#=GENOME_DIFF 1.0 #=AUTHOR breseq 0.25c #=CREATED 13:32:48 21 Feb 2015 #=REFSEQ /data/savita/refseq/NC_007779.gbk #=READSEQ 1_D10_GCCAAT_L003_R1_001.fastq SNP 1 77 NC_007779 66457 A frequency=1 SNP 2 83 NC_007779 97880 T frequency=1 SNP 3 110 NC_007779 167632 A frequency=1 SNP 4 130 NC_007779 274547 G frequency=1 DEL 5 960,976 NC_007779 274733 97240 frequency=1 SNP 6 162 NC_007779 547694 G frequency=1 INS 7 163 NC_007779 547831 G frequency=1 insert_position=1 SNP 8 165 NC_007779 556858 T frequency=1 SNP 9 172 NC_007779 569996 C frequency=1 DEL 10 961,981 NC_007779 654214 1199 frequency=1 SNP 11 197 NC_007779 749354 A frequency=1 SNP 12 199 NC_007779 758300 A frequency=1.660728e-02 SNP 13 201 NC_007779 758562 A frequency=8.984566e-03 SNP 14 202 NC_007779 758579 T frequency=1.133347e-02 SNP 15 203 NC_007779 758631 T frequency=1.209068e-02 SNP 16 221 NC_007779 887234 A frequency=1 SNP 17 233 NC_007779 987574 T frequency=1 SNP 18 255 NC_007779 1093686 C frequency=1 SNP 19 270 NC_007779 1170573 T frequency=1 SNP 20 276 NC_007779 1197797 T frequency=1.376152e-02 SNP 21 277 NC_007779 1197809 T frequency=1.304626e-02 SNP 22 280 NC_007779 1213001 C frequency=6.565714e-02 SNP 23 281 NC_007779 1213013 C frequency=4.814863e-02 SNP 24 282 NC_007779 1213026 T frequency=3.201580e-02 SNP 25 283 NC_007779 1213028 A frequency=3.163624e-02 SNP 26 284 NC_007779 1213058 C frequency=1.896763e-02 SNP 27 285 NC_007779 1213061 G frequency=1.322460e-02 DEL 28 963,988 NC_007779 1301041 1336 frequency=1 SNP 29 298 NC_007779 1318876 A frequency=1 DEL 30 964,991 NC_007779 1413639 23060 frequency=1 SNP 31 339 NC_007779 1483588 A frequency=1 DEL 32 340 NC_007779 1496775 1 frequency=1 SNP 33 384 NC_007779 1615814 A frequency=1 DEL 34 395 NC_007779 1669599 1 frequency=1 SNP 35 423 NC_007779 1844073 A frequency=1 SNP 36 439 NC_007779 1918872 A frequency=1 SNP 37 445 NC_007779 1973476 A frequency=1 SNP 38 452 NC_007779 2005401 T frequency=1 SNP 39 468 NC_007779 2170094 A frequency=1 SNP 40 482 NC_007779 2262756 C frequency=3.592968e-02 DEL 41 966,998 NC_007779 2320795 1336 frequency=1 SNP 42 505 NC_007779 2406075 T frequency=1 SNP 43 507 NC_007779 2416102 A frequency=1 SNP 44 525 NC_007779 2538628 T frequency=1 INS 45 1007 NC_007779 2865274 GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG frequency=3.232732e-01 INS 46 1008 NC_007779 2865278 TTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGC frequency=1.678952e-01 SNP 47 574 NC_007779 2866111 G frequency=1 SNP 48 594 NC_007779 3003330 A frequency=1 SNP 49 605 NC_007779 3049815 T frequency=1 SNP 50 658 NC_007779 3397813 G frequency=1 DEL 51 969,1018 NC_007779 3746911 1199 frequency=1 DEL 52 758 NC_007779 3750122 1 frequency=1 SNP 53 759 NC_007779 3750123 T frequency=4.039383e-02 DEL 54 970,1021 NC_007779 3750591 1199 frequency=1 SNP 55 789 NC_007779 3898657 G frequency=1 DEL 56 971,1023 NC_007779 3958123 34 frequency=1 SNP 57 847 NC_007779 4090749 T frequency=1 SNP 58 859 NC_007779 4165991 C frequency=1 DEL 59 972,1026 NC_007779 4310363 1199 frequency=1 DEL 60 917,918 NC_007779 4371271 2 frequency=1 SNP 61 940 NC_007779 4546535 A frequency=1 RA 62 . NC_007779 301 1 . T bias_e_value=3010460 bias_p_value=0.647922 fisher_strand_p_value=0.398231 frequency=1.059341e-02 genotype_quality=2247.8 ks_quality_p_value=0.726069 log10_base_likelihood=-20.3068 log10_qual_likelihood_position_model=4.31768 log10_strand_likelihood_position_model=0.640396 new_cov=1/4 polymorphism_quality=15.0 quality=15.0 quality_position_model=1.8214e-17 ref_cov=201/266 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=202/270 RA 63 . NC_007779 302 0 T . bias_e_value=3390970 bias_p_value=0.729817 fisher_strand_p_value=1 frequency=8.325577e-03 genotype_quality=1883.0 ks_quality_p_value=0.361985 log10_base_likelihood=-10.5012 log10_qual_likelihood_position_model=2.58085 log10_strand_likelihood_position_model=0.443528 new_cov=2/2 polymorphism_quality=5.1 quality=5.1 quality_position_model=1.91697e-09 ref_cov=202/273 reject=INDEL_HOMOPOLYMER tot_cov=205/275 RA 64 . NC_007779 847 0 A C bias_e_value=0.000266745 bias_p_value=5.74097e-11 fisher_strand_p_value=2.05785e-12 frequency=4.250431e-02 genotype_quality=879.7 ks_quality_p_value=0.999575 log10_base_likelihood=-14.415 log10_qual_likelihood_position_model=13.6758 log10_strand_likelihood_position_model=11.6866 new_cov=0/11 polymorphism_quality=9.1 quality=9.1 quality_position_model=Inf ref_cov=208/14 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=208/25 RA 65 . NC_007779 5595 0 G T bias_e_value=5.28322e-05 bias_p_value=1.13707e-11 fisher_strand_p_value=3.84311e-13 frequency=4.808044e-02 genotype_quality=1578.5 ks_quality_p_value=1 log10_base_likelihood=-17.1211 log10_qual_likelihood_position_model=23.8043 log10_strand_likelihood_position_model=12.4326 new_cov=0/41 polymorphism_quality=11.8 quality=11.8 quality_position_model=Inf ref_cov=242/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=243/260 RA 66 . NC_007779 10315 0 T . bias_e_value=3398970 bias_p_value=0.731537 fisher_strand_p_value=1 frequency=6.306648e-03 genotype_quality=1936.0 ks_quality_p_value=0.363682 log10_base_likelihood=-7.30938 log10_qual_likelihood_position_model=2.28913 log10_strand_likelihood_position_model=0.419635 new_cov=1/2 polymorphism_quality=1.8 quality=1.8 quality_position_model=1.80955e-06 ref_cov=233/238 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=235/240 RA 67 . NC_007779 11143 0 G T bias_e_value=4.11124e-07 bias_p_value=8.84836e-14 fisher_strand_p_value=2.55734e-15 frequency=5.545378e-02 genotype_quality=1472.0 ks_quality_p_value=1 log10_base_likelihood=-17.8288 log10_qual_likelihood_position_model=27.8784 log10_strand_likelihood_position_model=14.7416 new_cov=0/46 polymorphism_quality=12.5 quality=12.5 quality_position_model=Inf ref_cov=228/186 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=228/232 RA 68 . NC_007779 15382 0 A G bias_e_value=1.42725e-10 bias_p_value=3.07179e-17 fisher_strand_p_value=7.18081e-19 frequency=6.662703e-02 genotype_quality=1096.1 ks_quality_p_value=1 log10_base_likelihood=-13.6803 log10_qual_likelihood_position_model=28.394 log10_strand_likelihood_position_model=18.1438 new_cov=35/0 polymorphism_quality=8.3 quality=8.3 quality_position_model=Inf ref_cov=84/233 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=120/233 RA 69 . NC_007779 17050 0 A C bias_e_value=2.79541e-12 bias_p_value=6.01638e-19 fisher_strand_p_value=1.28554e-20 frequency=1.151938e-01 genotype_quality=973.0 ks_quality_p_value=1 log10_base_likelihood=-23.2639 log10_qual_likelihood_position_model=37.3128 log10_strand_likelihood_position_model=19.8909 new_cov=0/56 polymorphism_quality=18.0 quality=18.0 quality_position_model=Inf ref_cov=171/108 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=171/164 RA 70 . NC_007779 29496 0 T A bias_e_value=0.000106989 bias_p_value=2.30266e-11 fisher_strand_p_value=7.97964e-13 frequency=6.834316e-02 genotype_quality=1518.2 ks_quality_p_value=1 log10_base_likelihood=-24.9248 log10_qual_likelihood_position_model=48.4447 log10_strand_likelihood_position_model=12.098 new_cov=0/34 polymorphism_quality=19.7 quality=19.7 quality_position_model=Inf ref_cov=240/172 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=240/206 RA 71 . NC_007779 34111 1 . T bias_e_value=586925 bias_p_value=0.12632 fisher_strand_p_value=0.163612 frequency=1.026726e-02 genotype_quality=2391.0 ks_quality_p_value=0.168075 log10_base_likelihood=-21.2762 log10_qual_likelihood_position_model=2.56346 log10_strand_likelihood_position_model=1.09541 new_cov=1/4 polymorphism_quality=16.0 quality=16.0 quality_position_model=9.175e-20 ref_cov=288/194 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=289/198 RA 72 . NC_007779 34112 0 T . bias_e_value=4221520 bias_p_value=0.908571 fisher_strand_p_value=1 frequency=7.990837e-03 genotype_quality=2011.4 ks_quality_p_value=0.60409 log10_base_likelihood=-10.0758 log10_qual_likelihood_position_model=3.79133 log10_strand_likelihood_position_model=0.456985 new_cov=2/2 polymorphism_quality=4.6 quality=4.6 quality_position_model=9.61568e-08 ref_cov=296/200 reject=INDEL_HOMOPOLYMER tot_cov=298/202 RA 73 . NC_007779 36544 0 G T bias_e_value=5.78178 bias_p_value=1.24437e-06 fisher_strand_p_value=8.20539e-08 frequency=2.606201e-02 genotype_quality=1573.4 ks_quality_p_value=0.868745 log10_base_likelihood=-7.55075 log10_qual_likelihood_position_model=30.362 log10_strand_likelihood_position_model=7.23811 new_cov=0/28 polymorphism_quality=2.1 quality=2.1 quality_position_model=Inf ref_cov=215/250 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=215/279 RA 74 . NC_007779 39910 0 G T bias_e_value=768.147 bias_p_value=0.000165323 fisher_strand_p_value=1.36125e-05 frequency=3.815651e-02 genotype_quality=1059.1 ks_quality_p_value=0.994687 log10_base_likelihood=-8.65284 log10_qual_likelihood_position_model=22.1822 log10_strand_likelihood_position_model=4.95302 new_cov=0/29 polymorphism_quality=3.2 quality=3.2 quality_position_model=Inf ref_cov=116/226 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=116/257 RA 75 . NC_007779 47305 0 G T bias_e_value=1.06826e-17 bias_p_value=2.29914e-24 fisher_strand_p_value=3.87409e-26 frequency=1.109462e-01 genotype_quality=1458.8 ks_quality_p_value=0.997159 log10_base_likelihood=-46.7021 log10_qual_likelihood_position_model=38.7827 log10_strand_likelihood_position_model=25.4118 new_cov=0/73 polymorphism_quality=41.6 quality=41.6 quality_position_model=Inf ref_cov=250/168 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=250/241 RA 76 . NC_007779 48338 0 T G bias_e_value=17.4813 bias_p_value=3.76238e-06 fisher_strand_p_value=2.31098e-07 frequency=2.314472e-02 genotype_quality=823.8 ks_quality_p_value=1 log10_base_likelihood=-5.60544 log10_qual_likelihood_position_model=9.9905 log10_strand_likelihood_position_model=6.6362 new_cov=6/0 polymorphism_quality=0.0 quality=0.0 quality_position_model=Inf ref_cov=13/193 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=19/194 RA 77 . NC_007779 66457 0 C A frequency=1 genotype_quality=1965.8 new_cov=258/224 quality=1965.8 ref_cov=1/0 tot_cov=259/226 RA 78 . NC_007779 70602 0 G T bias_e_value=1.56842e-13 bias_p_value=3.3756e-20 fisher_strand_p_value=6.78623e-22 frequency=6.981707e-02 genotype_quality=1491.1 ks_quality_p_value=1 log10_base_likelihood=-15.6398 log10_qual_likelihood_position_model=45.5535 log10_strand_likelihood_position_model=21.1684 new_cov=0/57 polymorphism_quality=10.3 quality=10.3 quality_position_model=Inf ref_cov=250/157 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=250/214 RA 79 . NC_007779 72039 0 T G bias_e_value=12.6802 bias_p_value=2.72908e-06 fisher_strand_p_value=1.64182e-07 frequency=2.026939e-02 genotype_quality=1247.9 ks_quality_p_value=1 log10_base_likelihood=-6.02122 log10_qual_likelihood_position_model=17.0639 log10_strand_likelihood_position_model=6.78467 new_cov=12/0 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=87/250 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=99/250 RA 80 . NC_007779 75070 1 . G bias_e_value=1282910 bias_p_value=0.276112 fisher_strand_p_value=0.0907224 frequency=6.593704e-03 genotype_quality=2262.5 ks_quality_p_value=0.856013 log10_base_likelihood=-12.4115 log10_qual_likelihood_position_model=2.81893 log10_strand_likelihood_position_model=1.04229 new_cov=3/0 polymorphism_quality=7.0 quality=7.0 quality_position_model=1.51851e-10 ref_cov=202/250 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=205/250 RA 81 . NC_007779 75074 0 T G bias_e_value=2.96321e-49 bias_p_value=6.37752e-56 fisher_strand_p_value=4.79577e-58 frequency=1.847816e-01 genotype_quality=1179.2 ks_quality_p_value=1 log10_base_likelihood=-53.3746 log10_qual_likelihood_position_model=75.4602 log10_strand_likelihood_position_model=57.3191 new_cov=102/0 polymorphism_quality=48.3 quality=48.3 quality_position_model=Inf ref_cov=52/259 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=155/259 RA 82 . NC_007779 75079 0 C T bias_e_value=0.000405041 bias_p_value=8.71744e-11 fisher_strand_p_value=3.1727e-12 frequency=3.983784e-02 genotype_quality=1275.7 ks_quality_p_value=1 log10_base_likelihood=-11.935 log10_qual_likelihood_position_model=21.6608 log10_strand_likelihood_position_model=11.4986 new_cov=17/0 polymorphism_quality=6.5 quality=6.5 quality_position_model=Inf ref_cov=63/269 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=80/269 RA 83 . NC_007779 97880 0 C T frequency=1 genotype_quality=1876.2 new_cov=200/254 quality=1876.2 ref_cov=0/0 tot_cov=200/254 RA 84 . NC_007779 101231 0 T G bias_e_value=2.35112e-07 bias_p_value=5.06016e-14 fisher_strand_p_value=1.43856e-15 frequency=6.084633e-02 genotype_quality=994.6 ks_quality_p_value=1 log10_base_likelihood=-6.96152 log10_qual_likelihood_position_model=30.8036 log10_strand_likelihood_position_model=14.8421 new_cov=31/0 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=81/194 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=112/194 RA 85 . NC_007779 101240 1 . G bias_e_value=1860680 bias_p_value=0.400462 fisher_strand_p_value=0.138679 frequency=7.544518e-03 genotype_quality=1275.3 ks_quality_p_value=0.956001 log10_base_likelihood=-6.14368 log10_qual_likelihood_position_model=2.18021 log10_strand_likelihood_position_model=0.857989 new_cov=2/0 polymorphism_quality=0.6 quality=0.6 quality_position_model=6.76505e-05 ref_cov=97/166 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=99/166 RA 86 . NC_007779 101246 0 T G bias_e_value=3972.18 bias_p_value=0.000854906 fisher_strand_p_value=0.000119245 frequency=2.606010e-02 genotype_quality=854.0 ks_quality_p_value=0.688892 log10_base_likelihood=-14.1638 log10_qual_likelihood_position_model=5.23687 log10_strand_likelihood_position_model=3.92356 new_cov=6/0 polymorphism_quality=8.8 quality=8.8 quality_position_model=6.8859e-07 ref_cov=47/177 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=53/177 RA 87 . NC_007779 107544 1 . T bias_e_value=2597820 bias_p_value=0.559112 fisher_strand_p_value=0.227486 frequency=4.281998e-03 genotype_quality=2324.6 ks_quality_p_value=0.984628 log10_base_likelihood=-7.41231 log10_qual_likelihood_position_model=2.51816 log10_strand_likelihood_position_model=0.643045 new_cov=0/2 polymorphism_quality=1.9 quality=1.9 quality_position_model=4.19626e-06 ref_cov=244/221 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=244/223 RA 88 . NC_007779 116855 0 G T bias_e_value=0.000964493 bias_p_value=2.07582e-10 fisher_strand_p_value=7.81102e-12 frequency=2.542877e-02 genotype_quality=1660.6 ks_quality_p_value=1 log10_base_likelihood=-6.1038 log10_qual_likelihood_position_model=26.6885 log10_strand_likelihood_position_model=11.1073 new_cov=0/31 polymorphism_quality=0.6 quality=0.6 quality_position_model=Inf ref_cov=265/191 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=265/223 RA 89 . NC_007779 119384 0 T G bias_e_value=1.79661e-30 bias_p_value=3.86673e-37 fisher_strand_p_value=4.32832e-39 frequency=1.357155e-01 genotype_quality=1315.5 ks_quality_p_value=1 log10_base_likelihood=-38.6731 log10_qual_likelihood_position_model=62.1105 log10_strand_likelihood_position_model=38.3637 new_cov=98/0 polymorphism_quality=33.5 quality=33.5 quality_position_model=Inf ref_cov=124/249 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=223/250 RA 90 . NC_007779 119389 0 C A bias_e_value=0.0270513 bias_p_value=5.82208e-09 fisher_strand_p_value=2.52022e-10 frequency=2.687263e-02 genotype_quality=1631.9 ks_quality_p_value=1 log10_base_likelihood=-5.60915 log10_qual_likelihood_position_model=21.9755 log10_strand_likelihood_position_model=9.59856 new_cov=29/0 polymorphism_quality=0.0 quality=0.0 quality_position_model=Inf ref_cov=197/242 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=226/242 RA 91 . NC_007779 134366 0 G T bias_e_value=2.22128e-07 bias_p_value=4.78073e-14 fisher_strand_p_value=1.39256e-15 frequency=5.177307e-02 genotype_quality=1581.7 ks_quality_p_value=0.974366 log10_base_likelihood=-11.4645 log10_qual_likelihood_position_model=32.5234 log10_strand_likelihood_position_model=14.8562 new_cov=0/45 polymorphism_quality=6.1 quality=6.1 quality_position_model=Inf ref_cov=251/198 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=251/243 RA 92 . NC_007779 135495 1 . G bias_e_value=385621 bias_p_value=0.0829947 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2613.4 ks_quality_p_value=0.076922 log10_base_likelihood=-7.63923 log10_qual_likelihood_position_model=1.39795 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=1.79906e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 93 . NC_007779 135495 2 . G bias_e_value=385621 bias_p_value=0.0829947 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2613.4 ks_quality_p_value=0.076922 log10_base_likelihood=-7.63923 log10_qual_likelihood_position_model=1.39795 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=1.79906e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 94 . NC_007779 135495 3 . C bias_e_value=385621 bias_p_value=0.0829947 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2614.1 ks_quality_p_value=0.076922 log10_base_likelihood=-7.56368 log10_qual_likelihood_position_model=1.39795 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=2.1546e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 95 . NC_007779 135495 4 . A bias_e_value=385621 bias_p_value=0.0829947 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2603.9 ks_quality_p_value=0.076922 log10_base_likelihood=-7.63928 log10_qual_likelihood_position_model=1.39795 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=1.79885e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 96 . NC_007779 135495 5 . G bias_e_value=902530 bias_p_value=0.194246 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2612.8 ks_quality_p_value=0.228664 log10_base_likelihood=-7.64802 log10_qual_likelihood_position_model=2.03865 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=8.15295e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 97 . NC_007779 135495 6 . T bias_e_value=902530 bias_p_value=0.194246 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2605.6 ks_quality_p_value=0.228664 log10_base_likelihood=-7.67124 log10_qual_likelihood_position_model=2.03865 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=7.71168e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 98 . NC_007779 135495 7 . T bias_e_value=902530 bias_p_value=0.194246 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2605.6 ks_quality_p_value=0.228664 log10_base_likelihood=-7.67124 log10_qual_likelihood_position_model=2.03865 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=7.71168e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 99 . NC_007779 135495 8 . T bias_e_value=902530 bias_p_value=0.194246 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2605.6 ks_quality_p_value=0.228664 log10_base_likelihood=-7.67124 log10_qual_likelihood_position_model=2.03865 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=7.71168e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 100 . NC_007779 135495 9 . T bias_e_value=902530 bias_p_value=0.194246 fisher_strand_p_value=0.210623 frequency=3.860474e-03 genotype_quality=2605.6 ks_quality_p_value=0.228664 log10_base_likelihood=-7.67124 log10_qual_likelihood_position_model=2.03865 log10_strand_likelihood_position_model=0.676495 new_cov=2/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=7.71168e-07 ref_cov=236/280 reject=POLYMORPHISM_STRAND tot_cov=238/280 RA 101 . NC_007779 137009 0 G T bias_e_value=5.05628 bias_p_value=1.08823e-06 fisher_strand_p_value=6.89598e-08 frequency=3.034115e-02 genotype_quality=1465.2 ks_quality_p_value=0.89669 log10_base_likelihood=-10.02 log10_qual_likelihood_position_model=25.5806 log10_strand_likelihood_position_model=7.1614 new_cov=18/0 polymorphism_quality=4.6 quality=4.6 quality_position_model=Inf ref_cov=158/251 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=176/251 RA 102 . NC_007779 150546 0 A C bias_e_value=130707 bias_p_value=0.0281312 fisher_strand_p_value=0.0043735 frequency=2.634525e-02 genotype_quality=1552.1 ks_quality_p_value=1 log10_base_likelihood=-12.525 log10_qual_likelihood_position_model=18.8563 log10_strand_likelihood_position_model=2.62635 new_cov=13/1 polymorphism_quality=7.1 quality=7.1 quality_position_model=Inf ref_cov=210/181 reject=POLYMORPHISM_STRAND tot_cov=224/183 RA 103 . NC_007779 158557 0 G T bias_e_value=1.17697 bias_p_value=2.53312e-07 fisher_strand_p_value=1.32344e-08 frequency=3.004074e-02 genotype_quality=1297.7 ks_quality_p_value=1 log10_base_likelihood=-7.04927 log10_qual_likelihood_position_model=19.9254 log10_strand_likelihood_position_model=8.10135 new_cov=0/26 polymorphism_quality=1.5 quality=1.5 quality_position_model=Inf ref_cov=207/184 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=208/211 RA 104 . NC_007779 162886 0 C A bias_e_value=0.0594006 bias_p_value=1.27844e-08 fisher_strand_p_value=5.7384e-10 frequency=2.864075e-02 genotype_quality=1428.9 ks_quality_p_value=1 log10_base_likelihood=-6.08743 log10_qual_likelihood_position_model=21.2494 log10_strand_likelihood_position_model=9.24121 new_cov=26/0 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=173/236 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=199/236 RA 105 . NC_007779 164558 0 T G bias_e_value=3914.26 bias_p_value=0.000842441 fisher_strand_p_value=8.08233e-05 frequency=1.949406e-02 genotype_quality=794.1 ks_quality_p_value=1 log10_base_likelihood=-6.64652 log10_qual_likelihood_position_model=9.3575 log10_strand_likelihood_position_model=4.10007 new_cov=1/5 polymorphism_quality=1.1 quality=1.1 quality_position_model=Inf ref_cov=197/21 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=198/26 RA 106 . NC_007779 164569 0 C G bias_e_value=0.00292156 bias_p_value=6.28788e-10 fisher_strand_p_value=2.47331e-11 frequency=4.254246e-02 genotype_quality=725.7 ks_quality_p_value=1 log10_base_likelihood=-12.7484 log10_qual_likelihood_position_model=12.7527 log10_strand_likelihood_position_model=10.6067 new_cov=0/10 polymorphism_quality=7.4 quality=7.4 quality_position_model=Inf ref_cov=181/12 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=181/22 RA 107 . NC_007779 164574 0 T G bias_e_value=0.00129311 bias_p_value=2.78307e-10 fisher_strand_p_value=1.05938e-11 frequency=5.096960e-02 genotype_quality=553.4 ks_quality_p_value=1 log10_base_likelihood=-9.32726 log10_qual_likelihood_position_model=11.7248 log10_strand_likelihood_position_model=10.9787 new_cov=1/15 polymorphism_quality=3.9 quality=3.9 quality_position_model=Inf ref_cov=171/24 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=173/39 RA 108 . NC_007779 164576 0 A G bias_e_value=0.000660461 bias_p_value=1.42147e-10 fisher_strand_p_value=5.27476e-12 frequency=6.238794e-02 genotype_quality=602.5 ks_quality_p_value=0.999245 log10_base_likelihood=-13.469 log10_qual_likelihood_position_model=16.4264 log10_strand_likelihood_position_model=11.2813 new_cov=1/15 polymorphism_quality=8.1 quality=8.1 quality_position_model=Inf ref_cov=175/23 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=176/38 RA 109 . NC_007779 164597 1 . C bias_e_value=723747 bias_p_value=0.155767 fisher_strand_p_value=0.0436493 frequency=1.401901e-02 genotype_quality=916.8 ks_quality_p_value=0.825409 log10_base_likelihood=-13.0643 log10_qual_likelihood_position_model=3.34485 log10_strand_likelihood_position_model=1.36002 new_cov=3/0 polymorphism_quality=7.7 quality=7.7 quality_position_model=2.38207e-10 ref_cov=73/138 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=76/138 RA 110 . NC_007779 167632 0 C A frequency=1 genotype_quality=1777.4 new_cov=187/252 quality=1777.4 ref_cov=0/0 tot_cov=187/252 RA 111 . NC_007779 169737 1 . G bias_e_value=3771300 bias_p_value=0.811672 fisher_strand_p_value=0.49991 frequency=4.608154e-03 genotype_quality=2159.7 ks_quality_p_value=0.906058 log10_base_likelihood=-7.93732 log10_qual_likelihood_position_model=2.51658 log10_strand_likelihood_position_model=0.563843 new_cov=2/0 polymorphism_quality=2.5 quality=2.5 quality_position_model=9.78166e-07 ref_cov=225/207 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=227/207 RA 112 . NC_007779 175694 0 T G bias_e_value=5.93884e-27 bias_p_value=1.27818e-33 fisher_strand_p_value=1.57535e-35 frequency=1.110096e-01 genotype_quality=1346.3 ks_quality_p_value=1 log10_base_likelihood=-27.2688 log10_qual_likelihood_position_model=57.7938 log10_strand_likelihood_position_model=34.8026 new_cov=90/0 polymorphism_quality=22.1 quality=22.1 quality_position_model=Inf ref_cov=132/251 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=225/251 RA 113 . NC_007779 193496 0 A T bias_e_value=23.081 bias_p_value=4.96756e-06 fisher_strand_p_value=3.1078e-07 frequency=4.033375e-02 genotype_quality=1279.4 ks_quality_p_value=1 log10_base_likelihood=-12.2102 log10_qual_likelihood_position_model=24.0175 log10_strand_likelihood_position_model=6.50755 new_cov=16/0 polymorphism_quality=6.8 quality=6.8 quality_position_model=Inf ref_cov=127/210 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=143/210 RA 114 . NC_007779 194247 0 G T bias_e_value=2.71294e-07 bias_p_value=5.83889e-14 fisher_strand_p_value=1.66805e-15 frequency=7.158518e-02 genotype_quality=1176.0 ks_quality_p_value=0.999327 log10_base_likelihood=-19.4853 log10_qual_likelihood_position_model=33.4828 log10_strand_likelihood_position_model=14.7778 new_cov=0/41 polymorphism_quality=14.2 quality=14.2 quality_position_model=Inf ref_cov=197/132 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=197/174 RA 115 . NC_007779 207536 0 G T bias_e_value=0.00257188 bias_p_value=5.53529e-10 fisher_strand_p_value=2.16598e-11 frequency=4.169750e-02 genotype_quality=1331.7 ks_quality_p_value=1 log10_base_likelihood=-11.0772 log10_qual_likelihood_position_model=26.9201 log10_strand_likelihood_position_model=10.7713 new_cov=0/37 polymorphism_quality=5.7 quality=5.7 quality_position_model=Inf ref_cov=203/194 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=203/232 RA 116 . NC_007779 215133 1 . A bias_e_value=3040040 bias_p_value=0.654289 fisher_strand_p_value=0.502526 frequency=4.357338e-03 genotype_quality=2290.7 ks_quality_p_value=0.585664 log10_base_likelihood=-8.14182 log10_qual_likelihood_position_model=1.41634 log10_strand_likelihood_position_model=0.532027 new_cov=2/0 polymorphism_quality=2.7 quality=2.7 quality_position_model=4.02353e-08 ref_cov=247/210 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=249/210 RA 117 . NC_007779 215134 0 A . bias_e_value=4599700 bias_p_value=0.989964 fisher_strand_p_value=1 frequency=6.443977e-03 genotype_quality=1904.5 ks_quality_p_value=0.861712 log10_base_likelihood=-7.5021 log10_qual_likelihood_position_model=1.98466 log10_strand_likelihood_position_model=0.391574 new_cov=2/1 polymorphism_quality=2.0 quality=2.0 quality_position_model=5.13555e-07 ref_cov=251/211 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=253/212 RA 118 . NC_007779 218828 0 A . bias_e_value=4091700 bias_p_value=0.880631 fisher_strand_p_value=1 frequency=9.227753e-03 genotype_quality=1773.0 ks_quality_p_value=0.553059 log10_base_likelihood=-10.3545 log10_qual_likelihood_position_model=2.55591 log10_strand_likelihood_position_model=0.424026 new_cov=2/2 polymorphism_quality=4.9 quality=4.9 quality_position_model=2.44178e-09 ref_cov=212/216 reject=INDEL_HOMOPOLYMER tot_cov=215/218 RA 119 . NC_007779 221544 0 A . bias_e_value=1621710 bias_p_value=0.349031 fisher_strand_p_value=0.251275 frequency=7.448196e-03 genotype_quality=1641.8 ks_quality_p_value=0.430996 log10_base_likelihood=-7.21027 log10_qual_likelihood_position_model=3.52722 log10_strand_likelihood_position_model=0.824301 new_cov=3/0 polymorphism_quality=1.7 quality=1.7 quality_position_model=0.000123887 ref_cov=211/188 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=214/188 RA 120 . NC_007779 228904 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 121 . NC_007779 228905 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 122 . NC_007779 228906 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 123 . NC_007779 228907 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 124 . NC_007779 228908 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 125 . NC_007779 228909 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 126 . NC_007779 228910 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 127 . NC_007779 228911 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 128 . NC_007779 264190 1 . G bias_e_value=3822020 bias_p_value=0.822589 fisher_strand_p_value=0.501046 frequency=5.290985e-03 genotype_quality=1889.1 ks_quality_p_value=0.932059 log10_base_likelihood=-8.78928 log10_qual_likelihood_position_model=2.50256 log10_strand_likelihood_position_model=0.545286 new_cov=0/2 polymorphism_quality=3.3 quality=3.3 quality_position_model=1.18045e-07 ref_cov=176/200 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=176/202 RA 129 . NC_007779 265564 0 T G bias_e_value=1.27712e-07 bias_p_value=2.74866e-14 fisher_strand_p_value=7.67715e-16 frequency=4.296780e-02 genotype_quality=1225.4 ks_quality_p_value=1 log10_base_likelihood=-6.93985 log10_qual_likelihood_position_model=34.1879 log10_strand_likelihood_position_model=15.1148 new_cov=42/0 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=145/214 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=187/214 RA 130 . NC_007779 274547 0 A G frequency=1 genotype_quality=2050.0 new_cov=243/236 quality=2050.0 ref_cov=0/0 tot_cov=243/238 RA 131 . NC_007779 358275 0 G A deleted=1 frequency=1 genotype_quality=3.2 new_cov=0/1 quality=3.2 ref_cov=0/0 reject=EVALUE tot_cov=0/1 RA 132 . NC_007779 365386 0 A C deleted=1 frequency=1 genotype_quality=1.8 new_cov=0/1 quality=1.8 ref_cov=0/0 reject=EVALUE tot_cov=0/1 RA 133 . NC_007779 365514 0 C T deleted=1 frequency=1 genotype_quality=7.8 new_cov=1/1 quality=7.8 ref_cov=0/0 reject=EVALUE tot_cov=1/1 RA 134 . NC_007779 365524 0 G . deleted=1 frequency=1 genotype_quality=9.5 new_cov=1/1 quality=9.5 ref_cov=0/0 reject=EVALUE tot_cov=1/1 RA 135 . NC_007779 365626 0 G C deleted=1 frequency=1 genotype_quality=3.1 new_cov=0/1 quality=3.1 ref_cov=0/0 reject=EVALUE tot_cov=0/1 RA 136 . NC_007779 374799 0 T G bias_e_value=3.61869e-14 bias_p_value=7.78827e-21 fisher_strand_p_value=1.52001e-22 frequency=6.547928e-02 genotype_quality=1138.3 ks_quality_p_value=1 log10_base_likelihood=-12.7028 log10_qual_likelihood_position_model=32.781 log10_strand_likelihood_position_model=21.8182 new_cov=42/0 polymorphism_quality=7.3 quality=7.3 quality_position_model=Inf ref_cov=80/232 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=123/232 RA 137 . NC_007779 379236 1 . G bias_e_value=2900650 bias_p_value=0.624287 fisher_strand_p_value=0.652803 frequency=1.533699e-02 genotype_quality=1565.8 ks_quality_p_value=0.4145 log10_base_likelihood=-22.1109 log10_qual_likelihood_position_model=3.17876 log10_strand_likelihood_position_model=0.492217 new_cov=3/2 polymorphism_quality=16.8 quality=16.8 quality_position_model=1.34997e-20 ref_cov=220/101 reject=INDEL_HOMOPOLYMER tot_cov=223/103 RA 138 . NC_007779 379237 0 G . bias_e_value=3114000 bias_p_value=0.670206 fisher_strand_p_value=0.324478 frequency=5.336094e-02 genotype_quality=1428.0 ks_quality_p_value=0.947878 log10_base_likelihood=-63.8282 log10_qual_likelihood_position_model=7.54593 log10_strand_likelihood_position_model=0.992187 new_cov=10/9 polymorphism_quality=58.8 quality=58.8 quality_position_model=1.10919e-57 ref_cov=220/117 reject=INDEL_HOMOPOLYMER tot_cov=230/126 RA 139 . NC_007779 379266 0 G C bias_e_value=11.1457 bias_p_value=2.39881e-06 fisher_strand_p_value=2.32843e-07 frequency=4.118252e-02 genotype_quality=1088.7 ks_quality_p_value=0.614711 log10_base_likelihood=-10.3293 log10_qual_likelihood_position_model=30.4142 log10_strand_likelihood_position_model=6.93397 new_cov=22/0 polymorphism_quality=4.9 quality=4.9 quality_position_model=Inf ref_cov=150/172 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=172/172 RA 140 . NC_007779 387560 0 A C bias_e_value=3.18052e-12 bias_p_value=6.84522e-19 fisher_strand_p_value=1.46677e-20 frequency=4.362965e-02 genotype_quality=1398.6 ks_quality_p_value=1 log10_base_likelihood=-6.89578 log10_qual_likelihood_position_model=41.9752 log10_strand_likelihood_position_model=19.8336 new_cov=0/52 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=247/150 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=247/202 RA 141 . NC_007779 387917 0 T G bias_e_value=0.000127637 bias_p_value=2.74706e-11 fisher_strand_p_value=9.58035e-13 frequency=4.405212e-02 genotype_quality=799.9 ks_quality_p_value=1 log10_base_likelihood=-9.44989 log10_qual_likelihood_position_model=22.0245 log10_strand_likelihood_position_model=12.0252 new_cov=3/15 polymorphism_quality=4.0 quality=4.0 quality_position_model=Inf ref_cov=221/18 reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=225/33 RA 142 . NC_007779 387919 0 A G bias_e_value=7.94145e-12 bias_p_value=1.70919e-18 fisher_strand_p_value=3.73729e-20 frequency=6.870890e-02 genotype_quality=828.8 ks_quality_p_value=1 log10_base_likelihood=-25.2654 log10_qual_likelihood_position_model=17.0343 log10_strand_likelihood_position_model=19.4274 new_cov=0/19 polymorphism_quality=20.0 quality=20.0 quality_position_model=Inf ref_cov=222/14 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=222/33 RA 143 . NC_007779 421227 1 . C bias_e_value=3751320 bias_p_value=0.807373 fisher_strand_p_value=0.508507 frequency=4.629135e-03 genotype_quality=2118.0 ks_quality_p_value=0.880144 log10_base_likelihood=-7.05554 log10_qual_likelihood_position_model=3.15602 log10_strand_likelihood_position_model=0.48986 new_cov=0/2 polymorphism_quality=1.5 quality=1.5 quality_position_model=3.2201e-05 ref_cov=186/244 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=186/246 RA 144 . NC_007779 429744 1 . T bias_e_value=2480970 bias_p_value=0.533964 fisher_strand_p_value=1 frequency=4.405022e-03 genotype_quality=2257.9 ks_quality_p_value=0.207592 log10_base_likelihood=-7.83168 log10_qual_likelihood_position_model=2.03623 log10_strand_likelihood_position_model=0.30879 new_cov=1/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=2.16791e-07 ref_cov=258/194 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=259/195 RA 145 . NC_007779 432858 0 T G bias_e_value=8.31798e-14 bias_p_value=1.79022e-20 fisher_strand_p_value=3.5528e-22 frequency=7.175493e-02 genotype_quality=1182.8 ks_quality_p_value=1 log10_base_likelihood=-10.2511 log10_qual_likelihood_position_model=44.5465 log10_strand_likelihood_position_model=21.5718 new_cov=64/0 polymorphism_quality=4.8 quality=4.8 quality_position_model=Inf ref_cov=142/203 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=209/203 RA 146 . NC_007779 440767 0 G T bias_e_value=3.36201e-17 bias_p_value=7.23583e-24 fisher_strand_p_value=1.24009e-25 frequency=1.157436e-01 genotype_quality=1337.6 ks_quality_p_value=1 log10_base_likelihood=-43.3784 log10_qual_likelihood_position_model=37.4861 log10_strand_likelihood_position_model=24.9065 new_cov=0/67 polymorphism_quality=38.3 quality=38.3 quality_position_model=Inf ref_cov=243/147 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=243/217 RA 147 . NC_007779 455714 0 T . bias_e_value=3020300 bias_p_value=0.65004 fisher_strand_p_value=0.625674 frequency=7.512093e-03 genotype_quality=2146.6 ks_quality_p_value=0.464866 log10_base_likelihood=-10.3816 log10_qual_likelihood_position_model=1.98089 log10_strand_likelihood_position_model=0.55847 new_cov=1/3 polymorphism_quality=5.0 quality=5.0 quality_position_model=8.0789e-10 ref_cov=251/277 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=252/280 RA 148 . NC_007779 473544 1 . C bias_e_value=3876160 bias_p_value=0.83424 fisher_strand_p_value=1 frequency=4.237175e-03 genotype_quality=2274.0 ks_quality_p_value=0.482646 log10_base_likelihood=-8.34349 log10_qual_likelihood_position_model=1.62433 log10_strand_likelihood_position_model=0.303899 new_cov=1/1 polymorphism_quality=2.9 quality=2.9 quality_position_model=2.37469e-08 ref_cov=257/213 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=258/214 RA 149 . NC_007779 474686 0 G T bias_e_value=4.13463e-06 bias_p_value=8.89869e-13 fisher_strand_p_value=2.76679e-14 frequency=4.755402e-02 genotype_quality=1317.8 ks_quality_p_value=0.998208 log10_base_likelihood=-15.2069 log10_qual_likelihood_position_model=27.3245 log10_strand_likelihood_position_model=13.558 new_cov=0/39 polymorphism_quality=9.9 quality=9.9 quality_position_model=Inf ref_cov=230/168 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=230/208 RA 150 . NC_007779 487248 0 C A bias_e_value=234.883 bias_p_value=5.05524e-05 fisher_strand_p_value=3.74607e-06 frequency=3.712368e-02 genotype_quality=1374.2 ks_quality_p_value=1 log10_base_likelihood=-7.51038 log10_qual_likelihood_position_model=18.2525 log10_strand_likelihood_position_model=5.44236 new_cov=1/17 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=222/150 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=223/167 RA 151 . NC_007779 494823 0 T G bias_e_value=1.85417e-07 bias_p_value=3.99061e-14 fisher_strand_p_value=1.12667e-15 frequency=4.613781e-02 genotype_quality=1125.7 ks_quality_p_value=1 log10_base_likelihood=-6.49292 log10_qual_likelihood_position_model=44.1405 log10_strand_likelihood_position_model=14.9482 new_cov=37/0 polymorphism_quality=1.0 quality=1.0 quality_position_model=Inf ref_cov=108/194 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=146/194 RA 152 . NC_007779 500788 0 A C bias_e_value=9.49131e-06 bias_p_value=2.04275e-12 fisher_strand_p_value=6.5134e-14 frequency=3.194904e-02 genotype_quality=1277.2 ks_quality_p_value=1 log10_base_likelihood=-6.70616 log10_qual_likelihood_position_model=26.1043 log10_strand_likelihood_position_model=13.1862 new_cov=0/26 polymorphism_quality=1.2 quality=1.2 quality_position_model=Inf ref_cov=244/97 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=244/123 RA 153 . NC_007779 506364 0 A . bias_e_value=3455900 bias_p_value=0.743791 fisher_strand_p_value=1 frequency=5.817413e-03 genotype_quality=2121.6 ks_quality_p_value=0.376 log10_base_likelihood=-7.38936 log10_qual_likelihood_position_model=1.5031 log10_strand_likelihood_position_model=0.422607 new_cov=1/2 polymorphism_quality=1.9 quality=1.9 quality_position_model=2.29031e-07 ref_cov=255/257 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=256/259 RA 154 . NC_007779 513848 0 A C bias_e_value=1.71632e-25 bias_p_value=3.69393e-32 fisher_strand_p_value=4.75231e-34 frequency=1.064315e-01 genotype_quality=1068.6 ks_quality_p_value=1 log10_base_likelihood=-16.8215 log10_qual_likelihood_position_model=50.8951 log10_strand_likelihood_position_model=33.3231 new_cov=0/60 polymorphism_quality=11.5 quality=11.5 quality_position_model=Inf ref_cov=221/57 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=221/117 RA 155 . NC_007779 522430 1 . T bias_e_value=4362560 bias_p_value=0.938925 fisher_strand_p_value=1 frequency=5.076408e-03 genotype_quality=1972.1 ks_quality_p_value=0.671516 log10_base_likelihood=-7.81503 log10_qual_likelihood_position_model=1.98414 log10_strand_likelihood_position_model=0.313059 new_cov=1/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=2.01244e-07 ref_cov=230/162 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=231/163 RA 156 . NC_007779 522431 0 T . bias_e_value=3688510 bias_p_value=0.793854 fisher_strand_p_value=1 frequency=1.522064e-02 genotype_quality=1613.8 ks_quality_p_value=0.431123 log10_base_likelihood=-17.2698 log10_qual_likelihood_position_model=2.75775 log10_strand_likelihood_position_model=0.515064 new_cov=4/2 polymorphism_quality=12.0 quality=12.0 quality_position_model=4.28154e-16 ref_cov=226/160 reject=INDEL_HOMOPOLYMER tot_cov=231/163 RA 157 . NC_007779 524490 0 T G bias_e_value=9.68447e-10 bias_p_value=2.08433e-16 fisher_strand_p_value=5.10664e-18 frequency=7.453156e-02 genotype_quality=1256.9 ks_quality_p_value=1 log10_base_likelihood=-19.2053 log10_qual_likelihood_position_model=39.0792 log10_strand_likelihood_position_model=17.2919 new_cov=38/0 polymorphism_quality=13.9 quality=13.9 quality_position_model=Inf ref_cov=107/233 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=145/233 RA 158 . NC_007779 528271 1 . T bias_e_value=4625520 bias_p_value=0.995522 fisher_strand_p_value=1 frequency=5.375862e-03 genotype_quality=1870.1 ks_quality_p_value=0.906864 log10_base_likelihood=-7.80088 log10_qual_likelihood_position_model=2.11625 log10_strand_likelihood_position_model=0.301988 new_cov=1/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=2.7793e-07 ref_cov=198/172 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=199/173 RA 159 . NC_007779 535125 0 T G bias_e_value=9.30564e-10 bias_p_value=2.00279e-16 fisher_strand_p_value=4.90197e-18 frequency=5.423975e-02 genotype_quality=1228.7 ks_quality_p_value=1 log10_base_likelihood=-7.71995 log10_qual_likelihood_position_model=39.7744 log10_strand_likelihood_position_model=17.4251 new_cov=62/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=Inf ref_cov=185/196 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=248/196 RA 160 . NC_007779 535142 0 A G bias_e_value=30.0084 bias_p_value=6.45852e-06 fisher_strand_p_value=4.11265e-07 frequency=3.770065e-02 genotype_quality=1200.6 ks_quality_p_value=1 log10_base_likelihood=-8.24547 log10_qual_likelihood_position_model=15.0867 log10_strand_likelihood_position_model=6.47496 new_cov=23/1 polymorphism_quality=2.8 quality=2.8 quality_position_model=Inf ref_cov=162/197 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=186/198 RA 161 . NC_007779 544570 0 A C bias_e_value=1104400 bias_p_value=0.237693 fisher_strand_p_value=0.0633124 frequency=1.089478e-02 genotype_quality=1697.8 ks_quality_p_value=0.99805 log10_base_likelihood=-5.78459 log10_qual_likelihood_position_model=6.78755 log10_strand_likelihood_position_model=1.38724 new_cov=5/0 polymorphism_quality=0.2 quality=0.2 quality_position_model=Inf ref_cov=224/203 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=229/204 RA 162 . NC_007779 547694 0 A G frequency=1 genotype_quality=1623.0 new_cov=191/197 quality=1623.0 ref_cov=0/0 tot_cov=191/197 RA 163 . NC_007779 547831 1 . G frequency=1 genotype_quality=1750.3 new_cov=179/226 quality=1750.3 ref_cov=1/1 tot_cov=180/228 RA 164 . NC_007779 556653 0 A C bias_e_value=9.83841e-20 bias_p_value=2.11746e-26 fisher_strand_p_value=3.2941e-28 frequency=7.117271e-02 genotype_quality=1181.6 ks_quality_p_value=1 log10_base_likelihood=-13.8634 log10_qual_likelihood_position_model=40.5944 log10_strand_likelihood_position_model=27.4823 new_cov=0/46 polymorphism_quality=8.5 quality=8.5 quality_position_model=Inf ref_cov=249/62 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=249/109 RA 165 . NC_007779 556858 0 A T frequency=1 genotype_quality=1741.3 new_cov=225/201 quality=1741.3 ref_cov=0/0 tot_cov=225/201 RA 166 . NC_007779 562819 0 T C bias_e_value=8649.51 bias_p_value=0.00186158 fisher_strand_p_value=0.000196301 frequency=3.156471e-02 genotype_quality=1277.8 ks_quality_p_value=0.993841 log10_base_likelihood=-7.92694 log10_qual_likelihood_position_model=20.7587 log10_strand_likelihood_position_model=3.89401 new_cov=0/15 polymorphism_quality=2.4 quality=2.4 quality_position_model=Inf ref_cov=157/184 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=158/199 RA 167 . NC_007779 562821 0 C A bias_e_value=8685.38 bias_p_value=0.0018693 fisher_strand_p_value=0.000197679 frequency=2.580452e-02 genotype_quality=1398.2 ks_quality_p_value=0.991487 log10_base_likelihood=-6.4697 log10_qual_likelihood_position_model=22.0141 log10_strand_likelihood_position_model=3.88901 new_cov=0/15 polymorphism_quality=0.9 quality=0.9 quality_position_model=Inf ref_cov=160/188 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=160/203 RA 168 . NC_007779 562825 0 A G bias_e_value=369538 bias_p_value=0.0795333 fisher_strand_p_value=0.0153672 frequency=2.065277e-02 genotype_quality=1250.8 ks_quality_p_value=1 log10_base_likelihood=-5.92427 log10_qual_likelihood_position_model=16.5915 log10_strand_likelihood_position_model=2.01428 new_cov=1/11 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=147/185 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=148/196 RA 169 . NC_007779 562827 0 C A bias_e_value=30448.2 bias_p_value=0.00655318 fisher_strand_p_value=0.0008068 frequency=2.957821e-02 genotype_quality=1332.6 ks_quality_p_value=1 log10_base_likelihood=-7.03591 log10_qual_likelihood_position_model=17.8559 log10_strand_likelihood_position_model=3.25653 new_cov=0/13 polymorphism_quality=1.5 quality=1.5 quality_position_model=Inf ref_cov=149/184 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=149/197 RA 170 . NC_007779 562829 0 C A bias_e_value=257133 bias_p_value=0.0553412 fisher_strand_p_value=0.00985839 frequency=2.120399e-02 genotype_quality=1341.8 ks_quality_p_value=0.99874 log10_base_likelihood=-7.45454 log10_qual_likelihood_position_model=12.2964 log10_strand_likelihood_position_model=2.07122 new_cov=0/8 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=152/182 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=153/190 RA 171 . NC_007779 562836 0 C A bias_e_value=1984.33 bias_p_value=0.000427075 fisher_strand_p_value=3.86197e-05 frequency=3.798199e-02 genotype_quality=1345.8 ks_quality_p_value=0.989842 log10_base_likelihood=-15.5433 log10_qual_likelihood_position_model=22.5428 log10_strand_likelihood_position_model=4.44628 new_cov=0/16 polymorphism_quality=10.2 quality=10.2 quality_position_model=Inf ref_cov=159/169 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=159/185 RA 172 . NC_007779 569996 0 G C frequency=1 genotype_quality=2241.0 new_cov=242/270 quality=2241.0 ref_cov=0/0 tot_cov=242/270 RA 173 . NC_007779 583702 1 . T bias_e_value=2339550 bias_p_value=0.503526 fisher_strand_p_value=0.19105 frequency=5.181313e-03 genotype_quality=1932.9 ks_quality_p_value=0.98817 log10_base_likelihood=-7.86731 log10_qual_likelihood_position_model=2.01915 log10_strand_likelihood_position_model=0.718852 new_cov=0/2 polymorphism_quality=2.4 quality=2.4 quality_position_model=5.09339e-07 ref_cov=217/167 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=217/169 RA 174 . NC_007779 589157 0 T G bias_e_value=6.95012e-16 bias_p_value=1.49583e-22 fisher_strand_p_value=2.70658e-24 frequency=6.361723e-02 genotype_quality=1162.1 ks_quality_p_value=1 log10_base_likelihood=-9.02559 log10_qual_likelihood_position_model=53.2724 log10_strand_likelihood_position_model=23.5676 new_cov=50/0 polymorphism_quality=3.6 quality=3.6 quality_position_model=Inf ref_cov=92/228 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=144/228 RA 175 . NC_007779 593216 0 T G bias_e_value=1.56259e-15 bias_p_value=3.36307e-22 fisher_strand_p_value=6.17744e-24 frequency=6.985712e-02 genotype_quality=1089.0 ks_quality_p_value=1 log10_base_likelihood=-17.5056 log10_qual_likelihood_position_model=38.3529 log10_strand_likelihood_position_model=23.2092 new_cov=37/0 polymorphism_quality=12.2 quality=12.2 quality_position_model=Inf ref_cov=53/230 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=90/230 RA 176 . NC_007779 595481 0 T G bias_e_value=4.72109e-06 bias_p_value=1.01609e-12 fisher_strand_p_value=3.16703e-14 frequency=3.628254e-02 genotype_quality=1289.2 ks_quality_p_value=1 log10_base_likelihood=-6.71274 log10_qual_likelihood_position_model=28.2759 log10_strand_likelihood_position_model=13.4993 new_cov=39/0 polymorphism_quality=1.2 quality=1.2 quality_position_model=Inf ref_cov=161/220 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=202/220 RA 177 . NC_007779 598799 0 T G bias_e_value=2.15167e-35 bias_p_value=4.6309e-42 fisher_strand_p_value=4.59465e-44 frequency=1.508865e-01 genotype_quality=946.5 ks_quality_p_value=1 log10_base_likelihood=-36.1398 log10_qual_likelihood_position_model=56.8289 log10_strand_likelihood_position_model=43.3377 new_cov=55/0 polymorphism_quality=31.0 quality=31.0 quality_position_model=Inf ref_cov=19/224 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=74/224 RA 178 . NC_007779 606687 1 . T bias_e_value=1825980 bias_p_value=0.392994 fisher_strand_p_value=0.386298 frequency=1.054859e-02 genotype_quality=2329.5 ks_quality_p_value=0.333699 log10_base_likelihood=-21.899 log10_qual_likelihood_position_model=3.52349 log10_strand_likelihood_position_model=0.681179 new_cov=4/1 polymorphism_quality=16.6 quality=16.6 quality_position_model=7.66787e-20 ref_cov=258/211 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=262/212 RA 179 . NC_007779 606911 1 . G bias_e_value=108104 bias_p_value=0.0232665 fisher_strand_p_value=0.088806 frequency=7.672310e-03 genotype_quality=1971.1 ks_quality_p_value=0.03936 log10_base_likelihood=-12.356 log10_qual_likelihood_position_model=1.72213 log10_strand_likelihood_position_model=1.05156 new_cov=3/0 polymorphism_quality=7.0 quality=7.0 quality_position_model=1.33572e-11 ref_cov=172/216 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=175/216 RA 180 . NC_007779 612991 0 C G bias_e_value=0.0036713 bias_p_value=7.90149e-10 fisher_strand_p_value=3.13858e-11 frequency=4.460144e-02 genotype_quality=1101.2 ks_quality_p_value=0.999616 log10_base_likelihood=-13.2715 log10_qual_likelihood_position_model=18.8665 log10_strand_likelihood_position_model=10.5033 new_cov=0/15 polymorphism_quality=7.9 quality=7.9 quality_position_model=Inf ref_cov=224/48 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=224/64 RA 181 . NC_007779 617601 0 C A bias_e_value=0.0106951 bias_p_value=2.30184e-09 fisher_strand_p_value=9.56291e-11 frequency=4.025555e-02 genotype_quality=1370.6 ks_quality_p_value=1 log10_base_likelihood=-8.91685 log10_qual_likelihood_position_model=20.0058 log10_strand_likelihood_position_model=10.0194 new_cov=24/0 polymorphism_quality=3.5 quality=3.5 quality_position_model=Inf ref_cov=132/233 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=156/233 RA 182 . NC_007779 617621 0 G T bias_e_value=271.306 bias_p_value=5.83914e-05 fisher_strand_p_value=4.37748e-06 frequency=3.074265e-02 genotype_quality=1411.2 ks_quality_p_value=1 log10_base_likelihood=-8.85161 log10_qual_likelihood_position_model=15.1277 log10_strand_likelihood_position_model=5.35878 new_cov=13/0 polymorphism_quality=3.4 quality=3.4 quality_position_model=Inf ref_cov=132/220 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=145/220 RA 183 . NC_007779 634377 1 . T bias_e_value=1828280 bias_p_value=0.39349 fisher_strand_p_value=0.188049 frequency=4.175186e-03 genotype_quality=2392.7 ks_quality_p_value=0.686784 log10_base_likelihood=-7.76952 log10_qual_likelihood_position_model=1.50014 log10_strand_likelihood_position_model=0.72573 new_cov=0/2 polymorphism_quality=2.3 quality=2.3 quality_position_model=1.89216e-07 ref_cov=271/206 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=271/208 RA 184 . NC_007779 645970 0 T G bias_e_value=4.15934e-25 bias_p_value=8.95188e-32 fisher_strand_p_value=1.16512e-33 frequency=1.135082e-01 genotype_quality=1140.6 ks_quality_p_value=1 log10_base_likelihood=-35.8529 log10_qual_likelihood_position_model=49.3583 log10_strand_likelihood_position_model=32.9336 new_cov=47/0 polymorphism_quality=30.7 quality=30.7 quality_position_model=Inf ref_cov=39/246 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=86/246 RA 185 . NC_007779 646433 0 A C bias_e_value=2.36965e-05 bias_p_value=5.10005e-12 fisher_strand_p_value=1.67672e-13 frequency=3.112793e-02 genotype_quality=1268.1 ks_quality_p_value=1 log10_base_likelihood=-8.05009 log10_qual_likelihood_position_model=23.832 log10_strand_likelihood_position_model=12.7755 new_cov=0/14 polymorphism_quality=2.6 quality=2.6 quality_position_model=Inf ref_cov=289/33 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=289/47 RA 186 . NC_007779 646440 0 C A bias_e_value=5.14057e-14 bias_p_value=1.10637e-20 fisher_strand_p_value=2.17777e-22 frequency=5.782413e-02 genotype_quality=1333.3 ks_quality_p_value=0.998485 log10_base_likelihood=-37.6661 log10_qual_likelihood_position_model=22.6607 log10_strand_likelihood_position_model=21.662 new_cov=0/20 polymorphism_quality=32.5 quality=32.5 quality_position_model=Inf ref_cov=298/17 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=298/37 RA 187 . NC_007779 660356 0 T G bias_e_value=2.1289e-24 bias_p_value=4.5819e-31 fisher_strand_p_value=6.09475e-33 frequency=1.158099e-01 genotype_quality=1117.8 ks_quality_p_value=1 log10_base_likelihood=-25.3661 log10_qual_likelihood_position_model=47.788 log10_strand_likelihood_position_model=32.215 new_cov=66/0 polymorphism_quality=20.1 quality=20.1 quality_position_model=Inf ref_cov=78/227 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=144/227 RA 188 . NC_007779 665062 0 C A bias_e_value=31.0278 bias_p_value=6.67791e-06 fisher_strand_p_value=4.59165e-07 frequency=3.781605e-02 genotype_quality=1266.5 ks_quality_p_value=0.928215 log10_base_likelihood=-10.4957 log10_qual_likelihood_position_model=23.1846 log10_strand_likelihood_position_model=6.33803 new_cov=0/19 polymorphism_quality=5.1 quality=5.1 quality_position_model=Inf ref_cov=194/158 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=194/177 RA 189 . NC_007779 667452 0 G T bias_e_value=12556.3 bias_p_value=0.00270241 fisher_strand_p_value=0.000296168 frequency=3.209972e-02 genotype_quality=1580.4 ks_quality_p_value=1 log10_base_likelihood=-17.0425 log10_qual_likelihood_position_model=19.3425 log10_strand_likelihood_position_model=3.57505 new_cov=15/0 polymorphism_quality=11.7 quality=11.7 quality_position_model=Inf ref_cov=215/163 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=230/163 RA 190 . NC_007779 667899 1 . G bias_e_value=3894430 bias_p_value=0.838173 fisher_strand_p_value=0.498944 frequency=4.773140e-03 genotype_quality=2094.7 ks_quality_p_value=0.97824 log10_base_likelihood=-7.21767 log10_qual_likelihood_position_model=2.52739 log10_strand_likelihood_position_model=0.588675 new_cov=2/0 polymorphism_quality=1.7 quality=1.7 quality_position_model=6.01841e-06 ref_cov=211/206 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=213/206 RA 191 . NC_007779 686495 0 A C bias_e_value=5.03937e-27 bias_p_value=1.08459e-33 fisher_strand_p_value=1.33402e-35 frequency=1.195645e-01 genotype_quality=1169.3 ks_quality_p_value=1 log10_base_likelihood=-42.4149 log10_qual_likelihood_position_model=52.708 log10_strand_likelihood_position_model=34.8748 new_cov=0/53 polymorphism_quality=37.3 quality=37.3 quality_position_model=Inf ref_cov=252/46 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=252/99 RA 192 . NC_007779 687133 0 A C bias_e_value=0.00682475 bias_p_value=1.46885e-09 fisher_strand_p_value=5.98575e-11 frequency=2.221298e-02 genotype_quality=1459.5 ks_quality_p_value=1 log10_base_likelihood=-8.66462 log10_qual_likelihood_position_model=24.5457 log10_strand_likelihood_position_model=10.2229 new_cov=0/19 polymorphism_quality=3.2 quality=3.2 quality_position_model=Inf ref_cov=284/106 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=284/127 RA 193 . NC_007779 697558 1 . T bias_e_value=4413300 bias_p_value=0.949846 fisher_strand_p_value=1 frequency=4.192352e-03 genotype_quality=2368.8 ks_quality_p_value=0.700487 log10_base_likelihood=-7.85357 log10_qual_likelihood_position_model=1.53711 log10_strand_likelihood_position_model=0.302202 new_cov=1/1 polymorphism_quality=2.4 quality=2.4 quality_position_model=6.16287e-08 ref_cov=254/221 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=255/222 RA 194 . NC_007779 706385 1 . T bias_e_value=2699940 bias_p_value=0.581091 fisher_strand_p_value=0.372447 frequency=1.035213e-02 genotype_quality=2352.2 ks_quality_p_value=0.641726 log10_base_likelihood=-21.6083 log10_qual_likelihood_position_model=4.27287 log10_strand_likelihood_position_model=0.799885 new_cov=4/1 polymorphism_quality=16.3 quality=16.3 quality_position_model=1.1424e-18 ref_cov=239/239 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=243/240 RA 195 . NC_007779 706386 0 T . bias_e_value=4643310 bias_p_value=0.99935 fisher_strand_p_value=1 frequency=6.070137e-03 genotype_quality=1991.3 ks_quality_p_value=0.964161 log10_base_likelihood=-6.68855 log10_qual_likelihood_position_model=2.45799 log10_strand_likelihood_position_model=0.424205 new_cov=2/1 polymorphism_quality=1.2 quality=1.2 quality_position_model=1.22894e-05 ref_cov=245/245 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=247/246 RA 196 . NC_007779 710864 0 T G bias_e_value=4.58546e-05 bias_p_value=9.86899e-12 fisher_strand_p_value=3.3191e-13 frequency=2.299595e-02 genotype_quality=1057.6 ks_quality_p_value=1 log10_base_likelihood=-7.80884 log10_qual_likelihood_position_model=14.7933 log10_strand_likelihood_position_model=12.479 new_cov=10/0 polymorphism_quality=2.3 quality=2.3 quality_position_model=Inf ref_cov=10/254 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=20/254 RA 197 . NC_007779 749354 0 C A frequency=1 genotype_quality=1631.7 new_cov=183/211 quality=1631.7 ref_cov=0/0 tot_cov=183/211 RA 198 . NC_007779 752693 0 A C bias_e_value=5.25913e-12 bias_p_value=1.13189e-18 fisher_strand_p_value=2.45238e-20 frequency=5.798340e-02 genotype_quality=1514.8 ks_quality_p_value=1 log10_base_likelihood=-15.0676 log10_qual_likelihood_position_model=42.59 log10_strand_likelihood_position_model=19.6104 new_cov=0/43 polymorphism_quality=9.7 quality=9.7 quality_position_model=Inf ref_cov=283/131 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=283/175 RA 199 . NC_007779 758300 0 G A bias_e_value=3207460 bias_p_value=0.690321 fisher_strand_p_value=1 frequency=1.660728e-02 genotype_quality=1688.8 ks_quality_p_value=0.325039 log10_base_likelihood=-13.6296 log10_qual_likelihood_position_model=3.76398 log10_strand_likelihood_position_model=0.529281 new_cov=4/3 polymorphism_quality=8.3 quality=8.3 quality_position_model=2.38291e-11 ref_cov=231/182 tot_cov=235/185 RA 200 . NC_007779 758440 0 A T bias_e_value=825298 bias_p_value=0.177624 error=polymorphic_without_reference_base fisher_strand_p_value=0.0652764 frequency=6.719494e-02 genotype_quality=1885.7 ks_quality_p_value=0.655437 log10_base_likelihood=-104.944 log10_qual_likelihood_position_model=7.33928 log10_strand_likelihood_position_model=1.70033 new_cov=19/14 polymorphism_quality=100.0 quality=100.0 quality_position_model=2.05029e-98 ref_cov=182/276 reject=SURROUNDING_HOMOPOLYMER tot_cov=201/290 RA 201 . NC_007779 758562 0 T A bias_e_value=4633670 bias_p_value=0.997274 fisher_strand_p_value=1 frequency=8.984566e-03 genotype_quality=1782.1 ks_quality_p_value=0.927079 log10_base_likelihood=-8.6622 log10_qual_likelihood_position_model=2.37196 log10_strand_likelihood_position_model=0.424874 new_cov=2/2 polymorphism_quality=3.2 quality=3.2 quality_position_model=8.78585e-08 ref_cov=227/213 tot_cov=229/215 RA 202 . NC_007779 758579 0 A T bias_e_value=2905380 bias_p_value=0.625306 fisher_strand_p_value=1 frequency=1.133347e-02 genotype_quality=1707.5 ks_quality_p_value=0.271367 log10_base_likelihood=-12.2571 log10_qual_likelihood_position_model=3.37363 log10_strand_likelihood_position_model=0.485495 new_cov=3/2 polymorphism_quality=6.9 quality=6.9 quality_position_model=2.175e-10 ref_cov=227/208 tot_cov=231/210 RA 203 . NC_007779 758631 0 G T bias_e_value=3758390 bias_p_value=0.808894 fisher_strand_p_value=0.449491 frequency=1.209068e-02 genotype_quality=1735.9 ks_quality_p_value=0.999923 log10_base_likelihood=-10.1062 log10_qual_likelihood_position_model=7.04406 log10_strand_likelihood_position_model=0.770851 new_cov=2/5 polymorphism_quality=4.7 quality=4.7 quality_position_model=0.000504404 ref_cov=210/212 tot_cov=212/217 RA 204 . NC_007779 759019 0 C G bias_e_value=1.56807e-25 bias_p_value=3.37487e-32 fisher_strand_p_value=4.33672e-34 frequency=9.078074e-02 genotype_quality=1285.5 ks_quality_p_value=1 log10_base_likelihood=-60.8132 log10_qual_likelihood_position_model=32.7961 log10_strand_likelihood_position_model=33.3628 new_cov=0/30 polymorphism_quality=55.8 quality=55.8 quality_position_model=Inf ref_cov=284/10 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=284/40 RA 205 . NC_007779 771375 0 A . bias_e_value=4113660 bias_p_value=0.885356 fisher_strand_p_value=0.588149 frequency=8.255959e-03 genotype_quality=1474.8 ks_quality_p_value=0.954073 log10_base_likelihood=-7.67776 log10_qual_likelihood_position_model=2.0207 log10_strand_likelihood_position_model=0.479464 new_cov=1/2 polymorphism_quality=2.2 quality=2.2 quality_position_model=4.53761e-07 ref_cov=200/160 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=201/162 RA 206 . NC_007779 780786 0 C A bias_e_value=7.45266e-05 bias_p_value=1.60399e-11 fisher_strand_p_value=5.48725e-13 frequency=5.049515e-02 genotype_quality=1468.3 ks_quality_p_value=1 log10_base_likelihood=-13.1763 log10_qual_likelihood_position_model=33.2056 log10_strand_likelihood_position_model=12.2606 new_cov=38/0 polymorphism_quality=7.8 quality=7.8 quality_position_model=Inf ref_cov=186/226 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=226/226 RA 207 . NC_007779 817515 0 G T bias_e_value=7.82995e-10 bias_p_value=1.68519e-16 fisher_strand_p_value=4.11577e-18 frequency=7.059717e-02 genotype_quality=1400.5 ks_quality_p_value=0.997826 log10_base_likelihood=-19.4016 log10_qual_likelihood_position_model=33.1197 log10_strand_likelihood_position_model=17.3855 new_cov=0/52 polymorphism_quality=14.1 quality=14.1 quality_position_model=Inf ref_cov=235/177 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=235/230 RA 208 . NC_007779 827921 0 T G bias_e_value=1.79811e-14 bias_p_value=3.86995e-21 fisher_strand_p_value=7.44919e-23 frequency=6.018066e-02 genotype_quality=1193.5 ks_quality_p_value=1 log10_base_likelihood=-7.95116 log10_qual_likelihood_position_model=39.4548 log10_strand_likelihood_position_model=22.1279 new_cov=56/0 polymorphism_quality=2.5 quality=2.5 quality_position_model=Inf ref_cov=125/226 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=182/226 RA 209 . NC_007779 829585 0 G T bias_e_value=37.0472 bias_p_value=7.97342e-06 fisher_strand_p_value=5.20708e-07 frequency=3.464413e-02 genotype_quality=1073.5 ks_quality_p_value=0.989261 log10_base_likelihood=-9.94021 log10_qual_likelihood_position_model=21.0119 log10_strand_likelihood_position_model=6.28341 new_cov=13/0 polymorphism_quality=4.5 quality=4.5 quality_position_model=Inf ref_cov=90/198 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=104/198 RA 210 . NC_007779 835061 0 T . bias_e_value=1248610 bias_p_value=0.268731 fisher_strand_p_value=0.622632 frequency=6.293297e-03 genotype_quality=1915.1 ks_quality_p_value=0.120122 log10_base_likelihood=-7.24256 log10_qual_likelihood_position_model=2.47075 log10_strand_likelihood_position_model=0.426899 new_cov=2/1 polymorphism_quality=1.7 quality=1.7 quality_position_model=3.34737e-06 ref_cov=235/238 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=237/239 RA 211 . NC_007779 837857 0 A . bias_e_value=1229320 bias_p_value=0.264579 fisher_strand_p_value=0.0890466 frequency=7.102966e-03 genotype_quality=1735.6 ks_quality_p_value=0.822014 log10_base_likelihood=-7.86469 log10_qual_likelihood_position_model=1.67206 log10_strand_likelihood_position_model=1.05038 new_cov=3/0 polymorphism_quality=2.4 quality=2.4 quality_position_model=4.93812e-07 ref_cov=186/233 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/233 RA 212 . NC_007779 842195 0 C A bias_e_value=0.00301172 bias_p_value=6.48193e-10 fisher_strand_p_value=2.55282e-11 frequency=3.756237e-02 genotype_quality=1830.4 ks_quality_p_value=1 log10_base_likelihood=-15.5896 log10_qual_likelihood_position_model=32.9742 log10_strand_likelihood_position_model=10.7062 new_cov=43/0 polymorphism_quality=10.2 quality=10.2 quality_position_model=Inf ref_cov=291/242 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=335/242 RA 213 . NC_007779 845764 1 . T bias_e_value=657743 bias_p_value=0.141562 fisher_strand_p_value=0.271763 frequency=7.177353e-03 genotype_quality=2050.4 ks_quality_p_value=0.117127 log10_base_likelihood=-12.3842 log10_qual_likelihood_position_model=3.31778 log10_strand_likelihood_position_model=0.692915 new_cov=3/0 polymorphism_quality=7.0 quality=7.0 quality_position_model=2.30425e-10 ref_cov=243/172 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=246/172 RA 214 . NC_007779 845765 0 T . bias_e_value=4632850 bias_p_value=0.997099 fisher_strand_p_value=1 frequency=7.083893e-03 genotype_quality=1727.6 ks_quality_p_value=0.924796 log10_base_likelihood=-7.48585 log10_qual_likelihood_position_model=2.07301 log10_strand_likelihood_position_model=0.367025 new_cov=2/1 polymorphism_quality=2.0 quality=2.0 quality_position_model=6.22026e-07 ref_cov=247/172 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=249/174 RA 215 . NC_007779 847616 0 T C bias_e_value=0.161895 bias_p_value=3.48435e-08 fisher_strand_p_value=1.64142e-09 frequency=3.459358e-02 genotype_quality=1234.0 ks_quality_p_value=1 log10_base_likelihood=-8.70037 log10_qual_likelihood_position_model=30.0708 log10_strand_likelihood_position_model=8.78478 new_cov=20/0 polymorphism_quality=3.2 quality=3.2 quality_position_model=Inf ref_cov=124/235 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=144/235 RA 216 . NC_007779 847635 0 A C bias_e_value=0.000452693 bias_p_value=9.74302e-11 fisher_strand_p_value=3.56091e-12 frequency=3.184509e-02 genotype_quality=1401.7 ks_quality_p_value=1 log10_base_likelihood=-9.01279 log10_qual_likelihood_position_model=33.5074 log10_strand_likelihood_position_model=11.4484 new_cov=23/0 polymorphism_quality=3.6 quality=3.6 quality_position_model=Inf ref_cov=108/257 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=131/257 RA 217 . NC_007779 848585 0 C A bias_e_value=0.000181275 bias_p_value=3.90146e-11 fisher_strand_p_value=1.84722e-12 frequency=3.912163e-02 genotype_quality=1607.7 ks_quality_p_value=0.746045 log10_base_likelihood=-9.96627 log10_qual_likelihood_position_model=37.0611 log10_strand_likelihood_position_model=11.7335 new_cov=35/0 polymorphism_quality=4.5 quality=4.5 quality_position_model=Inf ref_cov=204/258 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=239/258 RA 218 . NC_007779 853114 0 C G bias_e_value=13.9812 bias_p_value=3.00908e-06 fisher_strand_p_value=1.82813e-07 frequency=2.937126e-02 genotype_quality=1297.2 ks_quality_p_value=0.996457 log10_base_likelihood=-13.7172 log10_qual_likelihood_position_model=13.5732 log10_strand_likelihood_position_model=6.73799 new_cov=0/12 polymorphism_quality=8.3 quality=8.3 quality_position_model=Inf ref_cov=239/84 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=239/96 RA 219 . NC_007779 854530 0 T C bias_e_value=29044.8 bias_p_value=0.00625113 fisher_strand_p_value=0.000764549 frequency=1.732540e-02 genotype_quality=1717.5 ks_quality_p_value=1 log10_base_likelihood=-9.51897 log10_qual_likelihood_position_model=13.1669 log10_strand_likelihood_position_model=3.11659 new_cov=10/0 polymorphism_quality=4.1 quality=4.1 quality_position_model=Inf ref_cov=207/223 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=218/223 RA 220 . NC_007779 884191 1 . T bias_e_value=1076940 bias_p_value=0.231784 fisher_strand_p_value=0.0610622 frequency=1.176262e-02 genotype_quality=2076.5 ks_quality_p_value=1 log10_base_likelihood=-17.2028 log10_qual_likelihood_position_model=7.55613 log10_strand_likelihood_position_model=1.50006 new_cov=0/5 polymorphism_quality=11.9 quality=11.9 quality_position_model=3.93653e-10 ref_cov=211/209 reject=POLYMORPHISM_STRAND tot_cov=211/214 RA 221 . NC_007779 887234 0 C A frequency=1 genotype_quality=1505.0 new_cov=207/183 quality=1505.0 ref_cov=0/0 tot_cov=207/184 RA 222 . NC_007779 889983 1 . A bias_e_value=1701050 bias_p_value=0.366107 fisher_strand_p_value=0.607367 frequency=6.681442e-03 genotype_quality=2224.9 ks_quality_p_value=0.191159 log10_base_likelihood=-12.7054 log10_qual_likelihood_position_model=2.92918 log10_strand_likelihood_position_model=0.446849 new_cov=2/1 polymorphism_quality=7.3 quality=7.3 quality_position_model=2.4223e-11 ref_cov=212/234 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=214/235 RA 223 . NC_007779 894943 0 T G bias_e_value=1.00821e-16 bias_p_value=2.16991e-23 fisher_strand_p_value=3.79144e-25 frequency=5.629253e-02 genotype_quality=1250.1 ks_quality_p_value=1 log10_base_likelihood=-8.14592 log10_qual_likelihood_position_model=60.0092 log10_strand_likelihood_position_model=24.4212 new_cov=55/0 polymorphism_quality=2.7 quality=2.7 quality_position_model=Inf ref_cov=107/238 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=164/238 RA 224 . NC_007779 895911 0 C A bias_e_value=0.000206767 bias_p_value=4.45011e-11 fisher_strand_p_value=1.57951e-12 frequency=4.828024e-02 genotype_quality=1269.9 ks_quality_p_value=1 log10_base_likelihood=-11.6348 log10_qual_likelihood_position_model=22.9448 log10_strand_likelihood_position_model=11.8015 new_cov=35/0 polymorphism_quality=6.2 quality=6.2 quality_position_model=Inf ref_cov=169/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=204/219 RA 225 . NC_007779 904838 0 C A bias_e_value=5.36246e-23 bias_p_value=1.15413e-29 fisher_strand_p_value=2.41989e-31 frequency=1.249471e-01 genotype_quality=1395.4 ks_quality_p_value=0.663266 log10_base_likelihood=-44.7811 log10_qual_likelihood_position_model=60.976 log10_strand_likelihood_position_model=30.6162 new_cov=76/0 polymorphism_quality=39.7 quality=39.7 quality_position_model=Inf ref_cov=131/256 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=207/256 RA 226 . NC_007779 911333 0 T G bias_e_value=7.45138e-11 bias_p_value=1.60371e-17 fisher_strand_p_value=3.69153e-19 frequency=4.666042e-02 genotype_quality=1064.5 ks_quality_p_value=1 log10_base_likelihood=-6.25868 log10_qual_likelihood_position_model=31.1408 log10_strand_likelihood_position_model=18.4328 new_cov=30/0 polymorphism_quality=0.7 quality=0.7 quality_position_model=Inf ref_cov=58/227 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=88/228 RA 227 . NC_007779 932353 0 T . bias_e_value=3785430 bias_p_value=0.814714 fisher_strand_p_value=0.622315 frequency=7.119179e-03 genotype_quality=1702.3 ks_quality_p_value=0.734048 log10_base_likelihood=-7.76725 log10_qual_likelihood_position_model=1.53995 log10_strand_likelihood_position_model=0.427026 new_cov=2/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=1.02598e-07 ref_cov=207/210 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=209/212 RA 228 . NC_007779 932754 1 . A bias_e_value=4627110 bias_p_value=0.995862 fisher_strand_p_value=1 frequency=4.366875e-03 genotype_quality=2301.0 ks_quality_p_value=0.910421 log10_base_likelihood=-7.97664 log10_qual_likelihood_position_model=1.41769 log10_strand_likelihood_position_model=0.300487 new_cov=1/1 polymorphism_quality=2.5 quality=2.5 quality_position_model=3.44718e-08 ref_cov=221/235 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=222/236 RA 229 . NC_007779 947970 0 C A bias_e_value=0.000364383 bias_p_value=7.84239e-11 fisher_strand_p_value=2.84287e-12 frequency=4.761219e-02 genotype_quality=1547.9 ks_quality_p_value=1 log10_base_likelihood=-18.5235 log10_qual_likelihood_position_model=23.6663 log10_strand_likelihood_position_model=11.5462 new_cov=36/0 polymorphism_quality=13.2 quality=13.2 quality_position_model=Inf ref_cov=196/234 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/234 RA 230 . NC_007779 954820 0 A C bias_e_value=9.58068e-13 bias_p_value=2.06199e-19 fisher_strand_p_value=4.30528e-21 frequency=6.876850e-02 genotype_quality=1146.2 ks_quality_p_value=1 log10_base_likelihood=-10.3926 log10_qual_likelihood_position_model=41.3745 log10_strand_likelihood_position_model=20.366 new_cov=0/51 polymorphism_quality=5.0 quality=5.0 quality_position_model=Inf ref_cov=211/115 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=211/166 RA 231 . NC_007779 969494 0 C A bias_e_value=9.30754e-05 bias_p_value=2.0032e-11 fisher_strand_p_value=6.93769e-13 frequency=5.034924e-02 genotype_quality=1228.4 ks_quality_p_value=0.995626 log10_base_likelihood=-13.5128 log10_qual_likelihood_position_model=24.0919 log10_strand_likelihood_position_model=12.1588 new_cov=35/0 polymorphism_quality=8.1 quality=8.1 quality_position_model=Inf ref_cov=153/209 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=190/210 RA 232 . NC_007779 975142 0 T G bias_e_value=0.0656948 bias_p_value=1.41391e-08 fisher_strand_p_value=6.37664e-10 frequency=2.627373e-02 genotype_quality=903.4 ks_quality_p_value=1 log10_base_likelihood=-7.96604 log10_qual_likelihood_position_model=11.4761 log10_strand_likelihood_position_model=9.19541 new_cov=8/0 polymorphism_quality=2.5 quality=2.5 quality_position_model=Inf ref_cov=12/214 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=20/214 RA 233 . NC_007779 987574 0 G T frequency=1 genotype_quality=1582.3 new_cov=134/247 quality=1582.3 ref_cov=0/0 tot_cov=134/247 RA 234 . NC_007779 987916 0 T G bias_e_value=3.2651e-08 bias_p_value=7.02727e-15 fisher_strand_p_value=1.88877e-16 frequency=4.311180e-02 genotype_quality=1031.2 ks_quality_p_value=1 log10_base_likelihood=-9.92602 log10_qual_likelihood_position_model=23.1029 log10_strand_likelihood_position_model=15.7238 new_cov=18/0 polymorphism_quality=4.5 quality=4.5 quality_position_model=Inf ref_cov=26/227 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=44/227 RA 235 . NC_007779 991407 0 G T bias_e_value=2.82201e-05 bias_p_value=6.07363e-12 fisher_strand_p_value=3.26931e-13 frequency=4.472256e-02 genotype_quality=1477.9 ks_quality_p_value=0.614421 log10_base_likelihood=-9.91172 log10_qual_likelihood_position_model=42.3973 log10_strand_likelihood_position_model=12.6296 new_cov=0/40 polymorphism_quality=4.5 quality=4.5 quality_position_model=Inf ref_cov=232/197 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/237 RA 236 . NC_007779 994634 0 G T bias_e_value=18.8251 bias_p_value=4.05161e-06 fisher_strand_p_value=2.50076e-07 frequency=2.273464e-02 genotype_quality=1525.7 ks_quality_p_value=1 log10_base_likelihood=-7.19951 log10_qual_likelihood_position_model=18.7652 log10_strand_likelihood_position_model=6.63277 new_cov=0/23 polymorphism_quality=1.7 quality=1.7 quality_position_model=Inf ref_cov=211/212 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=212/235 RA 237 . NC_007779 999606 0 A T bias_e_value=1476.66 bias_p_value=0.000317812 fisher_strand_p_value=2.76454e-05 frequency=5.778360e-02 genotype_quality=1200.5 ks_quality_p_value=1 log10_base_likelihood=-25.1233 log10_qual_likelihood_position_model=18.7202 log10_strand_likelihood_position_model=4.7094 new_cov=21/0 polymorphism_quality=19.9 quality=19.9 quality_position_model=0.00227539 ref_cov=180/129 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=201/129 RA 238 . NC_007779 999607 0 A C bias_e_value=76.2181 bias_p_value=1.64039e-05 fisher_strand_p_value=1.11544e-06 frequency=6.105471e-02 genotype_quality=1154.1 ks_quality_p_value=1 log10_base_likelihood=-24.7062 log10_qual_likelihood_position_model=23.8733 log10_strand_likelihood_position_model=6.15845 new_cov=27/0 polymorphism_quality=19.5 quality=19.5 quality_position_model=Inf ref_cov=173/129 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=200/129 RA 239 . NC_007779 999613 0 A T bias_e_value=8690.48 bias_p_value=0.0018704 fisher_strand_p_value=0.000196125 frequency=5.560541e-02 genotype_quality=1126.3 ks_quality_p_value=1 log10_base_likelihood=-28.8333 log10_qual_likelihood_position_model=20.7899 log10_strand_likelihood_position_model=3.95168 new_cov=18/0 polymorphism_quality=23.6 quality=23.6 quality_position_model=6.16461e-06 ref_cov=170/118 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=188/118 RA 240 . NC_007779 999623 0 A T bias_e_value=27878.6 bias_p_value=0.00600013 fisher_strand_p_value=0.000729686 frequency=4.942226e-02 genotype_quality=1043.7 ks_quality_p_value=1 log10_base_likelihood=-18.5372 log10_qual_likelihood_position_model=17.1093 log10_strand_likelihood_position_model=3.3862 new_cov=16/0 polymorphism_quality=13.2 quality=13.2 quality_position_model=Inf ref_cov=162/107 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=179/107 RA 241 . NC_007779 999625 0 T C bias_e_value=334168 bias_p_value=0.0719208 fisher_strand_p_value=0.0135703 frequency=2.494144e-02 genotype_quality=1045.8 ks_quality_p_value=1 log10_base_likelihood=-8.56087 log10_qual_likelihood_position_model=10.7983 log10_strand_likelihood_position_model=1.9646 new_cov=9/0 polymorphism_quality=3.1 quality=3.1 quality_position_model=Inf ref_cov=165/111 reject=POLYMORPHISM_STRAND tot_cov=174/111 RA 242 . NC_007779 1002640 0 G . bias_e_value=4272940 bias_p_value=0.919636 fisher_strand_p_value=1 frequency=6.811142e-03 genotype_quality=1893.6 ks_quality_p_value=0.626887 log10_base_likelihood=-7.73666 log10_qual_likelihood_position_model=1.99485 log10_strand_likelihood_position_model=0.398232 new_cov=2/1 polymorphism_quality=2.2 quality=2.2 quality_position_model=3.05122e-07 ref_cov=233/204 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=235/205 RA 243 . NC_007779 1006080 0 C A bias_e_value=5.27065e-09 bias_p_value=1.13437e-15 fisher_strand_p_value=2.90281e-17 frequency=8.262396e-02 genotype_quality=1320.7 ks_quality_p_value=1 log10_base_likelihood=-24.8436 log10_qual_likelihood_position_model=29.8232 log10_strand_likelihood_position_model=16.5372 new_cov=50/0 polymorphism_quality=19.6 quality=19.6 quality_position_model=Inf ref_cov=168/220 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=219/220 RA 244 . NC_007779 1013042 0 G C bias_e_value=0.000897011 bias_p_value=1.93058e-10 fisher_strand_p_value=7.27083e-12 frequency=5.072212e-02 genotype_quality=1077.7 ks_quality_p_value=0.996305 log10_base_likelihood=-14.2364 log10_qual_likelihood_position_model=16.1743 log10_strand_likelihood_position_model=11.1384 new_cov=0/18 polymorphism_quality=8.9 quality=8.9 quality_position_model=Inf ref_cov=225/62 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=226/80 RA 245 . NC_007779 1019391 0 A . bias_e_value=4633090 bias_p_value=0.997151 fisher_strand_p_value=1 frequency=1.256943e-02 genotype_quality=1932.7 ks_quality_p_value=0.92547 log10_base_likelihood=-16.309 log10_qual_likelihood_position_model=3.45805 log10_strand_likelihood_position_model=0.502491 new_cov=3/3 polymorphism_quality=11.0 quality=11.0 quality_position_model=2.0254e-14 ref_cov=237/233 reject=INDEL_HOMOPOLYMER tot_cov=241/236 RA 246 . NC_007779 1023337 0 T G bias_e_value=0.00563484 bias_p_value=1.21275e-09 fisher_strand_p_value=4.90369e-11 frequency=2.147770e-02 genotype_quality=1084.0 ks_quality_p_value=0.999702 log10_base_likelihood=-5.82262 log10_qual_likelihood_position_model=17.3881 log10_strand_likelihood_position_model=10.3095 new_cov=12/0 polymorphism_quality=0.3 quality=0.3 quality_position_model=Inf ref_cov=33/245 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=45/245 RA 247 . NC_007779 1035834 0 C A bias_e_value=0.000188009 bias_p_value=4.04639e-11 fisher_strand_p_value=1.43121e-12 frequency=3.893280e-02 genotype_quality=1441.7 ks_quality_p_value=1 log10_base_likelihood=-11.0357 log10_qual_likelihood_position_model=24.8249 log10_strand_likelihood_position_model=11.8443 new_cov=31/0 polymorphism_quality=5.6 quality=5.6 quality_position_model=Inf ref_cov=163/252 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=196/252 RA 248 . NC_007779 1037529 0 T G bias_e_value=242.286 bias_p_value=5.21457e-05 fisher_strand_p_value=3.89569e-06 frequency=1.879311e-02 genotype_quality=999.9 ks_quality_p_value=0.994369 log10_base_likelihood=-6.12286 log10_qual_likelihood_position_model=7.3009 log10_strand_likelihood_position_model=5.40942 new_cov=5/0 polymorphism_quality=0.6 quality=0.6 quality_position_model=Inf ref_cov=18/232 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=23/232 RA 249 . NC_007779 1037601 1 . G bias_e_value=1822290 bias_p_value=0.3922 fisher_strand_p_value=0.13103 frequency=6.600380e-03 genotype_quality=1496.8 ks_quality_p_value=0.980844 log10_base_likelihood=-7.98224 log10_qual_likelihood_position_model=2.85424 log10_strand_likelihood_position_model=0.88263 new_cov=2/0 polymorphism_quality=2.5 quality=2.5 quality_position_model=4.25469e-06 ref_cov=108/193 reject=POLYMORPHISM_STRAND tot_cov=110/193 RA 250 . NC_007779 1058914 0 A C bias_e_value=2.09574e-12 bias_p_value=4.51053e-19 fisher_strand_p_value=9.57753e-21 frequency=6.194973e-02 genotype_quality=1108.5 ks_quality_p_value=1 log10_base_likelihood=-12.4908 log10_qual_likelihood_position_model=35.5516 log10_strand_likelihood_position_model=20.0187 new_cov=0/33 polymorphism_quality=7.1 quality=7.1 quality_position_model=Inf ref_cov=232/60 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/93 RA 251 . NC_007779 1070200 0 A C bias_e_value=0.19679 bias_p_value=4.23539e-08 fisher_strand_p_value=2.01466e-09 frequency=3.677368e-02 genotype_quality=844.5 ks_quality_p_value=1 log10_base_likelihood=-5.71142 log10_qual_likelihood_position_model=16.5546 log10_strand_likelihood_position_model=8.70011 new_cov=1/11 polymorphism_quality=0.2 quality=0.2 quality_position_model=Inf ref_cov=191/23 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=192/34 RA 252 . NC_007779 1072428 0 T G bias_e_value=0.000335191 bias_p_value=7.21409e-11 fisher_strand_p_value=2.60692e-12 frequency=3.716469e-02 genotype_quality=1297.5 ks_quality_p_value=1 log10_base_likelihood=-8.01224 log10_qual_likelihood_position_model=26.1907 log10_strand_likelihood_position_model=11.5912 new_cov=30/1 polymorphism_quality=2.5 quality=2.5 quality_position_model=Inf ref_cov=125/236 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=155/237 RA 253 . NC_007779 1079882 0 T G bias_e_value=0.000242171 bias_p_value=5.2121e-11 fisher_strand_p_value=1.8608e-12 frequency=3.149700e-02 genotype_quality=954.9 ks_quality_p_value=1 log10_base_likelihood=-7.90783 log10_qual_likelihood_position_model=15.8465 log10_strand_likelihood_position_model=11.7303 new_cov=12/0 polymorphism_quality=2.4 quality=2.4 quality_position_model=Inf ref_cov=20/223 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=32/223 RA 254 . NC_007779 1092328 0 C A bias_e_value=0.0378379 bias_p_value=8.14362e-09 fisher_strand_p_value=3.58083e-10 frequency=4.174709e-02 genotype_quality=1445.3 ks_quality_p_value=0.999631 log10_base_likelihood=-10.0625 log10_qual_likelihood_position_model=24.6957 log10_strand_likelihood_position_model=9.46094 new_cov=32/0 polymorphism_quality=4.6 quality=4.6 quality_position_model=Inf ref_cov=195/206 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=227/206 RA 255 . NC_007779 1093686 0 T C frequency=1 genotype_quality=2339.9 new_cov=236/295 quality=2339.9 ref_cov=0/0 tot_cov=236/295 RA 256 . NC_007779 1097580 0 C T bias_e_value=3457.39 bias_p_value=0.000744112 fisher_strand_p_value=0.536325 frequency=2.150021e-01 genotype_quality=1285.5 ks_quality_p_value=0.00013138 log10_base_likelihood=-342.146 log10_qual_likelihood_position_model=30.0542 log10_strand_likelihood_position_model=1.17101 new_cov=63/56 polymorphism_quality=inf quality=inf quality_position_model=1.09814000001537e-313 ref_cov=215/218 reject=KS_QUALITY_P_VALUE tot_cov=278/274 RA 257 . NC_007779 1097583 1 . A bias_e_value=2713590 bias_p_value=0.584028 fisher_strand_p_value=0.242707 frequency=3.913879e-03 genotype_quality=1854.3 ks_quality_p_value=0.993241 log10_base_likelihood=-7.10949 log10_qual_likelihood_position_model=2.14601 log10_strand_likelihood_position_model=0.614917 new_cov=0/2 polymorphism_quality=1.6 quality=1.6 quality_position_model=3.31809e-06 ref_cov=259/250 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=259/252 RA 258 . NC_007779 1097765 0 A . bias_e_value=2210840 bias_p_value=0.475825 fisher_strand_p_value=0.653458 frequency=5.434036e-03 genotype_quality=3427.6 ks_quality_p_value=0.264138 log10_base_likelihood=-12.3396 log10_qual_likelihood_position_model=1.96036 log10_strand_likelihood_position_model=0.587159 new_cov=1/4 polymorphism_quality=6.9 quality=6.9 quality_position_model=8.15531e-12 ref_cov=367/547 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=368/551 RA 259 . NC_007779 1099903 0 G C bias_e_value=2119220 bias_p_value=0.456106 fisher_strand_p_value=0.161592 frequency=9.669304e-03 genotype_quality=1790.0 ks_quality_p_value=0.999944 log10_base_likelihood=-5.62543 log10_qual_likelihood_position_model=7.3327 log10_strand_likelihood_position_model=1.08538 new_cov=5/0 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=253/166 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=259/166 RA 260 . NC_007779 1115091 0 C A bias_e_value=9.17711 bias_p_value=1.97513e-06 fisher_strand_p_value=1.16416e-07 frequency=3.308582e-02 genotype_quality=1381.4 ks_quality_p_value=1 log10_base_likelihood=-8.09327 log10_qual_likelihood_position_model=17.09 log10_strand_likelihood_position_model=6.93399 new_cov=0/15 polymorphism_quality=2.6 quality=2.6 quality_position_model=Inf ref_cov=241/119 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=241/134 RA 261 . NC_007779 1116582 0 G C bias_e_value=1.78658e-28 bias_p_value=3.84515e-35 fisher_strand_p_value=4.54753e-37 frequency=1.595087e-01 genotype_quality=766.4 ks_quality_p_value=0.99849 log10_base_likelihood=-67.9081 log10_qual_likelihood_position_model=33.1532 log10_strand_likelihood_position_model=36.3428 new_cov=1/42 polymorphism_quality=62.9 quality=62.9 quality_position_model=Inf ref_cov=207/11 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=208/53 RA 262 . NC_007779 1148417 0 C A bias_e_value=0.000107596 bias_p_value=2.31573e-11 fisher_strand_p_value=1.05003e-12 frequency=5.234909e-02 genotype_quality=1580.9 ks_quality_p_value=0.76441 log10_base_likelihood=-16.9559 log10_qual_likelihood_position_model=36.2238 log10_strand_likelihood_position_model=12.0408 new_cov=39/0 polymorphism_quality=11.6 quality=11.6 quality_position_model=Inf ref_cov=215/243 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=255/243 RA 263 . NC_007779 1151485 0 C A bias_e_value=1.79572e-06 bias_p_value=3.86482e-13 fisher_strand_p_value=1.1683e-14 frequency=6.453085e-02 genotype_quality=1264.6 ks_quality_p_value=1 log10_base_likelihood=-12.0102 log10_qual_likelihood_position_model=27.7907 log10_strand_likelihood_position_model=13.9424 new_cov=45/0 polymorphism_quality=6.6 quality=6.6 quality_position_model=Inf ref_cov=165/195 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=211/195 RA 264 . NC_007779 1155150 0 T G bias_e_value=1.13884 bias_p_value=2.45106e-07 fisher_strand_p_value=1.27824e-08 frequency=1.951218e-02 genotype_quality=1081.6 ks_quality_p_value=1 log10_base_likelihood=-5.97534 log10_qual_likelihood_position_model=12.8819 log10_strand_likelihood_position_model=7.89339 new_cov=8/0 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=24/247 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=32/247 RA 265 . NC_007779 1158848 0 T G bias_e_value=2.49224e-24 bias_p_value=5.36388e-31 fisher_strand_p_value=7.15011e-33 frequency=1.018963e-01 genotype_quality=1406.2 ks_quality_p_value=1 log10_base_likelihood=-26.6984 log10_qual_likelihood_position_model=48.8453 log10_strand_likelihood_position_model=32.1457 new_cov=73/0 polymorphism_quality=21.5 quality=21.5 quality_position_model=Inf ref_cov=117/267 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=191/267 RA 266 . NC_007779 1164334 0 C G bias_e_value=1545.41 bias_p_value=0.000332608 fisher_strand_p_value=2.95067e-05 frequency=2.401257e-02 genotype_quality=897.5 ks_quality_p_value=0.984808 log10_base_likelihood=-5.81022 log10_qual_likelihood_position_model=7.97343 log10_strand_likelihood_position_model=4.53008 new_cov=0/6 polymorphism_quality=0.3 quality=0.3 quality_position_model=Inf ref_cov=185/36 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=185/42 RA 267 . NC_007779 1164938 1 . G bias_e_value=2460620 bias_p_value=0.529583 fisher_strand_p_value=0.221521 frequency=4.986763e-03 genotype_quality=2001.8 ks_quality_p_value=0.924594 log10_base_likelihood=-7.34123 log10_qual_likelihood_position_model=1.90854 log10_strand_likelihood_position_model=0.654585 new_cov=2/0 polymorphism_quality=1.8 quality=1.8 quality_position_model=1.18165e-06 ref_cov=187/212 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/212 RA 268 . NC_007779 1164944 0 T G bias_e_value=5.86239e-08 bias_p_value=1.26172e-14 fisher_strand_p_value=3.44697e-16 frequency=3.901863e-02 genotype_quality=1004.3 ks_quality_p_value=1 log10_base_likelihood=-7.94423 log10_qual_likelihood_position_model=31.0445 log10_strand_likelihood_position_model=15.4626 new_cov=23/0 polymorphism_quality=2.5 quality=2.5 quality_position_model=Inf ref_cov=46/213 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=69/213 RA 269 . NC_007779 1170375 1 . T bias_e_value=1292520 bias_p_value=0.278181 fisher_strand_p_value=0.182572 frequency=5.988121e-03 genotype_quality=1622.7 ks_quality_p_value=0.429807 log10_base_likelihood=-8.12173 log10_qual_likelihood_position_model=1.84207 log10_strand_likelihood_position_model=0.738566 new_cov=2/0 polymorphism_quality=2.6 quality=2.6 quality_position_model=1.90372e-07 ref_cov=141/191 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=143/191 RA 270 . NC_007779 1170573 0 C T frequency=1 genotype_quality=2091.5 new_cov=312/190 quality=2091.5 ref_cov=0/0 tot_cov=312/190 RA 271 . NC_007779 1176562 0 C . bias_e_value=939370 bias_p_value=0.202175 fisher_strand_p_value=0.26137 frequency=7.766724e-03 genotype_quality=1569.5 ks_quality_p_value=0.194358 log10_base_likelihood=-8.30637 log10_qual_likelihood_position_model=1.93542 log10_strand_likelihood_position_model=0.742835 new_cov=0/3 polymorphism_quality=2.8 quality=2.8 quality_position_model=1.54674e-07 ref_cov=166/214 reject=POLYMORPHISM_STRAND tot_cov=168/218 RA 272 . NC_007779 1176573 0 A G bias_e_value=108.05 bias_p_value=2.3255e-05 fisher_strand_p_value=1.62266e-06 frequency=4.044247e-02 genotype_quality=1421.9 ks_quality_p_value=1 log10_base_likelihood=-17.2635 log10_qual_likelihood_position_model=25.8599 log10_strand_likelihood_position_model=5.85433 new_cov=0/20 polymorphism_quality=11.9 quality=11.9 quality_position_model=Inf ref_cov=187/184 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=187/204 RA 273 . NC_007779 1176575 0 G T bias_e_value=2388.66 bias_p_value=0.000514096 fisher_strand_p_value=4.69111e-05 frequency=3.028107e-02 genotype_quality=1566.5 ks_quality_p_value=0.999167 log10_base_likelihood=-13.655 log10_qual_likelihood_position_model=19.0678 log10_strand_likelihood_position_model=4.55111 new_cov=0/15 polymorphism_quality=8.3 quality=8.3 quality_position_model=Inf ref_cov=191/181 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=191/197 RA 274 . NC_007779 1177683 0 A G bias_e_value=1.11198e-06 bias_p_value=2.39324e-13 fisher_strand_p_value=7.12809e-15 frequency=5.541420e-02 genotype_quality=1200.5 ks_quality_p_value=1 log10_base_likelihood=-12.4735 log10_qual_likelihood_position_model=26.3424 log10_strand_likelihood_position_model=14.147 new_cov=25/0 polymorphism_quality=7.1 quality=7.1 quality_position_model=Inf ref_cov=81/251 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=106/251 RA 275 . NC_007779 1192244 0 C A bias_e_value=0.049255 bias_p_value=1.06008e-08 fisher_strand_p_value=4.71679e-10 frequency=4.086494e-02 genotype_quality=1464.8 ks_quality_p_value=1 log10_base_likelihood=-12.2006 log10_qual_likelihood_position_model=25.5017 log10_strand_likelihood_position_model=9.47583 new_cov=33/0 polymorphism_quality=6.8 quality=6.8 quality_position_model=Inf ref_cov=217/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=250/221 RA 276 . NC_007779 1197797 0 C T bias_e_value=3448640 bias_p_value=0.742228 fisher_strand_p_value=0.417355 frequency=1.376152e-02 genotype_quality=1861.9 ks_quality_p_value=0.897092 log10_base_likelihood=-11.4219 log10_qual_likelihood_position_model=2.8862 log10_strand_likelihood_position_model=0.721554 new_cov=2/4 polymorphism_quality=6.0 quality=6.0 quality_position_model=8.6335e-10 ref_cov=235/193 tot_cov=237/197 RA 277 . NC_007779 1197809 0 C T bias_e_value=2894000 bias_p_value=0.622857 fisher_strand_p_value=0.422183 frequency=1.304626e-02 genotype_quality=1947.7 ks_quality_p_value=0.638334 log10_base_likelihood=-11.5543 log10_qual_likelihood_position_model=2.72004 log10_strand_likelihood_position_model=0.701736 new_cov=2/4 polymorphism_quality=6.1 quality=6.1 quality_position_model=4.06959e-10 ref_cov=244/208 tot_cov=246/212 RA 278 . NC_007779 1197822 0 T C bias_e_value=1284660 bias_p_value=0.276489 fisher_strand_p_value=0.333378 frequency=8.657455e-03 genotype_quality=1857.0 ks_quality_p_value=0.23339 log10_base_likelihood=-8.50075 log10_qual_likelihood_position_model=2.33046 log10_strand_likelihood_position_model=0.691496 new_cov=1/3 polymorphism_quality=3.0 quality=3.0 quality_position_model=2.20901e-07 ref_cov=251/206 reject=POLYMORPHISM_STRAND tot_cov=253/209 RA 279 . NC_007779 1197824 0 A G bias_e_value=2312040 bias_p_value=0.497605 fisher_strand_p_value=0.339098 frequency=8.583069e-03 genotype_quality=1872.9 ks_quality_p_value=0.546328 log10_base_likelihood=-8.17918 log10_qual_likelihood_position_model=2.10458 log10_strand_likelihood_position_model=0.675313 new_cov=1/3 polymorphism_quality=2.7 quality=2.7 quality_position_model=2.67095e-07 ref_cov=249/211 reject=POLYMORPHISM_STRAND tot_cov=251/214 RA 280 . NC_007779 1213001 0 T C bias_e_value=3796040 bias_p_value=0.816997 fisher_strand_p_value=0.580395 frequency=6.565714e-02 genotype_quality=1803.5 ks_quality_p_value=0.792106 log10_base_likelihood=-92.2838 log10_qual_likelihood_position_model=6.99752 log10_strand_likelihood_position_model=0.919596 new_cov=17/15 polymorphism_quality=87.3 quality=87.3 quality_position_model=7.53747e-87 ref_cov=267/188 tot_cov=284/203 RA 281 . NC_007779 1213013 0 T C bias_e_value=1829950 bias_p_value=0.393849 fisher_strand_p_value=0.293613 frequency=4.814863e-02 genotype_quality=1902.9 ks_quality_p_value=0.440459 log10_base_likelihood=-64.8972 log10_qual_likelihood_position_model=6.82871 log10_strand_likelihood_position_model=1.05641 new_cov=11/13 polymorphism_quality=59.9 quality=59.9 quality_position_model=2.07205e-59 ref_cov=273/201 tot_cov=284/214 RA 282 . NC_007779 1213026 0 C T bias_e_value=3811840 bias_p_value=0.820397 fisher_strand_p_value=0.598772 frequency=3.201580e-02 genotype_quality=1943.7 ks_quality_p_value=0.775148 log10_base_likelihood=-33.7542 log10_qual_likelihood_position_model=4.88245 log10_strand_likelihood_position_model=0.800107 new_cov=7/8 polymorphism_quality=28.6 quality=28.6 quality_position_model=2.56462e-30 ref_cov=254/198 tot_cov=261/207 RA 283 . NC_007779 1213028 0 G A bias_e_value=3835410 bias_p_value=0.825471 fisher_strand_p_value=0.602489 frequency=3.163624e-02 genotype_quality=1958.3 ks_quality_p_value=0.781441 log10_base_likelihood=-33.6995 log10_qual_likelihood_position_model=5.02922 log10_strand_likelihood_position_model=0.773562 new_cov=7/8 polymorphism_quality=28.5 quality=28.5 quality_position_model=3.8485e-30 ref_cov=252/206 tot_cov=259/214 RA 284 . NC_007779 1213058 0 T C bias_e_value=4612420 bias_p_value=0.992701 fisher_strand_p_value=1 frequency=1.896763e-02 genotype_quality=1685.7 ks_quality_p_value=0.881635 log10_base_likelihood=-18.5123 log10_qual_likelihood_position_model=3.34757 log10_strand_likelihood_position_model=0.560662 new_cov=4/4 polymorphism_quality=13.2 quality=13.2 quality_position_model=1.0365e-16 ref_cov=200/213 tot_cov=204/217 RA 285 . NC_007779 1213061 0 C G bias_e_value=4555640 bias_p_value=0.980482 fisher_strand_p_value=1 frequency=1.322460e-02 genotype_quality=1931.0 ks_quality_p_value=0.809042 log10_base_likelihood=-12.3035 log10_qual_likelihood_position_model=6.81449 log10_strand_likelihood_position_model=0.502541 new_cov=3/3 polymorphism_quality=6.9 quality=6.9 quality_position_model=7.1704e-07 ref_cov=217/224 tot_cov=220/227 RA 286 . NC_007779 1213064 0 G A bias_e_value=4541080 bias_p_value=0.977348 fisher_strand_p_value=1 frequency=1.343441e-02 genotype_quality=1841.9 ks_quality_p_value=0.794846 log10_base_likelihood=-10.7733 log10_qual_likelihood_position_model=3.55266 log10_strand_likelihood_position_model=0.502439 new_cov=3/3 polymorphism_quality=5.4 quality=5.4 quality_position_model=1.1567e-08 ref_cov=216/222 reject=SURROUNDING_HOMOPOLYMER tot_cov=219/225 RA 287 . NC_007779 1213658 0 C . bias_e_value=764129 bias_p_value=0.164459 fisher_strand_p_value=0.0767622 frequency=9.327888e-03 genotype_quality=1367.2 ks_quality_p_value=0.503791 log10_base_likelihood=-7.27029 log10_qual_likelihood_position_model=3.85363 log10_strand_likelihood_position_model=1.11485 new_cov=3/0 polymorphism_quality=1.8 quality=1.8 quality_position_model=0.000491358 ref_cov=134/184 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=137/184 RA 288 . NC_007779 1224173 0 G A bias_e_value=0.014142 bias_p_value=3.0437e-09 fisher_strand_p_value=1.28e-10 frequency=5.821371e-02 genotype_quality=1335.7 ks_quality_p_value=1 log10_base_likelihood=-11.942 log10_qual_likelihood_position_model=31.3968 log10_strand_likelihood_position_model=10.1591 new_cov=0/32 polymorphism_quality=6.5 quality=6.5 quality_position_model=Inf ref_cov=207/176 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=207/208 RA 289 . NC_007779 1245322 0 C A bias_e_value=58.5103 bias_p_value=1.25928e-05 fisher_strand_p_value=9.59834e-07 frequency=2.434349e-02 genotype_quality=1408.7 ks_quality_p_value=0.875249 log10_base_likelihood=-5.85757 log10_qual_likelihood_position_model=27.0472 log10_strand_likelihood_position_model=6.07687 new_cov=23/0 polymorphism_quality=0.3 quality=0.3 quality_position_model=Inf ref_cov=221/195 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=244/195 RA 290 . NC_007779 1246917 0 T . bias_e_value=1233530 bias_p_value=0.265486 fisher_strand_p_value=0.254931 frequency=5.887985e-03 genotype_quality=2080.4 ks_quality_p_value=0.288488 log10_base_likelihood=-7.59087 log10_qual_likelihood_position_model=1.93942 log10_strand_likelihood_position_model=0.790156 new_cov=3/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=9.67903e-07 ref_cov=275/231 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=278/231 RA 291 . NC_007779 1262472 0 A C bias_e_value=4.78161e-09 bias_p_value=1.02911e-15 fisher_strand_p_value=2.62675e-17 frequency=6.586742e-02 genotype_quality=1263.9 ks_quality_p_value=1 log10_base_likelihood=-12.5803 log10_qual_likelihood_position_model=41.6736 log10_strand_likelihood_position_model=16.5806 new_cov=0/49 polymorphism_quality=7.2 quality=7.2 quality_position_model=Inf ref_cov=209/153 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=209/202 RA 292 . NC_007779 1273399 0 T G bias_e_value=1.96174e-41 bias_p_value=4.22212e-48 fisher_strand_p_value=3.67694e-50 frequency=1.575069e-01 genotype_quality=1222.5 ks_quality_p_value=1 log10_base_likelihood=-61.1001 log10_qual_likelihood_position_model=68.5236 log10_strand_likelihood_position_model=49.4345 new_cov=79/0 polymorphism_quality=56.1 quality=56.1 quality_position_model=Inf ref_cov=47/268 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=126/268 RA 293 . NC_007779 1280617 0 G T bias_e_value=5.8485 bias_p_value=1.25873e-06 fisher_strand_p_value=7.21568e-08 frequency=2.762318e-02 genotype_quality=1404.5 ks_quality_p_value=1 log10_base_likelihood=-7.88755 log10_qual_likelihood_position_model=18.8393 log10_strand_likelihood_position_model=7.3308 new_cov=0/28 polymorphism_quality=2.4 quality=2.4 quality_position_model=Inf ref_cov=193/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=193/247 RA 294 . NC_007779 1288364 0 G A deleted=1 frequency=1 genotype_quality=183.0 new_cov=25/27 quality=183.0 ref_cov=0/0 tot_cov=25/27 RA 295 . NC_007779 1288370 0 A G deleted=1 frequency=1 genotype_quality=50.8 new_cov=12/7 quality=50.8 ref_cov=0/0 tot_cov=12/7 RA 296 . NC_007779 1288462 0 T C deleted=1 frequency=1 genotype_quality=60.4 new_cov=18/8 quality=60.4 ref_cov=0/0 tot_cov=18/8 RA 297 . NC_007779 1313924 0 C A bias_e_value=0.000351909 bias_p_value=7.57391e-11 fisher_strand_p_value=2.74195e-12 frequency=3.357315e-02 genotype_quality=1388.5 ks_quality_p_value=1 log10_base_likelihood=-6.88148 log10_qual_likelihood_position_model=22.1639 log10_strand_likelihood_position_model=11.5619 new_cov=21/0 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=86/247 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=107/247 RA 298 . NC_007779 1318876 0 G A frequency=1 genotype_quality=1831.8 new_cov=214/233 quality=1831.8 ref_cov=0/0 tot_cov=214/233 RA 299 . NC_007779 1325276 0 G T bias_e_value=0.00170892 bias_p_value=3.678e-10 fisher_strand_p_value=1.54936e-11 frequency=2.990723e-02 genotype_quality=1493.9 ks_quality_p_value=0.913707 log10_base_likelihood=-6.21216 log10_qual_likelihood_position_model=29.4172 log10_strand_likelihood_position_model=10.8098 new_cov=0/32 polymorphism_quality=0.7 quality=0.7 quality_position_model=Inf ref_cov=245/192 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=245/225 RA 300 . NC_007779 1330179 0 T G bias_e_value=0.00204499 bias_p_value=4.40131e-10 fisher_strand_p_value=1.70632e-11 frequency=2.717304e-02 genotype_quality=1273.7 ks_quality_p_value=1 log10_base_likelihood=-5.73533 log10_qual_likelihood_position_model=27.1632 log10_strand_likelihood_position_model=10.7679 new_cov=30/0 polymorphism_quality=0.2 quality=0.2 quality_position_model=Inf ref_cov=149/211 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=179/211 RA 301 . NC_007779 1336531 0 G T bias_e_value=0.0245692 bias_p_value=5.28788e-09 fisher_strand_p_value=2.27905e-10 frequency=3.827190e-02 genotype_quality=1527.9 ks_quality_p_value=1 log10_base_likelihood=-8.99518 log10_qual_likelihood_position_model=24.5092 log10_strand_likelihood_position_model=9.78462 new_cov=0/34 polymorphism_quality=3.5 quality=3.5 quality_position_model=Inf ref_cov=222/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=222/253 RA 302 . NC_007779 1352913 1 . T bias_e_value=357.221 bias_p_value=7.68823e-05 fisher_strand_p_value=7.0628e-06 frequency=3.169060e-02 genotype_quality=1307.3 ks_quality_p_value=0.834693 log10_base_likelihood=-41.9558 log10_qual_likelihood_position_model=7.32967 log10_strand_likelihood_position_model=5.15102 new_cov=9/0 polymorphism_quality=36.8 quality=36.8 quality_position_model=9.88846e-32 ref_cov=70/205 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER tot_cov=79/205 RA 303 . NC_007779 1371749 1 . T bias_e_value=890005 bias_p_value=0.19155 fisher_strand_p_value=0.143637 frequency=1.489353e-02 genotype_quality=2270.8 ks_quality_p_value=0.329133 log10_base_likelihood=-30.4018 log10_qual_likelihood_position_model=4.5986 log10_strand_likelihood_position_model=1.01362 new_cov=1/6 polymorphism_quality=25.2 quality=25.2 quality_position_model=5.21991e-27 ref_cov=204/259 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=205/265 RA 304 . NC_007779 1374596 0 C A bias_e_value=0.00332831 bias_p_value=7.16331e-10 fisher_strand_p_value=3.63151e-11 frequency=4.664946e-02 genotype_quality=1278.2 ks_quality_p_value=0.780056 log10_base_likelihood=-9.96112 log10_qual_likelihood_position_model=35.4716 log10_strand_likelihood_position_model=10.6748 new_cov=36/0 polymorphism_quality=4.5 quality=4.5 quality_position_model=Inf ref_cov=180/194 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=217/194 RA 305 . NC_007779 1378219 0 A C bias_e_value=2.72926e-13 bias_p_value=5.87401e-20 fisher_strand_p_value=1.19447e-21 frequency=7.759666e-02 genotype_quality=1180.1 ks_quality_p_value=1 log10_base_likelihood=-13.4454 log10_qual_likelihood_position_model=58.0693 log10_strand_likelihood_position_model=20.9228 new_cov=0/50 polymorphism_quality=8.1 quality=8.1 quality_position_model=Inf ref_cov=213/107 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=213/159 RA 306 . NC_007779 1405508 0 G T bias_e_value=0.0107949 bias_p_value=2.32332e-09 fisher_strand_p_value=1.01631e-10 frequency=5.046558e-02 genotype_quality=913.1 ks_quality_p_value=0.950106 log10_base_likelihood=-18.8675 log10_qual_likelihood_position_model=18.8191 log10_strand_likelihood_position_model=9.99297 new_cov=14/0 polymorphism_quality=13.6 quality=13.6 quality_position_model=Inf ref_cov=38/189 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=52/190 RA 307 . NC_007779 1409137 0 G T bias_e_value=8.0969e-25 bias_p_value=1.74264e-31 fisher_strand_p_value=2.29066e-33 frequency=1.479845e-01 genotype_quality=1238.1 ks_quality_p_value=0.998927 log10_base_likelihood=-44.6168 log10_qual_likelihood_position_model=40.414 log10_strand_likelihood_position_model=32.64 new_cov=0/90 polymorphism_quality=39.5 quality=39.5 quality_position_model=Inf ref_cov=232/135 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/225 RA 308 . NC_007779 1410956 1 . T bias_e_value=4196940 bias_p_value=0.90328 fisher_strand_p_value=0.671543 frequency=1.077557e-02 genotype_quality=2234.3 ks_quality_p_value=0.884187 log10_base_likelihood=-20.55 log10_qual_likelihood_position_model=3.73987 log10_strand_likelihood_position_model=0.52888 new_cov=3/2 polymorphism_quality=15.3 quality=15.3 quality_position_model=2.06729e-18 ref_cov=217/242 reject=INDEL_HOMOPOLYMER tot_cov=220/244 RA 309 . NC_007779 1412694 0 C A bias_e_value=8.20498e-05 bias_p_value=1.7659e-11 fisher_strand_p_value=6.06429e-13 frequency=4.442310e-02 genotype_quality=1376.2 ks_quality_p_value=0.999593 log10_base_likelihood=-10.4874 log10_qual_likelihood_position_model=24.2848 log10_strand_likelihood_position_model=12.2172 new_cov=31/0 polymorphism_quality=5.1 quality=5.1 quality_position_model=Inf ref_cov=142/233 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=174/233 RA 310 . NC_007779 1423611 0 T A deleted=1 frequency=1 genotype_quality=1.1 new_cov=0/1 quality=1.1 ref_cov=0/0 reject=EVALUE tot_cov=0/1 RA 311 . NC_007779 1435159 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 312 . NC_007779 1435160 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 313 . NC_007779 1435162 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 314 . NC_007779 1435165 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 315 . NC_007779 1435166 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 316 . NC_007779 1435169 0 G A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 317 . NC_007779 1435170 0 G A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 318 . NC_007779 1435171 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 319 . NC_007779 1435172 0 G A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 320 . NC_007779 1435174 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 321 . NC_007779 1435175 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 322 . NC_007779 1435176 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 323 . NC_007779 1435178 0 G A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 324 . NC_007779 1435179 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 325 . NC_007779 1435180 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 326 . NC_007779 1435181 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 327 . NC_007779 1435182 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 328 . NC_007779 1435183 0 G A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 329 . NC_007779 1435184 0 T A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 330 . NC_007779 1435185 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 331 . NC_007779 1435187 0 C A deleted=1 frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 332 . NC_007779 1437441 0 G A bias_e_value=0.00851749 bias_p_value=1.83316e-09 fisher_strand_p_value=7.54139e-11 frequency=3.926659e-02 genotype_quality=1281.3 ks_quality_p_value=1 log10_base_likelihood=-10.7651 log10_qual_likelihood_position_model=23.7023 log10_strand_likelihood_position_model=10.1225 new_cov=0/15 polymorphism_quality=5.3 quality=5.3 quality_position_model=Inf ref_cov=253/60 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=253/75 RA 333 . NC_007779 1437447 0 G C bias_e_value=5.03586e-11 bias_p_value=1.08384e-17 fisher_strand_p_value=2.47202e-19 frequency=7.128191e-02 genotype_quality=1238.2 ks_quality_p_value=1 log10_base_likelihood=-15.0151 log10_qual_likelihood_position_model=30.1915 log10_strand_likelihood_position_model=18.6069 new_cov=0/38 polymorphism_quality=9.7 quality=9.7 quality_position_model=Inf ref_cov=246/99 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=246/137 RA 334 . NC_007779 1438936 1 . T bias_e_value=3683780 bias_p_value=0.792836 fisher_strand_p_value=0.61699 frequency=8.086205e-03 genotype_quality=1810.4 ks_quality_p_value=0.696795 log10_base_likelihood=-12.4868 log10_qual_likelihood_position_model=2.2304 log10_strand_likelihood_position_model=0.433269 new_cov=1/2 polymorphism_quality=7.1 quality=7.1 quality_position_model=7.58099e-12 ref_cov=188/180 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/182 RA 335 . NC_007779 1438937 0 T . bias_e_value=2624800 bias_p_value=0.564918 fisher_strand_p_value=1 frequency=1.318455e-02 genotype_quality=1522.6 ks_quality_p_value=0.227892 log10_base_likelihood=-13.8414 log10_qual_likelihood_position_model=3.11093 log10_strand_likelihood_position_model=0.494042 new_cov=3/2 polymorphism_quality=8.5 quality=8.5 quality_position_model=2.86967e-12 ref_cov=190/183 reject=INDEL_HOMOPOLYMER tot_cov=194/185 RA 336 . NC_007779 1457194 0 C A bias_e_value=92.7563 bias_p_value=1.99633e-05 fisher_strand_p_value=1.3776e-06 frequency=3.110027e-02 genotype_quality=1346.9 ks_quality_p_value=0.999722 log10_base_likelihood=-8.08485 log10_qual_likelihood_position_model=18.4644 log10_strand_likelihood_position_model=6.05569 new_cov=22/0 polymorphism_quality=2.6 quality=2.6 quality_position_model=Inf ref_cov=200/187 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=223/187 RA 337 . NC_007779 1461304 0 G T bias_e_value=183.793 bias_p_value=3.95566e-05 fisher_strand_p_value=2.87486e-06 frequency=2.505398e-02 genotype_quality=1329.5 ks_quality_p_value=1 log10_base_likelihood=-5.63899 log10_qual_likelihood_position_model=17.3669 log10_strand_likelihood_position_model=5.70006 new_cov=0/21 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=177/193 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=177/215 RA 338 . NC_007779 1465121 0 T G bias_e_value=40.5673 bias_p_value=8.73104e-06 fisher_strand_p_value=5.67621e-07 frequency=1.109791e-02 genotype_quality=1346.4 ks_quality_p_value=1 log10_base_likelihood=-5.85694 log10_qual_likelihood_position_model=25.4967 log10_strand_likelihood_position_model=6.24594 new_cov=18/0 polymorphism_quality=0.3 quality=0.3 quality_position_model=Inf ref_cov=168/217 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=188/217 RA 339 . NC_007779 1483588 0 G A frequency=1 genotype_quality=1255.3 new_cov=231/83 quality=1255.3 ref_cov=0/0 tot_cov=232/83 RA 340 . NC_007779 1496775 0 T . frequency=1 genotype_quality=2119.6 new_cov=180/253 quality=2119.6 ref_cov=0/0 tot_cov=180/253 RA 341 . NC_007779 1498415 0 A . bias_e_value=915122 bias_p_value=0.196956 fisher_strand_p_value=0.123695 frequency=7.961273e-03 genotype_quality=2072.4 ks_quality_p_value=0.396605 log10_base_likelihood=-10.5109 log10_qual_likelihood_position_model=2.13157 log10_strand_likelihood_position_model=1.18172 new_cov=0/4 polymorphism_quality=5.1 quality=5.1 quality_position_model=3.71243e-09 ref_cov=247/251 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=247/255 RA 342 . NC_007779 1504851 0 C A bias_e_value=1696.97 bias_p_value=0.000365228 fisher_strand_p_value=3.21967e-05 frequency=3.355503e-02 genotype_quality=1026.4 ks_quality_p_value=1 log10_base_likelihood=-5.87539 log10_qual_likelihood_position_model=17.7536 log10_strand_likelihood_position_model=4.61259 new_cov=25/0 polymorphism_quality=0.3 quality=0.3 quality_position_model=Inf ref_cov=212/119 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=237/119 RA 343 . NC_007779 1512494 1 . A bias_e_value=4644380 bias_p_value=0.99958 fisher_strand_p_value=1 frequency=7.731438e-03 genotype_quality=1919.9 ks_quality_p_value=0.971144 log10_base_likelihood=-12.0558 log10_qual_likelihood_position_model=2.87662 log10_strand_likelihood_position_model=0.422615 new_cov=1/2 polymorphism_quality=6.7 quality=6.7 quality_position_model=9.33672e-11 ref_cov=192/193 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=193/195 RA 344 . NC_007779 1515709 0 A G bias_e_value=1.39907e-20 bias_p_value=3.01112e-27 fisher_strand_p_value=4.54433e-29 frequency=1.569915e-01 genotype_quality=1080.5 ks_quality_p_value=1 log10_base_likelihood=-55.0036 log10_qual_likelihood_position_model=67.4779 log10_strand_likelihood_position_model=28.3425 new_cov=73/0 polymorphism_quality=49.9 quality=49.9 quality_position_model=Inf ref_cov=118/221 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=192/221 RA 345 . NC_007779 1515714 0 A T bias_e_value=5.08603 bias_p_value=1.09463e-06 fisher_strand_p_value=6.22214e-08 frequency=4.029369e-02 genotype_quality=1273.0 ks_quality_p_value=1 log10_base_likelihood=-11.7723 log10_qual_likelihood_position_model=22.1512 log10_strand_likelihood_position_model=7.20606 new_cov=19/0 polymorphism_quality=6.4 quality=6.4 quality_position_model=Inf ref_cov=145/216 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=164/216 RA 346 . NC_007779 1527474 0 G A bias_e_value=1.14755e-07 bias_p_value=2.4698e-14 fisher_strand_p_value=6.87713e-16 frequency=9.197664e-02 genotype_quality=1370.1 ks_quality_p_value=1 log10_base_likelihood=-35.7532 log10_qual_likelihood_position_model=44.3611 log10_strand_likelihood_position_model=15.1626 new_cov=0/45 polymorphism_quality=30.6 quality=30.6 quality_position_model=Inf ref_cov=222/167 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=222/212 RA 347 . NC_007779 1527479 0 C A bias_e_value=1.30758 bias_p_value=2.81421e-07 fisher_strand_p_value=1.61066e-08 frequency=4.335022e-02 genotype_quality=1554.1 ks_quality_p_value=0.918178 log10_base_likelihood=-15.7989 log10_qual_likelihood_position_model=32.6108 log10_strand_likelihood_position_model=7.793 new_cov=0/24 polymorphism_quality=10.5 quality=10.5 quality_position_model=Inf ref_cov=225/190 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=225/214 RA 348 . NC_007779 1533124 0 C A bias_e_value=61601 bias_p_value=0.013258 fisher_strand_p_value=0.00181299 frequency=2.760601e-02 genotype_quality=1452.0 ks_quality_p_value=1 log10_base_likelihood=-8.89994 log10_qual_likelihood_position_model=17.8562 log10_strand_likelihood_position_model=2.83913 new_cov=0/12 polymorphism_quality=3.4 quality=3.4 quality_position_model=Inf ref_cov=143/191 reject=POLYMORPHISM_STRAND tot_cov=143/203 RA 349 . NC_007779 1533140 0 C A bias_e_value=1078300 bias_p_value=0.232076 fisher_strand_p_value=0.0613421 frequency=1.342487e-02 genotype_quality=1525.7 ks_quality_p_value=0.997139 log10_base_likelihood=-6.94528 log10_qual_likelihood_position_model=7.81461 log10_strand_likelihood_position_model=1.45083 new_cov=0/5 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=173/179 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=173/184 RA 350 . NC_007779 1537499 0 A G bias_e_value=2.5771e-08 bias_p_value=5.54652e-15 fisher_strand_p_value=1.4811e-16 frequency=8.563995e-02 genotype_quality=1252.9 ks_quality_p_value=1 log10_base_likelihood=-16.8996 log10_qual_likelihood_position_model=34.3658 log10_strand_likelihood_position_model=16.1095 new_cov=54/0 polymorphism_quality=11.6 quality=11.6 quality_position_model=Inf ref_cov=186/210 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=240/210 RA 351 . NC_007779 1540169 1 . T bias_e_value=2733880 bias_p_value=0.588396 fisher_strand_p_value=0.244355 frequency=4.122734e-03 genotype_quality=2430.8 ks_quality_p_value=0.999164 log10_base_likelihood=-6.70422 log10_qual_likelihood_position_model=2.70034 log10_strand_likelihood_position_model=0.611978 new_cov=2/0 polymorphism_quality=1.2 quality=1.2 quality_position_model=3.36243e-05 ref_cov=238/245 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=240/245 RA 352 . NC_007779 1552377 0 A C bias_e_value=3.1208e-20 bias_p_value=6.7167e-27 fisher_strand_p_value=1.02629e-28 frequency=1.109619e-01 genotype_quality=1126.0 ks_quality_p_value=1 log10_base_likelihood=-19.1337 log10_qual_likelihood_position_model=51.0268 log10_strand_likelihood_position_model=27.9887 new_cov=0/63 polymorphism_quality=13.8 quality=13.8 quality_position_model=Inf ref_cov=214/90 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=214/153 RA 353 . NC_007779 1572925 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 354 . NC_007779 1572927 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 355 . NC_007779 1572928 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 356 . NC_007779 1572929 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 357 . NC_007779 1572932 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 358 . NC_007779 1572933 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 359 . NC_007779 1572934 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 360 . NC_007779 1572936 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 361 . NC_007779 1572937 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 362 . NC_007779 1572938 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 363 . NC_007779 1572939 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 364 . NC_007779 1572940 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 365 . NC_007779 1572941 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 366 . NC_007779 1572942 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 367 . NC_007779 1572945 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 368 . NC_007779 1572946 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 369 . NC_007779 1572948 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 370 . NC_007779 1572949 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 371 . NC_007779 1572950 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 372 . NC_007779 1572952 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 373 . NC_007779 1572953 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 374 . NC_007779 1572954 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 375 . NC_007779 1572956 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 376 . NC_007779 1572957 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 377 . NC_007779 1572958 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 378 . NC_007779 1572959 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 379 . NC_007779 1572961 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 380 . NC_007779 1581577 1 . T bias_e_value=4566120 bias_p_value=0.982736 fisher_strand_p_value=1 frequency=4.444122e-03 genotype_quality=2244.5 ks_quality_p_value=0.820031 log10_base_likelihood=-7.9156 log10_qual_likelihood_position_model=1.22664 log10_strand_likelihood_position_model=0.300141 new_cov=1/1 polymorphism_quality=2.4 quality=2.4 quality_position_model=2.52868e-08 ref_cov=221/227 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=222/228 RA 381 . NC_007779 1595838 1 . C bias_e_value=3750070 bias_p_value=0.807103 fisher_strand_p_value=0.63862 frequency=1.069546e-02 genotype_quality=1816.8 ks_quality_p_value=0.700297 log10_base_likelihood=-17.0338 log10_qual_likelihood_position_model=2.7998 log10_strand_likelihood_position_model=0.493188 new_cov=1/3 polymorphism_quality=11.7 quality=11.7 quality_position_model=7.7924e-16 ref_cov=159/211 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=160/214 RA 382 . NC_007779 1595839 0 C . bias_e_value=4643570 bias_p_value=0.999407 fisher_strand_p_value=1 frequency=7.840157e-03 genotype_quality=1565.8 ks_quality_p_value=0.965747 log10_base_likelihood=-7.09553 log10_qual_likelihood_position_model=2.85945 log10_strand_likelihood_position_model=0.375891 new_cov=1/2 polymorphism_quality=1.6 quality=1.6 quality_position_model=1.07876e-05 ref_cov=163/216 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=164/218 RA 383 . NC_007779 1602599 0 C A bias_e_value=0.000875496 bias_p_value=1.88427e-10 fisher_strand_p_value=7.06353e-12 frequency=3.555489e-02 genotype_quality=1390.9 ks_quality_p_value=1 log10_base_likelihood=-7.08422 log10_qual_likelihood_position_model=28.4082 log10_strand_likelihood_position_model=11.2572 new_cov=36/0 polymorphism_quality=1.6 quality=1.6 quality_position_model=Inf ref_cov=182/211 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=218/211 RA 384 . NC_007779 1615814 0 C A frequency=1 genotype_quality=1480.1 new_cov=193/192 quality=1480.1 ref_cov=0/0 tot_cov=193/192 RA 385 . NC_007779 1624530 1 . A bias_e_value=2920670 bias_p_value=0.628596 fisher_strand_p_value=0.581172 frequency=7.299423e-03 genotype_quality=1964.5 ks_quality_p_value=0.471286 log10_base_likelihood=-12.0434 log10_qual_likelihood_position_model=3.09171 log10_strand_likelihood_position_model=0.495479 new_cov=2/1 polymorphism_quality=6.6 quality=6.6 quality_position_model=1.8958e-10 ref_cov=176/232 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=178/233 RA 386 . NC_007779 1628027 0 G T bias_e_value=2.70959e-06 bias_p_value=5.83167e-13 fisher_strand_p_value=2.02019e-14 frequency=1.676679e-01 genotype_quality=645.9 ks_quality_p_value=0.88396 log10_base_likelihood=-73.6724 log10_qual_likelihood_position_model=38.3187 log10_strand_likelihood_position_model=13.9054 new_cov=43/0 polymorphism_quality=68.7 quality=68.7 quality_position_model=1.22963e-23 ref_cov=84/116 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=127/116 RA 387 . NC_007779 1639433 0 T . bias_e_value=913229 bias_p_value=0.196548 fisher_strand_p_value=0.120831 frequency=8.374214e-03 genotype_quality=1479.3 ks_quality_p_value=0.404888 log10_base_likelihood=-8.21932 log10_qual_likelihood_position_model=1.69023 log10_strand_likelihood_position_model=0.917823 new_cov=0/3 polymorphism_quality=2.7 quality=2.7 quality_position_model=1.61018e-07 ref_cov=180/174 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=180/178 RA 388 . NC_007779 1640962 1 . T bias_e_value=2291900 bias_p_value=0.493272 fisher_strand_p_value=0.503819 frequency=4.761696e-03 genotype_quality=2100.1 ks_quality_p_value=0.362628 log10_base_likelihood=-8.12787 log10_qual_likelihood_position_model=1.89097 log10_strand_likelihood_position_model=0.520123 new_cov=0/2 polymorphism_quality=2.6 quality=2.6 quality_position_model=1.25195e-07 ref_cov=189/229 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/231 RA 389 . NC_007779 1640963 0 T . bias_e_value=2277150 bias_p_value=0.490097 fisher_strand_p_value=0.256057 frequency=7.119179e-03 genotype_quality=1719.6 ks_quality_p_value=0.706237 log10_base_likelihood=-7.82076 log10_qual_likelihood_position_model=1.96126 log10_strand_likelihood_position_model=0.778918 new_cov=0/3 polymorphism_quality=2.3 quality=2.3 quality_position_model=5.72347e-07 ref_cov=189/229 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/232 RA 390 . NC_007779 1641155 0 T . bias_e_value=3315490 bias_p_value=0.713571 fisher_strand_p_value=0.446376 frequency=1.332378e-02 genotype_quality=1798.1 ks_quality_p_value=0.775883 log10_base_likelihood=-16.5124 log10_qual_likelihood_position_model=3.62834 log10_strand_likelihood_position_model=0.637041 new_cov=2/4 polymorphism_quality=11.2 quality=11.2 quality_position_model=2.56853e-14 ref_cov=225/219 reject=INDEL_HOMOPOLYMER tot_cov=227/223 RA 391 . NC_007779 1646748 0 A C bias_e_value=1.77992e-08 bias_p_value=3.83082e-15 fisher_strand_p_value=1.01267e-16 frequency=6.040764e-02 genotype_quality=1418.3 ks_quality_p_value=1 log10_base_likelihood=-15.7293 log10_qual_likelihood_position_model=39.9424 log10_strand_likelihood_position_model=15.9945 new_cov=0/45 polymorphism_quality=10.4 quality=10.4 quality_position_model=Inf ref_cov=231/160 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/207 RA 392 . NC_007779 1651009 0 T G bias_e_value=4.61485e-23 bias_p_value=9.93224e-30 fisher_strand_p_value=1.37834e-31 frequency=1.290674e-01 genotype_quality=987.0 ks_quality_p_value=1 log10_base_likelihood=-36.15 log10_qual_likelihood_position_model=47.5845 log10_strand_likelihood_position_model=30.8606 new_cov=56/0 polymorphism_quality=31.0 quality=31.0 quality_position_model=Inf ref_cov=53/203 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=109/203 RA 393 . NC_007779 1660545 0 G T bias_e_value=0.347527 bias_p_value=7.4796e-08 fisher_strand_p_value=3.66193e-09 frequency=2.929974e-02 genotype_quality=1390.6 ks_quality_p_value=1 log10_base_likelihood=-7.07931 log10_qual_likelihood_position_model=19.7105 log10_strand_likelihood_position_model=8.43629 new_cov=0/23 polymorphism_quality=1.6 quality=1.6 quality_position_model=Inf ref_cov=228/160 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=228/184 RA 394 . NC_007779 1666683 0 T . bias_e_value=1654230 bias_p_value=0.35603 fisher_strand_p_value=0.124877 frequency=9.294510e-03 genotype_quality=1751.8 ks_quality_p_value=0.892621 log10_base_likelihood=-10.5539 log10_qual_likelihood_position_model=1.98736 log10_strand_likelihood_position_model=1.13071 new_cov=4/0 polymorphism_quality=5.1 quality=5.1 quality_position_model=2.11221e-09 ref_cov=221/205 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=225/205 RA 395 . NC_007779 1669599 0 C . frequency=1 genotype_quality=1903.8 new_cov=188/192 quality=1903.8 ref_cov=0/0 tot_cov=188/192 RA 396 . NC_007779 1669765 0 C A bias_e_value=75417.8 bias_p_value=0.0162317 fisher_strand_p_value=0.00229334 frequency=2.464104e-02 genotype_quality=1791.1 ks_quality_p_value=1 log10_base_likelihood=-12.2109 log10_qual_likelihood_position_model=18.9136 log10_strand_likelihood_position_model=2.8801 new_cov=0/13 polymorphism_quality=6.8 quality=6.8 quality_position_model=Inf ref_cov=175/256 reject=POLYMORPHISM_STRAND tot_cov=175/270 RA 397 . NC_007779 1669767 0 T G bias_e_value=128796 bias_p_value=0.0277199 fisher_strand_p_value=0.00429838 frequency=1.244545e-02 genotype_quality=1702.5 ks_quality_p_value=0.999887 log10_base_likelihood=-6.07642 log10_qual_likelihood_position_model=15.4413 log10_strand_likelihood_position_model=2.42616 new_cov=0/11 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=176/260 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=176/272 RA 398 . NC_007779 1669781 0 G A bias_e_value=13609.4 bias_p_value=0.00292906 fisher_strand_p_value=0.000325502 frequency=3.153706e-02 genotype_quality=1804.4 ks_quality_p_value=0.996073 log10_base_likelihood=-15.388 log10_qual_likelihood_position_model=19.2759 log10_strand_likelihood_position_model=3.66405 new_cov=0/16 polymorphism_quality=10.0 quality=10.0 quality_position_model=Inf ref_cov=185/258 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=185/275 RA 399 . NC_007779 1669786 0 G A bias_e_value=620.277 bias_p_value=0.000133498 fisher_strand_p_value=1.07314e-05 frequency=3.788471e-02 genotype_quality=1789.5 ks_quality_p_value=0.999792 log10_base_likelihood=-18.0553 log10_qual_likelihood_position_model=25.6038 log10_strand_likelihood_position_model=5.14615 new_cov=0/21 polymorphism_quality=12.7 quality=12.7 quality_position_model=Inf ref_cov=194/245 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=194/266 RA 400 . NC_007779 1671093 0 G T bias_e_value=7108.12 bias_p_value=0.00152984 fisher_strand_p_value=0.00015673 frequency=1.344776e-02 genotype_quality=1645.2 ks_quality_p_value=1 log10_base_likelihood=-6.77779 log10_qual_likelihood_position_model=13.8269 log10_strand_likelihood_position_model=3.85295 new_cov=0/14 polymorphism_quality=1.3 quality=1.3 quality_position_model=Inf ref_cov=218/239 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=218/256 RA 401 . NC_007779 1677110 0 G T bias_e_value=0.00023132 bias_p_value=4.97854e-11 fisher_strand_p_value=2.13824e-12 frequency=4.810715e-02 genotype_quality=1255.5 ks_quality_p_value=0.829843 log10_base_likelihood=-9.57067 log10_qual_likelihood_position_model=40.4803 log10_strand_likelihood_position_model=11.6979 new_cov=0/38 polymorphism_quality=4.1 quality=4.1 quality_position_model=Inf ref_cov=195/170 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=195/211 RA 402 . NC_007779 1681402 0 T G bias_e_value=2.98924e-12 bias_p_value=6.43355e-19 fisher_strand_p_value=1.37669e-20 frequency=5.107355e-02 genotype_quality=1402.5 ks_quality_p_value=1 log10_base_likelihood=-13.6314 log10_qual_likelihood_position_model=42.6562 log10_strand_likelihood_position_model=19.8612 new_cov=44/0 polymorphism_quality=8.3 quality=8.3 quality_position_model=Inf ref_cov=120/259 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=164/259 RA 403 . NC_007779 1698552 0 G T bias_e_value=0.00218943 bias_p_value=4.71217e-10 fisher_strand_p_value=1.83188e-11 frequency=4.526043e-02 genotype_quality=1354.5 ks_quality_p_value=1 log10_base_likelihood=-14.2027 log10_qual_likelihood_position_model=27.8441 log10_strand_likelihood_position_model=10.7371 new_cov=0/29 polymorphism_quality=8.8 quality=8.8 quality_position_model=Inf ref_cov=227/154 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=227/184 RA 404 . NC_007779 1703335 0 G C bias_e_value=0.0367885 bias_p_value=7.91774e-09 fisher_strand_p_value=3.48047e-10 frequency=3.941631e-02 genotype_quality=1058.8 ks_quality_p_value=0.99864 log10_base_likelihood=-15.9627 log10_qual_likelihood_position_model=14.3643 log10_strand_likelihood_position_model=9.45836 new_cov=13/0 polymorphism_quality=10.6 quality=10.6 quality_position_model=Inf ref_cov=45/225 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=58/225 RA 405 . NC_007779 1705204 0 A C bias_e_value=4.01335 bias_p_value=8.63768e-07 fisher_strand_p_value=4.84077e-08 frequency=3.869820e-02 genotype_quality=1492.1 ks_quality_p_value=1 log10_base_likelihood=-16.1319 log10_qual_likelihood_position_model=31.5207 log10_strand_likelihood_position_model=7.31509 new_cov=23/0 polymorphism_quality=10.8 quality=10.8 quality_position_model=Inf ref_cov=178/205 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=201/205 RA 406 . NC_007779 1705209 1 . T bias_e_value=2544890 bias_p_value=0.54772 fisher_strand_p_value=0.235564 frequency=5.088806e-03 genotype_quality=1917.1 ks_quality_p_value=0.918903 log10_base_likelihood=-7.81173 log10_qual_likelihood_position_model=3.04155 log10_strand_likelihood_position_model=0.627892 new_cov=2/0 polymorphism_quality=2.3 quality=2.3 quality_position_model=5.45558e-06 ref_cov=189/202 reject=POLYMORPHISM_STRAND tot_cov=191/202 RA 407 . NC_007779 1705210 0 G T bias_e_value=1.22215 bias_p_value=2.63036e-07 fisher_strand_p_value=1.37755e-08 frequency=5.344677e-02 genotype_quality=1492.7 ks_quality_p_value=0.999673 log10_base_likelihood=-25.5564 log10_qual_likelihood_position_model=30.3198 log10_strand_likelihood_position_model=7.86089 new_cov=24/0 polymorphism_quality=20.3 quality=20.3 quality_position_model=Inf ref_cov=168/203 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=192/203 RA 408 . NC_007779 1705224 0 G T bias_e_value=156.783 bias_p_value=3.37435e-05 fisher_strand_p_value=2.42468e-06 frequency=3.431416e-02 genotype_quality=1542.7 ks_quality_p_value=0.998982 log10_base_likelihood=-9.59544 log10_qual_likelihood_position_model=21.9853 log10_strand_likelihood_position_model=5.91638 new_cov=19/0 polymorphism_quality=4.2 quality=4.2 quality_position_model=Inf ref_cov=179/198 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=198/198 RA 409 . NC_007779 1716031 1 . T bias_e_value=136057 bias_p_value=0.0292827 fisher_strand_p_value=0.250382 frequency=7.462502e-03 genotype_quality=1963.7 ks_quality_p_value=0.0183177 log10_base_likelihood=-12.5662 log10_qual_likelihood_position_model=2.57776 log10_strand_likelihood_position_model=0.836593 new_cov=3/0 polymorphism_quality=7.2 quality=7.2 quality_position_model=3.67915e-11 ref_cov=209/190 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=212/190 RA 410 . NC_007779 1722510 0 G T bias_e_value=6.50166 bias_p_value=1.39931e-06 fisher_strand_p_value=8.07352e-08 frequency=2.746773e-02 genotype_quality=1554.7 ks_quality_p_value=1 log10_base_likelihood=-7.6557 log10_qual_likelihood_position_model=25.1609 log10_strand_likelihood_position_model=7.27101 new_cov=0/26 polymorphism_quality=2.2 quality=2.2 quality_position_model=Inf ref_cov=210/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=210/245 RA 411 . NC_007779 1739073 1 . A bias_e_value=3554920 bias_p_value=0.765102 fisher_strand_p_value=0.499033 frequency=3.929138e-03 genotype_quality=2561.4 ks_quality_p_value=0.798464 log10_base_likelihood=-8.05183 log10_qual_likelihood_position_model=1.56947 log10_strand_likelihood_position_model=0.597801 new_cov=2/0 polymorphism_quality=2.6 quality=2.6 quality_position_model=8.39318e-08 ref_cov=254/253 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=256/253 RA 412 . NC_007779 1743936 1 . A bias_e_value=2958700 bias_p_value=0.636781 fisher_strand_p_value=1 frequency=3.751755e-03 genotype_quality=2676.1 ks_quality_p_value=0.280276 log10_base_likelihood=-7.63042 log10_qual_likelihood_position_model=1.41219 log10_strand_likelihood_position_model=0.302091 new_cov=1/1 polymorphism_quality=2.1 quality=2.1 quality_position_model=7.785e-08 ref_cov=248/283 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=249/284 RA 413 . NC_007779 1744363 0 C A bias_e_value=0.000235635 bias_p_value=5.07143e-11 fisher_strand_p_value=1.80874e-12 frequency=5.898190e-02 genotype_quality=1414.3 ks_quality_p_value=1 log10_base_likelihood=-15.6021 log10_qual_likelihood_position_model=32.634 log10_strand_likelihood_position_model=11.8547 new_cov=46/0 polymorphism_quality=10.3 quality=10.3 quality_position_model=Inf ref_cov=219/196 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=265/196 RA 414 . NC_007779 1746048 0 C A bias_e_value=2.88051 bias_p_value=6.19954e-07 fisher_strand_p_value=3.41731e-08 frequency=4.184723e-02 genotype_quality=1422.2 ks_quality_p_value=0.997077 log10_base_likelihood=-9.98375 log10_qual_likelihood_position_model=23.1223 log10_strand_likelihood_position_model=7.67964 new_cov=29/0 polymorphism_quality=4.5 quality=4.5 quality_position_model=Inf ref_cov=215/193 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=244/193 RA 415 . NC_007779 1759411 1 . T bias_e_value=907744 bias_p_value=0.195368 fisher_strand_p_value=0.227322 frequency=4.525185e-03 genotype_quality=2182.6 ks_quality_p_value=0.213496 log10_base_likelihood=-7.8283 log10_qual_likelihood_position_model=3.04931 log10_strand_likelihood_position_model=0.643359 new_cov=2/0 polymorphism_quality=2.3 quality=2.3 quality_position_model=5.54395e-06 ref_cov=209/231 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=211/231 RA 416 . NC_007779 1763744 0 C A bias_e_value=2.67065e-14 bias_p_value=5.74786e-21 fisher_strand_p_value=1.12081e-22 frequency=8.557034e-02 genotype_quality=1426.3 ks_quality_p_value=0.994859 log10_base_likelihood=-33.719 log10_qual_likelihood_position_model=31.7948 log10_strand_likelihood_position_model=21.9505 new_cov=58/0 polymorphism_quality=28.5 quality=28.5 quality_position_model=Inf ref_cov=160/262 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=219/262 RA 417 . NC_007779 1801456 0 C G bias_e_value=262.899 bias_p_value=5.6582e-05 fisher_strand_p_value=4.2832e-06 frequency=2.323055e-02 genotype_quality=1530.2 ks_quality_p_value=0.987822 log10_base_likelihood=-7.1656 log10_qual_likelihood_position_model=21.6662 log10_strand_likelihood_position_model=5.36823 new_cov=0/17 polymorphism_quality=1.7 quality=1.7 quality_position_model=Inf ref_cov=218/195 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=218/212 RA 418 . NC_007779 1820099 0 A C bias_e_value=9.88685e-10 bias_p_value=2.12788e-16 fisher_strand_p_value=5.21607e-18 frequency=5.919123e-02 genotype_quality=1490.0 ks_quality_p_value=1 log10_base_likelihood=-13.5167 log10_qual_likelihood_position_model=37.535 log10_strand_likelihood_position_model=17.2827 new_cov=0/40 polymorphism_quality=8.1 quality=8.1 quality_position_model=Inf ref_cov=276/142 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=277/182 RA 419 . NC_007779 1823574 0 A . bias_e_value=2618720 bias_p_value=0.563609 fisher_strand_p_value=0.249271 frequency=6.318092e-03 genotype_quality=1945.1 ks_quality_p_value=0.91069 log10_base_likelihood=-7.13688 log10_qual_likelihood_position_model=2.55447 log10_strand_likelihood_position_model=0.862419 new_cov=3/0 polymorphism_quality=1.6 quality=1.6 quality_position_model=1.51503e-05 ref_cov=242/229 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=245/229 RA 420 . NC_007779 1832491 0 G T bias_e_value=0.0892255 bias_p_value=1.92034e-08 fisher_strand_p_value=8.81603e-10 frequency=3.227520e-02 genotype_quality=1308.3 ks_quality_p_value=0.996793 log10_base_likelihood=-9.44484 log10_qual_likelihood_position_model=22.0914 log10_strand_likelihood_position_model=9.05473 new_cov=0/25 polymorphism_quality=4.0 quality=4.0 quality_position_model=Inf ref_cov=212/150 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=212/175 RA 421 . NC_007779 1837206 0 G T bias_e_value=7.75941 bias_p_value=1.67001e-06 fisher_strand_p_value=9.86151e-08 frequency=4.361820e-02 genotype_quality=1223.4 ks_quality_p_value=0.987766 log10_base_likelihood=-11.8096 log10_qual_likelihood_position_model=26.8915 log10_strand_likelihood_position_model=7.01744 new_cov=18/1 polymorphism_quality=6.4 quality=6.4 quality_position_model=Inf ref_cov=109/215 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=127/217 RA 422 . NC_007779 1840899 0 G T bias_e_value=8.50426e-05 bias_p_value=1.83032e-11 fisher_strand_p_value=6.29094e-13 frequency=4.576874e-02 genotype_quality=1149.0 ks_quality_p_value=1 log10_base_likelihood=-6.10293 log10_qual_likelihood_position_model=29.5457 log10_strand_likelihood_position_model=12.2013 new_cov=0/36 polymorphism_quality=0.6 quality=0.6 quality_position_model=Inf ref_cov=188/141 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=188/179 RA 423 . NC_007779 1844073 0 G A frequency=1 genotype_quality=1950.1 new_cov=253/223 quality=1950.1 ref_cov=0/0 tot_cov=253/223 RA 424 . NC_007779 1844628 0 A G bias_e_value=6.93285e-09 bias_p_value=1.49211e-15 fisher_strand_p_value=3.84596e-17 frequency=6.481409e-02 genotype_quality=818.5 ks_quality_p_value=1 log10_base_likelihood=-13.4003 log10_qual_likelihood_position_model=23.0226 log10_strand_likelihood_position_model=16.415 new_cov=18/0 polymorphism_quality=8.0 quality=8.0 quality_position_model=Inf ref_cov=18/193 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=37/194 RA 425 . NC_007779 1846634 0 A . bias_e_value=4391420 bias_p_value=0.945138 fisher_strand_p_value=0.75167 frequency=2.177620e-02 genotype_quality=1872.4 ks_quality_p_value=0.914758 log10_base_likelihood=-29.5407 log10_qual_likelihood_position_model=6.22664 log10_strand_likelihood_position_model=0.668709 new_cov=4/6 polymorphism_quality=24.3 quality=24.3 quality_position_model=7.60657e-25 ref_cov=221/228 reject=INDEL_HOMOPOLYMER tot_cov=225/234 RA 426 . NC_007779 1861399 0 A C bias_e_value=2.33184e-16 bias_p_value=5.01867e-23 fisher_strand_p_value=8.90176e-25 frequency=6.029797e-02 genotype_quality=999.2 ks_quality_p_value=1 log10_base_likelihood=-9.98673 log10_qual_likelihood_position_model=39.8735 log10_strand_likelihood_position_model=24.0505 new_cov=0/39 polymorphism_quality=4.6 quality=4.6 quality_position_model=Inf ref_cov=216/50 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=216/89 RA 427 . NC_007779 1863580 0 G T bias_e_value=3509.71 bias_p_value=0.000755373 fisher_strand_p_value=7.16411e-05 frequency=2.226734e-02 genotype_quality=1606.8 ks_quality_p_value=1 log10_base_likelihood=-5.70257 log10_qual_likelihood_position_model=13.5109 log10_strand_likelihood_position_model=4.14484 new_cov=12/0 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=182/229 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=194/230 RA 428 . NC_007779 1865525 0 T . bias_e_value=1967360 bias_p_value=0.423422 fisher_strand_p_value=0.601539 frequency=6.874084e-03 genotype_quality=1796.9 ks_quality_p_value=0.239693 log10_base_likelihood=-7.70492 log10_qual_likelihood_position_model=1.59056 log10_strand_likelihood_position_model=0.45573 new_cov=2/1 polymorphism_quality=2.2 quality=2.2 quality_position_model=1.43817e-07 ref_cov=202/231 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=204/232 RA 429 . NC_007779 1879404 0 A C bias_e_value=3.53081e-25 bias_p_value=7.59913e-32 fisher_strand_p_value=9.86919e-34 frequency=8.757544e-02 genotype_quality=1238.6 ks_quality_p_value=1 log10_base_likelihood=-21.8447 log10_qual_likelihood_position_model=50.6053 log10_strand_likelihood_position_model=33.0057 new_cov=0/46 polymorphism_quality=16.6 quality=16.6 quality_position_model=Inf ref_cov=265/41 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=265/87 RA 430 . NC_007779 1879996 0 G T bias_e_value=3284.31 bias_p_value=0.000706861 fisher_strand_p_value=6.65773e-05 frequency=2.564907e-02 genotype_quality=1626.5 ks_quality_p_value=1 log10_base_likelihood=-6.43173 log10_qual_likelihood_position_model=17.0223 log10_strand_likelihood_position_model=4.21053 new_cov=14/2 polymorphism_quality=0.9 quality=0.9 quality_position_model=Inf ref_cov=159/270 reject=EVALUE,FISHER_STRAND_P_VALUE tot_cov=173/272 RA 431 . NC_007779 1881068 1 . T bias_e_value=2363170 bias_p_value=0.50861 fisher_strand_p_value=0.499189 frequency=4.414558e-03 genotype_quality=2212.4 ks_quality_p_value=0.384333 log10_base_likelihood=-7.84879 log10_qual_likelihood_position_model=1.57468 log10_strand_likelihood_position_model=0.582137 new_cov=0/2 polymorphism_quality=2.4 quality=2.4 quality_position_model=1.32823e-07 ref_cov=221/230 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=221/232 RA 432 . NC_007779 1889729 1 . A bias_e_value=4629610 bias_p_value=0.9964 fisher_strand_p_value=1 frequency=4.039764e-03 genotype_quality=2453.8 ks_quality_p_value=0.916358 log10_base_likelihood=-7.54436 log10_qual_likelihood_position_model=1.67636 log10_strand_likelihood_position_model=0.304085 new_cov=1/1 polymorphism_quality=2.0 quality=2.0 quality_position_model=1.80279e-07 ref_cov=270/223 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=271/224 RA 433 . NC_007779 1889730 0 A . bias_e_value=3158690 bias_p_value=0.679823 fisher_strand_p_value=0.33553 frequency=7.960320e-03 genotype_quality=2032.9 ks_quality_p_value=0.941244 log10_base_likelihood=-10.2902 log10_qual_likelihood_position_model=2.52738 log10_strand_likelihood_position_model=0.685593 new_cov=1/3 polymorphism_quality=4.9 quality=4.9 quality_position_model=4.9376e-09 ref_cov=272/226 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=273/229 RA 434 . NC_007779 1906475 1 . C bias_e_value=1368960 bias_p_value=0.294632 fisher_strand_p_value=0.17559 frequency=4.938126e-03 genotype_quality=1980.5 ks_quality_p_value=0.484309 log10_base_likelihood=-9.19403 log10_qual_likelihood_position_model=2.59059 log10_strand_likelihood_position_model=0.755501 new_cov=2/0 polymorphism_quality=3.7 quality=3.7 quality_position_model=9.15818e-08 ref_cov=168/235 reject=POLYMORPHISM_STRAND tot_cov=170/235 RA 435 . NC_007779 1906477 1 . G bias_e_value=14039.3 bias_p_value=0.00302158 fisher_strand_p_value=0.000335926 frequency=2.167892e-02 genotype_quality=1747.1 ks_quality_p_value=0.99952 log10_base_likelihood=-31.2991 log10_qual_likelihood_position_model=9.91633 log10_strand_likelihood_position_model=3.47376 new_cov=8/0 polymorphism_quality=26.1 quality=26.1 quality_position_model=4.64979e-20 ref_cov=130/231 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER tot_cov=138/231 RA 436 . NC_007779 1906488 0 G T bias_e_value=2.03264 bias_p_value=4.37471e-07 fisher_strand_p_value=2.35663e-08 frequency=3.191280e-02 genotype_quality=1354.6 ks_quality_p_value=1 log10_base_likelihood=-8.31721 log10_qual_likelihood_position_model=19.4245 log10_strand_likelihood_position_model=7.62771 new_cov=17/0 polymorphism_quality=2.8 quality=2.8 quality_position_model=Inf ref_cov=116/226 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=133/226 RA 437 . NC_007779 1907281 0 C A bias_e_value=1282780 bias_p_value=0.276084 fisher_strand_p_value=0.0776484 frequency=7.910728e-03 genotype_quality=3936.7 ks_quality_p_value=1 log10_base_likelihood=-13.4706 log10_qual_likelihood_position_model=7.76237 log10_strand_likelihood_position_model=1.29318 new_cov=1/7 polymorphism_quality=8.1 quality=8.1 quality_position_model=2.82729e-06 ref_cov=412/486 reject=POLYMORPHISM_STRAND tot_cov=413/493 RA 438 . NC_007779 1911198 0 G T bias_e_value=132.713 bias_p_value=2.8563e-05 fisher_strand_p_value=2.02463e-06 frequency=1.681900e-02 genotype_quality=1537.3 ks_quality_p_value=0.999818 log10_base_likelihood=-6.03154 log10_qual_likelihood_position_model=17.3484 log10_strand_likelihood_position_model=5.74028 new_cov=0/20 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=227/232 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=227/253 RA 439 . NC_007779 1918872 0 T A frequency=1 genotype_quality=1962.7 new_cov=271/231 quality=1962.7 ref_cov=0/1 tot_cov=271/232 RA 440 . NC_007779 1920746 0 G T bias_e_value=6.11965e-13 bias_p_value=1.31709e-19 fisher_strand_p_value=2.72396e-21 frequency=8.887434e-02 genotype_quality=1375.0 ks_quality_p_value=1 log10_base_likelihood=-33.6941 log10_qual_likelihood_position_model=27.8709 log10_strand_likelihood_position_model=20.5648 new_cov=0/52 polymorphism_quality=28.5 quality=28.5 quality_position_model=Inf ref_cov=240/136 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=240/189 RA 441 . NC_007779 1927640 0 T . bias_e_value=4392720 bias_p_value=0.945416 fisher_strand_p_value=1 frequency=7.328987e-03 genotype_quality=1647.2 ks_quality_p_value=0.68834 log10_base_likelihood=-7.88782 log10_qual_likelihood_position_model=2.25931 log10_strand_likelihood_position_model=0.419668 new_cov=1/2 polymorphism_quality=2.4 quality=2.4 quality_position_model=4.21084e-07 ref_cov=201/205 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=202/207 RA 442 . NC_007779 1941891 0 T . bias_e_value=4646320 bias_p_value=0.999997 fisher_strand_p_value=1 frequency=6.710052e-03 genotype_quality=1825.9 ks_quality_p_value=0.997543 log10_base_likelihood=-6.64619 log10_qual_likelihood_position_model=4.44429 log10_strand_likelihood_position_model=0.389609 new_cov=2/1 polymorphism_quality=1.1 quality=1.1 quality_position_model=0.00168206 ref_cov=242/201 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=244/202 RA 443 . NC_007779 1956118 0 C A bias_e_value=0.00262278 bias_p_value=5.64485e-10 fisher_strand_p_value=2.23456e-11 frequency=5.038643e-02 genotype_quality=1035.0 ks_quality_p_value=0.989285 log10_base_likelihood=-23.6004 log10_qual_likelihood_position_model=18.5876 log10_strand_likelihood_position_model=10.6508 new_cov=0/14 polymorphism_quality=18.4 quality=18.4 quality_position_model=Inf ref_cov=211/37 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=211/51 RA 444 . NC_007779 1971508 0 A C bias_e_value=8.62021e-21 bias_p_value=1.85527e-27 fisher_strand_p_value=2.77932e-29 frequency=8.630371e-02 genotype_quality=1088.9 ks_quality_p_value=1 log10_base_likelihood=-41.6075 log10_qual_likelihood_position_model=28.788 log10_strand_likelihood_position_model=28.5561 new_cov=0/30 polymorphism_quality=36.5 quality=36.5 quality_position_model=Inf ref_cov=256/18 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=256/48 RA 445 . NC_007779 1973476 0 G A frequency=1 genotype_quality=1469.1 new_cov=192/179 quality=1469.1 ref_cov=1/0 tot_cov=193/179 RA 446 . NC_007779 1978922 0 A . bias_e_value=1004350 bias_p_value=0.216159 fisher_strand_p_value=0.118589 frequency=6.485939e-03 genotype_quality=1886.5 ks_quality_p_value=0.468549 log10_base_likelihood=-7.46596 log10_qual_likelihood_position_model=1.5259 log10_strand_likelihood_position_model=0.925955 new_cov=0/3 polymorphism_quality=2.0 quality=2.0 quality_position_model=6.71111e-07 ref_cov=234/224 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=235/227 RA 447 . NC_007779 1993891 1 . C bias_e_value=878641 bias_p_value=0.189104 fisher_strand_p_value=0.0508163 frequency=9.341240e-03 genotype_quality=2029.8 ks_quality_p_value=0.914599 log10_base_likelihood=-12.3113 log10_qual_likelihood_position_model=5.07688 log10_strand_likelihood_position_model=1.294 new_cov=0/4 polymorphism_quality=6.9 quality=6.9 quality_position_model=7.34737e-08 ref_cov=224/200 reject=POLYMORPHISM_STRAND tot_cov=224/204 RA 448 . NC_007779 1993894 0 A C bias_e_value=9.80671e-11 bias_p_value=2.11063e-17 fisher_strand_p_value=4.89004e-19 frequency=8.969069e-02 genotype_quality=1437.1 ks_quality_p_value=1 log10_base_likelihood=-44.5403 log10_qual_likelihood_position_model=42.055 log10_strand_likelihood_position_model=18.3107 new_cov=0/52 polymorphism_quality=39.4 quality=39.4 quality_position_model=Inf ref_cov=237/164 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=237/219 RA 449 . NC_007779 1999234 0 T G bias_e_value=0.771555 bias_p_value=1.66057e-07 fisher_strand_p_value=8.47845e-09 frequency=3.000355e-02 genotype_quality=832.3 ks_quality_p_value=1 log10_base_likelihood=-5.96182 log10_qual_likelihood_position_model=17.7926 log10_strand_likelihood_position_model=8.07168 new_cov=20/0 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=85/146 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=105/146 RA 450 . NC_007779 2004055 0 A C bias_e_value=8.76027e-34 bias_p_value=1.88542e-40 fisher_strand_p_value=1.94284e-42 frequency=1.822748e-01 genotype_quality=1159.6 ks_quality_p_value=1 log10_base_likelihood=-75.793 log10_qual_likelihood_position_model=64.6511 log10_strand_likelihood_position_model=41.7116 new_cov=0/94 polymorphism_quality=70.8 quality=70.8 quality_position_model=Inf ref_cov=236/89 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=236/184 RA 451 . NC_007779 2004055 1 . C bias_e_value=1701770 bias_p_value=0.366262 fisher_strand_p_value=0.181191 frequency=5.073547e-03 genotype_quality=1851.3 ks_quality_p_value=0.641179 log10_base_likelihood=-5.75974 log10_qual_likelihood_position_model=3.63359 log10_strand_likelihood_position_model=0.741863 new_cov=0/2 polymorphism_quality=0.2 quality=0.2 quality_position_model=0.0050561 ref_cov=226/166 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=226/168 RA 452 . NC_007779 2005401 0 C T frequency=1 genotype_quality=1845.0 new_cov=219/227 quality=1845.0 ref_cov=0/1 tot_cov=219/228 RA 453 . NC_007779 2005920 1 . A bias_e_value=2294820 bias_p_value=0.493898 fisher_strand_p_value=0.248853 frequency=5.639076e-03 genotype_quality=2647.2 ks_quality_p_value=0.735646 log10_base_likelihood=-12.015 log10_qual_likelihood_position_model=2.06715 log10_strand_likelihood_position_model=0.881197 new_cov=0/3 polymorphism_quality=6.6 quality=6.6 quality_position_model=4.4966e-11 ref_cov=261/268 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=261/271 RA 454 . NC_007779 2014008 0 T . bias_e_value=4498640 bias_p_value=0.968214 fisher_strand_p_value=1 frequency=1.128006e-02 genotype_quality=1810.3 ks_quality_p_value=0.758699 log10_base_likelihood=-13.9988 log10_qual_likelihood_position_model=2.41953 log10_strand_likelihood_position_model=0.487968 new_cov=2/3 polymorphism_quality=8.6 quality=8.6 quality_position_model=3.85648e-13 ref_cov=211/227 reject=INDEL_HOMOPOLYMER tot_cov=213/230 RA 455 . NC_007779 2020389 1 . A bias_e_value=4412320 bias_p_value=0.949635 fisher_strand_p_value=1 frequency=6.772041e-03 genotype_quality=2185.7 ks_quality_p_value=0.699894 log10_base_likelihood=-12.2893 log10_qual_likelihood_position_model=2.55002 log10_strand_likelihood_position_model=0.407468 new_cov=2/1 polymorphism_quality=6.9 quality=6.9 quality_position_model=2.40838e-11 ref_cov=229/211 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=231/212 RA 456 . NC_007779 2023811 0 C A bias_e_value=0.163517 bias_p_value=3.51928e-08 fisher_strand_p_value=1.65869e-09 frequency=4.464531e-02 genotype_quality=1479.6 ks_quality_p_value=1 log10_base_likelihood=-16.2621 log10_qual_likelihood_position_model=31.3678 log10_strand_likelihood_position_model=8.82702 new_cov=31/1 polymorphism_quality=10.9 quality=10.9 quality_position_model=Inf ref_cov=191/229 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=222/230 RA 457 . NC_007779 2032185 0 G C bias_e_value=9.68034e-09 bias_p_value=2.08344e-15 fisher_strand_p_value=5.41797e-17 frequency=6.820059e-02 genotype_quality=900.5 ks_quality_p_value=1 log10_base_likelihood=-21.6777 log10_qual_likelihood_position_model=20.501 log10_strand_likelihood_position_model=16.2662 new_cov=18/0 polymorphism_quality=16.4 quality=16.4 quality_position_model=Inf ref_cov=19/196 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=37/196 RA 458 . NC_007779 2065611 0 C A bias_e_value=0.000855173 bias_p_value=1.84053e-10 fisher_strand_p_value=6.89326e-12 frequency=5.634212e-02 genotype_quality=1391.7 ks_quality_p_value=1 log10_base_likelihood=-16.3861 log10_qual_likelihood_position_model=28.5942 log10_strand_likelihood_position_model=11.1966 new_cov=39/0 polymorphism_quality=11.1 quality=11.1 quality_position_model=Inf ref_cov=195/201 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=234/201 RA 459 . NC_007779 2079936 0 G T bias_e_value=1.6871 bias_p_value=3.63105e-07 fisher_strand_p_value=1.93549e-08 frequency=2.797604e-02 genotype_quality=1532.1 ks_quality_p_value=1 log10_base_likelihood=-7.51038 log10_qual_likelihood_position_model=20.1252 log10_strand_likelihood_position_model=7.71321 new_cov=0/24 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=236/203 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=236/229 RA 460 . NC_007779 2095119 0 G . bias_e_value=1562650 bias_p_value=0.336318 fisher_strand_p_value=0.25204 frequency=7.804871e-03 genotype_quality=1616.6 ks_quality_p_value=0.407264 log10_base_likelihood=-7.77277 log10_qual_likelihood_position_model=1.47742 log10_strand_likelihood_position_model=0.814342 new_cov=0/3 polymorphism_quality=2.3 quality=2.3 quality_position_model=2.19735e-07 ref_cov=178/203 reject=POLYMORPHISM_STRAND tot_cov=178/206 RA 461 . NC_007779 2095120 0 C . bias_e_value=1490910 bias_p_value=0.320879 fisher_strand_p_value=0.251264 frequency=7.868767e-03 genotype_quality=1600.9 ks_quality_p_value=0.381919 log10_base_likelihood=-8.14086 log10_qual_likelihood_position_model=1.60884 log10_strand_likelihood_position_model=0.823304 new_cov=0/3 polymorphism_quality=2.7 quality=2.7 quality_position_model=1.27624e-07 ref_cov=178/200 reject=POLYMORPHISM_STRAND tot_cov=178/203 RA 462 . NC_007779 2095121 0 T . bias_e_value=1555800 bias_p_value=0.334844 fisher_strand_p_value=0.251086 frequency=8.014679e-03 genotype_quality=1508.4 ks_quality_p_value=0.406236 log10_base_likelihood=-7.94656 log10_qual_likelihood_position_model=1.50819 log10_strand_likelihood_position_model=0.825139 new_cov=0/3 polymorphism_quality=2.5 quality=2.5 quality_position_model=1.60266e-07 ref_cov=175/196 reject=POLYMORPHISM_STRAND tot_cov=175/199 RA 463 . NC_007779 2095122 0 G . bias_e_value=1682530 bias_p_value=0.36212 fisher_strand_p_value=0.251362 frequency=8.013725e-03 genotype_quality=1586.8 ks_quality_p_value=0.45456 log10_base_likelihood=-7.80726 log10_qual_likelihood_position_model=1.48026 log10_strand_likelihood_position_model=0.821641 new_cov=0/3 polymorphism_quality=2.3 quality=2.3 quality_position_model=2.07326e-07 ref_cov=174/196 reject=POLYMORPHISM_STRAND tot_cov=175/199 RA 464 . NC_007779 2095582 0 G T bias_e_value=1.77307e-06 bias_p_value=3.81606e-13 fisher_strand_p_value=1.15311e-14 frequency=6.987572e-02 genotype_quality=1368.6 ks_quality_p_value=1 log10_base_likelihood=-19.5185 log10_qual_likelihood_position_model=27.7724 log10_strand_likelihood_position_model=13.9881 new_cov=0/47 polymorphism_quality=14.2 quality=14.2 quality_position_model=Inf ref_cov=211/191 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=211/238 RA 465 . NC_007779 2098223 0 T G bias_e_value=2.78973e-16 bias_p_value=6.00415e-23 fisher_strand_p_value=1.06843e-24 frequency=6.691217e-02 genotype_quality=1230.1 ks_quality_p_value=1 log10_base_likelihood=-9.35359 log10_qual_likelihood_position_model=47.1597 log10_strand_likelihood_position_model=23.9713 new_cov=60/0 polymorphism_quality=3.9 quality=3.9 quality_position_model=Inf ref_cov=120/225 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=180/225 RA 466 . NC_007779 2107010 1 . A bias_e_value=4639860 bias_p_value=0.998607 fisher_strand_p_value=1 frequency=1.222515e-02 genotype_quality=1988.5 ks_quality_p_value=0.947675 log10_base_likelihood=-20.8012 log10_qual_likelihood_position_model=4.68532 log10_strand_likelihood_position_model=0.461724 new_cov=3/2 polymorphism_quality=15.5 quality=15.5 quality_position_model=8.92908e-18 ref_cov=232/172 reject=INDEL_HOMOPOLYMER tot_cov=235/174 RA 467 . NC_007779 2156661 0 C A bias_e_value=0.0026686 bias_p_value=5.74346e-10 fisher_strand_p_value=2.25236e-11 frequency=6.434536e-02 genotype_quality=1101.8 ks_quality_p_value=0.99932 log10_base_likelihood=-13.541 log10_qual_likelihood_position_model=29.6731 log10_strand_likelihood_position_model=10.7089 new_cov=47/0 polymorphism_quality=8.2 quality=8.2 quality_position_model=Inf ref_cov=197/152 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=245/152 RA 468 . NC_007779 2170094 0 C A frequency=1 genotype_quality=1992.9 new_cov=216/265 quality=1992.9 ref_cov=0/1 tot_cov=216/266 RA 469 . NC_007779 2172317 0 C A bias_e_value=4571970 bias_p_value=0.983996 fisher_strand_p_value=1 frequency=6.911278e-03 genotype_quality=1879.7 ks_quality_p_value=0.826512 log10_base_likelihood=-5.68381 log10_qual_likelihood_position_model=4.09904 log10_strand_likelihood_position_model=0.42529 new_cov=2/2 polymorphism_quality=0.1 quality=0.1 quality_position_model=0.00914906 ref_cov=227/210 reject=EVALUE tot_cov=229/212 RA 470 . NC_007779 2174678 0 C G bias_e_value=0.000519314 bias_p_value=1.11768e-10 fisher_strand_p_value=4.10634e-12 frequency=5.209780e-02 genotype_quality=1232.4 ks_quality_p_value=1 log10_base_likelihood=-14.1698 log10_qual_likelihood_position_model=21.855 log10_strand_likelihood_position_model=11.3865 new_cov=0/20 polymorphism_quality=8.8 quality=8.8 quality_position_model=Inf ref_cov=231/75 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=232/95 RA 471 . NC_007779 2199432 0 G C bias_e_value=0.00015167 bias_p_value=3.2643e-11 fisher_strand_p_value=1.14556e-12 frequency=3.507137e-02 genotype_quality=1365.7 ks_quality_p_value=1 log10_base_likelihood=-12.399 log10_qual_likelihood_position_model=20.2084 log10_strand_likelihood_position_model=11.941 new_cov=0/14 polymorphism_quality=7.0 quality=7.0 quality_position_model=Inf ref_cov=296/41 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=296/55 RA 472 . NC_007779 2200802 0 A . bias_e_value=4562930 bias_p_value=0.98205 fisher_strand_p_value=1 frequency=7.821083e-03 genotype_quality=2114.6 ks_quality_p_value=0.816608 log10_base_likelihood=-10.4342 log10_qual_likelihood_position_model=1.69485 log10_strand_likelihood_position_model=0.425016 new_cov=2/2 polymorphism_quality=5.0 quality=5.0 quality_position_model=2.64951e-10 ref_cov=246/261 reject=INDEL_HOMOPOLYMER tot_cov=248/263 RA 473 . NC_007779 2202934 0 G T bias_e_value=0.00175856 bias_p_value=3.78483e-10 fisher_strand_p_value=1.4607e-11 frequency=3.761864e-02 genotype_quality=1338.0 ks_quality_p_value=0.998461 log10_base_likelihood=-8.84943 log10_qual_likelihood_position_model=25.2318 log10_strand_likelihood_position_model=10.8354 new_cov=0/32 polymorphism_quality=3.4 quality=3.4 quality_position_model=Inf ref_cov=221/171 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=221/204 RA 474 . NC_007779 2203780 1 . A bias_e_value=2910500 bias_p_value=0.626407 fisher_strand_p_value=0.353906 frequency=1.015186e-02 genotype_quality=1948.1 ks_quality_p_value=0.769165 log10_base_likelihood=-16.9372 log10_qual_likelihood_position_model=2.06987 log10_strand_likelihood_position_model=0.639076 new_cov=3/1 polymorphism_quality=11.6 quality=11.6 quality_position_model=2.49391e-16 ref_cov=186/204 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/205 RA 475 . NC_007779 2211749 0 G C bias_e_value=216.387 bias_p_value=4.65716e-05 fisher_strand_p_value=3.42942e-06 frequency=2.281666e-02 genotype_quality=1053.4 ks_quality_p_value=0.999754 log10_base_likelihood=-8.30199 log10_qual_likelihood_position_model=12.7313 log10_strand_likelihood_position_model=5.46478 new_cov=9/0 polymorphism_quality=2.8 quality=2.8 quality_position_model=Inf ref_cov=62/204 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=71/204 RA 476 . NC_007779 2213133 1 . T bias_e_value=2564980 bias_p_value=0.552044 fisher_strand_p_value=0.223407 frequency=4.854202e-03 genotype_quality=2049.7 ks_quality_p_value=0.981606 log10_base_likelihood=-8.0515 log10_qual_likelihood_position_model=2.5641 log10_strand_likelihood_position_model=0.650903 new_cov=2/0 polymorphism_quality=2.6 quality=2.6 quality_position_model=1.0272e-06 ref_cov=193/217 reject=POLYMORPHISM_STRAND tot_cov=195/217 RA 477 . NC_007779 2213136 0 G T bias_e_value=7.48116e-17 bias_p_value=1.61012e-23 fisher_strand_p_value=2.81948e-25 frequency=1.305594e-01 genotype_quality=999.6 ks_quality_p_value=0.992554 log10_base_likelihood=-77.6862 log10_qual_likelihood_position_model=41.2347 log10_strand_likelihood_position_model=24.5498 new_cov=42/0 polymorphism_quality=72.7 quality=72.7 quality_position_model=5.76834e-14 ref_cov=54/211 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=96/211 RA 478 . NC_007779 2225700 0 T G bias_e_value=0.0138019 bias_p_value=2.9705e-09 fisher_strand_p_value=1.24815e-10 frequency=2.261639e-02 genotype_quality=1107.0 ks_quality_p_value=0.999782 log10_base_likelihood=-7.53538 log10_qual_likelihood_position_model=12.8599 log10_strand_likelihood_position_model=9.90373 new_cov=9/0 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=18/265 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=27/265 RA 479 . NC_007779 2226744 0 T G bias_e_value=0.000117533 bias_p_value=2.52959e-11 fisher_strand_p_value=8.79571e-13 frequency=5.793905e-02 genotype_quality=1322.6 ks_quality_p_value=1 log10_base_likelihood=-10.4908 log10_qual_likelihood_position_model=36.5017 log10_strand_likelihood_position_model=12.0998 new_cov=39/0 polymorphism_quality=5.1 quality=5.1 quality_position_model=Inf ref_cov=178/206 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=217/206 RA 480 . NC_007779 2232587 0 G A bias_e_value=114970 bias_p_value=0.0247443 fisher_strand_p_value=0.00379866 frequency=1.930428e-02 genotype_quality=912.5 ks_quality_p_value=0.989398 log10_base_likelihood=-9.75177 log10_qual_likelihood_position_model=4.93878 log10_strand_likelihood_position_model=2.42037 new_cov=6/0 polymorphism_quality=4.3 quality=4.3 quality_position_model=0.000391958 ref_cov=116/183 reject=POLYMORPHISM_STRAND tot_cov=122/183 RA 481 . NC_007779 2249963 0 T G bias_e_value=6.36001e-13 bias_p_value=1.36882e-19 fisher_strand_p_value=2.83325e-21 frequency=8.301163e-02 genotype_quality=1275.8 ks_quality_p_value=1 log10_base_likelihood=-19.1465 log10_qual_likelihood_position_model=53.7754 log10_strand_likelihood_position_model=20.5477 new_cov=57/0 polymorphism_quality=13.9 quality=13.9 quality_position_model=Inf ref_cov=143/221 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=200/221 RA 482 . NC_007779 2262756 0 A C bias_e_value=3806050 bias_p_value=0.819151 fisher_strand_p_value=0.466119 frequency=3.592968e-02 genotype_quality=1858.8 ks_quality_p_value=0.992273 log10_base_likelihood=-44.1466 log10_qual_likelihood_position_model=8.54496 log10_strand_likelihood_position_model=0.839222 new_cov=11/6 polymorphism_quality=39.0 quality=39.0 quality_position_model=4.70384e-37 ref_cov=249/206 tot_cov=260/212 RA 483 . NC_007779 2266892 0 G T bias_e_value=0.0406132 bias_p_value=8.74091e-09 fisher_strand_p_value=3.96869e-10 frequency=2.555180e-02 genotype_quality=1829.0 ks_quality_p_value=0.971253 log10_base_likelihood=-6.29965 log10_qual_likelihood_position_model=20.4148 log10_strand_likelihood_position_model=9.40135 new_cov=0/27 polymorphism_quality=0.8 quality=0.8 quality_position_model=Inf ref_cov=285/218 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=285/245 RA 484 . NC_007779 2271802 0 A . bias_e_value=350615 bias_p_value=0.0754606 fisher_strand_p_value=0.370385 frequency=8.205414e-03 genotype_quality=1975.5 ks_quality_p_value=0.0388766 log10_base_likelihood=-10.3804 log10_qual_likelihood_position_model=3.03069 log10_strand_likelihood_position_model=0.607483 new_cov=1/3 polymorphism_quality=5.0 quality=5.0 quality_position_model=1.09262e-08 ref_cov=244/239 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=245/242 RA 485 . NC_007779 2277624 0 G T bias_e_value=3.20177 bias_p_value=6.89097e-07 fisher_strand_p_value=3.81077e-08 frequency=2.328396e-02 genotype_quality=1606.5 ks_quality_p_value=1 log10_base_likelihood=-6.36513 log10_qual_likelihood_position_model=21.2899 log10_strand_likelihood_position_model=7.41899 new_cov=0/23 polymorphism_quality=0.8 quality=0.8 quality_position_model=Inf ref_cov=240/206 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=241/230 RA 486 . NC_007779 2295451 0 C A bias_e_value=0.0358394 bias_p_value=7.71349e-09 fisher_strand_p_value=3.38201e-10 frequency=2.456856e-02 genotype_quality=1550.6 ks_quality_p_value=1 log10_base_likelihood=-5.96063 log10_qual_likelihood_position_model=20.6709 log10_strand_likelihood_position_model=9.47082 new_cov=24/0 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=170/270 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=194/270 RA 487 . NC_007779 2307309 0 T C bias_e_value=0.000794474 bias_p_value=1.70989e-10 fisher_strand_p_value=6.38569e-12 frequency=4.004669e-02 genotype_quality=1174.4 ks_quality_p_value=1 log10_base_likelihood=-7.93065 log10_qual_likelihood_position_model=21.8703 log10_strand_likelihood_position_model=11.1948 new_cov=0/19 polymorphism_quality=2.4 quality=2.4 quality_position_model=Inf ref_cov=256/79 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=257/98 RA 488 . NC_007779 2331120 0 T G bias_e_value=1.33052e-26 bias_p_value=2.8636e-33 fisher_strand_p_value=3.56527e-35 frequency=1.211033e-01 genotype_quality=1255.3 ks_quality_p_value=1 log10_base_likelihood=-29.1294 log10_qual_likelihood_position_model=52.7447 log10_strand_likelihood_position_model=34.4479 new_cov=83/0 polymorphism_quality=23.9 quality=23.9 quality_position_model=Inf ref_cov=110/239 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=194/239 RA 489 . NC_007779 2332580 0 A C bias_e_value=4.43339e-23 bias_p_value=9.54171e-30 fisher_strand_p_value=1.3234e-31 frequency=6.656742e-02 genotype_quality=1243.6 ks_quality_p_value=1 log10_base_likelihood=-10.5516 log10_qual_likelihood_position_model=46.8927 log10_strand_likelihood_position_model=30.8783 new_cov=0/64 polymorphism_quality=5.1 quality=5.1 quality_position_model=Inf ref_cov=254/94 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=254/159 RA 490 . NC_007779 2342393 0 A C bias_e_value=3.95245e-14 bias_p_value=8.50659e-21 fisher_strand_p_value=1.66313e-22 frequency=8.182383e-02 genotype_quality=1240.7 ks_quality_p_value=1 log10_base_likelihood=-12.7163 log10_qual_likelihood_position_model=44.823 log10_strand_likelihood_position_model=21.7791 new_cov=0/46 polymorphism_quality=7.3 quality=7.3 quality_position_model=Inf ref_cov=240/99 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=240/145 RA 491 . NC_007779 2344586 0 C A bias_e_value=0.149825 bias_p_value=3.22458e-08 fisher_strand_p_value=1.51325e-09 frequency=3.399467e-02 genotype_quality=1394.7 ks_quality_p_value=1 log10_base_likelihood=-6.43769 log10_qual_likelihood_position_model=22.2452 log10_strand_likelihood_position_model=8.83901 new_cov=30/0 polymorphism_quality=0.9 quality=0.9 quality_position_model=Inf ref_cov=198/207 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=228/208 RA 492 . NC_007779 2348491 0 C A bias_e_value=9.89115 bias_p_value=2.12881e-06 fisher_strand_p_value=1.26066e-07 frequency=2.658653e-02 genotype_quality=1485.4 ks_quality_p_value=1 log10_base_likelihood=-5.77064 log10_qual_likelihood_position_model=13.252 log10_strand_likelihood_position_model=6.8994 new_cov=0/17 polymorphism_quality=0.2 quality=0.2 quality_position_model=Inf ref_cov=241/147 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=241/164 RA 493 . NC_007779 2351513 1 . G bias_e_value=1749920 bias_p_value=0.376625 fisher_strand_p_value=0.505102 frequency=3.936768e-03 genotype_quality=2548.5 ks_quality_p_value=0.239628 log10_base_likelihood=-8.15291 log10_qual_likelihood_position_model=2.66893 log10_strand_likelihood_position_model=0.511916 new_cov=0/2 polymorphism_quality=2.7 quality=2.7 quality_position_model=7.42217e-07 ref_cov=226/280 reject=POLYMORPHISM_STRAND tot_cov=226/282 RA 494 . NC_007779 2351513 2 . C bias_e_value=3708620 bias_p_value=0.798183 fisher_strand_p_value=0.505102 frequency=3.936768e-03 genotype_quality=2549.5 ks_quality_p_value=0.863798 log10_base_likelihood=-7.79266 log10_qual_likelihood_position_model=1.87659 log10_strand_likelihood_position_model=0.511916 new_cov=0/2 polymorphism_quality=2.3 quality=2.3 quality_position_model=2.64006e-07 ref_cov=226/280 reject=POLYMORPHISM_STRAND tot_cov=226/282 RA 495 . NC_007779 2351513 3 . A bias_e_value=3930160 bias_p_value=0.845863 fisher_strand_p_value=0.505102 frequency=3.936768e-03 genotype_quality=2540.6 ks_quality_p_value=0.987874 log10_base_likelihood=-7.43264 log10_qual_likelihood_position_model=2.91672 log10_strand_likelihood_position_model=0.511916 new_cov=0/2 polymorphism_quality=1.9 quality=1.9 quality_position_model=7.61839e-06 ref_cov=226/280 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=226/282 RA 496 . NC_007779 2351513 4 . C bias_e_value=1749920 bias_p_value=0.376625 fisher_strand_p_value=0.505102 frequency=3.936768e-03 genotype_quality=2549.7 ks_quality_p_value=0.239628 log10_base_likelihood=-7.59127 log10_qual_likelihood_position_model=2.66893 log10_strand_likelihood_position_model=0.511916 new_cov=0/2 polymorphism_quality=2.1 quality=2.1 quality_position_model=2.85897e-06 ref_cov=226/280 reject=POLYMORPHISM_STRAND tot_cov=226/282 RA 497 . NC_007779 2351513 5 . C bias_e_value=1508910 bias_p_value=0.324753 fisher_strand_p_value=0.505102 frequency=3.936768e-03 genotype_quality=2549.8 ks_quality_p_value=0.193271 log10_base_likelihood=-7.78231 log10_qual_likelihood_position_model=2.21775 log10_strand_likelihood_position_model=0.511916 new_cov=0/2 polymorphism_quality=2.3 quality=2.3 quality_position_model=6.11936e-07 ref_cov=226/280 reject=POLYMORPHISM_STRAND tot_cov=226/282 RA 498 . NC_007779 2351513 6 . T bias_e_value=1508910 bias_p_value=0.324753 fisher_strand_p_value=0.505102 frequency=3.936768e-03 genotype_quality=2541.8 ks_quality_p_value=0.193271 log10_base_likelihood=-7.92995 log10_qual_likelihood_position_model=2.21775 log10_strand_likelihood_position_model=0.511916 new_cov=0/2 polymorphism_quality=2.4 quality=2.4 quality_position_model=4.29789e-07 ref_cov=226/280 reject=POLYMORPHISM_STRAND tot_cov=226/282 RA 499 . NC_007779 2353815 0 A C bias_e_value=9.5963e-17 bias_p_value=2.06535e-23 fisher_strand_p_value=3.60557e-25 frequency=8.678579e-02 genotype_quality=1060.2 ks_quality_p_value=1 log10_base_likelihood=-29.032 log10_qual_likelihood_position_model=35.3009 log10_strand_likelihood_position_model=24.443 new_cov=0/37 polymorphism_quality=23.8 quality=23.8 quality_position_model=Inf ref_cov=225/45 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=225/82 RA 500 . NC_007779 2354291 0 A C bias_e_value=5.25632e-09 bias_p_value=1.13128e-15 fisher_strand_p_value=2.89471e-17 frequency=7.158804e-02 genotype_quality=1390.3 ks_quality_p_value=1 log10_base_likelihood=-13.3853 log10_qual_likelihood_position_model=43.6767 log10_strand_likelihood_position_model=16.5384 new_cov=0/45 polymorphism_quality=8.0 quality=8.0 quality_position_model=Inf ref_cov=240/158 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=240/204 RA 501 . NC_007779 2373239 0 A C bias_e_value=2.07486e-16 bias_p_value=4.46558e-23 fisher_strand_p_value=7.90407e-25 frequency=8.288765e-02 genotype_quality=1009.9 ks_quality_p_value=1 log10_base_likelihood=-15.5175 log10_qual_likelihood_position_model=37.5659 log10_strand_likelihood_position_model=24.1021 new_cov=0/45 polymorphism_quality=10.2 quality=10.2 quality_position_model=Inf ref_cov=211/65 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=213/112 RA 502 . NC_007779 2379901 0 T . bias_e_value=1494500 bias_p_value=0.321652 fisher_strand_p_value=1 frequency=7.255554e-03 genotype_quality=1625.2 ks_quality_p_value=0.0962925 log10_base_likelihood=-7.5855 log10_qual_likelihood_position_model=3.46253 log10_strand_likelihood_position_model=0.394156 new_cov=2/1 polymorphism_quality=2.1 quality=2.1 quality_position_model=1.48298e-05 ref_cov=221/189 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=223/190 RA 503 . NC_007779 2387486 1 . A bias_e_value=2040710 bias_p_value=0.439208 fisher_strand_p_value=0.501594 frequency=4.140854e-03 genotype_quality=2436.7 ks_quality_p_value=0.303944 log10_base_likelihood=-7.81968 log10_qual_likelihood_position_model=1.2678 log10_strand_likelihood_position_model=0.542075 new_cov=0/2 polymorphism_quality=2.3 quality=2.3 quality_position_model=6.22853e-08 ref_cov=224/257 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=224/259 RA 504 . NC_007779 2387487 0 A . bias_e_value=4646080 bias_p_value=0.999946 fisher_strand_p_value=1 frequency=5.919456e-03 genotype_quality=2110.8 ks_quality_p_value=0.989658 log10_base_likelihood=-7.11459 log10_qual_likelihood_position_model=3.00297 log10_strand_likelihood_position_model=0.40296 new_cov=1/2 polymorphism_quality=1.6 quality=1.6 quality_position_model=1.55727e-05 ref_cov=238/265 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=239/267 RA 505 . NC_007779 2406075 0 C T frequency=1 genotype_quality=1667.4 new_cov=220/191 quality=1667.4 ref_cov=0/0 tot_cov=220/191 RA 506 . NC_007779 2410316 0 A C bias_e_value=1.67249e-12 bias_p_value=3.59958e-19 fisher_strand_p_value=7.60603e-21 frequency=9.887314e-02 genotype_quality=1207.9 ks_quality_p_value=1 log10_base_likelihood=-36.6476 log10_qual_likelihood_position_model=38.6642 log10_strand_likelihood_position_model=20.1188 new_cov=0/58 polymorphism_quality=31.5 quality=31.5 quality_position_model=Inf ref_cov=207/141 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=207/200 RA 507 . NC_007779 2416102 0 G A frequency=1 genotype_quality=1789.1 new_cov=214/232 quality=1789.1 ref_cov=0/0 tot_cov=214/232 RA 508 . NC_007779 2417605 0 C A bias_e_value=7.23416e-12 bias_p_value=1.55696e-18 fisher_strand_p_value=1.42203e-19 frequency=7.001638e-02 genotype_quality=1439.7 ks_quality_p_value=0.238909 log10_base_likelihood=-15.5002 log10_qual_likelihood_position_model=54.9384 log10_strand_likelihood_position_model=19.0446 new_cov=58/0 polymorphism_quality=10.2 quality=10.2 quality_position_model=Inf ref_cov=183/239 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=242/239 RA 509 . NC_007779 2420902 0 G C bias_e_value=42.0674 bias_p_value=9.0539e-06 fisher_strand_p_value=6.15781e-07 frequency=2.322865e-02 genotype_quality=1320.9 ks_quality_p_value=0.958296 log10_base_likelihood=-6.38722 log10_qual_likelihood_position_model=18.3584 log10_strand_likelihood_position_model=6.21057 new_cov=14/0 polymorphism_quality=0.9 quality=0.9 quality_position_model=Inf ref_cov=122/230 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=137/230 RA 510 . NC_007779 2426889 0 A C bias_e_value=3.5076e-10 bias_p_value=7.54917e-17 fisher_strand_p_value=1.80357e-18 frequency=4.595757e-02 genotype_quality=1169.4 ks_quality_p_value=1 log10_base_likelihood=-13.2264 log10_qual_likelihood_position_model=26.1345 log10_strand_likelihood_position_model=17.7439 new_cov=0/21 polymorphism_quality=7.9 quality=7.9 quality_position_model=Inf ref_cov=261/33 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=261/54 RA 511 . NC_007779 2441855 0 C A bias_e_value=0.406332 bias_p_value=8.74522e-08 fisher_strand_p_value=4.31631e-09 frequency=2.384377e-02 genotype_quality=1723.1 ks_quality_p_value=1 log10_base_likelihood=-5.56613 log10_qual_likelihood_position_model=21.2422 log10_strand_likelihood_position_model=8.36489 new_cov=26/0 polymorphism_quality=0.0 quality=0.0 quality_position_model=Inf ref_cov=219/255 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=246/256 RA 512 . NC_007779 2465370 0 C A bias_e_value=0.0234629 bias_p_value=5.04977e-09 fisher_strand_p_value=2.18931e-10 frequency=5.179262e-02 genotype_quality=982.3 ks_quality_p_value=0.99206 log10_base_likelihood=-21.8842 log10_qual_likelihood_position_model=20.0563 log10_strand_likelihood_position_model=9.65969 new_cov=0/15 polymorphism_quality=16.6 quality=16.6 quality_position_model=Inf ref_cov=190/48 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=190/63 RA 513 . NC_007779 2468326 1 . C bias_e_value=1009260 bias_p_value=0.217217 fisher_strand_p_value=0.193112 frequency=4.608154e-03 genotype_quality=2082.8 ks_quality_p_value=0.289633 log10_base_likelihood=-7.87085 log10_qual_likelihood_position_model=1.54303 log10_strand_likelihood_position_model=0.714191 new_cov=2/0 polymorphism_quality=2.4 quality=2.4 quality_position_model=1.60116e-07 ref_cov=189/243 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=191/243 RA 514 . NC_007779 2468327 0 C . bias_e_value=1020480 bias_p_value=0.219632 fisher_strand_p_value=0.0652997 frequency=3.415871e-02 genotype_quality=1787.6 ks_quality_p_value=0.869394 log10_base_likelihood=-47.7572 log10_qual_likelihood_position_model=7.52185 log10_strand_likelihood_position_model=1.47285 new_cov=3/12 polymorphism_quality=42.7 quality=42.7 quality_position_model=4.45649e-41 ref_cov=191/232 reject=INDEL_HOMOPOLYMER tot_cov=194/245 RA 515 . NC_007779 2475095 1 . T bias_e_value=4558080 bias_p_value=0.981006 fisher_strand_p_value=1 frequency=5.916595e-03 genotype_quality=1700.1 ks_quality_p_value=0.811536 log10_base_likelihood=-7.9633 log10_qual_likelihood_position_model=2.79173 log10_strand_likelihood_position_model=0.314608 new_cov=1/1 polymorphism_quality=2.5 quality=2.5 quality_position_model=9.78005e-07 ref_cov=199/137 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=200/138 RA 516 . NC_007779 2476279 0 C G bias_e_value=114734 bias_p_value=0.0246935 fisher_strand_p_value=0.00375778 frequency=2.443790e-02 genotype_quality=1475.6 ks_quality_p_value=0.997736 log10_base_likelihood=-17.5697 log10_qual_likelihood_position_model=8.21901 log10_strand_likelihood_position_model=2.59094 new_cov=0/9 polymorphism_quality=12.3 quality=12.3 quality_position_model=1.04812e-08 ref_cov=173/179 reject=POLYMORPHISM_STRAND tot_cov=174/188 RA 517 . NC_007779 2476287 0 T G bias_e_value=199728 bias_p_value=0.0429862 fisher_strand_p_value=0.0072535 frequency=1.449871e-02 genotype_quality=1412.0 ks_quality_p_value=1 log10_base_likelihood=-7.77574 log10_qual_likelihood_position_model=10.9709 log10_strand_likelihood_position_model=2.40368 new_cov=0/8 polymorphism_quality=2.3 quality=2.3 quality_position_model=Inf ref_cov=182/178 reject=POLYMORPHISM_STRAND tot_cov=183/186 RA 518 . NC_007779 2476289 0 A T bias_e_value=195737 bias_p_value=0.0421271 fisher_strand_p_value=0.00707954 frequency=1.202011e-02 genotype_quality=1420.1 ks_quality_p_value=1 log10_base_likelihood=-5.90659 log10_qual_likelihood_position_model=8.9554 log10_strand_likelihood_position_model=2.15 new_cov=0/7 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=182/173 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=183/180 RA 519 . NC_007779 2478675 0 C A bias_e_value=0.00362567 bias_p_value=7.80331e-10 fisher_strand_p_value=3.09679e-11 frequency=3.265095e-02 genotype_quality=1518.4 ks_quality_p_value=1 log10_base_likelihood=-10.0722 log10_qual_likelihood_position_model=24.17 log10_strand_likelihood_position_model=10.5091 new_cov=28/0 polymorphism_quality=4.6 quality=4.6 quality_position_model=Inf ref_cov=170/253 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=199/253 RA 520 . NC_007779 2487343 0 A . bias_e_value=961070 bias_p_value=0.206845 fisher_strand_p_value=0.248439 frequency=6.586075e-03 genotype_quality=1876.6 ks_quality_p_value=0.210815 log10_base_likelihood=-7.56512 log10_qual_likelihood_position_model=2.71938 log10_strand_likelihood_position_model=0.891667 new_cov=3/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=8.59579e-06 ref_cov=227/225 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=230/225 RA 521 . NC_007779 2489981 1 . A bias_e_value=3278480 bias_p_value=0.705606 fisher_strand_p_value=0.510935 frequency=4.566193e-03 genotype_quality=2192.6 ks_quality_p_value=0.663292 log10_base_likelihood=-7.94985 log10_qual_likelihood_position_model=1.08766 log10_strand_likelihood_position_model=0.477434 new_cov=0/2 polymorphism_quality=2.5 quality=2.5 quality_position_model=2.55324e-08 ref_cov=185/251 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=185/253 RA 522 . NC_007779 2501527 0 G T bias_e_value=107.224 bias_p_value=2.30772e-05 fisher_strand_p_value=1.60937e-06 frequency=1.772213e-02 genotype_quality=1493.3 ks_quality_p_value=0.999972 log10_base_likelihood=-7.30524 log10_qual_likelihood_position_model=17.057 log10_strand_likelihood_position_model=5.86832 new_cov=0/20 polymorphism_quality=1.8 quality=1.8 quality_position_model=Inf ref_cov=205/202 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=206/222 RA 523 . NC_007779 2517218 0 A C bias_e_value=9.05214e-15 bias_p_value=1.94823e-21 fisher_strand_p_value=3.70028e-23 frequency=6.243086e-02 genotype_quality=1024.7 ks_quality_p_value=1 log10_base_likelihood=-11.6589 log10_qual_likelihood_position_model=53.091 log10_strand_likelihood_position_model=22.4318 new_cov=0/45 polymorphism_quality=6.3 quality=6.3 quality_position_model=Inf ref_cov=204/73 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=205/118 RA 524 . NC_007779 2536601 0 T G bias_e_value=1.60555e-07 bias_p_value=3.45552e-14 fisher_strand_p_value=9.71535e-16 frequency=7.539749e-02 genotype_quality=1362.2 ks_quality_p_value=1 log10_base_likelihood=-15.9743 log10_qual_likelihood_position_model=48.2499 log10_strand_likelihood_position_model=15.0187 new_cov=44/1 polymorphism_quality=10.6 quality=10.6 quality_position_model=Inf ref_cov=148/231 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=192/232 RA 525 . NC_007779 2538628 0 C T frequency=1 genotype_quality=2034.6 new_cov=249/249 quality=2034.6 ref_cov=0/1 tot_cov=249/251 RA 526 . NC_007779 2556426 0 G T bias_e_value=1.12864e-17 bias_p_value=2.4291e-24 fisher_strand_p_value=8.15903e-26 frequency=9.959888e-02 genotype_quality=1397.7 ks_quality_p_value=0.500708 log10_base_likelihood=-32.8702 log10_qual_likelihood_position_model=59.972 log10_strand_likelihood_position_model=25.0884 new_cov=0/68 polymorphism_quality=27.7 quality=27.7 quality_position_model=Inf ref_cov=249/153 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=249/223 RA 527 . NC_007779 2579404 0 G T bias_e_value=0.00164865 bias_p_value=3.54828e-10 fisher_strand_p_value=1.36377e-11 frequency=4.354572e-02 genotype_quality=1633.6 ks_quality_p_value=1 log10_base_likelihood=-12.8967 log10_qual_likelihood_position_model=24.9494 log10_strand_likelihood_position_model=10.8653 new_cov=0/34 polymorphism_quality=7.5 quality=7.5 quality_position_model=Inf ref_cov=247/210 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=247/244 RA 528 . NC_007779 2581402 0 A . bias_e_value=669246 bias_p_value=0.144037 fisher_strand_p_value=0.0458718 frequency=1.004410e-02 genotype_quality=1633.5 ks_quality_p_value=0.709613 log10_base_likelihood=-11.1268 log10_qual_likelihood_position_model=1.86272 log10_strand_likelihood_position_model=1.33845 new_cov=4/0 polymorphism_quality=5.7 quality=5.7 quality_position_model=6.63416e-10 ref_cov=181/213 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=185/213 RA 529 . NC_007779 2581900 0 G T bias_e_value=0.000143373 bias_p_value=3.08572e-11 fisher_strand_p_value=1.08068e-12 frequency=3.115845e-02 genotype_quality=1725.0 ks_quality_p_value=1 log10_base_likelihood=-5.96952 log10_qual_likelihood_position_model=31.3428 log10_strand_likelihood_position_model=11.9663 new_cov=0/37 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=265/221 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=266/259 RA 530 . NC_007779 2601998 0 A C bias_e_value=2.60326e-07 bias_p_value=5.60282e-14 fisher_strand_p_value=1.5976e-15 frequency=5.982447e-02 genotype_quality=1091.5 ks_quality_p_value=1 log10_base_likelihood=-15.9486 log10_qual_likelihood_position_model=30.3192 log10_strand_likelihood_position_model=14.802 new_cov=2/21 polymorphism_quality=10.6 quality=10.6 quality_position_model=Inf ref_cov=238/33 reject=FISHER_STRAND_P_VALUE tot_cov=241/54 RA 531 . NC_007779 2616347 0 A C bias_e_value=1.45973e-17 bias_p_value=3.14169e-24 fisher_strand_p_value=5.30707e-26 frequency=7.942295e-02 genotype_quality=1130.3 ks_quality_p_value=1 log10_base_likelihood=-12.8573 log10_qual_likelihood_position_model=38.6485 log10_strand_likelihood_position_model=25.2751 new_cov=0/48 polymorphism_quality=7.5 quality=7.5 quality_position_model=Inf ref_cov=232/75 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=232/123 RA 532 . NC_007779 2618382 0 A C bias_e_value=45.7183 bias_p_value=9.83964e-06 fisher_strand_p_value=6.45056e-07 frequency=1.450729e-02 genotype_quality=1120.0 ks_quality_p_value=1 log10_base_likelihood=-7.35532 log10_qual_likelihood_position_model=9.43095 log10_strand_likelihood_position_model=6.1904 new_cov=0/6 polymorphism_quality=1.9 quality=1.9 quality_position_model=Inf ref_cov=258/23 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=258/29 RA 533 . NC_007779 2618856 1 . A bias_e_value=3525220 bias_p_value=0.75871 fisher_strand_p_value=0.511538 frequency=4.228592e-03 genotype_quality=2360.2 ks_quality_p_value=0.765491 log10_base_likelihood=-7.81874 log10_qual_likelihood_position_model=1.23054 log10_strand_likelihood_position_model=0.47489 new_cov=0/2 polymorphism_quality=2.3 quality=2.3 quality_position_model=4.86857e-08 ref_cov=199/272 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=199/274 RA 534 . NC_007779 2618857 0 A . bias_e_value=1523230 bias_p_value=0.327835 fisher_strand_p_value=0.575886 frequency=6.309509e-03 genotype_quality=1951.1 ks_quality_p_value=0.171822 log10_base_likelihood=-7.67748 log10_qual_likelihood_position_model=1.75135 log10_strand_likelihood_position_model=0.509827 new_cov=2/1 polymorphism_quality=2.2 quality=2.2 quality_position_model=2.56453e-07 ref_cov=198/273 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=200/275 RA 535 . NC_007779 2623159 0 T G bias_e_value=4.59979e-33 bias_p_value=9.89984e-40 fisher_strand_p_value=1.03806e-41 frequency=1.180625e-01 genotype_quality=1328.2 ks_quality_p_value=1 log10_base_likelihood=-41.2532 log10_qual_likelihood_position_model=55.5012 log10_strand_likelihood_position_model=40.9838 new_cov=76/0 polymorphism_quality=36.1 quality=36.1 quality_position_model=Inf ref_cov=76/275 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=154/275 RA 536 . NC_007779 2623173 0 G T bias_e_value=0.158744 bias_p_value=3.41654e-08 fisher_strand_p_value=1.60791e-09 frequency=2.995205e-02 genotype_quality=1583.2 ks_quality_p_value=1 log10_base_likelihood=-5.98014 log10_qual_likelihood_position_model=19.3995 log10_strand_likelihood_position_model=8.79374 new_cov=21/0 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=150/261 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=172/262 RA 537 . NC_007779 2641345 0 T G bias_e_value=3.19862e-14 bias_p_value=6.88417e-21 fisher_strand_p_value=1.34027e-22 frequency=8.383989e-02 genotype_quality=897.2 ks_quality_p_value=1 log10_base_likelihood=-22.9823 log10_qual_likelihood_position_model=31.8936 log10_strand_likelihood_position_model=21.8728 new_cov=32/0 polymorphism_quality=17.7 quality=17.7 quality_position_model=Inf ref_cov=36/197 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=69/197 RA 538 . NC_007779 2648595 0 A C bias_e_value=2.21186e-10 bias_p_value=4.76045e-17 fisher_strand_p_value=1.12463e-18 frequency=5.990982e-02 genotype_quality=952.2 ks_quality_p_value=1 log10_base_likelihood=-17.5032 log10_qual_likelihood_position_model=27.3258 log10_strand_likelihood_position_model=17.949 new_cov=0/21 polymorphism_quality=12.2 quality=12.2 quality_position_model=Inf ref_cov=218/25 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=218/46 RA 539 . NC_007779 2672817 0 A C bias_e_value=4.82516e-14 bias_p_value=1.03849e-20 fisher_strand_p_value=2.03846e-22 frequency=1.082544e-01 genotype_quality=930.4 ks_quality_p_value=1 log10_base_likelihood=-18.1412 log10_qual_likelihood_position_model=46.1038 log10_strand_likelihood_position_model=21.6943 new_cov=1/57 polymorphism_quality=12.8 quality=12.8 quality_position_model=Inf ref_cov=176/86 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=177/143 RA 540 . NC_007779 2676695 0 T G bias_e_value=1.54341e-11 bias_p_value=3.32178e-18 fisher_strand_p_value=7.3729e-20 frequency=6.495142e-02 genotype_quality=1029.8 ks_quality_p_value=1 log10_base_likelihood=-6.32632 log10_qual_likelihood_position_model=54.953 log10_strand_likelihood_position_model=19.1324 new_cov=47/0 polymorphism_quality=0.8 quality=0.8 quality_position_model=Inf ref_cov=93/180 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=140/180 RA 541 . NC_007779 2708935 0 A C bias_e_value=0.000275211 bias_p_value=5.92318e-11 fisher_strand_p_value=2.12473e-12 frequency=6.055355e-02 genotype_quality=1422.1 ks_quality_p_value=1 log10_base_likelihood=-15.1465 log10_qual_likelihood_position_model=34.6984 log10_strand_likelihood_position_model=11.8656 new_cov=0/44 polymorphism_quality=9.8 quality=9.8 quality_position_model=Inf ref_cov=210/222 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=210/267 RA 542 . NC_007779 2724454 1 . T bias_e_value=2718540 bias_p_value=0.585094 fisher_strand_p_value=0.247653 frequency=3.759384e-03 genotype_quality=2672.4 ks_quality_p_value=0.976435 log10_base_likelihood=-7.60221 log10_qual_likelihood_position_model=2.21346 log10_strand_likelihood_position_model=0.606156 new_cov=2/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=1.169e-06 ref_cov=263/267 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=265/267 RA 543 . NC_007779 2733191 1 . C bias_e_value=235698 bias_p_value=0.0507277 fisher_strand_p_value=0.238848 frequency=4.291534e-03 genotype_quality=2230.5 ks_quality_p_value=0.037089 log10_base_likelihood=-7.77864 log10_qual_likelihood_position_model=2.35357 log10_strand_likelihood_position_model=0.621878 new_cov=2/0 polymorphism_quality=2.3 quality=2.3 quality_position_model=1.11262e-06 ref_cov=226/238 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=228/238 RA 544 . NC_007779 2756639 0 T . bias_e_value=2417080 bias_p_value=0.520213 fisher_strand_p_value=0.714877 frequency=1.638508e-02 genotype_quality=1734.3 ks_quality_p_value=0.278315 log10_base_likelihood=-19.8729 log10_qual_likelihood_position_model=3.62568 log10_strand_likelihood_position_model=0.58006 new_cov=4/3 polymorphism_quality=14.6 quality=14.6 quality_position_model=8.66206e-18 ref_cov=201/219 reject=INDEL_HOMOPOLYMER tot_cov=205/222 RA 545 . NC_007779 2757983 1 . A bias_e_value=865931 bias_p_value=0.186369 fisher_strand_p_value=0.238591 frequency=3.689766e-03 genotype_quality=2729.2 ks_quality_p_value=0.191072 log10_base_likelihood=-7.56917 log10_qual_likelihood_position_model=1.19489 log10_strand_likelihood_position_model=0.622347 new_cov=2/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=1.15129e-07 ref_cov=263/277 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=265/277 RA 546 . NC_007779 2771144 0 G T bias_e_value=8.65802e-06 bias_p_value=1.86341e-12 fisher_strand_p_value=9.08111e-14 frequency=5.571699e-02 genotype_quality=1276.9 ks_quality_p_value=0.652303 log10_base_likelihood=-12.5097 log10_qual_likelihood_position_model=39.9904 log10_strand_likelihood_position_model=13.0419 new_cov=0/40 polymorphism_quality=7.1 quality=7.1 quality_position_model=Inf ref_cov=217/174 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=217/214 RA 547 . NC_007779 2791171 0 G T bias_e_value=0.00198155 bias_p_value=4.26476e-10 fisher_strand_p_value=1.65129e-11 frequency=4.052258e-02 genotype_quality=1204.5 ks_quality_p_value=1 log10_base_likelihood=-5.75085 log10_qual_likelihood_position_model=22.3537 log10_strand_likelihood_position_model=10.7822 new_cov=0/29 polymorphism_quality=0.2 quality=0.2 quality_position_model=Inf ref_cov=204/136 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=205/165 RA 548 . NC_007779 2791635 0 C T bias_e_value=1.98771e-07 bias_p_value=4.27801e-14 fisher_strand_p_value=1.21088e-15 frequency=5.810928e-02 genotype_quality=1225.5 ks_quality_p_value=0.999488 log10_base_likelihood=-10.2569 log10_qual_likelihood_position_model=27.0208 log10_strand_likelihood_position_model=14.9169 new_cov=0/32 polymorphism_quality=4.8 quality=4.8 quality_position_model=Inf ref_cov=233/105 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=233/137 RA 549 . NC_007779 2791639 0 C G bias_e_value=839.02 bias_p_value=0.000180577 fisher_strand_p_value=1.4996e-05 frequency=2.178097e-02 genotype_quality=1410.7 ks_quality_p_value=0.994055 log10_base_likelihood=-9.3194 log10_qual_likelihood_position_model=16.9996 log10_strand_likelihood_position_model=4.82403 new_cov=0/11 polymorphism_quality=3.9 quality=3.9 quality_position_model=Inf ref_cov=232/127 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/138 RA 550 . NC_007779 2793036 1 . G bias_e_value=515246 bias_p_value=0.110893 fisher_strand_p_value=0.246147 frequency=4.414558e-03 genotype_quality=2259.6 ks_quality_p_value=0.0946604 log10_base_likelihood=-7.6095 log10_qual_likelihood_position_model=2.50235 log10_strand_likelihood_position_model=0.608806 new_cov=2/0 polymorphism_quality=2.1 quality=2.1 quality_position_model=2.31389e-06 ref_cov=223/228 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=225/228 RA 551 . NC_007779 2797644 0 C A bias_e_value=4817.78 bias_p_value=0.0010369 fisher_strand_p_value=0.00010174 frequency=2.468491e-02 genotype_quality=1624.2 ks_quality_p_value=0.999843 log10_base_likelihood=-6.38308 log10_qual_likelihood_position_model=16.2569 log10_strand_likelihood_position_model=4.02687 new_cov=2/13 polymorphism_quality=0.8 quality=0.8 quality_position_model=Inf ref_cov=276/154 reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=278/167 RA 552 . NC_007779 2804706 0 C A bias_e_value=4109.94 bias_p_value=0.000884556 fisher_strand_p_value=8.53055e-05 frequency=1.837063e-02 genotype_quality=1251.6 ks_quality_p_value=1 log10_base_likelihood=-6.08683 log10_qual_likelihood_position_model=12.998 log10_strand_likelihood_position_model=4.20207 new_cov=18/0 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=221/164 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=240/164 RA 553 . NC_007779 2815240 1 . A bias_e_value=964349 bias_p_value=0.207551 fisher_strand_p_value=0.504923 frequency=5.050659e-03 genotype_quality=1977.3 ks_quality_p_value=0.104202 log10_base_likelihood=-7.84236 log10_qual_likelihood_position_model=1.52035 log10_strand_likelihood_position_model=0.511425 new_cov=2/0 polymorphism_quality=2.4 quality=2.4 quality_position_model=1.00108e-07 ref_cov=218/176 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=220/176 RA 554 . NC_007779 2816615 0 G C bias_e_value=8.87463e-12 bias_p_value=1.91003e-18 fisher_strand_p_value=4.55545e-20 frequency=7.834625e-02 genotype_quality=1254.9 ks_quality_p_value=0.919085 log10_base_likelihood=-29.0694 log10_qual_likelihood_position_model=41.0644 log10_strand_likelihood_position_model=19.3415 new_cov=36/0 polymorphism_quality=23.9 quality=23.9 quality_position_model=Inf ref_cov=84/249 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=120/249 RA 555 . NC_007779 2816615 1 . C bias_e_value=1224740 bias_p_value=0.263593 fisher_strand_p_value=0.103283 frequency=5.509377e-03 genotype_quality=1628.8 ks_quality_p_value=0.70506 log10_base_likelihood=-7.86539 log10_qual_likelihood_position_model=2.85854 log10_strand_likelihood_position_model=0.985971 new_cov=2/0 polymorphism_quality=2.4 quality=2.4 quality_position_model=7.31411e-06 ref_cov=115/246 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=117/246 RA 556 . NC_007779 2817028 1 . C bias_e_value=1164590 bias_p_value=0.250648 fisher_strand_p_value=0.0679514 frequency=6.710052e-03 genotype_quality=1857.7 ks_quality_p_value=0.999879 log10_base_likelihood=-10.2192 log10_qual_likelihood_position_model=5.78964 log10_strand_likelihood_position_model=1.1678 new_cov=3/0 polymorphism_quality=4.8 quality=4.8 quality_position_model=4.61784e-05 ref_cov=180/264 reject=POLYMORPHISM_STRAND tot_cov=183/264 RA 557 . NC_007779 2817030 0 G C bias_e_value=4.34945e-21 bias_p_value=9.36105e-28 fisher_strand_p_value=2.20759e-29 frequency=1.096444e-01 genotype_quality=1285.0 ks_quality_p_value=0.628699 log10_base_likelihood=-46.7415 log10_qual_likelihood_position_model=55.7892 log10_strand_likelihood_position_model=28.6561 new_cov=51/0 polymorphism_quality=41.6 quality=41.6 quality_position_model=Inf ref_cov=77/269 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=128/269 RA 558 . NC_007779 2820080 1 . C bias_e_value=4140190 bias_p_value=0.891067 fisher_strand_p_value=1 frequency=7.910728e-03 genotype_quality=1857.0 ks_quality_p_value=0.571175 log10_base_likelihood=-10.4628 log10_qual_likelihood_position_model=3.14355 log10_strand_likelihood_position_model=0.410609 new_cov=1/2 polymorphism_quality=5.0 quality=5.0 quality_position_model=7.36293e-09 ref_cov=182/194 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=183/196 RA 559 . NC_007779 2833496 0 C A bias_e_value=1431.41 bias_p_value=0.000308073 fisher_strand_p_value=2.67189e-05 frequency=1.366615e-02 genotype_quality=1675.6 ks_quality_p_value=1 log10_base_likelihood=-5.63539 log10_qual_likelihood_position_model=12.7413 log10_strand_likelihood_position_model=4.57318 new_cov=14/0 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=211/245 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=225/245 RA 560 . NC_007779 2833875 0 A C bias_e_value=6.77282e-07 bias_p_value=1.45767e-13 fisher_strand_p_value=4.27649e-15 frequency=3.995800e-02 genotype_quality=1291.1 ks_quality_p_value=1 log10_base_likelihood=-6.74043 log10_qual_likelihood_position_model=35.9287 log10_strand_likelihood_position_model=14.3689 new_cov=0/41 polymorphism_quality=1.2 quality=1.2 quality_position_model=Inf ref_cov=209/148 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=209/191 RA 561 . NC_007779 2833904 0 A C bias_e_value=5.85955e-08 bias_p_value=1.26111e-14 fisher_strand_p_value=3.44525e-16 frequency=3.754330e-02 genotype_quality=1262.0 ks_quality_p_value=1 log10_base_likelihood=-8.38693 log10_qual_likelihood_position_model=31.0299 log10_strand_likelihood_position_model=15.4628 new_cov=0/42 polymorphism_quality=2.9 quality=2.9 quality_position_model=Inf ref_cov=224/147 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=225/189 RA 562 . NC_007779 2833989 0 A C bias_e_value=1.25378e-18 bias_p_value=2.69844e-25 fisher_strand_p_value=4.37389e-27 frequency=6.603527e-02 genotype_quality=1203.2 ks_quality_p_value=1 log10_base_likelihood=-13.0721 log10_qual_likelihood_position_model=40.3129 log10_strand_likelihood_position_model=26.3591 new_cov=0/42 polymorphism_quality=7.7 quality=7.7 quality_position_model=Inf ref_cov=254/58 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=254/100 RA 563 . NC_007779 2839296 0 A G bias_e_value=1.45012e-05 bias_p_value=3.121e-12 fisher_strand_p_value=1.00923e-13 frequency=5.927277e-02 genotype_quality=1129.9 ks_quality_p_value=1 log10_base_likelihood=-13.4444 log10_qual_likelihood_position_model=24.3535 log10_strand_likelihood_position_model=12.996 new_cov=24/0 polymorphism_quality=8.1 quality=8.1 quality_position_model=Inf ref_cov=81/231 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=105/231 RA 564 . NC_007779 2847445 0 G T bias_e_value=1.25092e-08 bias_p_value=2.69227e-15 fisher_strand_p_value=7.04949e-17 frequency=8.355474e-02 genotype_quality=1352.8 ks_quality_p_value=1 log10_base_likelihood=-28.341 log10_qual_likelihood_position_model=29.3109 log10_strand_likelihood_position_model=16.1651 new_cov=0/54 polymorphism_quality=23.1 quality=23.1 quality_position_model=Inf ref_cov=212/187 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=212/241 RA 565 . NC_007779 2854569 0 A . bias_e_value=2429080 bias_p_value=0.522795 fisher_strand_p_value=0.373036 frequency=1.189709e-02 genotype_quality=1702.6 ks_quality_p_value=0.537654 log10_base_likelihood=-13.8796 log10_qual_likelihood_position_model=2.79295 log10_strand_likelihood_position_model=0.771583 new_cov=4/1 polymorphism_quality=8.5 quality=8.5 quality_position_model=2.38559e-12 ref_cov=212/203 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=216/204 RA 566 . NC_007779 2862768 0 C A bias_e_value=1148.92 bias_p_value=0.000247274 fisher_strand_p_value=2.10078e-05 frequency=3.082466e-02 genotype_quality=1775.8 ks_quality_p_value=1 log10_base_likelihood=-12.3066 log10_qual_likelihood_position_model=29.6129 log10_strand_likelihood_position_model=4.85477 new_cov=0/20 polymorphism_quality=6.9 quality=6.9 quality_position_model=Inf ref_cov=183/234 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=183/255 RA 567 . NC_007779 2862769 0 T A bias_e_value=102912 bias_p_value=0.022149 fisher_strand_p_value=0.00329923 frequency=2.191734e-02 genotype_quality=1705.0 ks_quality_p_value=0.999882 log10_base_likelihood=-10.0821 log10_qual_likelihood_position_model=15.9061 log10_strand_likelihood_position_model=2.64343 new_cov=0/11 polymorphism_quality=4.6 quality=4.6 quality_position_model=Inf ref_cov=184/243 reject=POLYMORPHISM_STRAND tot_cov=184/254 RA 568 . NC_007779 2862772 0 A . bias_e_value=1311270 bias_p_value=0.282216 fisher_strand_p_value=0.0801849 frequency=1.225758e-02 genotype_quality=1623.7 ks_quality_p_value=0.998473 log10_base_likelihood=-11.2218 log10_qual_likelihood_position_model=7.23545 log10_strand_likelihood_position_model=1.16356 new_cov=0/5 polymorphism_quality=5.8 quality=5.8 quality_position_model=0.00013534 ref_cov=168/234 reject=POLYMORPHISM_STRAND tot_cov=168/239 RA 569 . NC_007779 2862781 0 C G bias_e_value=693171 bias_p_value=0.149187 fisher_strand_p_value=0.084214 frequency=1.194000e-02 genotype_quality=1724.3 ks_quality_p_value=0.404504 log10_base_likelihood=-11.5272 log10_qual_likelihood_position_model=3.71597 log10_strand_likelihood_position_model=1.132 new_cov=0/5 polymorphism_quality=6.1 quality=6.1 quality_position_model=1.2688e-08 ref_cov=169/244 reject=POLYMORPHISM_STRAND tot_cov=169/249 RA 570 . NC_007779 2862782 0 C A bias_e_value=107961 bias_p_value=0.0232357 fisher_strand_p_value=0.003492 frequency=1.982594e-02 genotype_quality=1581.7 ks_quality_p_value=0.999417 log10_base_likelihood=-6.07234 log10_qual_likelihood_position_model=16.2069 log10_strand_likelihood_position_model=2.57347 new_cov=0/11 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=162/221 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=162/232 RA 571 . NC_007779 2862783 1 . T bias_e_value=1314720 bias_p_value=0.282958 fisher_strand_p_value=0.0803612 frequency=1.198864e-02 genotype_quality=2051.3 ks_quality_p_value=0.999942 log10_base_likelihood=-18.1786 log10_qual_likelihood_position_model=8.41335 log10_strand_likelihood_position_model=1.16223 new_cov=0/5 polymorphism_quality=12.9 quality=12.9 quality_position_model=1.34096e-10 ref_cov=172/240 reject=POLYMORPHISM_STRAND tot_cov=172/245 RA 572 . NC_007779 2862844 0 T C bias_e_value=3379120 bias_p_value=0.727266 fisher_strand_p_value=0.372147 frequency=1.103401e-02 genotype_quality=1679.1 ks_quality_p_value=0.965973 log10_base_likelihood=-7.65098 log10_qual_likelihood_position_model=4.22436 log10_strand_likelihood_position_model=0.795949 new_cov=1/4 polymorphism_quality=2.2 quality=2.2 quality_position_model=0.000217318 ref_cov=209/210 reject=POLYMORPHISM_STRAND tot_cov=211/214 RA 573 . NC_007779 2865228 0 A G bias_e_value=3131600 bias_p_value=0.673994 fisher_strand_p_value=0.354189 frequency=7.388115e-03 genotype_quality=2144.0 ks_quality_p_value=0.877477 log10_base_likelihood=-6.11539 log10_qual_likelihood_position_model=2.46465 log10_strand_likelihood_position_model=0.639556 new_cov=3/1 polymorphism_quality=0.6 quality=0.6 quality_position_model=8.52218e-05 ref_cov=253/277 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=256/278 RA 574 . NC_007779 2866111 0 A G frequency=1 genotype_quality=1957.5 new_cov=213/237 quality=1957.5 ref_cov=0/0 tot_cov=213/237 RA 575 . NC_007779 2868094 0 C A bias_e_value=0.781528 bias_p_value=1.68203e-07 fisher_strand_p_value=8.59399e-09 frequency=3.530312e-02 genotype_quality=1612.3 ks_quality_p_value=1 log10_base_likelihood=-8.40399 log10_qual_likelihood_position_model=24.9422 log10_strand_likelihood_position_model=8.33615 new_cov=31/0 polymorphism_quality=2.9 quality=2.9 quality_position_model=Inf ref_cov=235/215 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=266/215 RA 576 . NC_007779 2895131 0 A C bias_e_value=5.23867e-19 bias_p_value=1.12749e-25 fisher_strand_p_value=1.80164e-27 frequency=1.356683e-01 genotype_quality=1006.5 ks_quality_p_value=1 log10_base_likelihood=-35.8076 log10_qual_likelihood_position_model=60.9119 log10_strand_likelihood_position_model=26.7469 new_cov=1/61 polymorphism_quality=30.6 quality=30.6 quality_position_model=Inf ref_cov=191/71 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=192/132 RA 577 . NC_007779 2895144 0 G C bias_e_value=14.153 bias_p_value=3.04607e-06 fisher_strand_p_value=1.8455e-07 frequency=3.803158e-02 genotype_quality=1019.4 ks_quality_p_value=1 log10_base_likelihood=-5.58721 log10_qual_likelihood_position_model=16.778 log10_strand_likelihood_position_model=6.74582 new_cov=1/18 polymorphism_quality=0.0 quality=0.0 quality_position_model=Inf ref_cov=186/99 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=187/117 RA 578 . NC_007779 2898837 0 G T bias_e_value=2.4198e-05 bias_p_value=5.20799e-12 fisher_strand_p_value=1.71343e-13 frequency=3.482819e-02 genotype_quality=1860.5 ks_quality_p_value=1 log10_base_likelihood=-9.42709 log10_qual_likelihood_position_model=29.8309 log10_strand_likelihood_position_model=12.7661 new_cov=0/35 polymorphism_quality=4.0 quality=4.0 quality_position_model=Inf ref_cov=297/208 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=297/244 RA 579 . NC_007779 2898953 1 . A bias_e_value=3900990 bias_p_value=0.839584 fisher_strand_p_value=0.600218 frequency=6.622314e-03 genotype_quality=2233.6 ks_quality_p_value=0.816469 log10_base_likelihood=-11.7704 log10_qual_likelihood_position_model=2.24148 log10_strand_likelihood_position_model=0.457975 new_cov=2/1 polymorphism_quality=6.4 quality=6.4 quality_position_model=4.45134e-11 ref_cov=209/241 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=211/242 RA 580 . NC_007779 2898954 0 A . bias_e_value=1040860 bias_p_value=0.224018 fisher_strand_p_value=0.105059 frequency=1.281357e-02 genotype_quality=1915.6 ks_quality_p_value=0.554993 log10_base_likelihood=-16.9388 log10_qual_likelihood_position_model=3.27441 log10_strand_likelihood_position_model=1.13448 new_cov=5/1 polymorphism_quality=11.6 quality=11.6 quality_position_model=1.32432e-14 ref_cov=216/246 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=221/247 RA 581 . NC_007779 2899215 1 . T bias_e_value=4596970 bias_p_value=0.989377 fisher_strand_p_value=1 frequency=4.651070e-03 genotype_quality=2130.6 ks_quality_p_value=0.857823 log10_base_likelihood=-7.88655 log10_qual_likelihood_position_model=2.28729 log10_strand_likelihood_position_model=0.300056 new_cov=1/1 polymorphism_quality=2.4 quality=2.4 quality_position_model=3.39258e-07 ref_cov=212/216 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=213/217 RA 582 . NC_007779 2905194 1 . G bias_e_value=759556 bias_p_value=0.163474 fisher_strand_p_value=0.0430493 frequency=9.614944e-03 genotype_quality=1536.1 ks_quality_p_value=0.891301 log10_base_likelihood=-12.5978 log10_qual_likelihood_position_model=2.22711 log10_strand_likelihood_position_model=1.36603 new_cov=3/0 polymorphism_quality=7.2 quality=7.2 quality_position_model=5.20357e-11 ref_cov=107/202 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=110/202 RA 583 . NC_007779 2911644 0 G T bias_e_value=0.0305298 bias_p_value=6.57073e-09 fisher_strand_p_value=3.34413e-10 frequency=4.624939e-02 genotype_quality=1319.0 ks_quality_p_value=0.855212 log10_base_likelihood=-12.7107 log10_qual_likelihood_position_model=33.6707 log10_strand_likelihood_position_model=9.58088 new_cov=0/31 polymorphism_quality=7.3 quality=7.3 quality_position_model=Inf ref_cov=203/180 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=203/213 RA 584 . NC_007779 2915479 0 C G bias_e_value=3.29158 bias_p_value=7.08426e-07 fisher_strand_p_value=3.97491e-08 frequency=2.718449e-02 genotype_quality=1228.1 ks_quality_p_value=0.987197 log10_base_likelihood=-8.71716 log10_qual_likelihood_position_model=15.6299 log10_strand_likelihood_position_model=7.40067 new_cov=0/13 polymorphism_quality=3.3 quality=3.3 quality_position_model=Inf ref_cov=230/78 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=231/91 RA 585 . NC_007779 2926157 0 T G bias_e_value=1.12126e-25 bias_p_value=2.41321e-32 fisher_strand_p_value=3.0875e-34 frequency=6.575871e-02 genotype_quality=1098.2 ks_quality_p_value=1 log10_base_likelihood=-9.86286 log10_qual_likelihood_position_model=43.1384 log10_strand_likelihood_position_model=33.5104 new_cov=39/0 polymorphism_quality=4.4 quality=4.4 quality_position_model=Inf ref_cov=23/257 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=62/257 RA 586 . NC_007779 2939008 0 A C bias_e_value=7.28503e-06 bias_p_value=1.56791e-12 fisher_strand_p_value=4.95617e-14 frequency=4.876232e-02 genotype_quality=1586.3 ks_quality_p_value=1 log10_base_likelihood=-12.7248 log10_qual_likelihood_position_model=32.5903 log10_strand_likelihood_position_model=13.3049 new_cov=0/35 polymorphism_quality=7.3 quality=7.3 quality_position_model=Inf ref_cov=271/176 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=271/211 RA 587 . NC_007779 2941549 1 . T bias_e_value=1815680 bias_p_value=0.390776 fisher_strand_p_value=0.240159 frequency=3.454208e-03 genotype_quality=2854.8 ks_quality_p_value=0.532259 log10_base_likelihood=-7.63522 log10_qual_likelihood_position_model=1.61292 log10_strand_likelihood_position_model=0.619502 new_cov=0/2 polymorphism_quality=2.1 quality=2.1 quality_position_model=2.64859e-07 ref_cov=295/282 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=295/284 RA 588 . NC_007779 2942972 0 G T bias_e_value=5.54398e-08 bias_p_value=1.19319e-14 fisher_strand_p_value=4.81407e-16 frequency=6.421661e-02 genotype_quality=1512.5 ks_quality_p_value=0.676069 log10_base_likelihood=-24.4933 log10_qual_likelihood_position_model=40.4461 log10_strand_likelihood_position_model=15.3455 new_cov=0/49 polymorphism_quality=19.3 quality=19.3 quality_position_model=Inf ref_cov=236/199 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=236/250 RA 589 . NC_007779 2953753 0 C . bias_e_value=1746010 bias_p_value=0.375782 fisher_strand_p_value=0.1254 frequency=8.621216e-03 genotype_quality=1879.7 ks_quality_p_value=0.962025 log10_base_likelihood=-9.3535 log10_qual_likelihood_position_model=3.37489 log10_strand_likelihood_position_model=1.12126 new_cov=4/0 polymorphism_quality=3.9 quality=3.9 quality_position_model=9.7711e-07 ref_cov=239/219 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=243/220 RA 590 . NC_007779 2983097 0 A C bias_e_value=8.01399e-16 bias_p_value=1.7248e-22 fisher_strand_p_value=3.1291e-24 frequency=8.064270e-02 genotype_quality=1055.4 ks_quality_p_value=1 log10_base_likelihood=-11.2407 log10_qual_likelihood_position_model=63.1348 log10_strand_likelihood_position_model=23.5046 new_cov=0/59 polymorphism_quality=5.8 quality=5.8 quality_position_model=Inf ref_cov=196/102 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=196/162 RA 591 . NC_007779 2987535 0 A C bias_e_value=1.63901e-13 bias_p_value=3.52753e-20 fisher_strand_p_value=7.09806e-22 frequency=6.294060e-02 genotype_quality=1563.1 ks_quality_p_value=1 log10_base_likelihood=-15.4499 log10_qual_likelihood_position_model=59.9538 log10_strand_likelihood_position_model=21.1489 new_cov=0/58 polymorphism_quality=10.1 quality=10.1 quality_position_model=Inf ref_cov=273/179 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=273/240 RA 592 . NC_007779 2988137 0 A . bias_e_value=4155960 bias_p_value=0.89446 fisher_strand_p_value=0.583967 frequency=8.142471e-03 genotype_quality=1522.6 ks_quality_p_value=0.988568 log10_base_likelihood=-7.45788 log10_qual_likelihood_position_model=2.94101 log10_strand_likelihood_position_model=0.488506 new_cov=1/2 polymorphism_quality=2.0 quality=2.0 quality_position_model=7.183e-06 ref_cov=205/159 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=207/161 RA 593 . NC_007779 2994664 0 T . bias_e_value=4644330 bias_p_value=0.999569 fisher_strand_p_value=1 frequency=8.629799e-03 genotype_quality=1900.0 ks_quality_p_value=0.970794 log10_base_likelihood=-10.1504 log10_qual_likelihood_position_model=2.66718 log10_strand_likelihood_position_model=0.44319 new_cov=2/2 polymorphism_quality=4.7 quality=4.7 quality_position_model=5.39254e-09 ref_cov=263/195 reject=INDEL_HOMOPOLYMER tot_cov=266/197 RA 594 . NC_007779 3003330 0 G A frequency=1 genotype_quality=1876.5 new_cov=240/217 quality=1876.5 ref_cov=1/0 tot_cov=242/217 RA 595 . NC_007779 3012136 1 . G bias_e_value=955841 bias_p_value=0.205719 fisher_strand_p_value=0.0519935 frequency=9.672165e-03 genotype_quality=2048.2 ks_quality_p_value=1 log10_base_likelihood=-11.2363 log10_qual_likelihood_position_model=7.99808 log10_strand_likelihood_position_model=1.28405 new_cov=4/0 polymorphism_quality=5.8 quality=5.8 quality_position_model=0.00117456 ref_cov=194/215 reject=POLYMORPHISM_STRAND tot_cov=198/215 RA 596 . NC_007779 3029385 0 C A bias_e_value=5.91349e-05 bias_p_value=1.27272e-11 fisher_strand_p_value=4.46159e-13 frequency=3.576565e-02 genotype_quality=1397.1 ks_quality_p_value=0.967954 log10_base_likelihood=-15.7926 log10_qual_likelihood_position_model=26.0235 log10_strand_likelihood_position_model=12.3505 new_cov=0/17 polymorphism_quality=10.5 quality=10.5 quality_position_model=Inf ref_cov=289/58 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=289/75 RA 597 . NC_007779 3031146 0 C A bias_e_value=0.093954 bias_p_value=2.02211e-08 fisher_strand_p_value=9.27644e-10 frequency=4.521179e-02 genotype_quality=1334.9 ks_quality_p_value=1 log10_base_likelihood=-12.9488 log10_qual_likelihood_position_model=21.5536 log10_strand_likelihood_position_model=9.08803 new_cov=30/0 polymorphism_quality=7.6 quality=7.6 quality_position_model=Inf ref_cov=187/204 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=218/204 RA 598 . NC_007779 3034413 0 A C bias_e_value=1.07657e-28 bias_p_value=2.31703e-35 fisher_strand_p_value=2.71967e-37 frequency=9.236622e-02 genotype_quality=1198.1 ks_quality_p_value=1 log10_base_likelihood=-22.414 log10_qual_likelihood_position_model=49.0117 log10_strand_likelihood_position_model=36.5655 new_cov=0/59 polymorphism_quality=17.2 quality=17.2 quality_position_model=Inf ref_cov=259/54 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=259/114 RA 599 . NC_007779 3035390 0 T C bias_e_value=3.39374e-17 bias_p_value=7.30414e-24 fisher_strand_p_value=1.252e-25 frequency=1.368818e-01 genotype_quality=865.0 ks_quality_p_value=1 log10_base_likelihood=-42.6104 log10_qual_likelihood_position_model=38.4302 log10_strand_likelihood_position_model=24.9024 new_cov=0/51 polymorphism_quality=37.5 quality=37.5 quality_position_model=Inf ref_cov=209/76 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=214/127 RA 600 . NC_007779 3035883 0 C A bias_e_value=10268.1 bias_p_value=0.00220995 fisher_strand_p_value=0.000249557 frequency=1.594448e-02 genotype_quality=1513.1 ks_quality_p_value=0.947091 log10_base_likelihood=-6.0668 log10_qual_likelihood_position_model=11.8651 log10_strand_likelihood_position_model=3.60283 new_cov=11/0 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=193/224 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=204/225 RA 601 . NC_007779 3044705 1 . T bias_e_value=839607 bias_p_value=0.180703 fisher_strand_p_value=0.0631579 frequency=7.017136e-03 genotype_quality=1333.5 ks_quality_p_value=0.69295 log10_base_likelihood=-8.47181 log10_qual_likelihood_position_model=1.21832 log10_strand_likelihood_position_model=1.19957 new_cov=2/0 polymorphism_quality=3.0 quality=3.0 quality_position_model=5.60774e-08 ref_cov=70/213 reject=POLYMORPHISM_STRAND tot_cov=72/213 RA 602 . NC_007779 3044707 1 . C bias_e_value=795629 bias_p_value=0.171238 fisher_strand_p_value=0.0421336 frequency=7.517815e-03 genotype_quality=1224.4 ks_quality_p_value=0.967723 log10_base_likelihood=-7.29681 log10_qual_likelihood_position_model=2.9908 log10_strand_likelihood_position_model=1.37537 new_cov=2/0 polymorphism_quality=1.8 quality=1.8 quality_position_model=0.000103834 ref_cov=53/211 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=55/211 RA 603 . NC_007779 3044712 0 T C bias_e_value=0.0178927 bias_p_value=3.85093e-09 fisher_strand_p_value=1.65534e-10 frequency=3.672791e-02 genotype_quality=852.0 ks_quality_p_value=0.988542 log10_base_likelihood=-10.1105 log10_qual_likelihood_position_model=14.0936 log10_strand_likelihood_position_model=9.78111 new_cov=10/0 polymorphism_quality=4.7 quality=4.7 quality_position_model=Inf ref_cov=21/224 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=31/224 RA 604 . NC_007779 3044714 0 A C bias_e_value=332.176 bias_p_value=7.14921e-05 fisher_strand_p_value=5.44906e-06 frequency=2.582932e-02 genotype_quality=749.7 ks_quality_p_value=1 log10_base_likelihood=-6.41768 log10_qual_likelihood_position_model=12.0633 log10_strand_likelihood_position_model=5.28083 new_cov=8/3 polymorphism_quality=0.9 quality=0.9 quality_position_model=Inf ref_cov=26/219 reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=34/222 RA 605 . NC_007779 3049815 0 G T frequency=1 genotype_quality=1916.4 new_cov=224/246 quality=1916.4 ref_cov=0/0 tot_cov=224/246 RA 606 . NC_007779 3051976 0 G T bias_e_value=81.3164 bias_p_value=1.75012e-05 fisher_strand_p_value=1.1957e-06 frequency=2.246380e-02 genotype_quality=1469.2 ks_quality_p_value=1 log10_base_likelihood=-6.81128 log10_qual_likelihood_position_model=18.4623 log10_strand_likelihood_position_model=6.14351 new_cov=0/20 polymorphism_quality=1.3 quality=1.3 quality_position_model=Inf ref_cov=203/187 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=203/208 RA 607 . NC_007779 3059420 1 . T bias_e_value=2315400 bias_p_value=0.498328 fisher_strand_p_value=0.248551 frequency=5.975723e-03 genotype_quality=2501.4 ks_quality_p_value=0.747081 log10_base_likelihood=-11.9247 log10_qual_likelihood_position_model=2.23123 log10_strand_likelihood_position_model=0.895317 new_cov=0/3 polymorphism_quality=6.5 quality=6.5 quality_position_model=8.46504e-11 ref_cov=249/250 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=249/253 RA 608 . NC_007779 3074129 0 G T bias_e_value=0.0155639 bias_p_value=3.34971e-09 fisher_strand_p_value=1.41464e-10 frequency=2.637672e-02 genotype_quality=1685.9 ks_quality_p_value=1 log10_base_likelihood=-5.66954 log10_qual_likelihood_position_model=22.6672 log10_strand_likelihood_position_model=9.84936 new_cov=0/29 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=263/207 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=263/236 RA 609 . NC_007779 3084663 0 C A bias_e_value=3.7965e-07 bias_p_value=8.17096e-14 fisher_strand_p_value=2.35598e-15 frequency=3.812218e-02 genotype_quality=1885.8 ks_quality_p_value=1 log10_base_likelihood=-12.9813 log10_qual_likelihood_position_model=33.5274 log10_strand_likelihood_position_model=14.6678 new_cov=50/0 polymorphism_quality=7.6 quality=7.6 quality_position_model=Inf ref_cov=259/274 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=310/274 RA 610 . NC_007779 3085177 1 . A bias_e_value=4094770 bias_p_value=0.881291 fisher_strand_p_value=0.594769 frequency=6.011963e-03 genotype_quality=2491.8 ks_quality_p_value=0.931751 log10_base_likelihood=-11.9673 log10_qual_likelihood_position_model=2.9624 log10_strand_likelihood_position_model=0.467635 new_cov=1/2 polymorphism_quality=6.6 quality=6.6 quality_position_model=1.56586e-10 ref_cov=270/226 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=271/228 RA 611 . NC_007779 3085178 0 A . bias_e_value=4585670 bias_p_value=0.986944 fisher_strand_p_value=1 frequency=5.933762e-03 genotype_quality=2084.5 ks_quality_p_value=0.842822 log10_base_likelihood=-7.50786 log10_qual_likelihood_position_model=1.38973 log10_strand_likelihood_position_model=0.392643 new_cov=2/1 polymorphism_quality=2.0 quality=2.0 quality_position_model=1.22622e-07 ref_cov=272/230 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=274/231 RA 612 . NC_007779 3088549 0 G T bias_e_value=0.146325 bias_p_value=3.14926e-08 fisher_strand_p_value=1.5061e-09 frequency=5.422497e-02 genotype_quality=1308.4 ks_quality_p_value=0.980134 log10_base_likelihood=-14.7944 log10_qual_likelihood_position_model=22.0075 log10_strand_likelihood_position_model=8.89925 new_cov=0/37 polymorphism_quality=9.4 quality=9.4 quality_position_model=Inf ref_cov=181/226 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=181/264 RA 613 . NC_007779 3090796 0 A C bias_e_value=0.0332652 bias_p_value=7.15946e-09 fisher_strand_p_value=3.12841e-10 frequency=2.838326e-02 genotype_quality=1239.8 ks_quality_p_value=1 log10_base_likelihood=-8.69809 log10_qual_likelihood_position_model=23.9198 log10_strand_likelihood_position_model=9.52214 new_cov=0/32 polymorphism_quality=3.2 quality=3.2 quality_position_model=Inf ref_cov=197/184 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=197/218 RA 614 . NC_007779 3100116 1 . A bias_e_value=3930630 bias_p_value=0.845965 fisher_strand_p_value=0.501493 frequency=4.039764e-03 genotype_quality=2476.2 ks_quality_p_value=0.995274 log10_base_likelihood=-7.15361 log10_qual_likelihood_position_model=2.94429 log10_strand_likelihood_position_model=0.543482 new_cov=2/0 polymorphism_quality=1.6 quality=1.6 quality_position_model=1.72769e-05 ref_cov=263/230 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=265/230 RA 615 . NC_007779 3106674 0 C A bias_e_value=2.60615e-08 bias_p_value=5.60905e-15 fisher_strand_p_value=1.49826e-16 frequency=4.335117e-02 genotype_quality=1628.3 ks_quality_p_value=1 log10_base_likelihood=-12.6324 log10_qual_likelihood_position_model=28.7781 log10_strand_likelihood_position_model=15.8244 new_cov=43/0 polymorphism_quality=7.2 quality=7.2 quality_position_model=Inf ref_cov=187/278 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=231/278 RA 616 . NC_007779 3110517 0 A C bias_e_value=4.70736e-06 bias_p_value=1.01313e-12 fisher_strand_p_value=3.15752e-14 frequency=4.207230e-02 genotype_quality=1178.0 ks_quality_p_value=1 log10_base_likelihood=-7.46251 log10_qual_likelihood_position_model=31.4892 log10_strand_likelihood_position_model=13.5056 new_cov=1/26 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=230/72 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=231/99 RA 617 . NC_007779 3110532 0 C A bias_e_value=24.5624 bias_p_value=5.2864e-06 fisher_strand_p_value=3.47504e-07 frequency=3.258514e-02 genotype_quality=1209.4 ks_quality_p_value=0.95569 log10_base_likelihood=-16.201 log10_qual_likelihood_position_model=15.8059 log10_strand_likelihood_position_model=6.45904 new_cov=0/11 polymorphism_quality=10.9 quality=10.9 quality_position_model=Inf ref_cov=229/74 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=229/85 RA 618 . NC_007779 3126794 0 T . bias_e_value=2464700 bias_p_value=0.530461 fisher_strand_p_value=0.3399 frequency=7.596970e-03 genotype_quality=2139.5 ks_quality_p_value=0.604211 log10_base_likelihood=-10.2874 log10_qual_likelihood_position_model=2.25547 log10_strand_likelihood_position_model=0.673693 new_cov=1/3 polymorphism_quality=4.9 quality=4.9 quality_position_model=2.53799e-09 ref_cov=282/240 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=283/243 RA 619 . NC_007779 3152854 1 . A bias_e_value=2604330 bias_p_value=0.560514 fisher_strand_p_value=0.335135 frequency=9.259224e-03 genotype_quality=2131.8 ks_quality_p_value=0.671156 log10_base_likelihood=-17.4256 log10_qual_likelihood_position_model=2.3943 log10_strand_likelihood_position_model=0.686002 new_cov=1/3 polymorphism_quality=12.1 quality=12.1 quality_position_model=1.89718e-16 ref_cov=234/194 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=235/197 RA 620 . NC_007779 3160153 0 G C bias_e_value=0.150687 bias_p_value=3.24313e-08 fisher_strand_p_value=1.5228e-09 frequency=3.171158e-02 genotype_quality=1073.3 ks_quality_p_value=0.999724 log10_base_likelihood=-10.9294 log10_qual_likelihood_position_model=13.7219 log10_strand_likelihood_position_model=8.81736 new_cov=10/0 polymorphism_quality=5.5 quality=5.5 quality_position_model=Inf ref_cov=30/234 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=40/234 RA 621 . NC_007779 3162929 0 G C bias_e_value=1175.55 bias_p_value=0.000253006 fisher_strand_p_value=2.27393e-05 frequency=1.880169e-02 genotype_quality=1332.9 ks_quality_p_value=0.947281 log10_base_likelihood=-6.30171 log10_qual_likelihood_position_model=20.8614 log10_strand_likelihood_position_model=4.86271 new_cov=16/0 polymorphism_quality=0.8 quality=0.8 quality_position_model=Inf ref_cov=185/196 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=201/197 RA 622 . NC_007779 3188902 1 . A bias_e_value=1837490 bias_p_value=0.39547 fisher_strand_p_value=0.248622 frequency=5.780220e-03 genotype_quality=2585.6 ks_quality_p_value=0.523359 log10_base_likelihood=-11.9891 log10_qual_likelihood_position_model=2.23595 log10_strand_likelihood_position_model=0.893073 new_cov=3/0 polymorphism_quality=6.6 quality=6.6 quality_position_model=7.31558e-11 ref_cov=259/257 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=262/257 RA 623 . NC_007779 3188903 0 A . bias_e_value=3113160 bias_p_value=0.670026 fisher_strand_p_value=1 frequency=5.685806e-03 genotype_quality=2175.4 ks_quality_p_value=0.307413 log10_base_likelihood=-7.4229 log10_qual_likelihood_position_model=2.39607 log10_strand_likelihood_position_model=0.419468 new_cov=2/1 polymorphism_quality=1.9 quality=1.9 quality_position_model=1.78044e-06 ref_cov=265/259 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=267/260 RA 624 . NC_007779 3195962 0 G T bias_e_value=20.4789 bias_p_value=4.40754e-06 fisher_strand_p_value=2.73561e-07 frequency=3.868103e-02 genotype_quality=1221.0 ks_quality_p_value=1 log10_base_likelihood=-6.35015 log10_qual_likelihood_position_model=20.4819 log10_strand_likelihood_position_model=6.64279 new_cov=0/28 polymorphism_quality=0.8 quality=0.8 quality_position_model=Inf ref_cov=163/210 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=163/241 RA 625 . NC_007779 3212355 0 G C bias_e_value=4.11746 bias_p_value=8.86175e-07 fisher_strand_p_value=5.06388e-08 frequency=3.357983e-02 genotype_quality=1296.0 ks_quality_p_value=0.982233 log10_base_likelihood=-12.7098 log10_qual_likelihood_position_model=18.9484 log10_strand_likelihood_position_model=7.29552 new_cov=17/0 polymorphism_quality=7.3 quality=7.3 quality_position_model=Inf ref_cov=121/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=138/219 RA 626 . NC_007779 3216602 0 C A bias_e_value=758844 bias_p_value=0.163321 fisher_strand_p_value=0.254715 frequency=6.371498e-03 genotype_quality=1919.3 ks_quality_p_value=0.150454 log10_base_likelihood=-5.6819 log10_qual_likelihood_position_model=2.54538 log10_strand_likelihood_position_model=0.791122 new_cov=0/3 polymorphism_quality=0.1 quality=0.1 quality_position_model=0.000440801 ref_cov=213/253 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=213/256 RA 627 . NC_007779 3223274 0 G T bias_e_value=0.00297012 bias_p_value=6.39239e-10 fisher_strand_p_value=2.51612e-11 frequency=6.699705e-02 genotype_quality=1110.6 ks_quality_p_value=1 log10_base_likelihood=-13.1463 log10_qual_likelihood_position_model=25.2331 log10_strand_likelihood_position_model=10.6267 new_cov=0/39 polymorphism_quality=7.8 quality=7.8 quality_position_model=Inf ref_cov=161/165 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=161/206 RA 628 . NC_007779 3231832 1 . G bias_e_value=883928 bias_p_value=0.190242 fisher_strand_p_value=0.0534061 frequency=7.614136e-03 genotype_quality=1962.9 ks_quality_p_value=0.877201 log10_base_likelihood=-11.6743 log10_qual_likelihood_position_model=2.79018 log10_strand_likelihood_position_model=1.27241 new_cov=3/0 polymorphism_quality=6.3 quality=6.3 quality_position_model=1.39328e-09 ref_cov=146/245 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=149/245 RA 629 . NC_007779 3232800 0 T . bias_e_value=553582 bias_p_value=0.119144 fisher_strand_p_value=0.116849 frequency=6.041527e-03 genotype_quality=2047.2 ks_quality_p_value=0.218423 log10_base_likelihood=-7.49067 log10_qual_likelihood_position_model=1.79774 log10_strand_likelihood_position_model=0.932375 new_cov=3/0 polymorphism_quality=2.0 quality=2.0 quality_position_model=1.23247e-06 ref_cov=240/253 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=243/253 RA 630 . NC_007779 3238315 1 . T bias_e_value=2811280 bias_p_value=0.605054 fisher_strand_p_value=0.258298 frequency=1.229477e-02 genotype_quality=1093.9 ks_quality_p_value=0.991769 log10_base_likelihood=-12.1792 log10_qual_likelihood_position_model=2.98949 log10_strand_likelihood_position_model=0.756218 new_cov=3/0 polymorphism_quality=6.8 quality=6.8 quality_position_model=2.00018e-10 ref_cov=134/107 reject=POLYMORPHISM_STRAND tot_cov=137/107 RA 631 . NC_007779 3238317 1 . C bias_e_value=1038440 bias_p_value=0.223496 fisher_strand_p_value=0.0601608 frequency=2.231979e-02 genotype_quality=957.1 ks_quality_p_value=0.966136 log10_base_likelihood=-19.828 log10_qual_likelihood_position_model=5.74405 log10_strand_likelihood_position_model=1.4665 new_cov=5/0 polymorphism_quality=14.5 quality=14.5 quality_position_model=1.07893e-14 ref_cov=110/109 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=115/109 RA 632 . NC_007779 3238322 0 T C bias_e_value=595.414 bias_p_value=0.000128147 fisher_strand_p_value=1.02624e-05 frequency=4.243374e-02 genotype_quality=637.6 ks_quality_p_value=1 log10_base_likelihood=-9.54497 log10_qual_likelihood_position_model=12.6387 log10_strand_likelihood_position_model=4.98875 new_cov=12/0 polymorphism_quality=4.1 quality=4.1 quality_position_model=Inf ref_cov=74/129 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=87/129 RA 633 . NC_007779 3238324 0 A C bias_e_value=872.293 bias_p_value=0.000187738 fisher_strand_p_value=1.5563e-05 frequency=4.353905e-02 genotype_quality=586.7 ks_quality_p_value=0.999322 log10_base_likelihood=-8.30844 log10_qual_likelihood_position_model=11.7606 log10_strand_likelihood_position_model=4.82408 new_cov=14/1 polymorphism_quality=2.8 quality=2.8 quality_position_model=Inf ref_cov=74/129 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=88/130 RA 634 . NC_007779 3243783 1 . T bias_e_value=1841410 bias_p_value=0.396316 fisher_strand_p_value=0.498875 frequency=4.773140e-03 genotype_quality=2005.1 ks_quality_p_value=0.261655 log10_base_likelihood=-7.89081 log10_qual_likelihood_position_model=1.94673 log10_strand_likelihood_position_model=0.592772 new_cov=0/2 polymorphism_quality=2.4 quality=2.4 quality_position_model=2.99531e-07 ref_cov=207/210 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=207/212 RA 635 . NC_007779 3249265 0 G T bias_e_value=0.0491864 bias_p_value=1.05861e-08 fisher_strand_p_value=5.3191e-10 frequency=2.852345e-02 genotype_quality=1816.4 ks_quality_p_value=0.88547 log10_base_likelihood=-8.45433 log10_qual_likelihood_position_model=35.9352 log10_strand_likelihood_position_model=9.33791 new_cov=0/31 polymorphism_quality=3.0 quality=3.0 quality_position_model=Inf ref_cov=260/244 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=260/276 RA 636 . NC_007779 3258468 0 G T bias_e_value=0.276477 bias_p_value=5.95043e-08 fisher_strand_p_value=2.88661e-09 frequency=3.450871e-02 genotype_quality=1507.4 ks_quality_p_value=0.997496 log10_base_likelihood=-8.23117 log10_qual_likelihood_position_model=21.3381 log10_strand_likelihood_position_model=8.53961 new_cov=0/27 polymorphism_quality=2.8 quality=2.8 quality_position_model=Inf ref_cov=228/199 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=228/227 RA 637 . NC_007779 3259711 0 A C bias_e_value=2.46822e-16 bias_p_value=5.31219e-23 fisher_strand_p_value=9.43206e-25 frequency=1.030617e-01 genotype_quality=1150.3 ks_quality_p_value=1 log10_base_likelihood=-22.7527 log10_qual_likelihood_position_model=44.2274 log10_strand_likelihood_position_model=24.0288 new_cov=1/63 polymorphism_quality=17.5 quality=17.5 quality_position_model=Inf ref_cov=225/115 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=226/178 RA 638 . NC_007779 3267102 0 A . bias_e_value=4637890 bias_p_value=0.998184 fisher_strand_p_value=1 frequency=1.143456e-02 genotype_quality=1824.6 ks_quality_p_value=0.940337 log10_base_likelihood=-14.0027 log10_qual_likelihood_position_model=1.8664 log10_strand_likelihood_position_model=0.459602 new_cov=2/3 polymorphism_quality=8.6 quality=8.6 quality_position_model=9.77255e-14 ref_cov=167/264 reject=INDEL_HOMOPOLYMER tot_cov=170/267 RA 639 . NC_007779 3271027 0 C . bias_e_value=3854870 bias_p_value=0.82966 fisher_strand_p_value=0.592956 frequency=6.266594e-03 genotype_quality=1972.7 ks_quality_p_value=0.803456 log10_base_likelihood=-7.24633 log10_qual_likelihood_position_model=2.47795 log10_strand_likelihood_position_model=0.470878 new_cov=2/1 polymorphism_quality=1.7 quality=1.7 quality_position_model=3.75235e-06 ref_cov=215/260 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=217/261 RA 640 . NC_007779 3280326 0 A C bias_e_value=1.23691e-35 bias_p_value=2.66213e-42 fisher_strand_p_value=2.62672e-44 frequency=1.465244e-01 genotype_quality=1176.6 ks_quality_p_value=1 log10_base_likelihood=-31.8877 log10_qual_likelihood_position_model=67.278 log10_strand_likelihood_position_model=43.5806 new_cov=0/93 polymorphism_quality=26.7 quality=26.7 quality_position_model=Inf ref_cov=245/83 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=245/180 RA 641 . NC_007779 3287872 1 . G bias_e_value=816250 bias_p_value=0.175676 fisher_strand_p_value=0.24834 frequency=7.556915e-03 genotype_quality=1955.6 ks_quality_p_value=0.1698 log10_base_likelihood=-12.1204 log10_qual_likelihood_position_model=3.92715 log10_strand_likelihood_position_model=0.883505 new_cov=3/0 polymorphism_quality=6.7 quality=6.7 quality_position_model=2.84673e-09 ref_cov=199/195 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=202/195 RA 642 . NC_007779 3293230 1 . A bias_e_value=2383000 bias_p_value=0.512877 fisher_strand_p_value=1 frequency=4.015923e-03 genotype_quality=2499.6 ks_quality_p_value=0.19445 log10_base_likelihood=-7.74638 log10_qual_likelihood_position_model=1.19323 log10_strand_likelihood_position_model=0.3005 new_cov=1/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=3.49513e-08 ref_cov=255/241 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=256/242 RA 643 . NC_007779 3300073 0 T G bias_e_value=1.07498e-11 bias_p_value=2.31362e-18 fisher_strand_p_value=5.09341e-20 frequency=9.300613e-02 genotype_quality=1107.2 ks_quality_p_value=1 log10_base_likelihood=-21.06 log10_qual_likelihood_position_model=54.2519 log10_strand_likelihood_position_model=19.3843 new_cov=58/0 polymorphism_quality=15.8 quality=15.8 quality_position_model=Inf ref_cov=134/188 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=193/188 RA 644 . NC_007779 3325139 0 G T bias_e_value=0.71652 bias_p_value=1.54212e-07 fisher_strand_p_value=7.84247e-09 frequency=3.124714e-02 genotype_quality=1447.7 ks_quality_p_value=1 log10_base_likelihood=-8.02738 log10_qual_likelihood_position_model=23.253 log10_strand_likelihood_position_model=8.39147 new_cov=0/31 polymorphism_quality=2.5 quality=2.5 quality_position_model=Inf ref_cov=197/212 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=197/243 RA 645 . NC_007779 3333612 0 T G bias_e_value=0.000115854 bias_p_value=2.49344e-11 fisher_strand_p_value=8.66553e-13 frequency=2.637100e-02 genotype_quality=1170.4 ks_quality_p_value=1 log10_base_likelihood=-9.42413 log10_qual_likelihood_position_model=17.8552 log10_strand_likelihood_position_model=12.0622 new_cov=12/0 polymorphism_quality=4.0 quality=4.0 quality_position_model=Inf ref_cov=23/267 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=35/267 RA 646 . NC_007779 3334554 0 G C bias_e_value=7180.68 bias_p_value=0.00154545 fisher_strand_p_value=0.000158513 frequency=1.672077e-02 genotype_quality=1556.7 ks_quality_p_value=1 log10_base_likelihood=-7.28859 log10_qual_likelihood_position_model=14.0069 log10_strand_likelihood_position_model=3.81765 new_cov=9/1 polymorphism_quality=1.8 quality=1.8 quality_position_model=Inf ref_cov=112/268 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=121/269 RA 647 . NC_007779 3350033 0 C . bias_e_value=4106120 bias_p_value=0.883734 fisher_strand_p_value=0.596096 frequency=6.779671e-03 genotype_quality=1872.5 ks_quality_p_value=0.936664 log10_base_likelihood=-7.53157 log10_qual_likelihood_position_model=1.1804 log10_strand_likelihood_position_model=0.464947 new_cov=1/2 polymorphism_quality=2.0 quality=2.0 quality_position_model=8.35994e-08 ref_cov=238/201 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=239/203 RA 648 . NC_007779 3350708 0 A C bias_e_value=4.32399e-06 bias_p_value=9.30624e-13 fisher_strand_p_value=2.89246e-14 frequency=3.834152e-02 genotype_quality=1246.7 ks_quality_p_value=1 log10_base_likelihood=-5.56464 log10_qual_likelihood_position_model=38.2107 log10_strand_likelihood_position_model=13.548 new_cov=0/44 polymorphism_quality=0.0 quality=0.0 quality_position_model=Inf ref_cov=198/170 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=198/215 RA 649 . NC_007779 3362866 1 . A bias_e_value=2064960 bias_p_value=0.444428 fisher_strand_p_value=0.246784 frequency=3.683090e-03 genotype_quality=2728.2 ks_quality_p_value=0.629074 log10_base_likelihood=-7.76282 log10_qual_likelihood_position_model=1.17903 log10_strand_likelihood_position_model=0.607683 new_cov=0/2 polymorphism_quality=2.3 quality=2.3 quality_position_model=6.74892e-08 ref_cov=273/268 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=273/270 RA 650 . NC_007779 3362867 0 A . bias_e_value=4562850 bias_p_value=0.982032 fisher_strand_p_value=1 frequency=5.436897e-03 genotype_quality=2260.7 ks_quality_p_value=0.81652 log10_base_likelihood=-7.34987 log10_qual_likelihood_position_model=1.84563 log10_strand_likelihood_position_model=0.424391 new_cov=2/1 polymorphism_quality=1.8 quality=1.8 quality_position_model=5.7335e-07 ref_cov=274/274 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=276/275 RA 651 . NC_007779 3377611 0 A . bias_e_value=1073760 bias_p_value=0.231098 fisher_strand_p_value=0.108477 frequency=5.750656e-03 genotype_quality=2139.5 ks_quality_p_value=0.560643 log10_base_likelihood=-7.39913 log10_qual_likelihood_position_model=2.11134 log10_strand_likelihood_position_model=0.96466 new_cov=3/0 polymorphism_quality=1.9 quality=1.9 quality_position_model=3.52769e-06 ref_cov=246/272 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=249/272 RA 652 . NC_007779 3379905 0 A . bias_e_value=3349530 bias_p_value=0.720899 fisher_strand_p_value=1 frequency=6.076813e-03 genotype_quality=2004.2 ks_quality_p_value=0.353312 log10_base_likelihood=-7.33451 log10_qual_likelihood_position_model=2.07876 log10_strand_likelihood_position_model=0.374517 new_cov=2/1 polymorphism_quality=1.8 quality=1.8 quality_position_model=9.2271e-07 ref_cov=281/209 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=283/210 RA 653 . NC_007779 3380462 0 G T bias_e_value=0.00549442 bias_p_value=1.18253e-09 fisher_strand_p_value=4.77632e-11 frequency=3.426743e-02 genotype_quality=1683.2 ks_quality_p_value=0.99972 log10_base_likelihood=-9.07696 log10_qual_likelihood_position_model=31.2079 log10_strand_likelihood_position_model=10.3341 new_cov=0/35 polymorphism_quality=3.6 quality=3.6 quality_position_model=Inf ref_cov=247/236 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=247/272 RA 654 . NC_007779 3385700 1 . T bias_e_value=3348240 bias_p_value=0.72062 fisher_strand_p_value=0.603642 frequency=6.223679e-03 genotype_quality=2358.6 ks_quality_p_value=0.584856 log10_base_likelihood=-11.4075 log10_qual_likelihood_position_model=3.91073 log10_strand_likelihood_position_model=0.452638 new_cov=2/1 polymorphism_quality=6.0 quality=6.0 quality_position_model=5.34033e-09 ref_cov=225/254 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=227/255 RA 655 . NC_007779 3389914 0 A C bias_e_value=5.47938e-08 bias_p_value=1.17929e-14 fisher_strand_p_value=3.21566e-16 frequency=4.358482e-02 genotype_quality=1142.6 ks_quality_p_value=1 log10_base_likelihood=-6.88833 log10_qual_likelihood_position_model=32.3838 log10_strand_likelihood_position_model=15.4927 new_cov=0/46 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=193/142 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=193/188 RA 656 . NC_007779 3392267 0 C A bias_e_value=3.10816e-08 bias_p_value=6.6895e-15 fisher_strand_p_value=1.79555e-16 frequency=3.480530e-02 genotype_quality=1777.0 ks_quality_p_value=1 log10_base_likelihood=-10.5377 log10_qual_likelihood_position_model=28.9348 log10_strand_likelihood_position_model=15.7458 new_cov=40/0 polymorphism_quality=5.1 quality=5.1 quality_position_model=Inf ref_cov=186/304 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=230/304 RA 657 . NC_007779 3397405 0 A C bias_e_value=1.80514e-34 bias_p_value=3.88509e-41 fisher_strand_p_value=3.93864e-43 frequency=1.035109e-01 genotype_quality=1301.0 ks_quality_p_value=1 log10_base_likelihood=-23.6605 log10_qual_likelihood_position_model=59.9262 log10_strand_likelihood_position_model=42.4047 new_cov=0/78 polymorphism_quality=18.4 quality=18.4 quality_position_model=Inf ref_cov=276/74 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=276/153 RA 658 . NC_007779 3397813 0 C G frequency=1 genotype_quality=1875.3 new_cov=203/230 quality=1875.3 ref_cov=0/0 tot_cov=203/231 RA 659 . NC_007779 3404070 0 T G bias_e_value=5.7579e-06 bias_p_value=1.23924e-12 fisher_strand_p_value=3.88738e-14 frequency=5.899096e-02 genotype_quality=1083.7 ks_quality_p_value=1 log10_base_likelihood=-9.17333 log10_qual_likelihood_position_model=33.4834 log10_strand_likelihood_position_model=13.4895 new_cov=42/0 polymorphism_quality=3.7 quality=3.7 quality_position_model=Inf ref_cov=139/175 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=182/175 RA 660 . NC_007779 3412753 0 C T bias_e_value=6.3801e-13 bias_p_value=1.37315e-19 fisher_strand_p_value=2.84239e-21 frequency=7.311487e-02 genotype_quality=1387.9 ks_quality_p_value=1 log10_base_likelihood=-18.8444 log10_qual_likelihood_position_model=38.6616 log10_strand_likelihood_position_model=20.5463 new_cov=0/38 polymorphism_quality=13.5 quality=13.5 quality_position_model=Inf ref_cov=274/92 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=274/130 RA 661 . NC_007779 3412756 0 G T bias_e_value=2.77937e-06 bias_p_value=5.98187e-13 fisher_strand_p_value=1.83324e-14 frequency=2.884674e-02 genotype_quality=1491.8 ks_quality_p_value=1 log10_base_likelihood=-6.57031 log10_qual_likelihood_position_model=25.4573 log10_strand_likelihood_position_model=13.7368 new_cov=0/26 polymorphism_quality=1.0 quality=1.0 quality_position_model=Inf ref_cov=276/103 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=277/129 RA 662 . NC_007779 3412772 0 A C bias_e_value=7.2762e-22 bias_p_value=1.56601e-28 fisher_strand_p_value=2.261e-30 frequency=4.480076e-02 genotype_quality=1308.6 ks_quality_p_value=1 log10_base_likelihood=-7.56338 log10_qual_likelihood_position_model=47.6167 log10_strand_likelihood_position_model=29.6457 new_cov=0/45 polymorphism_quality=2.1 quality=2.1 quality_position_model=Inf ref_cov=280/57 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=280/102 RA 663 . NC_007779 3421203 0 T C bias_e_value=5.03526e-16 bias_p_value=1.08371e-22 fisher_strand_p_value=1.9493e-24 frequency=8.575630e-02 genotype_quality=1326.9 ks_quality_p_value=1 log10_base_likelihood=-20.3034 log10_qual_likelihood_position_model=39.333 log10_strand_likelihood_position_model=23.7101 new_cov=0/48 polymorphism_quality=15.0 quality=15.0 quality_position_model=Inf ref_cov=268/103 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=268/151 RA 664 . NC_007779 3423128 1 . G bias_e_value=1714900 bias_p_value=0.369086 fisher_strand_p_value=0.248147 frequency=8.595467e-03 genotype_quality=1272.6 ks_quality_p_value=0.473474 log10_base_likelihood=-11.6664 log10_qual_likelihood_position_model=3.60703 log10_strand_likelihood_position_model=0.880828 new_cov=3/0 polymorphism_quality=6.3 quality=6.3 quality_position_model=3.88399e-09 ref_cov=175/171 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=178/171 RA 665 . NC_007779 3423142 0 G C bias_e_value=7.45785 bias_p_value=1.6051e-06 fisher_strand_p_value=9.33936e-08 frequency=3.307533e-02 genotype_quality=980.4 ks_quality_p_value=1 log10_base_likelihood=-8.7698 log10_qual_likelihood_position_model=16.0784 log10_strand_likelihood_position_model=7.02968 new_cov=11/0 polymorphism_quality=3.3 quality=3.3 quality_position_model=Inf ref_cov=54/201 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=65/201 RA 666 . NC_007779 3423145 0 A C bias_e_value=35256.2 bias_p_value=0.00758796 fisher_strand_p_value=0.000953861 frequency=2.755737e-02 genotype_quality=810.8 ks_quality_p_value=1 log10_base_likelihood=-6.77639 log10_qual_likelihood_position_model=12.7622 log10_strand_likelihood_position_model=3.06414 new_cov=8/3 polymorphism_quality=1.3 quality=1.3 quality_position_model=Inf ref_cov=61/203 reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=69/208 RA 667 . NC_007779 3423149 0 T C bias_e_value=2541.47 bias_p_value=0.000546984 fisher_strand_p_value=5.02552e-05 frequency=2.190971e-02 genotype_quality=1089.7 ks_quality_p_value=0.998558 log10_base_likelihood=-7.5418 log10_qual_likelihood_position_model=7.60287 log10_strand_likelihood_position_model=4.29882 new_cov=7/0 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=68/224 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=75/224 RA 668 . NC_007779 3428589 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 669 . NC_007779 3428591 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 670 . NC_007779 3431259 0 T G bias_e_value=850667 bias_p_value=0.183084 fisher_strand_p_value=0.0445282 frequency=1.400757e-02 genotype_quality=1440.9 ks_quality_p_value=1 log10_base_likelihood=-8.90367 log10_qual_likelihood_position_model=7.52791 log10_strand_likelihood_position_model=1.61894 new_cov=0/7 polymorphism_quality=3.4 quality=3.4 quality_position_model=Inf ref_cov=154/215 reject=POLYMORPHISM_STRAND tot_cov=155/223 RA 671 . NC_007779 3439587 0 A C bias_e_value=39.052 bias_p_value=8.4049e-06 fisher_strand_p_value=5.44976e-07 frequency=6.076717e-02 genotype_quality=1145.2 ks_quality_p_value=1 log10_base_likelihood=-28.1554 log10_qual_likelihood_position_model=20.2019 log10_strand_likelihood_position_model=6.48584 new_cov=23/0 polymorphism_quality=22.9 quality=22.9 quality_position_model=0.00407044 ref_cov=149/147 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=172/147 RA 672 . NC_007779 3439592 0 G . bias_e_value=196619 bias_p_value=0.0423169 fisher_strand_p_value=0.0071179 frequency=2.610016e-02 genotype_quality=1148.4 ks_quality_p_value=1 log10_base_likelihood=-19.8728 log10_qual_likelihood_position_model=8.9159 log10_strand_likelihood_position_model=2.41444 new_cov=8/0 polymorphism_quality=14.6 quality=14.6 quality_position_model=1.54679e-10 ref_cov=143/148 reject=POLYMORPHISM_STRAND tot_cov=157/149 RA 673 . NC_007779 3439594 0 C T bias_e_value=105946 bias_p_value=0.0228021 fisher_strand_p_value=0.00341431 frequency=2.510166e-02 genotype_quality=1041.8 ks_quality_p_value=0.999754 log10_base_likelihood=-6.76377 log10_qual_likelihood_position_model=9.32245 log10_strand_likelihood_position_model=2.75333 new_cov=9/0 polymorphism_quality=1.2 quality=1.2 quality_position_model=Inf ref_cov=129/137 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=147/137 RA 674 . NC_007779 3439598 1 . T bias_e_value=620155 bias_p_value=0.133472 fisher_strand_p_value=0.0307512 frequency=2.173901e-02 genotype_quality=1300.3 ks_quality_p_value=0.959614 log10_base_likelihood=-25.6111 log10_qual_likelihood_position_model=6.25338 log10_strand_likelihood_position_model=1.69899 new_cov=6/0 polymorphism_quality=20.4 quality=20.4 quality_position_model=8.33123e-20 ref_cov=139/131 reject=POLYMORPHISM_STRAND tot_cov=145/131 RA 675 . NC_007779 3439601 0 G T bias_e_value=1174.52 bias_p_value=0.000252784 fisher_strand_p_value=2.15199e-05 frequency=5.013847e-02 genotype_quality=1130.8 ks_quality_p_value=1 log10_base_likelihood=-19.0655 log10_qual_likelihood_position_model=17.8781 log10_strand_likelihood_position_model=4.68706 new_cov=17/0 polymorphism_quality=13.8 quality=13.8 quality_position_model=Inf ref_cov=149/140 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=166/140 RA 676 . NC_007779 3439605 0 T C bias_e_value=1781.25 bias_p_value=0.000383366 fisher_strand_p_value=3.39548e-05 frequency=4.884386e-02 genotype_quality=1118.8 ks_quality_p_value=1 log10_base_likelihood=-17.3464 log10_qual_likelihood_position_model=20.8309 log10_strand_likelihood_position_model=4.5103 new_cov=18/0 polymorphism_quality=12.0 quality=12.0 quality_position_model=Inf ref_cov=161/133 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=179/133 RA 677 . NC_007779 3439607 0 G T bias_e_value=73.37 bias_p_value=1.5791e-05 fisher_strand_p_value=1.07078e-06 frequency=6.311607e-02 genotype_quality=1188.6 ks_quality_p_value=1 log10_base_likelihood=-21.7539 log10_qual_likelihood_position_model=25.4929 log10_strand_likelihood_position_model=6.09094 new_cov=24/0 polymorphism_quality=16.5 quality=16.5 quality_position_model=Inf ref_cov=154/132 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=178/133 RA 678 . NC_007779 3439608 0 T G bias_e_value=168922 bias_p_value=0.036356 fisher_strand_p_value=0.00593362 frequency=2.225208e-02 genotype_quality=1112.5 ks_quality_p_value=1 log10_base_likelihood=-6.55483 log10_qual_likelihood_position_model=11.0898 log10_strand_likelihood_position_model=2.48263 new_cov=10/0 polymorphism_quality=1.0 quality=1.0 quality_position_model=Inf ref_cov=167/133 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=178/133 RA 679 . NC_007779 3440270 0 C A bias_e_value=2.97964e-08 bias_p_value=6.41289e-15 fisher_strand_p_value=1.7193e-16 frequency=7.670641e-02 genotype_quality=1424.0 ks_quality_p_value=1 log10_base_likelihood=-18.2221 log10_qual_likelihood_position_model=32.5344 log10_strand_likelihood_position_model=15.9898 new_cov=58/0 polymorphism_quality=12.9 quality=12.9 quality_position_model=Inf ref_cov=215/216 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=275/216 RA 680 . NC_007779 3440600 0 A C bias_e_value=8.3633e-12 bias_p_value=1.79998e-18 fisher_strand_p_value=3.94037e-20 frequency=4.312229e-02 genotype_quality=1306.9 ks_quality_p_value=1 log10_base_likelihood=-6.06911 log10_qual_likelihood_position_model=37.7663 log10_strand_likelihood_position_model=19.4045 new_cov=0/45 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=245/122 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=245/168 RA 681 . NC_007779 3441442 0 C A bias_e_value=0.0699931 bias_p_value=1.50642e-08 fisher_strand_p_value=6.83611e-10 frequency=2.623844e-02 genotype_quality=1363.0 ks_quality_p_value=0.996803 log10_base_likelihood=-5.65223 log10_qual_likelihood_position_model=28.5858 log10_strand_likelihood_position_model=9.17502 new_cov=27/1 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=150/233 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=177/234 RA 682 . NC_007779 3459714 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 683 . NC_007779 3459715 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 684 . NC_007779 3459716 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 685 . NC_007779 3459717 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 686 . NC_007779 3459719 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 687 . NC_007779 3459720 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 688 . NC_007779 3459722 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 689 . NC_007779 3459723 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 690 . NC_007779 3459724 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 691 . NC_007779 3459726 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 692 . NC_007779 3459727 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 693 . NC_007779 3459728 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 694 . NC_007779 3459729 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 695 . NC_007779 3459731 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 696 . NC_007779 3459732 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 697 . NC_007779 3459734 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 698 . NC_007779 3459735 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 699 . NC_007779 3459737 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 700 . NC_007779 3459738 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 701 . NC_007779 3459739 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 702 . NC_007779 3459742 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 703 . NC_007779 3459743 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 704 . NC_007779 3459745 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 705 . NC_007779 3459748 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 706 . NC_007779 3459749 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 707 . NC_007779 3459750 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 708 . NC_007779 3459751 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 709 . NC_007779 3459752 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 710 . NC_007779 3459753 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 711 . NC_007779 3459755 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 712 . NC_007779 3459756 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 713 . NC_007779 3459757 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 714 . NC_007779 3475527 0 T G bias_e_value=1.25534e-20 bias_p_value=2.70179e-27 fisher_strand_p_value=4.07073e-29 frequency=1.136374e-01 genotype_quality=1317.6 ks_quality_p_value=1 log10_base_likelihood=-34.9078 log10_qual_likelihood_position_model=50.3576 log10_strand_likelihood_position_model=28.3903 new_cov=77/0 polymorphism_quality=29.7 quality=29.7 quality_position_model=Inf ref_cov=138/234 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=216/234 RA 715 . NC_007779 3475533 0 C T bias_e_value=5.93367e-13 bias_p_value=1.27707e-19 fisher_strand_p_value=2.63945e-21 frequency=1.195221e-01 genotype_quality=1340.9 ks_quality_p_value=1 log10_base_likelihood=-54.692 log10_qual_likelihood_position_model=72.1778 log10_strand_likelihood_position_model=20.5785 new_cov=59/0 polymorphism_quality=49.6 quality=49.6 quality_position_model=Inf ref_cov=165/239 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=224/239 RA 716 . NC_007779 3475539 0 G T bias_e_value=185.625 bias_p_value=3.99509e-05 fisher_strand_p_value=2.90577e-06 frequency=3.092575e-02 genotype_quality=1375.3 ks_quality_p_value=1 log10_base_likelihood=-7.75647 log10_qual_likelihood_position_model=12.7241 log10_strand_likelihood_position_model=5.53674 new_cov=14/0 polymorphism_quality=2.3 quality=2.3 quality_position_model=Inf ref_cov=144/225 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=158/225 RA 717 . NC_007779 3478395 1 . T bias_e_value=3464370 bias_p_value=0.745613 fisher_strand_p_value=1 frequency=3.846169e-03 genotype_quality=2529.5 ks_quality_p_value=0.377868 log10_base_likelihood=-7.83228 log10_qual_likelihood_position_model=1.6204 log10_strand_likelihood_position_model=0.308136 new_cov=1/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=8.01819e-08 ref_cov=224/294 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=225/295 RA 718 . NC_007779 3484372 0 A C bias_e_value=8.80659e-12 bias_p_value=1.89539e-18 fisher_strand_p_value=4.15403e-20 frequency=5.970955e-02 genotype_quality=1106.3 ks_quality_p_value=1 log10_base_likelihood=-8.6998 log10_qual_likelihood_position_model=35.1186 log10_strand_likelihood_position_model=19.3815 new_cov=0/51 polymorphism_quality=3.2 quality=3.2 quality_position_model=Inf ref_cov=207/123 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=207/176 RA 719 . NC_007779 3485086 0 G T bias_e_value=0.0271278 bias_p_value=5.83855e-09 fisher_strand_p_value=2.52767e-10 frequency=2.789974e-02 genotype_quality=1563.3 ks_quality_p_value=1 log10_base_likelihood=-6.60695 log10_qual_likelihood_position_model=25.2618 log10_strand_likelihood_position_model=9.59728 new_cov=0/30 polymorphism_quality=1.1 quality=1.1 quality_position_model=Inf ref_cov=242/207 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=242/237 RA 720 . NC_007779 3498149 0 T G bias_e_value=8.44851e-11 bias_p_value=1.81832e-17 fisher_strand_p_value=4.19794e-19 frequency=4.679823e-02 genotype_quality=1023.3 ks_quality_p_value=1 log10_base_likelihood=-9.4643 log10_qual_likelihood_position_model=29.7815 log10_strand_likelihood_position_model=18.377 new_cov=34/0 polymorphism_quality=4.0 quality=4.0 quality_position_model=Inf ref_cov=67/207 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=101/207 RA 721 . NC_007779 3499066 0 A C bias_e_value=1.21684e-09 bias_p_value=2.61893e-16 fisher_strand_p_value=6.45343e-18 frequency=7.472420e-02 genotype_quality=1211.2 ks_quality_p_value=1 log10_base_likelihood=-22.8821 log10_qual_likelihood_position_model=35.9767 log10_strand_likelihood_position_model=17.1902 new_cov=0/31 polymorphism_quality=17.6 quality=17.6 quality_position_model=Inf ref_cov=239/77 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=240/109 RA 722 . NC_007779 3499693 1 . C bias_e_value=4646290 bias_p_value=0.999992 fisher_strand_p_value=1 frequency=4.254341e-03 genotype_quality=2348.0 ks_quality_p_value=0.995917 log10_base_likelihood=-7.02087 log10_qual_likelihood_position_model=4.13915 log10_strand_likelihood_position_model=0.302123 new_cov=1/1 polymorphism_quality=1.5 quality=1.5 quality_position_model=0.000246557 ref_cov=250/218 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=251/219 RA 723 . NC_007779 3520391 0 C G bias_e_value=2.47861e-06 bias_p_value=5.33456e-13 fisher_strand_p_value=1.62976e-14 frequency=5.558348e-02 genotype_quality=1068.5 ks_quality_p_value=0.999509 log10_base_likelihood=-13.1738 log10_qual_likelihood_position_model=23.8028 log10_strand_likelihood_position_model=13.7906 new_cov=17/1 polymorphism_quality=7.8 quality=7.8 quality_position_model=Inf ref_cov=27/235 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=45/236 RA 724 . NC_007779 3523734 0 G T bias_e_value=2.53373e-09 bias_p_value=5.45318e-16 fisher_strand_p_value=1.36912e-17 frequency=5.481672e-02 genotype_quality=1707.8 ks_quality_p_value=1 log10_base_likelihood=-13.4614 log10_qual_likelihood_position_model=42.4592 log10_strand_likelihood_position_model=16.9851 new_cov=0/53 polymorphism_quality=8.1 quality=8.1 quality_position_model=Inf ref_cov=259/211 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=259/264 RA 725 . NC_007779 3543517 0 C G bias_e_value=1.38382 bias_p_value=2.97832e-07 fisher_strand_p_value=1.57046e-08 frequency=2.264404e-02 genotype_quality=1363.4 ks_quality_p_value=0.999741 log10_base_likelihood=-6.28835 log10_qual_likelihood_position_model=16.5388 log10_strand_likelihood_position_model=7.80397 new_cov=0/15 polymorphism_quality=0.8 quality=0.8 quality_position_model=Inf ref_cov=238/95 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=238/112 RA 726 . NC_007779 3543547 0 A C bias_e_value=2.20137e-35 bias_p_value=4.73787e-42 fisher_strand_p_value=4.70186e-44 frequency=1.859975e-01 genotype_quality=1144.6 ks_quality_p_value=1 log10_base_likelihood=-56.2001 log10_qual_likelihood_position_model=87.0495 log10_strand_likelihood_position_model=43.3277 new_cov=0/99 polymorphism_quality=51.1 quality=51.1 quality_position_model=Inf ref_cov=231/87 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=231/188 RA 727 . NC_007779 3550877 0 C A bias_e_value=1.23835 bias_p_value=2.66522e-07 fisher_strand_p_value=1.39637e-08 frequency=3.127861e-02 genotype_quality=1564.8 ks_quality_p_value=1 log10_base_likelihood=-9.1589 log10_qual_likelihood_position_model=19.9838 log10_strand_likelihood_position_model=7.98423 new_cov=30/1 polymorphism_quality=3.7 quality=3.7 quality_position_model=Inf ref_cov=212/232 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=242/233 RA 728 . NC_007779 3560478 0 G T bias_e_value=0.00582935 bias_p_value=1.25461e-09 fisher_strand_p_value=5.07872e-11 frequency=4.163265e-02 genotype_quality=1562.7 ks_quality_p_value=1 log10_base_likelihood=-12.2102 log10_qual_likelihood_position_model=24.5396 log10_strand_likelihood_position_model=10.426 new_cov=0/36 polymorphism_quality=6.8 quality=6.8 quality_position_model=Inf ref_cov=222/216 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=222/254 RA 729 . NC_007779 3571350 0 A . bias_e_value=4015730 bias_p_value=0.864279 fisher_strand_p_value=0.62268 frequency=6.163597e-03 genotype_quality=1998.3 ks_quality_p_value=0.845606 log10_base_likelihood=-7.2331 log10_qual_likelihood_position_model=1.87686 log10_strand_likelihood_position_model=0.42688 new_cov=1/2 polymorphism_quality=1.7 quality=1.7 quality_position_model=8.22181e-07 ref_cov=243/240 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=244/242 RA 730 . NC_007779 3576400 1 . A bias_e_value=4030620 bias_p_value=0.867483 fisher_strand_p_value=1 frequency=4.219055e-03 genotype_quality=2341.1 ks_quality_p_value=0.531575 log10_base_likelihood=-7.77756 log10_qual_likelihood_position_model=1.31409 log10_strand_likelihood_position_model=0.304222 new_cov=1/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=4.36455e-08 ref_cov=213/259 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=214/260 RA 731 . NC_007779 3580297 0 G T bias_e_value=0.051678 bias_p_value=1.11223e-08 fisher_strand_p_value=4.9599e-10 frequency=2.521992e-02 genotype_quality=2000.9 ks_quality_p_value=1 log10_base_likelihood=-7.44647 log10_qual_likelihood_position_model=23.3516 log10_strand_likelihood_position_model=9.30453 new_cov=0/29 polymorphism_quality=1.9 quality=1.9 quality_position_model=Inf ref_cov=295/255 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=295/285 RA 732 . NC_007779 3581565 0 A C bias_e_value=181892 bias_p_value=0.0391474 fisher_strand_p_value=0.00648338 frequency=1.143169e-02 genotype_quality=1667.7 ks_quality_p_value=0.99992 log10_base_likelihood=-5.90587 log10_qual_likelihood_position_model=9.9057 log10_strand_likelihood_position_model=2.1882 new_cov=7/0 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=200/215 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=207/216 RA 733 . NC_007779 3581567 0 C . bias_e_value=943600 bias_p_value=0.203085 fisher_strand_p_value=0.0523166 frequency=9.355545e-03 genotype_quality=1815.6 ks_quality_p_value=0.976842 log10_base_likelihood=-9.87683 log10_qual_likelihood_position_model=3.56672 log10_strand_likelihood_position_model=1.28136 new_cov=4/0 polymorphism_quality=4.4 quality=4.4 quality_position_model=6.47976e-07 ref_cov=201/222 reject=POLYMORPHISM_STRAND tot_cov=205/222 RA 734 . NC_007779 3583865 0 C A bias_e_value=0.00855468 bias_p_value=1.84117e-09 fisher_strand_p_value=7.57574e-11 frequency=3.637791e-02 genotype_quality=1628.4 ks_quality_p_value=1 log10_base_likelihood=-12.9298 log10_qual_likelihood_position_model=23.5814 log10_strand_likelihood_position_model=10.1206 new_cov=31/0 polymorphism_quality=7.5 quality=7.5 quality_position_model=Inf ref_cov=202/244 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=237/244 RA 735 . NC_007779 3603950 0 A C bias_e_value=2.03394e-07 bias_p_value=4.37752e-14 fisher_strand_p_value=1.23924e-15 frequency=4.099369e-02 genotype_quality=1332.9 ks_quality_p_value=1 log10_base_likelihood=-8.16825 log10_qual_likelihood_position_model=49.0548 log10_strand_likelihood_position_model=14.9068 new_cov=0/36 polymorphism_quality=2.7 quality=2.7 quality_position_model=Inf ref_cov=244/135 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=244/174 RA 736 . NC_007779 3615064 0 C A bias_e_value=429.141 bias_p_value=9.23611e-05 fisher_strand_p_value=7.1918e-06 frequency=1.868534e-02 genotype_quality=1778.4 ks_quality_p_value=1 log10_base_likelihood=-5.94764 log10_qual_likelihood_position_model=19.8959 log10_strand_likelihood_position_model=5.25299 new_cov=20/0 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=258/223 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=278/223 RA 737 . NC_007779 3627545 0 T . bias_e_value=3616590 bias_p_value=0.778375 fisher_strand_p_value=0.592011 frequency=6.068230e-03 genotype_quality=1975.8 ks_quality_p_value=0.697921 log10_base_likelihood=-6.69216 log10_qual_likelihood_position_model=3.29256 log10_strand_likelihood_position_model=0.472751 new_cov=1/2 polymorphism_quality=1.2 quality=1.2 quality_position_model=0.000104806 ref_cov=269/221 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=270/223 RA 738 . NC_007779 3651632 0 C T bias_e_value=60338.1 bias_p_value=0.0129862 fisher_strand_p_value=0.00177799 frequency=1.591873e-02 genotype_quality=1889.1 ks_quality_p_value=0.995516 log10_base_likelihood=-6.49754 log10_qual_likelihood_position_model=15.2562 log10_strand_likelihood_position_model=3.01519 new_cov=10/0 polymorphism_quality=1.0 quality=1.0 quality_position_model=Inf ref_cov=228/234 reject=EVALUE,POLYMORPHISM_STRAND tot_cov=239/234 RA 739 . NC_007779 3651641 0 G C bias_e_value=9362.3 bias_p_value=0.00201499 fisher_strand_p_value=0.000213147 frequency=1.703835e-02 genotype_quality=1991.4 ks_quality_p_value=1 log10_base_likelihood=-9.78487 log10_qual_likelihood_position_model=16.4565 log10_strand_likelihood_position_model=3.87907 new_cov=13/0 polymorphism_quality=4.3 quality=4.3 quality_position_model=Inf ref_cov=237/241 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=250/241 RA 740 . NC_007779 3651647 0 G T bias_e_value=19051 bias_p_value=0.00410023 fisher_strand_p_value=0.000479492 frequency=1.576614e-02 genotype_quality=2006.8 ks_quality_p_value=0.988025 log10_base_likelihood=-7.10685 log10_qual_likelihood_position_model=19.0403 log10_strand_likelihood_position_model=3.4509 new_cov=12/0 polymorphism_quality=1.6 quality=1.6 quality_position_model=Inf ref_cov=247/238 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=259/239 RA 741 . NC_007779 3651649 0 A T bias_e_value=1558.58 bias_p_value=0.000335443 fisher_strand_p_value=2.93298e-05 frequency=2.251244e-02 genotype_quality=1944.1 ks_quality_p_value=1 log10_base_likelihood=-6.12891 log10_qual_likelihood_position_model=22.3065 log10_strand_likelihood_position_model=4.62979 new_cov=16/0 polymorphism_quality=0.6 quality=0.6 quality_position_model=Inf ref_cov=245/240 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=261/240 RA 742 . NC_007779 3654011 0 A C bias_e_value=0.028713 bias_p_value=6.17971e-09 fisher_strand_p_value=2.68226e-10 frequency=2.192879e-02 genotype_quality=1683.5 ks_quality_p_value=1 log10_base_likelihood=-7.18506 log10_qual_likelihood_position_model=27.1559 log10_strand_likelihood_position_model=9.5715 new_cov=0/23 polymorphism_quality=1.7 quality=1.7 quality_position_model=Inf ref_cov=289/168 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=289/192 RA 743 . NC_007779 3665059 0 C A bias_e_value=0.0360971 bias_p_value=7.76895e-09 fisher_strand_p_value=3.40745e-10 frequency=3.551865e-02 genotype_quality=1644.5 ks_quality_p_value=1 log10_base_likelihood=-10.0361 log10_qual_likelihood_position_model=25.2267 log10_strand_likelihood_position_model=9.51219 new_cov=38/0 polymorphism_quality=4.6 quality=4.6 quality_position_model=Inf ref_cov=272/227 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=311/228 RA 744 . NC_007779 3673380 0 G T bias_e_value=0.012681 bias_p_value=2.72925e-09 fisher_strand_p_value=1.87839e-10 frequency=4.313660e-02 genotype_quality=1399.5 ks_quality_p_value=0.608121 log10_base_likelihood=-16.755 log10_qual_likelihood_position_model=41.6194 log10_strand_likelihood_position_model=9.75113 new_cov=0/37 polymorphism_quality=11.4 quality=11.4 quality_position_model=Inf ref_cov=200/221 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=200/259 RA 745 . NC_007779 3677212 0 C G bias_e_value=131.105 bias_p_value=2.82168e-05 fisher_strand_p_value=1.99787e-06 frequency=1.829624e-02 genotype_quality=1030.0 ks_quality_p_value=1 log10_base_likelihood=-5.63278 log10_qual_likelihood_position_model=8.94323 log10_strand_likelihood_position_model=5.69943 new_cov=0/6 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=225/25 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=225/31 RA 746 . NC_007779 3686204 1 . A bias_e_value=1746030 bias_p_value=0.375786 fisher_strand_p_value=0.165541 frequency=4.158020e-03 genotype_quality=2392.2 ks_quality_p_value=0.728762 log10_base_likelihood=-7.82582 log10_qual_likelihood_position_model=1.54109 log10_strand_likelihood_position_model=0.781096 new_cov=0/2 polymorphism_quality=2.3 quality=2.3 quality_position_model=2.08178e-07 ref_cov=285/194 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=285/196 RA 747 . NC_007779 3686205 0 A . bias_e_value=4079550 bias_p_value=0.878016 fisher_strand_p_value=0.569477 frequency=6.188393e-03 genotype_quality=1973.3 ks_quality_p_value=0.963468 log10_base_likelihood=-7.1001 log10_qual_likelihood_position_model=2.13263 log10_strand_likelihood_position_model=0.530114 new_cov=1/2 polymorphism_quality=1.6 quality=1.6 quality_position_model=2.67954e-06 ref_cov=286/195 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=287/197 RA 748 . NC_007779 3688858 0 A C bias_e_value=1.18932e-26 bias_p_value=2.5597e-33 fisher_strand_p_value=3.18241e-35 frequency=1.413894e-01 genotype_quality=1063.4 ks_quality_p_value=1 log10_base_likelihood=-30.9345 log10_qual_likelihood_position_model=51.8613 log10_strand_likelihood_position_model=34.4972 new_cov=0/82 polymorphism_quality=25.7 quality=25.7 quality_position_model=Inf ref_cov=205/87 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=206/169 RA 749 . NC_007779 3701118 0 G T bias_e_value=2.24961e-12 bias_p_value=4.84169e-19 fisher_strand_p_value=1.02965e-20 frequency=8.853865e-02 genotype_quality=1360.7 ks_quality_p_value=1 log10_base_likelihood=-22.3908 log10_qual_likelihood_position_model=34.5023 log10_strand_likelihood_position_model=19.9873 new_cov=0/54 polymorphism_quality=17.1 quality=17.1 quality_position_model=Inf ref_cov=232/146 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/200 RA 750 . NC_007779 3705119 1 . C bias_e_value=3523020 bias_p_value=0.758237 fisher_strand_p_value=0.50324 frequency=4.319191e-03 genotype_quality=2278.7 ks_quality_p_value=0.777112 log10_base_likelihood=-7.42953 log10_qual_likelihood_position_model=1.02599 log10_strand_likelihood_position_model=0.525702 new_cov=0/2 polymorphism_quality=1.9 quality=1.9 quality_position_model=8.52859e-08 ref_cov=210/251 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=210/253 RA 751 . NC_007779 3727557 0 A G bias_e_value=9.47674e-08 bias_p_value=2.03962e-14 fisher_strand_p_value=5.64835e-16 frequency=4.499245e-02 genotype_quality=1213.1 ks_quality_p_value=1 log10_base_likelihood=-7.91511 log10_qual_likelihood_position_model=23.1743 log10_strand_likelihood_position_model=15.2481 new_cov=22/0 polymorphism_quality=2.4 quality=2.4 quality_position_model=Inf ref_cov=57/268 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=79/268 RA 752 . NC_007779 3728146 1 . T bias_e_value=1528910 bias_p_value=0.329057 fisher_strand_p_value=0.103078 frequency=8.163452e-03 genotype_quality=1203.7 ks_quality_p_value=0.965082 log10_base_likelihood=-8.45895 log10_qual_likelihood_position_model=1.21809 log10_strand_likelihood_position_model=0.986834 new_cov=2/0 polymorphism_quality=3.0 quality=3.0 quality_position_model=3.4837e-08 ref_cov=77/166 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=79/166 RA 753 . NC_007779 3728155 0 T C bias_e_value=364.29 bias_p_value=7.84039e-05 fisher_strand_p_value=6.2015e-06 frequency=2.715206e-02 genotype_quality=711.0 ks_quality_p_value=0.971013 log10_base_likelihood=-6.05357 log10_qual_likelihood_position_model=9.24873 log10_strand_likelihood_position_model=5.2075 new_cov=6/0 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=24/175 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=30/175 RA 754 . NC_007779 3731041 1 . T bias_e_value=4179330 bias_p_value=0.899491 fisher_strand_p_value=0.618513 frequency=6.535530e-03 genotype_quality=2267.0 ks_quality_p_value=0.948376 log10_base_likelihood=-12.3075 log10_qual_likelihood_position_model=2.32996 log10_strand_likelihood_position_model=0.431826 new_cov=2/1 polymorphism_quality=6.9 quality=6.9 quality_position_model=1.45584e-11 ref_cov=224/232 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=226/233 RA 755 . NC_007779 3731042 0 T . bias_e_value=2378180 bias_p_value=0.511841 fisher_strand_p_value=0.623969 frequency=8.576393e-03 genotype_quality=1815.1 ks_quality_p_value=0.31062 log10_base_likelihood=-10.5341 log10_qual_likelihood_position_model=2.60839 log10_strand_likelihood_position_model=0.578302 new_cov=1/3 polymorphism_quality=5.1 quality=5.1 quality_position_model=2.60391e-09 ref_cov=225/236 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=227/239 RA 756 . NC_007779 3732310 0 G T bias_e_value=2.21971e-08 bias_p_value=4.77733e-15 fisher_strand_p_value=1.2705e-16 frequency=7.045364e-02 genotype_quality=1465.1 ks_quality_p_value=1 log10_base_likelihood=-27.7291 log10_qual_likelihood_position_model=27.6943 log10_strand_likelihood_position_model=15.896 new_cov=0/45 polymorphism_quality=22.5 quality=22.5 quality_position_model=Inf ref_cov=239/168 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=239/213 RA 757 . NC_007779 3734126 0 G T bias_e_value=0.100696 bias_p_value=2.1672e-08 fisher_strand_p_value=9.97529e-10 frequency=3.536892e-02 genotype_quality=1735.7 ks_quality_p_value=1 log10_base_likelihood=-11.9058 log10_qual_likelihood_position_model=25.9326 log10_strand_likelihood_position_model=9.01377 new_cov=0/31 polymorphism_quality=6.5 quality=6.5 quality_position_model=Inf ref_cov=240/236 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=241/267 RA 758 . NC_007779 3750122 0 C . bias_e_value=18380.4 bias_p_value=0.00395588 fisher_strand_p_value=0.504207 frequency=1 genotype_quality=2281.8 ks_quality_p_value=0.000902295 log10_base_likelihood=-100.012 log10_qual_likelihood_position_model=10.448 log10_strand_likelihood_position_model=0.844438 new_cov=228/247 polymorphism_changed_to_consensus=1 polymorphism_quality=95.1 quality=95.1 quality_position_model=3.26191e-91 ref_cov=8/12 tot_cov=236/260 RA 759 . NC_007779 3750123 0 C T bias_e_value=3134080 bias_p_value=0.674527 fisher_strand_p_value=0.504207 frequency=4.039383e-02 genotype_quality=1920.3 ks_quality_p_value=0.617305 log10_base_likelihood=-45.2333 log10_qual_likelihood_position_model=12.4327 log10_strand_likelihood_position_model=0.844438 new_cov=8/12 polymorphism_quality=40.1 quality=40.1 quality_position_model=3.13904e-34 ref_cov=228/247 tot_cov=236/260 RA 760 . NC_007779 3761469 0 A C bias_e_value=1.06447e-06 bias_p_value=2.29099e-13 fisher_strand_p_value=6.81707e-15 frequency=3.103161e-02 genotype_quality=1036.7 ks_quality_p_value=0.999613 log10_base_likelihood=-6.66604 log10_qual_likelihood_position_model=19.7463 log10_strand_likelihood_position_model=14.1664 new_cov=0/15 polymorphism_quality=1.1 quality=1.1 quality_position_model=Inf ref_cov=247/24 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=247/39 RA 761 . NC_007779 3762475 0 T G bias_e_value=1.29682 bias_p_value=2.79107e-07 fisher_strand_p_value=1.46639e-08 frequency=2.904892e-02 genotype_quality=1431.6 ks_quality_p_value=0.999761 log10_base_likelihood=-7.76247 log10_qual_likelihood_position_model=23.6976 log10_strand_likelihood_position_model=7.83375 new_cov=21/0 polymorphism_quality=2.3 quality=2.3 quality_position_model=Inf ref_cov=167/242 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=189/242 RA 762 . NC_007779 3780902 0 T G bias_e_value=3.50983 bias_p_value=7.55399e-07 fisher_strand_p_value=4.20002e-08 frequency=1.908875e-02 genotype_quality=1126.2 ks_quality_p_value=1 log10_base_likelihood=-6.10823 log10_qual_likelihood_position_model=12.1636 log10_strand_likelihood_position_model=7.37675 new_cov=10/0 polymorphism_quality=0.6 quality=0.6 quality_position_model=Inf ref_cov=49/243 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=60/243 RA 763 . NC_007779 3788380 0 G T bias_e_value=9.75526e-09 bias_p_value=2.09956e-15 fisher_strand_p_value=5.46102e-17 frequency=8.261585e-02 genotype_quality=1426.1 ks_quality_p_value=1 log10_base_likelihood=-27.8336 log10_qual_likelihood_position_model=32.3053 log10_strand_likelihood_position_model=16.3002 new_cov=0/58 polymorphism_quality=22.6 quality=22.6 quality_position_model=Inf ref_cov=208/200 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=208/260 RA 764 . NC_007779 3789663 0 T . bias_e_value=1527950 bias_p_value=0.328851 fisher_strand_p_value=0.352052 frequency=8.667946e-03 genotype_quality=1816.2 ks_quality_p_value=0.282315 log10_base_likelihood=-10.2828 log10_qual_likelihood_position_model=2.76125 log10_strand_likelihood_position_model=0.643737 new_cov=1/3 polymorphism_quality=4.9 quality=4.9 quality_position_model=7.92126e-09 ref_cov=240/217 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=241/220 RA 765 . NC_007779 3812429 0 G T bias_e_value=0.00223509 bias_p_value=4.81045e-10 fisher_strand_p_value=1.87223e-11 frequency=3.541374e-02 genotype_quality=1595.0 ks_quality_p_value=0.999693 log10_base_likelihood=-8.79188 log10_qual_likelihood_position_model=26.5004 log10_strand_likelihood_position_model=10.7276 new_cov=0/31 polymorphism_quality=3.3 quality=3.3 quality_position_model=Inf ref_cov=247/187 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=247/219 RA 766 . NC_007779 3824606 1 . T bias_e_value=2378370 bias_p_value=0.511881 fisher_strand_p_value=1 frequency=4.484177e-03 genotype_quality=2180.6 ks_quality_p_value=0.193842 log10_base_likelihood=-7.92237 log10_qual_likelihood_position_model=2.01394 log10_strand_likelihood_position_model=0.300614 new_cov=1/1 polymorphism_quality=2.4 quality=2.4 quality_position_model=1.62351e-07 ref_cov=214/230 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=215/231 RA 767 . NC_007779 3824607 0 T . bias_e_value=4260710 bias_p_value=0.917006 fisher_strand_p_value=0.624661 frequency=8.746147e-03 genotype_quality=1853.3 ks_quality_p_value=0.994632 log10_base_likelihood=-9.64605 log10_qual_likelihood_position_model=3.24938 log10_strand_likelihood_position_model=0.567059 new_cov=1/3 polymorphism_quality=4.2 quality=4.2 quality_position_model=9.56707e-08 ref_cov=217/234 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=219/237 RA 768 . NC_007779 3828029 0 G T bias_e_value=0.185466 bias_p_value=3.99166e-08 fisher_strand_p_value=2.13379e-09 frequency=5.389690e-02 genotype_quality=1587.8 ks_quality_p_value=0.887215 log10_base_likelihood=-23.4901 log10_qual_likelihood_position_model=36.439 log10_strand_likelihood_position_model=8.81772 new_cov=31/0 polymorphism_quality=18.2 quality=18.2 quality_position_model=Inf ref_cov=221/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=252/219 RA 769 . NC_007779 3835358 1 . A bias_e_value=1517050 bias_p_value=0.326506 fisher_strand_p_value=0.144612 frequency=6.250381e-03 genotype_quality=1604.5 ks_quality_p_value=0.680274 log10_base_likelihood=-8.51763 log10_qual_likelihood_position_model=1.7714 log10_strand_likelihood_position_model=0.839795 new_cov=2/0 polymorphism_quality=3.0 quality=3.0 quality_position_model=7.96689e-08 ref_cov=120/198 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=122/198 RA 770 . NC_007779 3838979 0 A . bias_e_value=4637350 bias_p_value=0.998066 fisher_strand_p_value=1 frequency=6.402016e-03 genotype_quality=1953.5 ks_quality_p_value=0.938452 log10_base_likelihood=-7.46947 log10_qual_likelihood_position_model=1.83364 log10_strand_likelihood_position_model=0.377349 new_cov=1/2 polymorphism_quality=2.0 quality=2.0 quality_position_model=3.73949e-07 ref_cov=201/264 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=202/266 RA 771 . NC_007779 3841755 1 . A bias_e_value=4646320 bias_p_value=0.999998 fisher_strand_p_value=1 frequency=4.183769e-03 genotype_quality=2400.0 ks_quality_p_value=0.998244 log10_base_likelihood=-7.27576 log10_qual_likelihood_position_model=2.31498 log10_strand_likelihood_position_model=0.301613 new_cov=1/1 polymorphism_quality=1.8 quality=1.8 quality_position_model=1.57211e-06 ref_cov=252/224 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=253/225 RA 772 . NC_007779 3841756 0 A . bias_e_value=2875840 bias_p_value=0.618949 fisher_strand_p_value=0.266543 frequency=1.445103e-02 genotype_quality=1999.5 ks_quality_p_value=0.999939 log10_base_likelihood=-19.2105 log10_qual_likelihood_position_model=4.74706 log10_strand_likelihood_position_model=0.849113 new_cov=2/5 polymorphism_quality=13.9 quality=13.9 quality_position_model=1.04739e-15 ref_cov=251/226 reject=INDEL_HOMOPOLYMER tot_cov=253/231 RA 773 . NC_007779 3845596 0 G T bias_e_value=5.72119e-05 bias_p_value=1.23133e-11 fisher_strand_p_value=4.17332e-13 frequency=4.119968e-02 genotype_quality=1532.7 ks_quality_p_value=1 log10_base_likelihood=-7.46011 log10_qual_likelihood_position_model=33.252 log10_strand_likelihood_position_model=12.4077 new_cov=0/43 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=225/217 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=225/260 RA 774 . NC_007779 3846240 0 G C bias_e_value=1.73135 bias_p_value=3.72627e-07 fisher_strand_p_value=1.98915e-08 frequency=3.671932e-02 genotype_quality=1151.8 ks_quality_p_value=1 log10_base_likelihood=-8.40092 log10_qual_likelihood_position_model=17.6083 log10_strand_likelihood_position_model=7.71119 new_cov=1/18 polymorphism_quality=2.9 quality=2.9 quality_position_model=Inf ref_cov=226/99 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=227/118 RA 775 . NC_007779 3855276 1 . T bias_e_value=4373920 bias_p_value=0.941372 fisher_strand_p_value=1 frequency=7.712364e-03 genotype_quality=1917.5 ks_quality_p_value=0.677731 log10_base_likelihood=-12.3424 log10_qual_likelihood_position_model=2.47949 log10_strand_likelihood_position_model=0.368584 new_cov=2/1 polymorphism_quality=7.0 quality=7.0 quality_position_model=1.64294e-11 ref_cov=226/160 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=228/161 RA 776 . NC_007779 3859254 1 . T bias_e_value=411719 bias_p_value=0.0886115 fisher_strand_p_value=0.0248273 frequency=1.101875e-02 genotype_quality=1781.9 ks_quality_p_value=0.708 log10_base_likelihood=-17.5408 log10_qual_likelihood_position_model=1.31905 log10_strand_likelihood_position_model=1.60507 new_cov=4/0 polymorphism_quality=12.2 quality=12.2 quality_position_model=1.0064e-16 ref_cov=141/218 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=145/218 RA 777 . NC_007779 3859258 1 . C bias_e_value=620219 bias_p_value=0.133486 fisher_strand_p_value=0.0303982 frequency=1.567745e-02 genotype_quality=1493.0 ks_quality_p_value=0.970884 log10_base_likelihood=-14.5409 log10_qual_likelihood_position_model=4.33606 log10_strand_likelihood_position_model=1.51715 new_cov=3/0 polymorphism_quality=9.2 quality=9.2 quality_position_model=1.09827e-10 ref_cov=96/216 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=101/216 RA 778 . NC_007779 3859258 2 . C bias_e_value=655184 bias_p_value=0.141011 fisher_strand_p_value=0.0316884 frequency=9.462357e-03 genotype_quality=1507.9 ks_quality_p_value=0.999458 log10_base_likelihood=-11.1674 log10_qual_likelihood_position_model=3.69972 log10_strand_likelihood_position_model=1.4991 new_cov=3/0 polymorphism_quality=5.8 quality=5.8 quality_position_model=6.87088e-08 ref_cov=98/216 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=101/216 RA 779 . NC_007779 3859263 0 T C bias_e_value=2.06739e-10 bias_p_value=4.44952e-17 fisher_strand_p_value=1.04946e-18 frequency=7.848310e-02 genotype_quality=927.3 ks_quality_p_value=1 log10_base_likelihood=-24.6178 log10_qual_likelihood_position_model=28.3796 log10_strand_likelihood_position_model=17.979 new_cov=29/0 polymorphism_quality=19.4 quality=19.4 quality_position_model=Inf ref_cov=56/223 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=85/223 RA 780 . NC_007779 3859265 0 A C bias_e_value=7.04953e-09 bias_p_value=1.51722e-15 fisher_strand_p_value=3.91241e-17 frequency=8.127546e-02 genotype_quality=804.8 ks_quality_p_value=1 log10_base_likelihood=-25.9176 log10_qual_likelihood_position_model=14.927 log10_strand_likelihood_position_model=16.4143 new_cov=30/2 polymorphism_quality=20.7 quality=20.7 quality_position_model=Inf ref_cov=53/220 reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=83/224 RA 781 . NC_007779 3859270 0 G C bias_e_value=1.01116e-08 bias_p_value=2.17625e-15 fisher_strand_p_value=5.66591e-17 frequency=6.904078e-02 genotype_quality=1153.9 ks_quality_p_value=1 log10_base_likelihood=-33.8535 log10_qual_likelihood_position_model=21.9775 log10_strand_likelihood_position_model=16.2467 new_cov=23/0 polymorphism_quality=28.7 quality=28.7 quality_position_model=Inf ref_cov=45/231 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=68/231 RA 782 . NC_007779 3859271 0 G C bias_e_value=4445.36 bias_p_value=0.000956747 fisher_strand_p_value=9.30469e-05 frequency=1.760578e-02 genotype_quality=1187.8 ks_quality_p_value=1 log10_base_likelihood=-6.78627 log10_qual_likelihood_position_model=7.60239 log10_strand_likelihood_position_model=4.0313 new_cov=6/0 polymorphism_quality=1.3 quality=1.3 quality_position_model=Inf ref_cov=59/231 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=65/231 RA 783 . NC_007779 3859275 0 T C bias_e_value=1406.6 bias_p_value=0.000302734 fisher_strand_p_value=2.63058e-05 frequency=2.672577e-02 genotype_quality=1036.5 ks_quality_p_value=0.996447 log10_base_likelihood=-7.76136 log10_qual_likelihood_position_model=11.208 log10_strand_likelihood_position_model=4.59154 new_cov=8/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=Inf ref_cov=55/225 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=63/228 RA 784 . NC_007779 3859381 0 T G bias_e_value=0.000596434 bias_p_value=1.28367e-10 fisher_strand_p_value=4.7412e-12 frequency=3.683567e-02 genotype_quality=786.5 ks_quality_p_value=1 log10_base_likelihood=-8.00493 log10_qual_likelihood_position_model=14.3487 log10_strand_likelihood_position_model=11.3241 new_cov=0/11 polymorphism_quality=2.5 quality=2.5 quality_position_model=Inf ref_cov=211/16 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=212/27 RA 785 . NC_007779 3859383 0 A G bias_e_value=5.39313e-08 bias_p_value=1.16073e-14 fisher_strand_p_value=3.16364e-16 frequency=4.835653e-02 genotype_quality=800.2 ks_quality_p_value=1 log10_base_likelihood=-11.2091 log10_qual_likelihood_position_model=17.0065 log10_strand_likelihood_position_model=15.4998 new_cov=0/13 polymorphism_quality=5.8 quality=5.8 quality_position_model=Inf ref_cov=211/8 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=212/21 RA 786 . NC_007779 3866109 0 G T bias_e_value=1.35325 bias_p_value=2.91251e-07 fisher_strand_p_value=1.5376e-08 frequency=3.766441e-02 genotype_quality=1384.2 ks_quality_p_value=0.997302 log10_base_likelihood=-15.5434 log10_qual_likelihood_position_model=17.8372 log10_strand_likelihood_position_model=7.9837 new_cov=0/32 polymorphism_quality=10.2 quality=10.2 quality_position_model=Inf ref_cov=202/244 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=202/276 RA 787 . NC_007779 3873375 0 T . bias_e_value=2582770 bias_p_value=0.555874 fisher_strand_p_value=0.416706 frequency=1.208782e-02 genotype_quality=2005.4 ks_quality_p_value=0.532345 log10_base_likelihood=-16.3187 log10_qual_likelihood_position_model=3.65936 log10_strand_likelihood_position_model=0.72678 new_cov=4/2 polymorphism_quality=11.0 quality=11.0 quality_position_model=5.36536e-14 ref_cov=220/270 reject=INDEL_HOMOPOLYMER tot_cov=224/272 RA 788 . NC_007779 3893880 0 G T bias_e_value=5.07367e-11 bias_p_value=1.09197e-17 fisher_strand_p_value=2.49102e-19 frequency=6.088972e-02 genotype_quality=1438.2 ks_quality_p_value=1 log10_base_likelihood=-21.8069 log10_qual_likelihood_position_model=38.6765 log10_strand_likelihood_position_model=18.6036 new_cov=0/51 polymorphism_quality=16.5 quality=16.5 quality_position_model=Inf ref_cov=249/164 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=249/215 RA 789 . NC_007779 3898657 0 C G frequency=1 genotype_quality=1915.9 new_cov=207/241 quality=1915.9 ref_cov=0/0 tot_cov=207/241 RA 790 . NC_007779 3900676 1 . G bias_e_value=89714.8 bias_p_value=0.0193087 fisher_strand_p_value=0.00312527 frequency=1.639366e-02 genotype_quality=2089.3 ks_quality_p_value=0.898643 log10_base_likelihood=-30.8872 log10_qual_likelihood_position_model=3.53819 log10_strand_likelihood_position_model=2.50511 new_cov=7/0 polymorphism_quality=25.7 quality=25.7 quality_position_model=4.60128e-27 ref_cov=182/238 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/238 RA 791 . NC_007779 3900680 0 T G bias_e_value=2.45494e-26 bias_p_value=5.28361e-33 fisher_strand_p_value=6.62946e-35 frequency=8.786535e-02 genotype_quality=1113.5 ks_quality_p_value=1 log10_base_likelihood=-20.0628 log10_qual_likelihood_position_model=46.3124 log10_strand_likelihood_position_model=34.1785 new_cov=38/0 polymorphism_quality=14.8 quality=14.8 quality_position_model=Inf ref_cov=19/254 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=59/254 RA 792 . NC_007779 3900687 0 G T bias_e_value=0.000316169 bias_p_value=6.80469e-11 fisher_strand_p_value=2.4536e-12 frequency=3.549290e-02 genotype_quality=1296.8 ks_quality_p_value=1 log10_base_likelihood=-9.29756 log10_qual_likelihood_position_model=20.5253 log10_strand_likelihood_position_model=11.6102 new_cov=15/0 polymorphism_quality=3.8 quality=3.8 quality_position_model=Inf ref_cov=44/256 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=59/256 RA 793 . NC_007779 3903804 0 G T bias_e_value=0.631679 bias_p_value=1.35952e-07 fisher_strand_p_value=6.86923e-09 frequency=2.823925e-02 genotype_quality=1622.6 ks_quality_p_value=0.999747 log10_base_likelihood=-6.64842 log10_qual_likelihood_position_model=20.7735 log10_strand_likelihood_position_model=8.41507 new_cov=0/27 polymorphism_quality=1.1 quality=1.1 quality_position_model=Inf ref_cov=237/212 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=237/239 RA 794 . NC_007779 3904581 1 . G bias_e_value=1957290 bias_p_value=0.421255 fisher_strand_p_value=0.189954 frequency=4.618645e-03 genotype_quality=2167.7 ks_quality_p_value=0.753174 log10_base_likelihood=-7.71581 log10_qual_likelihood_position_model=2.05396 log10_strand_likelihood_position_model=0.721352 new_cov=2/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=8.00531e-07 ref_cov=187/244 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=189/244 RA 795 . NC_007779 3910746 0 C A bias_e_value=3.61581e-07 bias_p_value=7.78206e-14 fisher_strand_p_value=2.24175e-15 frequency=8.752108e-02 genotype_quality=1527.9 ks_quality_p_value=0.999489 log10_base_likelihood=-37.8046 log10_qual_likelihood_position_model=45.5218 log10_strand_likelihood_position_model=14.925 new_cov=63/0 polymorphism_quality=32.7 quality=32.7 quality_position_model=Inf ref_cov=257/209 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=322/209 RA 796 . NC_007779 3912296 1 . G bias_e_value=2958360 bias_p_value=0.636709 fisher_strand_p_value=1 frequency=5.797386e-03 genotype_quality=1659.4 ks_quality_p_value=0.280219 log10_base_likelihood=-8.09667 log10_qual_likelihood_position_model=1.7839 log10_strand_likelihood_position_model=0.304793 new_cov=1/1 polymorphism_quality=2.6 quality=2.6 quality_position_model=6.25571e-08 ref_cov=190/153 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=191/154 RA 797 . NC_007779 3914102 0 T . bias_e_value=1177860 bias_p_value=0.253504 fisher_strand_p_value=0.124267 frequency=7.655144e-03 genotype_quality=2104.3 ks_quality_p_value=0.555324 log10_base_likelihood=-10.3441 log10_qual_likelihood_position_model=2.00909 log10_strand_likelihood_position_model=1.1564 new_cov=4/0 polymorphism_quality=4.9 quality=4.9 quality_position_model=3.88329e-09 ref_cov=265/253 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=269/253 RA 798 . NC_007779 3930443 0 T G bias_e_value=3.75511e-24 bias_p_value=8.08188e-31 fisher_strand_p_value=1.08332e-32 frequency=1.029415e-01 genotype_quality=1101.1 ks_quality_p_value=1 log10_base_likelihood=-19.2706 log10_qual_likelihood_position_model=46.0754 log10_strand_likelihood_position_model=31.9652 new_cov=61/0 polymorphism_quality=14.0 quality=14.0 quality_position_model=Inf ref_cov=68/227 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=133/227 RA 799 . NC_007779 3933153 0 G T bias_e_value=0.027428 bias_p_value=5.90315e-09 fisher_strand_p_value=2.56001e-10 frequency=3.147030e-02 genotype_quality=1544.4 ks_quality_p_value=0.998787 log10_base_likelihood=-7.4795 log10_qual_likelihood_position_model=26.1927 log10_strand_likelihood_position_model=9.59176 new_cov=0/30 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=232/198 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/228 RA 800 . NC_007779 3952095 1 . G bias_e_value=9.72793 bias_p_value=2.09368e-06 fisher_strand_p_value=3.39042e-07 frequency=4.010677e-02 genotype_quality=1717.6 ks_quality_p_value=0.365311 log10_base_likelihood=-71.4775 log10_qual_likelihood_position_model=5.70817 log10_strand_likelihood_position_model=6.46975 new_cov=15/0 polymorphism_quality=66.5 quality=66.5 quality_position_model=1.04813e-61 ref_cov=128/231 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER tot_cov=143/231 RA 801 . NC_007779 3952099 0 T G bias_e_value=0.0228099 bias_p_value=4.90923e-09 fisher_strand_p_value=2.1088e-10 frequency=2.940464e-02 genotype_quality=1069.3 ks_quality_p_value=1 log10_base_likelihood=-7.50474 log10_qual_likelihood_position_model=17.0155 log10_strand_likelihood_position_model=9.67596 new_cov=10/0 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=24/243 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=34/243 RA 802 . NC_007779 3968984 1 . G bias_e_value=2168020 bias_p_value=0.46661 fisher_strand_p_value=0.174965 frequency=5.988121e-03 genotype_quality=1675.7 ks_quality_p_value=0.956773 log10_base_likelihood=-7.71391 log10_qual_likelihood_position_model=1.15143 log10_strand_likelihood_position_model=0.757048 new_cov=2/0 polymorphism_quality=2.2 quality=2.2 quality_position_model=1.01346e-07 ref_cov=138/194 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=140/194 RA 803 . NC_007779 3973343 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 804 . NC_007779 3973344 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 805 . NC_007779 3973345 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 806 . NC_007779 3973346 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 807 . NC_007779 3973347 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 808 . NC_007779 3973348 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 809 . NC_007779 3973350 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 810 . NC_007779 3973351 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 811 . NC_007779 3973352 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 812 . NC_007779 3973353 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 813 . NC_007779 3973354 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 814 . NC_007779 3973356 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 815 . NC_007779 3973357 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 816 . NC_007779 3973358 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 817 . NC_007779 3973359 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 818 . NC_007779 3973360 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 819 . NC_007779 3976303 1 . A bias_e_value=4576740 bias_p_value=0.985021 fisher_strand_p_value=1 frequency=4.301071e-03 genotype_quality=2335.5 ks_quality_p_value=0.831987 log10_base_likelihood=-7.62764 log10_qual_likelihood_position_model=2.05981 log10_strand_likelihood_position_model=0.300676 new_cov=1/1 polymorphism_quality=2.1 quality=2.1 quality_position_model=3.66277e-07 ref_cov=223/240 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=224/241 RA 820 . NC_007779 3986830 0 T . bias_e_value=1454750 bias_p_value=0.313096 fisher_strand_p_value=0.384978 frequency=1.195431e-02 genotype_quality=1722.8 ks_quality_p_value=0.240705 log10_base_likelihood=-14.0416 log10_qual_likelihood_position_model=2.56929 log10_strand_likelihood_position_model=0.650953 new_cov=2/3 polymorphism_quality=8.7 quality=8.7 quality_position_model=7.26597e-13 ref_cov=252/161 reject=INDEL_HOMOPOLYMER tot_cov=254/164 RA 821 . NC_007779 3989287 0 A . bias_e_value=3660070 bias_p_value=0.787733 fisher_strand_p_value=0.648892 frequency=9.041786e-03 genotype_quality=1829.8 ks_quality_p_value=0.653298 log10_base_likelihood=-10.4319 log10_qual_likelihood_position_model=2.35652 log10_strand_likelihood_position_model=0.46853 new_cov=1/3 polymorphism_quality=5.0 quality=5.0 quality_position_model=1.4094e-09 ref_cov=179/259 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=180/262 RA 822 . NC_007779 3989387 1 . T bias_e_value=3485420 bias_p_value=0.750144 fisher_strand_p_value=0.502241 frequency=4.566193e-03 genotype_quality=2204.5 ks_quality_p_value=0.761692 log10_base_likelihood=-7.93854 log10_qual_likelihood_position_model=1.32627 log10_strand_likelihood_position_model=0.534295 new_cov=2/0 polymorphism_quality=2.5 quality=2.5 quality_position_model=5.29564e-08 ref_cov=235/201 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=237/201 RA 823 . NC_007779 3989388 0 T . bias_e_value=1750550 bias_p_value=0.37676 fisher_strand_p_value=1 frequency=9.062767e-03 genotype_quality=1822.7 ks_quality_p_value=0.121101 log10_base_likelihood=-10.6593 log10_qual_likelihood_position_model=1.67238 log10_strand_likelihood_position_model=0.429849 new_cov=2/2 polymorphism_quality=5.2 quality=5.2 quality_position_model=1.4944e-10 ref_cov=236/200 reject=INDEL_HOMOPOLYMER tot_cov=239/202 RA 824 . NC_007779 4000222 0 C G bias_e_value=61.4735 bias_p_value=1.32305e-05 fisher_strand_p_value=9.94023e-07 frequency=3.325844e-02 genotype_quality=1689.1 ks_quality_p_value=0.891093 log10_base_likelihood=-12.6564 log10_qual_likelihood_position_model=27.8368 log10_strand_likelihood_position_model=6.09328 new_cov=1/22 polymorphism_quality=7.3 quality=7.3 quality_position_model=Inf ref_cov=253/215 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=255/238 RA 825 . NC_007779 4000535 1 . A bias_e_value=3817660 bias_p_value=0.82165 fisher_strand_p_value=0.579049 frequency=5.659103e-03 genotype_quality=2639.1 ks_quality_p_value=0.804376 log10_base_likelihood=-10.1569 log10_qual_likelihood_position_model=5.03428 log10_strand_likelihood_position_model=0.501667 new_cov=1/2 polymorphism_quality=4.7 quality=4.7 quality_position_model=1.72325e-06 ref_cov=302/225 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=303/227 RA 826 . NC_007779 4023064 1 . G bias_e_value=1879980 bias_p_value=0.404617 fisher_strand_p_value=0.257776 frequency=8.620262e-03 genotype_quality=1726.7 ks_quality_p_value=0.52232 log10_base_likelihood=-12.3675 log10_qual_likelihood_position_model=1.38347 log10_strand_likelihood_position_model=0.764325 new_cov=3/0 polymorphism_quality=7.0 quality=7.0 quality_position_model=2.98467e-12 ref_cov=191/154 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=194/154 RA 827 . NC_007779 4023068 0 T G bias_e_value=3.48473e-05 bias_p_value=7.49995e-12 fisher_strand_p_value=2.49849e-13 frequency=5.243301e-02 genotype_quality=813.6 ks_quality_p_value=1 log10_base_likelihood=-6.90243 log10_qual_likelihood_position_model=23.5564 log10_strand_likelihood_position_model=12.6023 new_cov=25/0 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=60/159 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=85/159 RA 828 . NC_007779 4029622 1 . G bias_e_value=839469 bias_p_value=0.180673 fisher_strand_p_value=0.0860069 frequency=8.152008e-03 genotype_quality=1787.4 ks_quality_p_value=0.508747 log10_base_likelihood=-12.0955 log10_qual_likelihood_position_model=2.30348 log10_strand_likelihood_position_model=1.06547 new_cov=3/0 polymorphism_quality=6.7 quality=6.7 quality_position_model=1.00213e-10 ref_cov=160/205 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=163/205 RA 829 . NC_007779 4029633 0 T G bias_e_value=4.40093e-21 bias_p_value=9.47183e-28 fisher_strand_p_value=1.40458e-29 frequency=1.075096e-01 genotype_quality=1016.8 ks_quality_p_value=1 log10_base_likelihood=-30.5037 log10_qual_likelihood_position_model=42.9385 log10_strand_likelihood_position_model=28.8525 new_cov=42/0 polymorphism_quality=25.3 quality=25.3 quality_position_model=Inf ref_cov=37/220 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=79/220 RA 830 . NC_007779 4031691 1 . T bias_e_value=5138.24 bias_p_value=0.00110587 fisher_strand_p_value=0.000131954 frequency=1.960754e-02 genotype_quality=1479.7 ks_quality_p_value=0.827987 log10_base_likelihood=-27.2558 log10_qual_likelihood_position_model=3.45725 log10_strand_likelihood_position_model=3.87958 new_cov=6/0 polymorphism_quality=22.0 quality=22.0 quality_position_model=4.31402e-22 ref_cov=65/235 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER tot_cov=71/235 RA 831 . NC_007779 4035478 0 A C bias_e_value=0.874337 bias_p_value=1.88178e-07 fisher_strand_p_value=9.67301e-09 frequency=2.057362e-02 genotype_quality=1244.7 ks_quality_p_value=1 log10_base_likelihood=-5.63431 log10_qual_likelihood_position_model=14.3387 log10_strand_likelihood_position_model=8.01444 new_cov=0/9 polymorphism_quality=0.1 quality=0.1 quality_position_model=Inf ref_cov=277/36 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=277/45 RA 832 . NC_007779 4036507 0 G T bias_e_value=0.00608491 bias_p_value=1.30962e-09 fisher_strand_p_value=5.99849e-11 frequency=3.164864e-02 genotype_quality=1553.5 ks_quality_p_value=0.885385 log10_base_likelihood=-8.42039 log10_qual_likelihood_position_model=38.3258 log10_strand_likelihood_position_model=10.2602 new_cov=0/34 polymorphism_quality=2.9 quality=2.9 quality_position_model=Inf ref_cov=237/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=237/254 RA 833 . NC_007779 4037805 0 G T bias_e_value=0.000246381 bias_p_value=5.3027e-11 fisher_strand_p_value=1.89435e-12 frequency=3.974438e-02 genotype_quality=1476.9 ks_quality_p_value=1 log10_base_likelihood=-8.93402 log10_qual_likelihood_position_model=26.0618 log10_strand_likelihood_position_model=11.7225 new_cov=0/33 polymorphism_quality=3.5 quality=3.5 quality_position_model=Inf ref_cov=235/169 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=235/202 RA 834 . NC_007779 4043703 0 C A bias_e_value=5.30633e-05 bias_p_value=1.14205e-11 fisher_strand_p_value=3.86051e-13 frequency=5.387163e-02 genotype_quality=1324.2 ks_quality_p_value=1 log10_base_likelihood=-11.7918 log10_qual_likelihood_position_model=27.1488 log10_strand_likelihood_position_model=12.4318 new_cov=43/0 polymorphism_quality=6.4 quality=6.4 quality_position_model=Inf ref_cov=190/200 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=233/200 RA 835 . NC_007779 4047202 1 . A bias_e_value=2370050 bias_p_value=0.510091 fisher_strand_p_value=0.2131 frequency=4.713058e-03 genotype_quality=2111.6 ks_quality_p_value=0.904518 log10_base_likelihood=-6.28776 log10_qual_likelihood_position_model=3.59095 log10_strand_likelihood_position_model=0.671416 new_cov=2/0 polymorphism_quality=0.8 quality=0.8 quality_position_model=0.000981596 ref_cov=194/228 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=196/228 RA 836 . NC_007779 4052978 0 G T bias_e_value=5.0362e-09 bias_p_value=1.08391e-15 fisher_strand_p_value=2.77037e-17 frequency=4.883862e-02 genotype_quality=1443.5 ks_quality_p_value=1 log10_base_likelihood=-12.4249 log10_qual_likelihood_position_model=28.3682 log10_strand_likelihood_position_model=16.5575 new_cov=0/47 polymorphism_quality=7.0 quality=7.0 quality_position_model=Inf ref_cov=243/171 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=243/219 RA 837 . NC_007779 4055100 0 G T bias_e_value=0.0632025 bias_p_value=1.36027e-08 fisher_strand_p_value=6.22605e-10 frequency=3.394413e-02 genotype_quality=1495.2 ks_quality_p_value=0.983536 log10_base_likelihood=-9.12971 log10_qual_likelihood_position_model=32.454 log10_strand_likelihood_position_model=9.20579 new_cov=22/0 polymorphism_quality=3.7 quality=3.7 quality_position_model=Inf ref_cov=146/255 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=168/255 RA 838 . NC_007779 4055329 0 T G bias_e_value=1.12078e-31 bias_p_value=2.41218e-38 fisher_strand_p_value=2.61792e-40 frequency=1.024709e-01 genotype_quality=1199.3 ks_quality_p_value=1 log10_base_likelihood=-26.5337 log10_qual_likelihood_position_model=55.2176 log10_strand_likelihood_position_model=39.582 new_cov=57/0 polymorphism_quality=21.3 quality=21.3 quality_position_model=Inf ref_cov=43/275 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=100/275 RA 839 . NC_007779 4059484 1 . T bias_e_value=1440990 bias_p_value=0.310134 fisher_strand_p_value=0.622414 frequency=6.880760e-03 genotype_quality=2120.3 ks_quality_p_value=0.146887 log10_base_likelihood=-12.5136 log10_qual_likelihood_position_model=2.28435 log10_strand_likelihood_position_model=0.426987 new_cov=2/1 polymorphism_quality=7.1 quality=7.1 quality_position_model=7.9622e-12 ref_cov=215/218 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=217/219 RA 840 . NC_007779 4059485 0 T . bias_e_value=4218540 bias_p_value=0.907928 fisher_strand_p_value=1 frequency=1.117897e-02 genotype_quality=1823.5 ks_quality_p_value=0.602818 log10_base_likelihood=-13.9315 log10_qual_likelihood_position_model=2.08928 log10_strand_likelihood_position_model=0.498435 new_cov=2/3 polymorphism_quality=8.6 quality=8.6 quality_position_model=2.13301e-13 ref_cov=219/223 reject=INDEL_HOMOPOLYMER tot_cov=221/226 RA 841 . NC_007779 4062114 0 T G bias_e_value=7.30064e-25 bias_p_value=1.57127e-31 fisher_strand_p_value=2.06034e-33 frequency=1.144581e-01 genotype_quality=1043.4 ks_quality_p_value=1 log10_base_likelihood=-28.4269 log10_qual_likelihood_position_model=50.9836 log10_strand_likelihood_position_model=32.6861 new_cov=57/0 polymorphism_quality=23.2 quality=23.2 quality_position_model=Inf ref_cov=54/222 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=111/222 RA 842 . NC_007779 4064463 0 G T bias_e_value=2.47026e-05 bias_p_value=5.31659e-12 fisher_strand_p_value=1.75039e-13 frequency=6.610394e-02 genotype_quality=1227.6 ks_quality_p_value=1 log10_base_likelihood=-15.3921 log10_qual_likelihood_position_model=26.379 log10_strand_likelihood_position_model=12.7712 new_cov=0/44 polymorphism_quality=10.0 quality=10.0 quality_position_model=Inf ref_cov=192/180 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=192/224 RA 843 . NC_007779 4074542 0 C A bias_e_value=1234.57 bias_p_value=0.000265708 fisher_strand_p_value=2.27255e-05 frequency=2.604008e-02 genotype_quality=1319.3 ks_quality_p_value=1 log10_base_likelihood=-7.87808 log10_qual_likelihood_position_model=18.7632 log10_strand_likelihood_position_model=4.6604 new_cov=1/13 polymorphism_quality=2.4 quality=2.4 quality_position_model=Inf ref_cov=222/124 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=223/137 RA 844 . NC_007779 4076934 0 A C bias_e_value=0.000210225 bias_p_value=4.52453e-11 fisher_strand_p_value=1.60691e-12 frequency=5.494785e-02 genotype_quality=1328.2 ks_quality_p_value=1 log10_base_likelihood=-13.2596 log10_qual_likelihood_position_model=30.5416 log10_strand_likelihood_position_model=11.794 new_cov=0/34 polymorphism_quality=7.9 quality=7.9 quality_position_model=Inf ref_cov=219/162 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=219/197 RA 845 . NC_007779 4084209 0 A G bias_e_value=0.000781932 bias_p_value=1.6829e-10 fisher_strand_p_value=6.28101e-12 frequency=4.249477e-02 genotype_quality=1350.7 ks_quality_p_value=1 log10_base_likelihood=-6.9477 log10_qual_likelihood_position_model=22.6372 log10_strand_likelihood_position_model=11.202 new_cov=30/0 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=158/236 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=188/236 RA 846 . NC_007779 4087369 0 T . bias_e_value=3948810 bias_p_value=0.849877 fisher_strand_p_value=1 frequency=1.110363e-02 genotype_quality=1848.0 ks_quality_p_value=0.504799 log10_base_likelihood=-13.6094 log10_qual_likelihood_position_model=2.36055 log10_strand_likelihood_position_model=0.485887 new_cov=3/2 polymorphism_quality=8.2 quality=8.2 quality_position_model=8.33326e-13 ref_cov=232/213 reject=INDEL_HOMOPOLYMER tot_cov=235/215 RA 847 . NC_007779 4090749 0 A T frequency=1 genotype_quality=1989.4 new_cov=216/275 quality=1989.4 ref_cov=0/0 tot_cov=216/275 RA 848 . NC_007779 4098730 0 G T bias_e_value=4.61851e-15 bias_p_value=9.94013e-22 fisher_strand_p_value=1.86365e-23 frequency=9.211063e-02 genotype_quality=1406.4 ks_quality_p_value=1 log10_base_likelihood=-33.1824 log10_qual_likelihood_position_model=33.7318 log10_strand_likelihood_position_model=22.7296 new_cov=0/62 polymorphism_quality=28.0 quality=28.0 quality_position_model=Inf ref_cov=255/162 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=255/224 RA 849 . NC_007779 4115400 0 T C bias_e_value=3.72276e-07 bias_p_value=8.01225e-14 fisher_strand_p_value=2.30887e-15 frequency=5.782700e-02 genotype_quality=1060.0 ks_quality_p_value=1 log10_base_likelihood=-7.5074 log10_qual_likelihood_position_model=27.0525 log10_strand_likelihood_position_model=14.6366 new_cov=0/27 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=215/73 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=215/101 RA 850 . NC_007779 4115400 1 . C bias_e_value=246868 bias_p_value=0.0531319 fisher_strand_p_value=0.00937036 frequency=1.323223e-02 genotype_quality=1434.2 ks_quality_p_value=1 log10_base_likelihood=-11.6264 log10_qual_likelihood_position_model=5.33803 log10_strand_likelihood_position_model=2.02824 new_cov=0/4 polymorphism_quality=6.2 quality=6.2 quality_position_model=4.10601e-06 ref_cov=207/91 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=207/95 RA 851 . NC_007779 4124974 0 G T bias_e_value=1.26548e-16 bias_p_value=2.72361e-23 fisher_strand_p_value=4.77821e-25 frequency=1.072030e-01 genotype_quality=1502.5 ks_quality_p_value=1 log10_base_likelihood=-47.821 log10_qual_likelihood_position_model=32.0997 log10_strand_likelihood_position_model=24.3207 new_cov=0/71 polymorphism_quality=42.7 quality=42.7 quality_position_model=Inf ref_cov=254/177 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=254/248 RA 852 . NC_007779 4128669 1 . T bias_e_value=3765420 bias_p_value=0.810408 fisher_strand_p_value=0.501929 frequency=4.453659e-03 genotype_quality=2221.4 ks_quality_p_value=0.899239 log10_base_likelihood=-7.47691 log10_qual_likelihood_position_model=2.18295 log10_strand_likelihood_position_model=0.537692 new_cov=0/2 polymorphism_quality=2.0 quality=2.0 quality_position_model=1.24522e-06 ref_cov=207/240 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=207/242 RA 853 . NC_007779 4128670 0 T . bias_e_value=2411000 bias_p_value=0.518904 fisher_strand_p_value=0.252302 frequency=6.585121e-03 genotype_quality=1801.1 ks_quality_p_value=0.785376 log10_base_likelihood=-7.46232 log10_qual_likelihood_position_model=1.65402 log10_strand_likelihood_position_model=0.814354 new_cov=0/3 polymorphism_quality=2.0 quality=2.0 quality_position_model=7.04315e-07 ref_cov=211/241 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=211/244 RA 854 . NC_007779 4148399 0 A C bias_e_value=1.14609e-21 bias_p_value=2.46665e-28 fisher_strand_p_value=3.58521e-30 frequency=8.459949e-02 genotype_quality=1324.6 ks_quality_p_value=1 log10_base_likelihood=-18.3638 log10_qual_likelihood_position_model=50.7036 log10_strand_likelihood_position_model=29.4455 new_cov=0/67 polymorphism_quality=13.1 quality=13.1 quality_position_model=Inf ref_cov=249/110 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=249/178 RA 855 . NC_007779 4148399 1 . C bias_e_value=624410 bias_p_value=0.134388 fisher_strand_p_value=0.0297696 frequency=9.415627e-03 genotype_quality=1980.5 ks_quality_p_value=1 log10_base_likelihood=-9.12348 log10_qual_likelihood_position_model=3.71158 log10_strand_likelihood_position_model=1.52623 new_cov=0/4 polymorphism_quality=3.7 quality=3.7 quality_position_model=1.01423e-05 ref_cov=247/173 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=247/177 RA 856 . NC_007779 4157323 0 C A bias_e_value=3.67751e-06 bias_p_value=7.91486e-13 fisher_strand_p_value=2.7674e-14 frequency=5.932665e-02 genotype_quality=1257.1 ks_quality_p_value=0.884331 log10_base_likelihood=-15.8172 log10_qual_likelihood_position_model=35.7254 log10_strand_likelihood_position_model=13.5579 new_cov=37/0 polymorphism_quality=10.5 quality=10.5 quality_position_model=Inf ref_cov=140/210 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=180/210 RA 857 . NC_007779 4158580 1 . A bias_e_value=1807090 bias_p_value=0.388928 fisher_strand_p_value=0.127208 frequency=1.315498e-02 genotype_quality=1504.3 ks_quality_p_value=0.997809 log10_base_likelihood=-13.3046 log10_qual_likelihood_position_model=8.06556 log10_strand_likelihood_position_model=1.07952 new_cov=0/4 polymorphism_quality=7.9 quality=7.9 quality_position_model=5.23332e-06 ref_cov=140/160 reject=POLYMORPHISM_STRAND tot_cov=140/164 RA 858 . NC_007779 4163966 1 . T bias_e_value=597922 bias_p_value=0.128687 fisher_strand_p_value=0.500108 frequency=4.525185e-03 genotype_quality=2181.2 ks_quality_p_value=0.0563078 log10_base_likelihood=-7.80934 log10_qual_likelihood_position_model=2.51171 log10_strand_likelihood_position_model=0.560761 new_cov=2/0 polymorphism_quality=2.3 quality=2.3 quality_position_model=1.30456e-06 ref_cov=230/210 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=232/210 RA 859 . NC_007779 4165991 0 A C frequency=1 genotype_quality=2009.3 new_cov=235/234 quality=2009.3 ref_cov=0/0 tot_cov=235/234 RA 860 . NC_007779 4169961 0 T G frequency=1 genotype_quality=-0.2 new_cov=1/0 quality=-0.2 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 861 . NC_007779 4169964 0 T G frequency=1 genotype_quality=-0.2 new_cov=1/0 quality=-0.2 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 862 . NC_007779 4174730 0 T . bias_e_value=919183 bias_p_value=0.19783 fisher_strand_p_value=0.12331 frequency=9.188652e-03 genotype_quality=1766.1 ks_quality_p_value=0.400198 log10_base_likelihood=-10.7793 log10_qual_likelihood_position_model=2.30629 log10_strand_likelihood_position_model=1.19814 new_cov=4/0 polymorphism_quality=5.4 quality=5.4 quality_position_model=3.09171e-09 ref_cov=215/216 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=219/216 RA 863 . NC_007779 4197139 0 T G bias_e_value=7.89231e-26 bias_p_value=1.69861e-32 fisher_strand_p_value=2.16339e-34 frequency=1.172090e-01 genotype_quality=996.0 ks_quality_p_value=1 log10_base_likelihood=-31.9897 log10_qual_likelihood_position_model=48.9694 log10_strand_likelihood_position_model=33.6649 new_cov=48/0 polymorphism_quality=26.8 quality=26.8 quality_position_model=Inf ref_cov=32/219 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=80/219 RA 864 . NC_007779 4200820 0 A C bias_e_value=8.66358e-05 bias_p_value=1.86461e-11 fisher_strand_p_value=6.41303e-13 frequency=3.272533e-02 genotype_quality=1464.8 ks_quality_p_value=1 log10_base_likelihood=-7.51608 log10_qual_likelihood_position_model=29.0363 log10_strand_likelihood_position_model=12.456 new_cov=0/39 polymorphism_quality=2.0 quality=2.0 quality_position_model=Inf ref_cov=232/194 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=232/234 RA 865 . NC_007779 4200831 1 . G bias_e_value=920234 bias_p_value=0.198056 fisher_strand_p_value=0.096955 frequency=6.396294e-03 genotype_quality=2345.4 ks_quality_p_value=0.509756 log10_base_likelihood=-11.7813 log10_qual_likelihood_position_model=3.75983 log10_strand_likelihood_position_model=1.01343 new_cov=3/0 polymorphism_quality=6.4 quality=6.4 quality_position_model=5.81721e-09 ref_cov=213/253 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=216/253 RA 866 . NC_007779 4207565 0 C A bias_e_value=4.3783e-11 bias_p_value=9.42312e-18 fisher_strand_p_value=2.14224e-19 frequency=9.366798e-02 genotype_quality=1355.6 ks_quality_p_value=1 log10_base_likelihood=-28.2715 log10_qual_likelihood_position_model=42.7465 log10_strand_likelihood_position_model=18.6969 new_cov=65/0 polymorphism_quality=23.1 quality=23.1 quality_position_model=Inf ref_cov=196/214 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=261/214 RA 867 . NC_007779 4211591 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 868 . NC_007779 4211592 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 869 . NC_007779 4211595 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 870 . NC_007779 4211596 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 871 . NC_007779 4211597 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 872 . NC_007779 4211598 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 873 . NC_007779 4211599 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 874 . NC_007779 4211602 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 875 . NC_007779 4211604 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 876 . NC_007779 4211605 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 877 . NC_007779 4211606 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 878 . NC_007779 4211609 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 879 . NC_007779 4211611 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 880 . NC_007779 4211612 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 881 . NC_007779 4211613 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 882 . NC_007779 4211616 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 883 . NC_007779 4211617 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 884 . NC_007779 4211618 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 885 . NC_007779 4211620 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 886 . NC_007779 4211621 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 887 . NC_007779 4211623 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 888 . NC_007779 4211624 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 889 . NC_007779 4211627 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 890 . NC_007779 4211628 0 T A frequency=1 genotype_quality=-0.5 new_cov=1/0 quality=-0.5 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 891 . NC_007779 4211629 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 892 . NC_007779 4211630 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 893 . NC_007779 4211633 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 894 . NC_007779 4211634 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 895 . NC_007779 4211635 0 C A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 896 . NC_007779 4211636 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 897 . NC_007779 4211637 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 898 . NC_007779 4211638 0 T A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=1/0 reject=EVALUE tot_cov=1/0 RA 899 . NC_007779 4211639 0 G A frequency=1 genotype_quality=-0.5 new_cov=0/0 quality=-0.5 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 900 . NC_007779 4224248 1 . T bias_e_value=4646330 bias_p_value=1 fisher_strand_p_value=1 frequency=3.958702e-03 genotype_quality=2541.1 ks_quality_p_value=0.999858 log10_base_likelihood=-6.46169 log10_qual_likelihood_position_model=3.32654 log10_strand_likelihood_position_model=0.306553 new_cov=1/1 polymorphism_quality=0.9 quality=0.9 quality_position_model=0.000133422 ref_cov=221/282 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=222/283 RA 901 . NC_007779 4226513 0 C A bias_e_value=2.92556e-05 bias_p_value=6.29648e-12 fisher_strand_p_value=2.08501e-13 frequency=3.249741e-02 genotype_quality=1630.5 ks_quality_p_value=1 log10_base_likelihood=-6.05908 log10_qual_likelihood_position_model=25.7881 log10_strand_likelihood_position_model=12.6809 new_cov=34/0 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=185/275 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=220/275 RA 902 . NC_007779 4227183 0 T G bias_e_value=5.76627e-19 bias_p_value=1.24104e-25 fisher_strand_p_value=1.98618e-27 frequency=6.557322e-02 genotype_quality=1403.0 ks_quality_p_value=1 log10_base_likelihood=-13.6042 log10_qual_likelihood_position_model=46.5041 log10_strand_likelihood_position_model=26.702 new_cov=59/0 polymorphism_quality=8.2 quality=8.2 quality_position_model=Inf ref_cov=119/271 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=178/271 RA 903 . NC_007779 4241272 0 G T bias_e_value=8.24367e-05 bias_p_value=1.77423e-11 fisher_strand_p_value=6.09142e-13 frequency=2.849674e-02 genotype_quality=1640.6 ks_quality_p_value=1 log10_base_likelihood=-6.19631 log10_qual_likelihood_position_model=25.2897 log10_strand_likelihood_position_model=12.2153 new_cov=0/30 polymorphism_quality=0.7 quality=0.7 quality_position_model=Inf ref_cov=280/165 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=282/196 RA 904 . NC_007779 4244592 0 G C bias_e_value=6898.15 bias_p_value=0.00148464 fisher_strand_p_value=0.000151581 frequency=2.183342e-02 genotype_quality=933.9 ks_quality_p_value=1 log10_base_likelihood=-6.8911 log10_qual_likelihood_position_model=7.91035 log10_strand_likelihood_position_model=3.82835 new_cov=1/5 polymorphism_quality=1.4 quality=1.4 quality_position_model=Inf ref_cov=206/26 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=207/31 RA 905 . NC_007779 4254117 0 T . bias_e_value=4615310 bias_p_value=0.993324 fisher_strand_p_value=1 frequency=6.456375e-03 genotype_quality=1893.6 ks_quality_p_value=0.886699 log10_base_likelihood=-6.56676 log10_qual_likelihood_position_model=3.96535 log10_strand_likelihood_position_model=0.416797 new_cov=1/2 polymorphism_quality=1.0 quality=1.0 quality_position_model=0.000658376 ref_cov=226/234 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=227/236 RA 906 . NC_007779 4289840 0 G T bias_e_value=0.00284618 bias_p_value=6.12564e-10 fisher_strand_p_value=2.40692e-11 frequency=4.116631e-02 genotype_quality=1282.4 ks_quality_p_value=1 log10_base_likelihood=-8.61978 log10_qual_likelihood_position_model=22.113 log10_strand_likelihood_position_model=10.7134 new_cov=0/37 polymorphism_quality=3.2 quality=3.2 quality_position_model=Inf ref_cov=211/204 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=211/241 RA 907 . NC_007779 4296690 0 G . bias_e_value=4646130 bias_p_value=0.999956 fisher_strand_p_value=1 frequency=7.376671e-03 genotype_quality=1737.0 ks_quality_p_value=0.990656 log10_base_likelihood=-7.24546 log10_qual_likelihood_position_model=3.61478 log10_strand_likelihood_position_model=0.422764 new_cov=1/2 polymorphism_quality=1.7 quality=1.7 quality_position_model=5.26657e-05 ref_cov=201/202 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=202/204 RA 908 . NC_007779 4304641 0 T G bias_e_value=1.17083e-11 bias_p_value=2.5199e-18 fisher_strand_p_value=5.55823e-20 frequency=5.425358e-02 genotype_quality=1058.0 ks_quality_p_value=1 log10_base_likelihood=-7.43227 log10_qual_likelihood_position_model=33.5632 log10_strand_likelihood_position_model=19.2551 new_cov=43/0 polymorphism_quality=1.9 quality=1.9 quality_position_model=Inf ref_cov=92/204 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=135/204 RA 909 . NC_007779 4310408 0 G T deleted=1 frequency=1 genotype_quality=0.6 new_cov=0/1 quality=0.6 ref_cov=0/0 reject=EVALUE tot_cov=0/1 RA 910 . NC_007779 4311992 0 G C bias_e_value=6.35657 bias_p_value=1.36808e-06 fisher_strand_p_value=7.88474e-08 frequency=2.724552e-02 genotype_quality=815.6 ks_quality_p_value=0.999712 log10_base_likelihood=-6.02777 log10_qual_likelihood_position_model=8.83065 log10_strand_likelihood_position_model=7.10321 new_cov=0/6 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=191/10 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=192/16 RA 911 . NC_007779 4318994 0 A G bias_e_value=0.00841639 bias_p_value=1.8114e-09 fisher_strand_p_value=7.46062e-11 frequency=2.281761e-02 genotype_quality=1020.5 ks_quality_p_value=0.998317 log10_base_likelihood=-5.9307 log10_qual_likelihood_position_model=12.2156 log10_strand_likelihood_position_model=10.1272 new_cov=0/7 polymorphism_quality=0.4 quality=0.4 quality_position_model=Inf ref_cov=264/6 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=264/13 RA 912 . NC_007779 4321435 0 G C bias_e_value=1.12968 bias_p_value=2.43134e-07 fisher_strand_p_value=1.26873e-08 frequency=2.368450e-02 genotype_quality=874.3 ks_quality_p_value=0.998952 log10_base_likelihood=-5.8099 log10_qual_likelihood_position_model=10.052 log10_strand_likelihood_position_model=7.89663 new_cov=6/0 polymorphism_quality=0.3 quality=0.3 quality_position_model=Inf ref_cov=7/204 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=13/204 RA 913 . NC_007779 4337469 0 A C bias_e_value=1.227e-23 bias_p_value=2.6408e-30 fisher_strand_p_value=3.5977e-32 frequency=1.207681e-01 genotype_quality=1107.1 ks_quality_p_value=1 log10_base_likelihood=-35.6076 log10_qual_likelihood_position_model=48.5778 log10_strand_likelihood_position_model=31.444 new_cov=0/60 polymorphism_quality=30.4 quality=30.4 quality_position_model=Inf ref_cov=226/68 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=226/129 RA 914 . NC_007779 4345371 0 T . bias_e_value=2851230 bias_p_value=0.613651 fisher_strand_p_value=0.263332 frequency=6.069183e-03 genotype_quality=2022.1 ks_quality_p_value=0.996999 log10_base_likelihood=-6.63115 log10_qual_likelihood_position_model=3.74144 log10_strand_likelihood_position_model=0.646632 new_cov=1/2 polymorphism_quality=1.1 quality=1.1 quality_position_model=0.000568875 ref_cov=326/164 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=327/166 RA 915 . NC_007779 4351353 0 T G bias_e_value=1.25053e-17 bias_p_value=2.69143e-24 fisher_strand_p_value=4.53442e-26 frequency=6.669426e-02 genotype_quality=1157.1 ks_quality_p_value=1 log10_base_likelihood=-11.2409 log10_qual_likelihood_position_model=61.3823 log10_strand_likelihood_position_model=25.3435 new_cov=54/0 polymorphism_quality=5.8 quality=5.8 quality_position_model=Inf ref_cov=90/226 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=147/226 RA 916 . NC_007779 4361112 1 . G bias_e_value=2114380 bias_p_value=0.455064 fisher_strand_p_value=0.172051 frequency=4.281998e-03 genotype_quality=2314.4 ks_quality_p_value=0.935839 log10_base_likelihood=-7.12326 log10_qual_likelihood_position_model=2.95749 log10_strand_likelihood_position_model=0.764344 new_cov=2/0 polymorphism_quality=1.6 quality=1.6 quality_position_model=3.28534e-05 ref_cov=192/273 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=194/273 RA 917 . NC_007779 4371271 0 A . frequency=1 genotype_quality=1853.3 new_cov=177/187 quality=1853.3 ref_cov=0/0 tot_cov=177/187 RA 918 . NC_007779 4371272 0 A . frequency=1 genotype_quality=1853.3 new_cov=177/187 quality=1853.3 ref_cov=0/0 tot_cov=177/187 RA 919 . NC_007779 4396934 0 A . bias_e_value=3759060 bias_p_value=0.809038 fisher_strand_p_value=0.59324 frequency=5.944252e-03 genotype_quality=2060.5 ks_quality_p_value=0.757933 log10_base_likelihood=-7.27913 log10_qual_likelihood_position_model=1.89422 log10_strand_likelihood_position_model=0.470478 new_cov=2/1 polymorphism_quality=1.8 quality=1.8 quality_position_model=8.52139e-07 ref_cov=227/274 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=229/275 RA 920 . NC_007779 4403831 0 G T bias_e_value=458.669 bias_p_value=9.87164e-05 fisher_strand_p_value=7.7301e-06 frequency=1.671028e-02 genotype_quality=1467.3 ks_quality_p_value=1 log10_base_likelihood=-6.09775 log10_qual_likelihood_position_model=12.3734 log10_strand_likelihood_position_model=5.11181 new_cov=0/16 polymorphism_quality=0.6 quality=0.6 quality_position_model=Inf ref_cov=220/194 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=220/210 RA 921 . NC_007779 4413560 0 A . bias_e_value=3208300 bias_p_value=0.690502 fisher_strand_p_value=1 frequency=9.062767e-03 genotype_quality=1775.6 ks_quality_p_value=0.3252 log10_base_likelihood=-10.58 log10_qual_likelihood_position_model=3.32649 log10_strand_likelihood_position_model=0.428892 new_cov=2/2 polymorphism_quality=5.2 quality=5.2 quality_position_model=8.98637e-09 ref_cov=235/202 reject=INDEL_HOMOPOLYMER tot_cov=237/204 RA 922 . NC_007779 4414724 1 . T bias_e_value=1280200 bias_p_value=0.275529 fisher_strand_p_value=0.138601 frequency=9.259224e-03 genotype_quality=2141.7 ks_quality_p_value=0.558663 log10_base_likelihood=-16.1793 log10_qual_likelihood_position_model=3.426 log10_strand_likelihood_position_model=0.915138 new_cov=3/1 polymorphism_quality=10.8 quality=10.8 quality_position_model=6.69379e-14 ref_cov=154/274 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=157/275 RA 923 . NC_007779 4419586 0 T G bias_e_value=3.00069e-09 bias_p_value=6.45819e-16 fisher_strand_p_value=1.62854e-17 frequency=7.772636e-02 genotype_quality=1432.9 ks_quality_p_value=1 log10_base_likelihood=-17.8602 log10_qual_likelihood_position_model=43.4335 log10_strand_likelihood_position_model=16.7882 new_cov=50/0 polymorphism_quality=12.5 quality=12.5 quality_position_model=Inf ref_cov=175/233 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=225/233 RA 924 . NC_007779 4429120 0 G T bias_e_value=5.82476e-14 bias_p_value=1.25362e-20 fisher_strand_p_value=9.50131e-22 frequency=6.377411e-02 genotype_quality=1672.9 ks_quality_p_value=0.259971 log10_base_likelihood=-18.8766 log10_qual_likelihood_position_model=64.5453 log10_strand_likelihood_position_model=21.0222 new_cov=0/62 polymorphism_quality=13.6 quality=13.6 quality_position_model=Inf ref_cov=281/207 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=282/269 RA 925 . NC_007779 4429129 1 . A bias_e_value=2301170 bias_p_value=0.495266 fisher_strand_p_value=1 frequency=3.830910e-03 genotype_quality=2607.8 ks_quality_p_value=0.183875 log10_base_likelihood=-7.54123 log10_qual_likelihood_position_model=2.11644 log10_strand_likelihood_position_model=0.300204 new_cov=1/1 polymorphism_quality=2.0 quality=2.0 quality_position_model=5.15134e-07 ref_cov=261/259 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=262/260 RA 926 . NC_007779 4429130 0 A . bias_e_value=4643100 bias_p_value=0.999305 fisher_strand_p_value=1 frequency=5.629539e-03 genotype_quality=2180.9 ks_quality_p_value=0.962953 log10_base_likelihood=-7.06184 log10_qual_likelihood_position_model=2.55237 log10_strand_likelihood_position_model=0.424331 new_cov=1/2 polymorphism_quality=1.5 quality=1.5 quality_position_model=6.26247e-06 ref_cov=264/264 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=265/267 RA 927 . NC_007779 4455463 0 T G bias_e_value=1.2919e-05 bias_p_value=2.78048e-12 fisher_strand_p_value=8.95663e-14 frequency=5.569410e-02 genotype_quality=1225.1 ks_quality_p_value=1 log10_base_likelihood=-13.3683 log10_qual_likelihood_position_model=34.6122 log10_strand_likelihood_position_model=13.0537 new_cov=29/1 polymorphism_quality=8.0 quality=8.0 quality_position_model=Inf ref_cov=97/237 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=127/238 RA 928 . NC_007779 4460712 0 A . bias_e_value=4192000 bias_p_value=0.902216 fisher_strand_p_value=1 frequency=6.665230e-03 genotype_quality=1831.1 ks_quality_p_value=0.591735 log10_base_likelihood=-6.9091 log10_qual_likelihood_position_model=3.60795 log10_strand_likelihood_position_model=0.411151 new_cov=2/1 polymorphism_quality=1.4 quality=1.4 quality_position_model=0.000114731 ref_cov=230/216 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=232/217 RA 929 . NC_007779 4479134 0 G T bias_e_value=1.0962 bias_p_value=2.35929e-07 fisher_strand_p_value=1.23071e-08 frequency=2.598476e-02 genotype_quality=1389.8 ks_quality_p_value=0.997639 log10_base_likelihood=-6.5057 log10_qual_likelihood_position_model=19.5985 log10_strand_likelihood_position_model=7.90984 new_cov=0/25 polymorphism_quality=1.0 quality=1.0 quality_position_model=Inf ref_cov=226/198 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=226/223 RA 930 . NC_007779 4484644 1 . T bias_e_value=4635170 bias_p_value=0.997599 fisher_strand_p_value=1 frequency=4.357338e-03 genotype_quality=2290.3 ks_quality_p_value=0.931503 log10_base_likelihood=-7.62827 log10_qual_likelihood_position_model=1.91173 log10_strand_likelihood_position_model=0.302333 new_cov=1/1 polymorphism_quality=2.1 quality=2.1 quality_position_model=2.57743e-07 ref_cov=245/212 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=246/213 RA 931 . NC_007779 4494104 0 C A bias_e_value=0.728408 bias_p_value=1.5677e-07 fisher_strand_p_value=7.98237e-09 frequency=3.513813e-02 genotype_quality=1451.8 ks_quality_p_value=0.999654 log10_base_likelihood=-5.85429 log10_qual_likelihood_position_model=24.6883 log10_strand_likelihood_position_model=8.30073 new_cov=31/0 polymorphism_quality=0.3 quality=0.3 quality_position_model=Inf ref_cov=213/195 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=245/195 RA 932 . NC_007779 4510866 0 A . bias_e_value=4603010 bias_p_value=0.990675 fisher_strand_p_value=1 frequency=7.774353e-03 genotype_quality=2132.7 ks_quality_p_value=0.866582 log10_base_likelihood=-10.4206 log10_qual_likelihood_position_model=1.69477 log10_strand_likelihood_position_model=0.428098 new_cov=2/2 polymorphism_quality=5.0 quality=5.0 quality_position_model=2.75543e-10 ref_cov=272/238 reject=INDEL_HOMOPOLYMER tot_cov=274/240 RA 933 . NC_007779 4512976 0 C A frequency=1 genotype_quality=-0.2 new_cov=1/0 quality=-0.2 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 934 . NC_007779 4512982 0 C T frequency=1 genotype_quality=-0.2 new_cov=1/0 quality=-0.2 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 935 . NC_007779 4513001 0 C T frequency=1 genotype_quality=-0.1 new_cov=1/0 quality=-0.1 ref_cov=0/0 reject=EVALUE tot_cov=1/0 RA 936 . NC_007779 4515952 0 G T bias_e_value=0.229477 bias_p_value=4.93888e-08 fisher_strand_p_value=2.36747e-09 frequency=4.174995e-02 genotype_quality=1353.2 ks_quality_p_value=1 log10_base_likelihood=-14.5101 log10_qual_likelihood_position_model=29.1057 log10_strand_likelihood_position_model=8.71079 new_cov=0/33 polymorphism_quality=9.2 quality=9.2 quality_position_model=Inf ref_cov=203/226 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=203/262 RA 937 . NC_007779 4533946 0 T G bias_e_value=0.000946526 bias_p_value=2.03715e-10 fisher_strand_p_value=7.65988e-12 frequency=2.009392e-02 genotype_quality=1420.6 ks_quality_p_value=1 log10_base_likelihood=-6.07071 log10_qual_likelihood_position_model=27.9328 log10_strand_likelihood_position_model=11.1158 new_cov=30/0 polymorphism_quality=0.5 quality=0.5 quality_position_model=Inf ref_cov=160/236 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=191/236 RA 938 . NC_007779 4540870 0 T G bias_e_value=1.06186e-36 bias_p_value=2.28536e-43 fisher_strand_p_value=2.20112e-45 frequency=1.127911e-01 genotype_quality=1472.2 ks_quality_p_value=1 log10_base_likelihood=-32.3084 log10_qual_likelihood_position_model=65.4935 log10_strand_likelihood_position_model=44.6574 new_cov=85/0 polymorphism_quality=27.1 quality=27.1 quality_position_model=Inf ref_cov=88/301 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=176/302 RA 939 . NC_007779 4540877 0 A T bias_e_value=8.85486e-16 bias_p_value=1.90578e-22 fisher_strand_p_value=3.46381e-24 frequency=8.899212e-02 genotype_quality=1623.7 ks_quality_p_value=1 log10_base_likelihood=-31.5742 log10_qual_likelihood_position_model=36.8829 log10_strand_likelihood_position_model=23.4604 new_cov=49/0 polymorphism_quality=26.4 quality=26.4 quality_position_model=Inf ref_cov=128/306 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=177/306 RA 940 . NC_007779 4546535 0 T A frequency=1 genotype_quality=1881.8 new_cov=269/182 quality=1881.8 ref_cov=0/0 tot_cov=269/182 RA 941 . NC_007779 4553745 0 C A bias_e_value=3.92997e-05 bias_p_value=8.45821e-12 fisher_strand_p_value=2.84083e-13 frequency=5.412960e-02 genotype_quality=1378.0 ks_quality_p_value=0.995994 log10_base_likelihood=-15.6645 log10_qual_likelihood_position_model=34.7622 log10_strand_likelihood_position_model=12.7087 new_cov=40/0 polymorphism_quality=10.3 quality=10.3 quality_position_model=Inf ref_cov=184/220 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=228/222 RA 942 . NC_007779 4554525 1 . T bias_e_value=704182 bias_p_value=0.151557 fisher_strand_p_value=0.051801 frequency=8.849144e-03 genotype_quality=1621.0 ks_quality_p_value=0.671189 log10_base_likelihood=-12.871 log10_qual_likelihood_position_model=1.98045 log10_strand_likelihood_position_model=1.28566 new_cov=3/0 polymorphism_quality=7.5 quality=7.5 quality_position_model=1.26663e-11 ref_cov=124/212 reject=POLYMORPHISM_STRAND tot_cov=127/212 RA 943 . NC_007779 4554527 1 . C bias_e_value=770658 bias_p_value=0.165864 fisher_strand_p_value=0.0400354 frequency=9.833336e-03 genotype_quality=1422.6 ks_quality_p_value=0.976759 log10_base_likelihood=-10.3176 log10_qual_likelihood_position_model=5.19334 log10_strand_likelihood_position_model=1.39756 new_cov=3/0 polymorphism_quality=4.9 quality=4.9 quality_position_model=1.4906e-05 ref_cov=102/200 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=105/200 RA 944 . NC_007779 4554532 0 T C bias_e_value=0.00203978 bias_p_value=4.39009e-10 fisher_strand_p_value=1.70259e-11 frequency=5.222178e-02 genotype_quality=919.3 ks_quality_p_value=0.999537 log10_base_likelihood=-17.1884 log10_qual_likelihood_position_model=15.8987 log10_strand_likelihood_position_model=10.7689 new_cov=19/0 polymorphism_quality=11.9 quality=11.9 quality_position_model=Inf ref_cov=68/209 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=87/210 RA 945 . NC_007779 4554534 0 A C bias_e_value=85125.5 bias_p_value=0.018321 fisher_strand_p_value=0.00264125 frequency=3.948498e-02 genotype_quality=832.8 ks_quality_p_value=1 log10_base_likelihood=-8.82761 log10_qual_likelihood_position_model=23.2349 log10_strand_likelihood_position_model=2.75125 new_cov=13/9 polymorphism_quality=3.4 quality=3.4 quality_position_model=Inf ref_cov=73/200 reject=SURROUNDING_HOMOPOLYMER tot_cov=86/211 RA 946 . NC_007779 4557828 0 A . bias_e_value=4088940 bias_p_value=0.880037 fisher_strand_p_value=0.607116 frequency=5.953789e-03 genotype_quality=2028.7 ks_quality_p_value=0.909312 log10_base_likelihood=-6.97726 log10_qual_likelihood_position_model=3.66815 log10_strand_likelihood_position_model=0.44746 new_cov=1/2 polymorphism_quality=1.5 quality=1.5 quality_position_model=0.000123007 ref_cov=262/237 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=263/240 RA 947 . NC_007779 4561440 1 . T bias_e_value=4645150 bias_p_value=0.999746 fisher_strand_p_value=1 frequency=7.555962e-03 genotype_quality=1971.6 ks_quality_p_value=0.977543 log10_base_likelihood=-11.8996 log10_qual_likelihood_position_model=2.92619 log10_strand_likelihood_position_model=0.357562 new_cov=2/1 polymorphism_quality=6.5 quality=6.5 quality_position_model=1.301e-10 ref_cov=243/151 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=245/152 RA 948 . NC_007779 4573184 0 T G bias_e_value=3.82581e-15 bias_p_value=8.23403e-22 fisher_strand_p_value=1.53824e-23 frequency=5.216074e-02 genotype_quality=1550.4 ks_quality_p_value=1 log10_base_likelihood=-7.25415 log10_qual_likelihood_position_model=45.919 log10_strand_likelihood_position_model=22.8362 new_cov=73/0 polymorphism_quality=1.7 quality=1.7 quality_position_model=Inf ref_cov=207/256 reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=283/256 RA 949 . NC_007779 4583431 0 T . bias_e_value=948940 bias_p_value=0.204234 fisher_strand_p_value=0.125487 frequency=8.379936e-03 genotype_quality=1937.6 ks_quality_p_value=0.410337 log10_base_likelihood=-10.7821 log10_qual_likelihood_position_model=2.09151 log10_strand_likelihood_position_model=1.12033 new_cov=0/4 polymorphism_quality=5.4 quality=5.4 quality_position_model=1.53679e-09 ref_cov=226/247 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=226/251 RA 950 . NC_007779 4584556 0 C A bias_e_value=5.20517e-07 bias_p_value=1.12027e-13 fisher_strand_p_value=3.2607e-15 frequency=5.319071e-02 genotype_quality=1646.3 ks_quality_p_value=1 log10_base_likelihood=-21.0415 log10_qual_likelihood_position_model=39.1141 log10_strand_likelihood_position_model=14.5074 new_cov=47/0 polymorphism_quality=15.8 quality=15.8 quality_position_model=Inf ref_cov=218/250 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=265/250 RA 951 . NC_007779 4599760 0 C A bias_e_value=1.37503e-15 bias_p_value=2.95939e-22 fisher_strand_p_value=5.42297e-24 frequency=7.036781e-02 genotype_quality=1782.9 ks_quality_p_value=1 log10_base_likelihood=-29.7927 log10_qual_likelihood_position_model=35.8629 log10_strand_likelihood_position_model=23.2658 new_cov=55/0 polymorphism_quality=24.6 quality=24.6 quality_position_model=Inf ref_cov=167/320 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=222/320 RA 952 . NC_007779 4610781 0 A C bias_e_value=4.50218e-14 bias_p_value=9.68974e-21 fisher_strand_p_value=1.89938e-22 frequency=6.985426e-02 genotype_quality=1600.7 ks_quality_p_value=1 log10_base_likelihood=-23.5763 log10_qual_likelihood_position_model=47.5857 log10_strand_likelihood_position_model=21.7214 new_cov=0/52 polymorphism_quality=18.3 quality=18.3 quality_position_model=Inf ref_cov=292/155 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=292/208 RA 953 . NC_007779 4610781 1 . C bias_e_value=1436000 bias_p_value=0.309061 fisher_strand_p_value=0.176311 frequency=4.183769e-03 genotype_quality=2222.6 ks_quality_p_value=0.515999 log10_base_likelihood=-7.37911 log10_qual_likelihood_position_model=3.1761 log10_strand_likelihood_position_model=0.75372 new_cov=0/2 polymorphism_quality=1.9 quality=1.9 quality_position_model=2.92403e-05 ref_cov=277/199 reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=277/201 RA 954 . NC_007779 4611002 1 . G bias_e_value=4542350 bias_p_value=0.97762 fisher_strand_p_value=1 frequency=4.962921e-03 genotype_quality=1984.1 ks_quality_p_value=0.796033 log10_base_likelihood=-7.76006 log10_qual_likelihood_position_model=2.17611 log10_strand_likelihood_position_model=0.302873 new_cov=1/1 polymorphism_quality=2.3 quality=2.3 quality_position_model=3.5428e-07 ref_cov=217/184 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=218/185 RA 955 . NC_007779 4636470 0 C G bias_e_value=2.06841e-07 bias_p_value=4.45171e-14 fisher_strand_p_value=1.26139e-15 frequency=4.648256e-02 genotype_quality=1283.8 ks_quality_p_value=0.999581 log10_base_likelihood=-8.78455 log10_qual_likelihood_position_model=23.8299 log10_strand_likelihood_position_model=14.8992 new_cov=25/0 polymorphism_quality=3.3 quality=3.3 quality_position_model=Inf ref_cov=75/258 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER tot_cov=100/258 RA 956 . NC_007779 4636473 0 A G bias_e_value=1.68087e-11 bias_p_value=3.61763e-18 fisher_strand_p_value=8.04514e-20 frequency=5.171537e-02 genotype_quality=1162.8 ks_quality_p_value=1 log10_base_likelihood=-9.11435 log10_qual_likelihood_position_model=32.5804 log10_strand_likelihood_position_model=19.0945 new_cov=24/0 polymorphism_quality=3.7 quality=3.7 quality_position_model=Inf ref_cov=38/262 reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE tot_cov=63/262 RA 957 . NC_007779 4639643 1 . G bias_e_value=289769 bias_p_value=0.0623651 fisher_strand_p_value=0.0120418 frequency=1.226997e-02 genotype_quality=1609.2 ks_quality_p_value=0.945957 log10_base_likelihood=-16.8476 log10_qual_likelihood_position_model=3.58654 log10_strand_likelihood_position_model=1.91931 new_cov=4/0 polymorphism_quality=11.5 quality=11.5 quality_position_model=2.1432e-13 ref_cov=105/217 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=109/217 RA 958 . NC_007779 4642414 1 . A bias_e_value=4005120 bias_p_value=0.861997 fisher_strand_p_value=0.635218 frequency=9.546280e-03 genotype_quality=2052.0 ks_quality_p_value=0.823344 log10_base_likelihood=-16.7057 log10_qual_likelihood_position_model=2.69411 log10_strand_likelihood_position_model=0.504913 new_cov=1/3 polymorphism_quality=11.4 quality=11.4 quality_position_model=1.34719e-15 ref_cov=182/233 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=183/236 RA 959 . NC_007779 4644245 0 T . bias_e_value=2950550 bias_p_value=0.635027 fisher_strand_p_value=1 frequency=6.389618e-03 genotype_quality=1854.3 ks_quality_p_value=0.278899 log10_base_likelihood=-7.51741 log10_qual_likelihood_position_model=2.82012 log10_strand_likelihood_position_model=0.383937 new_cov=2/1 polymorphism_quality=2.0 quality=2.0 quality_position_model=3.61179e-06 ref_cov=259/207 reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER tot_cov=261/208 MC 960 . NC_007779 274733 371972 0 0 left_inside_cov=0 left_outside_cov=457 right_inside_cov=0 right_outside_cov=460 MC 961 . NC_007779 654214 655412 1197 0 left_inside_cov=0 left_outside_cov=504 right_inside_cov=0 right_outside_cov=502 MC 962 . NC_007779 1288308 1288521 76 68 left_inside_cov=337 left_outside_cov=341 right_inside_cov=339 right_outside_cov=342 MC 963 . NC_007779 1301041 1302376 1329 0 left_inside_cov=0 left_outside_cov=513 right_inside_cov=0 right_outside_cov=516 MC 964 . NC_007779 1413639 1436698 0 0 left_inside_cov=1 left_outside_cov=570 right_inside_cov=3 right_outside_cov=578 MC 965 . NC_007779 2176983 2178208 0 0 left_inside_cov=0 left_outside_cov=534 right_inside_cov=0 right_outside_cov=424 MC 966 . NC_007779 2320795 2322130 1327 0 left_inside_cov=0 left_outside_cov=453 right_inside_cov=1 right_outside_cov=460 MC 967 . NC_007779 3128828 3147473 1174 0 left_inside_cov=337 left_outside_cov=341 right_inside_cov=0 right_outside_cov=418 MC 968 . NC_007779 3261134 3262337 1198 0 left_inside_cov=1 left_outside_cov=471 right_inside_cov=0 right_outside_cov=400 MC 969 . NC_007779 3746911 3748109 0 0 left_inside_cov=0 left_outside_cov=552 right_inside_cov=1 right_outside_cov=553 MC 970 . NC_007779 3750591 3751789 1198 0 left_inside_cov=0 left_outside_cov=589 right_inside_cov=0 right_outside_cov=587 MC 971 . NC_007779 3958123 3958156 0 0 left_inside_cov=0 left_outside_cov=490 right_inside_cov=0 right_outside_cov=489 MC 972 . NC_007779 4310363 4311561 0 0 left_inside_cov=1 left_outside_cov=551 right_inside_cov=0 right_outside_cov=553 JC 973 . NC_007779 1 1 NC_007779 4646332 -1 0 alignment_overlap=0 circular_chromosome=1 coverage_minus=223 coverage_plus=234 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__1__1__NC_007779__4646332__-1__0____101__101__0__0 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.05 new_junction_frequency=1.000000e+00 new_junction_read_count=458 pos_hash_score=165 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=457 JC 974 . NC_007779 273179 1 NC_007779 657843 1 0 alignment_overlap=0 coverage_minus=158 coverage_plus=126 flanking_left=101 flanking_right=101 frequency=6.753555e-01 junction_possible_overlap_registers=90 key=NC_007779__273179__1__NC_007779__657843__1__0____101__101__1__0 max_left=88 max_left_minus=88 max_left_plus=88 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=49 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.65 new_junction_frequency=6.753555e-01 new_junction_read_count=285 pos_hash_score=131 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.31 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=137 side_2_redundant=0 total_non_overlap_reads=284 JC 975 . NC_007779 273180 1 NC_007779 656434 1 0 alignment_overlap=1 coverage_minus=3 coverage_plus=1 flanking_left=101 flanking_right=101 frequency=8.660716e-03 junction_possible_overlap_registers=89 key=NC_007779__273179__1__NC_007779__656434__1__1____101__101__1__0 max_left=67 max_left_minus=47 max_left_plus=67 max_min_left=47 max_min_left_minus=47 max_min_left_plus=0 max_min_right=33 max_min_right_minus=0 max_min_right_plus=33 max_pos_hash_score=178 max_right=85 max_right_minus=85 max_right_plus=33 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.01 new_junction_frequency=8.660716e-03 new_junction_read_count=4 pos_hash_score=4 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.06 side_2_overlap=1 side_2_possible_overlap_registers=90 side_2_read_count=463 side_2_redundant=0 total_non_overlap_reads=4 JC 976 . NC_007779 274732 -1 NC_007779 371973 1 0 alignment_overlap=10 coverage_minus=171 coverage_plus=186 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=80 key=NC_007779__274732__-1__NC_007779__371963__1__10____101__101__0__0 max_left=85 max_left_minus=85 max_left_plus=85 max_min_left=45 max_min_left_minus=45 max_min_left_plus=45 max_min_right=45 max_min_right_minus=45 max_min_right_plus=45 max_pos_hash_score=160 max_right=85 max_right_minus=85 max_right_plus=85 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.92 new_junction_frequency=1.000000e+00 new_junction_read_count=358 pos_hash_score=136 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=10 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=80 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=357 JC 977 . NC_007779 289856 1 NC_007779 2176982 -1 -33 alignment_overlap=-33 coverage_minus=178 coverage_plus=157 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=57 key=NC_007779__289856__1__NC_007779__2176982__-1__-33__CTATTGCAATACCGCATTGTGAGGCGATTCATG__101__101__1__0 max_left=62 max_left_minus=62 max_left_plus=62 max_min_left=33 max_min_left_minus=33 max_min_left_plus=33 max_min_right=34 max_min_right_minus=34 max_min_right_plus=34 max_pos_hash_score=114 max_right=62 max_right_minus=62 max_right_plus=62 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.21 new_junction_frequency=1.000000e+00 new_junction_read_count=335 pos_hash_score=109 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=335 unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG JC 978 . NC_007779 380484 1 NC_007779 381407 -1 0 alignment_overlap=0 coverage_minus=265 coverage_plus=151 flanking_left=101 flanking_right=101 frequency=NA junction_possible_overlap_registers=90 key=NC_007779__380484__1__NC_007779__381407__-1__0____101__101__1__1 max_left=90 max_left_minus=90 max_left_plus=90 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=94 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.96 new_junction_frequency=NA new_junction_read_count=418 pos_hash_score=146 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=416 JC 979 . NC_007779 381401 1 NC_007779 381812 -1 0 alignment_overlap=2 coverage_minus=186 coverage_plus=197 flanking_left=101 flanking_right=101 frequency=NA junction_possible_overlap_registers=88 key=NC_007779__381401__1__NC_007779__381814__-1__2____101__101__1__1 max_left=93 max_left_minus=93 max_left_plus=93 max_min_left=49 max_min_left_minus=48 max_min_left_plus=49 max_min_right=49 max_min_right_minus=48 max_min_right_plus=49 max_pos_hash_score=176 max_right=93 max_right_minus=93 max_right_plus=93 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.90 new_junction_frequency=NA new_junction_read_count=383 pos_hash_score=146 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=2 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=383 JC 980 . NC_007779 608570 -1 NC_007779 1305025 1 0 alignment_overlap=3 coverage_minus=193 coverage_plus=248 flanking_left=101 flanking_right=101 frequency=9.580014e-01 junction_possible_overlap_registers=87 key=NC_007779__608573__-1__NC_007779__1305025__1__3____101__101__1__0 max_left=92 max_left_minus=92 max_left_plus=92 max_min_left=48 max_min_left_minus=48 max_min_left_plus=47 max_min_right=49 max_min_right_minus=49 max_min_right_plus=49 max_pos_hash_score=174 max_right=92 max_right_minus=92 max_right_plus=92 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.05 new_junction_frequency=9.580014e-01 new_junction_read_count=441 pos_hash_score=154 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.05 side_2_overlap=3 side_2_possible_overlap_registers=90 side_2_read_count=20 side_2_redundant=0 total_non_overlap_reads=441 JC 981 . NC_007779 654213 -1 NC_007779 655413 1 0 alignment_overlap=5 coverage_minus=231 coverage_plus=192 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=85 key=NC_007779__654213__-1__NC_007779__655408__1__5____101__101__0__0 max_left=90 max_left_minus=90 max_left_plus=90 max_min_left=47 max_min_left_minus=47 max_min_left_plus=46 max_min_right=48 max_min_right_minus=48 max_min_right_plus=48 max_pos_hash_score=170 max_right=90 max_right_minus=90 max_right_plus=90 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.03 new_junction_frequency=1.000000e+00 new_junction_read_count=426 pos_hash_score=156 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=5 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=85 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=423 JC 982 . NC_007779 654213 1 NC_007779 657846 -1 0 alignment_overlap=0 coverage_minus=121 coverage_plus=142 flanking_left=101 flanking_right=101 frequency=6.550868e-01 junction_possible_overlap_registers=90 key=NC_007779__654213__1__NC_007779__657846__-1__0____101__101__1__0 max_left=88 max_left_minus=88 max_left_plus=88 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.61 new_junction_frequency=6.550868e-01 new_junction_read_count=264 pos_hash_score=129 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.32 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=139 side_2_redundant=0 total_non_overlap_reads=263 JC 983 . NC_007779 655407 -1 NC_007779 656438 -1 0 alignment_overlap=0 coverage_minus=0 coverage_plus=6 flanking_left=101 flanking_right=101 frequency=1.290323e-02 junction_possible_overlap_registers=90 key=NC_007779__655407__-1__NC_007779__656438__-1__0____101__101__1__0 max_left=75 max_left_minus=0 max_left_plus=75 max_min_left=46 max_min_left_minus=0 max_min_left_plus=46 max_min_right=32 max_min_right_minus=0 max_min_right_plus=32 max_pos_hash_score=180 max_right=79 max_right_minus=0 max_right_plus=79 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.01 new_junction_frequency=1.290323e-02 new_junction_read_count=6 pos_hash_score=6 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.05 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=459 side_2_redundant=0 total_non_overlap_reads=6 JC 984 . NC_007779 1209367 1 NC_007779 1211196 1 0 alignment_overlap=16 coverage_minus=57 coverage_plus=77 flanking_left=101 flanking_right=101 frequency=3.371254e-01 junction_possible_overlap_registers=74 key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0 max_left=79 max_left_minus=78 max_left_plus=79 max_min_left=40 max_min_left_minus=40 max_min_left_plus=40 max_min_right=42 max_min_right_minus=42 max_min_right_plus=41 max_pos_hash_score=148 max_right=79 max_right_minus=79 max_right_plus=79 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.38 new_junction_frequency=3.371254e-01 new_junction_read_count=135 pos_hash_score=82 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.71 side_1_overlap=16 side_1_possible_overlap_registers=90 side_1_read_count=310 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.77 side_2_overlap=0 side_2_possible_overlap_registers=74 side_2_read_count=276 side_2_redundant=0 total_non_overlap_reads=134 JC 985 . NC_007779 1209382 -1 NC_007779 1211179 -1 0 alignment_overlap=16 coverage_minus=62 coverage_plus=58 flanking_left=101 flanking_right=101 frequency=3.157064e-01 junction_possible_overlap_registers=74 key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0 max_left=78 max_left_minus=78 max_left_plus=78 max_min_left=42 max_min_left_minus=42 max_min_left_plus=42 max_min_right=42 max_min_right_minus=42 max_min_right_plus=41 max_pos_hash_score=148 max_right=79 max_right_minus=79 max_right_plus=79 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.33 new_junction_frequency=3.157064e-01 new_junction_read_count=120 pos_hash_score=87 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.68 side_1_overlap=16 side_1_possible_overlap_registers=90 side_1_read_count=297 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.77 side_2_overlap=0 side_2_possible_overlap_registers=74 side_2_read_count=276 side_2_redundant=0 total_non_overlap_reads=120 JC 986 . NC_007779 1221489 1 NC_007779 1301041 1 0 alignment_overlap=2 coverage_minus=179 coverage_plus=241 flanking_left=101 flanking_right=101 frequency=9.795729e-01 junction_possible_overlap_registers=88 key=NC_007779__1221489__1__NC_007779__1301039__1__2____101__101__0__1 max_left=93 max_left_minus=92 max_left_plus=93 max_min_left=49 max_min_left_minus=47 max_min_left_plus=49 max_min_right=49 max_min_right_minus=49 max_min_right_plus=49 max_pos_hash_score=176 max_right=86 max_right_minus=86 max_right_plus=86 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.99 new_junction_frequency=9.795729e-01 new_junction_read_count=422 pos_hash_score=146 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.02 side_1_overlap=2 side_1_possible_overlap_registers=90 side_1_read_count=9 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=420 JC 987 . NC_007779 1221495 -1 NC_007779 1302369 -1 0 alignment_overlap=0 coverage_minus=229 coverage_plus=144 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__1221495__-1__NC_007779__1302369__-1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=90 max_right_minus=90 max_right_plus=88 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.87 new_junction_frequency=1.000000e+00 new_junction_read_count=378 pos_hash_score=147 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=373 JC 988 . NC_007779 1301040 -1 NC_007779 1302377 1 0 alignment_overlap=7 coverage_minus=199 coverage_plus=210 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=83 key=NC_007779__1301040__-1__NC_007779__1302370__1__7____101__101__0__0 max_left=88 max_left_minus=88 max_left_plus=88 max_min_left=46 max_min_left_minus=46 max_min_left_plus=46 max_min_right=47 max_min_right_minus=47 max_min_right_plus=47 max_pos_hash_score=166 max_right=88 max_right_minus=88 max_right_plus=88 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.02 new_junction_frequency=1.000000e+00 new_junction_read_count=409 pos_hash_score=150 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=7 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=83 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=409 JC 989 . NC_007779 1305037 -1 NC_007779 2519723 1 0 alignment_overlap=4 coverage_minus=218 coverage_plus=220 flanking_left=101 flanking_right=101 frequency=9.443726e-01 junction_possible_overlap_registers=86 key=NC_007779__1305037__-1__NC_007779__2519719__1__4____101__101__0__1 max_left=91 max_left_minus=91 max_left_plus=91 max_min_left=48 max_min_left_minus=48 max_min_left_plus=48 max_min_right=48 max_min_right_minus=48 max_min_right_plus=48 max_pos_hash_score=172 max_right=91 max_right_minus=91 max_right_plus=91 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.05 new_junction_frequency=9.443726e-01 new_junction_read_count=438 pos_hash_score=152 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.06 side_1_overlap=4 side_1_possible_overlap_registers=90 side_1_read_count=27 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=438 JC 990 . NC_007779 1397758 1 NC_007779 1672777 1 0 alignment_overlap=0 coverage_minus=185 coverage_plus=212 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__1397758__1__NC_007779__1672777__1__0____101__101__1__0 max_left=89 max_left_minus=89 max_left_plus=89 max_min_left=50 max_min_left_minus=48 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.92 new_junction_frequency=1.000000e+00 new_junction_read_count=403 pos_hash_score=151 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=397 JC 991 . NC_007779 1413638 -1 NC_007779 1436699 1 0 alignment_overlap=26 coverage_minus=164 coverage_plus=177 flanking_left=101 flanking_right=101 frequency=9.974973e-01 junction_possible_overlap_registers=64 key=NC_007779__1413638__-1__NC_007779__1436673__1__26____101__101__0__0 max_left=69 max_left_minus=69 max_left_plus=69 max_min_left=37 max_min_left_minus=37 max_min_left_plus=37 max_min_right=37 max_min_right_minus=37 max_min_right_plus=37 max_pos_hash_score=128 max_right=69 max_right_minus=69 max_right_plus=69 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.10 new_junction_frequency=9.974973e-01 new_junction_read_count=341 pos_hash_score=117 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=26 side_1_possible_overlap_registers=90 side_1_read_count=1 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=64 side_2_read_count=1 side_2_redundant=0 total_non_overlap_reads=341 JC 992 . NC_007779 1672780 -1 NC_007779 1980209 1 0 alignment_overlap=0 coverage_minus=226 coverage_plus=217 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__1672780__-1__NC_007779__1980209__1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.02 new_junction_frequency=1.000000e+00 new_junction_read_count=445 pos_hash_score=164 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=443 JC 993 . NC_007779 1907280 1 NC_007779 2412225 -1 0 alignment_overlap=0 coverage_minus=214 coverage_plus=209 flanking_left=101 flanking_right=101 frequency=9.593679e-01 junction_possible_overlap_registers=90 key=NC_007779__1907280__1__NC_007779__2412225__-1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=94 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.97 new_junction_frequency=9.593679e-01 new_junction_read_count=425 pos_hash_score=166 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.04 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=18 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=423 JC 994 . NC_007779 1907288 -1 NC_007779 2411458 1 0 alignment_overlap=0 coverage_minus=176 coverage_plus=226 flanking_left=101 flanking_right=101 frequency=9.350348e-01 junction_possible_overlap_registers=90 key=NC_007779__1907288__-1__NC_007779__2411458__1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=49 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.92 new_junction_frequency=9.350348e-01 new_junction_read_count=403 pos_hash_score=161 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.06 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=28 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=402 JC 995 . NC_007779 1980091 1 NC_007779 1980209 1 0 alignment_overlap=0 coverage_minus=192 coverage_plus=78 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__1980091__1__NC_007779__1980209__1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=41 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=93 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.62 new_junction_frequency=1.000000e+00 new_junction_read_count=271 pos_hash_score=117 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=270 JC 996 . NC_007779 1980095 -1 NC_007779 2176984 1 0 alignment_overlap=1 coverage_minus=268 coverage_plus=218 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=89 key=NC_007779__1980095__-1__NC_007779__2176983__1__1____101__101__0__1 max_left=94 max_left_minus=94 max_left_plus=94 max_min_left=49 max_min_left_minus=49 max_min_left_plus=49 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=178 max_right=94 max_right_minus=94 max_right_plus=94 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.13 new_junction_frequency=1.000000e+00 new_junction_read_count=488 pos_hash_score=168 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=1 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=486 JC 997 . NC_007779 2178209 1 NC_007779 2412225 -1 0 alignment_overlap=0 coverage_minus=189 coverage_plus=189 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=89 max_right_minus=87 max_right_plus=89 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.87 new_junction_frequency=1.000000e+00 new_junction_read_count=380 pos_hash_score=149 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=378 JC 998 . NC_007779 2320794 -1 NC_007779 2322131 1 0 alignment_overlap=6 coverage_minus=184 coverage_plus=195 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=84 key=NC_007779__2320794__-1__NC_007779__2322125__1__6____101__101__0__0 max_left=89 max_left_minus=89 max_left_plus=89 max_min_left=47 max_min_left_minus=47 max_min_left_plus=47 max_min_right=47 max_min_right_minus=47 max_min_right_plus=47 max_pos_hash_score=168 max_right=89 max_right_minus=89 max_right_plus=89 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.93 new_junction_frequency=1.000000e+00 new_junction_read_count=380 pos_hash_score=145 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=6 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=84 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=379 JC 999 . NC_007779 2320794 1 NC_007779 2589834 -1 0 alignment_overlap=0 coverage_minus=154 coverage_plus=302 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__2320794__1__NC_007779__2589834__-1__0____101__101__1__0 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=49 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.05 new_junction_frequency=1.000000e+00 new_junction_read_count=457 pos_hash_score=158 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=456 JC 1000 . NC_007779 2322124 -1 NC_007779 2589830 1 0 alignment_overlap=0 coverage_minus=292 coverage_plus=238 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__2322124__-1__NC_007779__2589830__1__0____101__101__1__0 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.22 new_junction_frequency=1.000000e+00 new_junction_read_count=534 pos_hash_score=169 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=530 JC 1001 . NC_007779 2411458 1 NC_007779 2941519 1 0 alignment_overlap=0 coverage_minus=28 coverage_plus=32 flanking_left=101 flanking_right=101 frequency=1.134216e-01 junction_possible_overlap_registers=90 key=NC_007779__2411458__1__NC_007779__2941519__1__0____101__101__1__0 max_left=83 max_left_minus=83 max_left_plus=73 max_min_left=50 max_min_left_minus=50 max_min_left_plus=49 max_min_right=49 max_min_right_minus=45 max_min_right_plus=49 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=94 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.14 new_junction_frequency=1.134216e-01 new_junction_read_count=60 pos_hash_score=45 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.08 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=469 side_2_redundant=0 total_non_overlap_reads=60 JC 1002 . NC_007779 2411458 1 NC_007779 2985055 -1 0 alignment_overlap=0 coverage_minus=223 coverage_plus=233 flanking_left=101 flanking_right=101 frequency=9.600840e-01 junction_possible_overlap_registers=90 key=NC_007779__2411458__1__NC_007779__2985055__-1__0____101__101__1__0 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=49 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.05 new_junction_frequency=9.600840e-01 new_junction_read_count=457 pos_hash_score=160 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.04 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=19 side_2_redundant=0 total_non_overlap_reads=456 JC 1003 . NC_007779 2411459 1 NC_007779 2941509 1 0 alignment_overlap=1 coverage_minus=11 coverage_plus=9 flanking_left=101 flanking_right=101 frequency=4.159542e-02 junction_possible_overlap_registers=89 key=NC_007779__2411458__1__NC_007779__2941509__1__1____101__101__1__0 max_left=86 max_left_minus=83 max_left_plus=86 max_min_left=41 max_min_left_minus=39 max_min_left_plus=41 max_min_right=48 max_min_right_minus=48 max_min_right_plus=44 max_pos_hash_score=178 max_right=93 max_right_minus=93 max_right_plus=83 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.05 new_junction_frequency=4.159542e-02 new_junction_read_count=20 pos_hash_score=18 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.07 side_2_overlap=1 side_2_possible_overlap_registers=90 side_2_read_count=466 side_2_redundant=0 total_non_overlap_reads=20 JC 1004 . NC_007779 2412225 -1 NC_007779 2941518 -1 0 alignment_overlap=0 coverage_minus=11 coverage_plus=6 flanking_left=101 flanking_right=101 frequency=3.497942e-02 junction_possible_overlap_registers=90 key=NC_007779__2412225__-1__NC_007779__2941518__-1__0____101__101__1__0 max_left=84 max_left_minus=77 max_left_plus=84 max_min_left=50 max_min_left_minus=50 max_min_left_plus=34 max_min_right=47 max_min_right_minus=45 max_min_right_plus=47 max_pos_hash_score=180 max_right=92 max_right_minus=92 max_right_plus=78 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.04 new_junction_frequency=3.497942e-02 new_junction_read_count=17 pos_hash_score=16 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.08 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=469 side_2_redundant=0 total_non_overlap_reads=17 JC 1005 . NC_007779 2412225 -1 NC_007779 2941525 -1 0 alignment_overlap=0 coverage_minus=30 coverage_plus=40 flanking_left=101 flanking_right=101 frequency=1.256732e-01 junction_possible_overlap_registers=90 key=NC_007779__2412225__-1__NC_007779__2941525__-1__0____101__101__1__0 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=45 max_min_right=50 max_min_right_minus=46 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.16 new_junction_frequency=1.256732e-01 new_junction_read_count=70 pos_hash_score=58 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=1.12 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=487 side_2_redundant=0 total_non_overlap_reads=70 JC 1006 . NC_007779 2412225 -1 NC_007779 2985047 1 0 alignment_overlap=0 coverage_minus=208 coverage_plus=197 flanking_left=101 flanking_right=101 frequency=9.511628e-01 junction_possible_overlap_registers=90 key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0 max_left=88 max_left_minus=88 max_left_plus=88 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.94 new_junction_frequency=9.511628e-01 new_junction_read_count=409 pos_hash_score=149 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.05 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=21 side_2_redundant=0 total_non_overlap_reads=405 JC 1007 . NC_007779 2865229 1 NC_007779 2865274 -1 0 alignment_overlap=4 coverage_minus=70 coverage_plus=70 flanking_left=101 flanking_right=101 frequency=3.232732e-01 junction_possible_overlap_registers=86 key=NC_007779__2865229__1__NC_007779__2865278__-1__4____101__101__0__0 max_left=91 max_left_minus=91 max_left_plus=91 max_min_left=46 max_min_left_minus=46 max_min_left_plus=46 max_min_right=46 max_min_right_minus=44 max_min_right_plus=46 max_pos_hash_score=172 max_right=91 max_right_minus=91 max_right_plus=91 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.42 new_junction_frequency=3.232732e-01 new_junction_read_count=174 pos_hash_score=97 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.90 side_1_overlap=4 side_1_possible_overlap_registers=90 side_1_read_count=394 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.84 side_2_overlap=0 side_2_possible_overlap_registers=86 side_2_read_count=352 side_2_redundant=0 total_non_overlap_reads=140 JC 1008 . NC_007779 2865229 1 NC_007779 2865278 -1 -42 alignment_overlap=-42 coverage_minus=24 coverage_plus=17 flanking_left=101 flanking_right=101 frequency=1.678952e-01 junction_possible_overlap_registers=48 key=NC_007779__2865229__1__NC_007779__2865278__-1__-42__CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA__101__101__0__0 max_left=45 max_left_minus=45 max_left_plus=42 max_min_left=28 max_min_left_minus=27 max_min_left_plus=28 max_min_right=28 max_min_right_minus=27 max_min_right_plus=28 max_pos_hash_score=96 max_right=44 max_right_minus=44 max_right_plus=44 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.18 new_junction_frequency=1.678952e-01 new_junction_read_count=41 pos_hash_score=28 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.90 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=394 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.84 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=368 side_2_redundant=0 total_non_overlap_reads=41 unique_read_sequence=CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA JC 1009 . NC_007779 3147474 1 NC_007779 3262328 -1 0 alignment_overlap=0 coverage_minus=178 coverage_plus=211 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__3147474__1__NC_007779__3262328__-1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=90 max_right_minus=90 max_right_plus=87 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.90 new_junction_frequency=1.000000e+00 new_junction_read_count=391 pos_hash_score=142 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=389 JC 1010 . NC_007779 3186081 -1 NC_007779 3512753 1 0 alignment_overlap=1 coverage_minus=202 coverage_plus=173 flanking_left=101 flanking_right=101 frequency=9.973699e-01 junction_possible_overlap_registers=89 key=NC_007779__3186082__-1__NC_007779__3512753__1__1____101__101__1__0 max_left=91 max_left_minus=84 max_left_plus=91 max_min_left=49 max_min_left_minus=49 max_min_left_plus=49 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=178 max_right=95 max_right_minus=95 max_right_plus=93 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.87 new_junction_frequency=9.973699e-01 new_junction_read_count=375 pos_hash_score=140 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=1 side_2_possible_overlap_registers=90 side_2_read_count=1 side_2_redundant=0 total_non_overlap_reads=375 JC 1011 . NC_007779 3261133 -1 NC_007779 3748109 -1 -6 alignment_overlap=-6 coverage_minus=230 coverage_plus=189 flanking_left=101 flanking_right=101 frequency=9.977827e-01 junction_possible_overlap_registers=84 key=NC_007779__3261133__-1__NC_007779__3748109__-1__-6__CTTTGC__101__101__0__1 max_left=89 max_left_minus=89 max_left_plus=88 max_min_left=47 max_min_left_minus=46 max_min_left_plus=47 max_min_right=47 max_min_right_minus=47 max_min_right_plus=47 max_pos_hash_score=168 max_right=89 max_right_minus=89 max_right_plus=89 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.03 new_junction_frequency=9.977827e-01 new_junction_read_count=420 pos_hash_score=148 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=1 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=419 unique_read_sequence=CTTTGC JC 1012 . NC_007779 3261134 1 NC_007779 3265774 1 0 alignment_overlap=0 coverage_minus=216 coverage_plus=220 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=49 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.01 new_junction_frequency=1.000000e+00 new_junction_read_count=440 pos_hash_score=156 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=436 JC 1013 . NC_007779 3261135 1 NC_007779 3262338 1 0 alignment_overlap=1 coverage_minus=183 coverage_plus=187 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=89 key=NC_007779__3261134__1__NC_007779__3262338__1__1____101__101__1__0 max_left=90 max_left_minus=89 max_left_plus=90 max_min_left=49 max_min_left_minus=48 max_min_left_plus=49 max_min_right=50 max_min_right_minus=50 max_min_right_plus=49 max_pos_hash_score=178 max_right=94 max_right_minus=94 max_right_plus=94 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.86 new_junction_frequency=1.000000e+00 new_junction_read_count=372 pos_hash_score=137 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=1 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=370 JC 1014 . NC_007779 3265777 -1 NC_007779 3365411 1 0 alignment_overlap=0 coverage_minus=263 coverage_plus=201 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=49 max_min_left_minus=49 max_min_left_plus=49 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=93 max_right_minus=93 max_right_plus=93 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.07 new_junction_frequency=1.000000e+00 new_junction_read_count=467 pos_hash_score=162 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=464 JC 1015 . NC_007779 3512759 -1 NC_007779 3744262 -1 0 alignment_overlap=1 coverage_minus=184 coverage_plus=265 flanking_left=101 flanking_right=101 frequency=9.848834e-01 junction_possible_overlap_registers=89 key=NC_007779__3512759__-1__NC_007779__3744263__-1__1____101__101__0__1 max_left=94 max_left_minus=94 max_left_plus=94 max_min_left=49 max_min_left_minus=49 max_min_left_plus=49 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=178 max_right=87 max_right_minus=87 max_right_plus=86 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.05 new_junction_frequency=9.848834e-01 new_junction_read_count=451 pos_hash_score=152 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.02 side_1_overlap=1 side_1_possible_overlap_registers=90 side_1_read_count=7 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=449 JC 1016 . NC_007779 3742935 -1 NC_007779 3744272 1 0 alignment_overlap=8 coverage_minus=226 coverage_plus=228 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=82 key=NC_007779__3742935__-1__NC_007779__3744264__1__8____101__101__0__0 max_left=87 max_left_minus=87 max_left_plus=87 max_min_left=46 max_min_left_minus=46 max_min_left_plus=46 max_min_right=46 max_min_right_minus=46 max_min_right_plus=46 max_pos_hash_score=164 max_right=87 max_right_minus=87 max_right_plus=87 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.14 new_junction_frequency=1.000000e+00 new_junction_read_count=455 pos_hash_score=151 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=8 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=82 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=454 JC 1017 . NC_007779 3744263 -1 NC_007779 3903274 1 0 alignment_overlap=0 coverage_minus=283 coverage_plus=195 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__3744263__-1__NC_007779__3903274__1__0____101__101__1__0 max_left=88 max_left_minus=88 max_left_plus=88 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.10 new_junction_frequency=1.000000e+00 new_junction_read_count=481 pos_hash_score=152 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=478 JC 1018 . NC_007779 3746910 -1 NC_007779 3748110 1 0 alignment_overlap=3 coverage_minus=231 coverage_plus=233 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=86 key=NC_007779__3746910__-1__NC_007779__3748107__1__3____101__101__0__0 max_left=92 max_left_minus=92 max_left_plus=92 max_min_left=48 max_min_left_minus=48 max_min_left_plus=48 max_min_right=49 max_min_right_minus=49 max_min_right_plus=49 max_pos_hash_score=172 max_right=92 max_right_minus=92 max_right_plus=92 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.10 new_junction_frequency=1.000000e+00 new_junction_read_count=459 pos_hash_score=159 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=3 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=1 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=86 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=464 JC 1019 . NC_007779 3746911 1 NC_007779 3748646 -1 0 alignment_overlap=0 coverage_minus=230 coverage_plus=201 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__3746911__1__NC_007779__3748646__-1__0____101__101__1__0 max_left=92 max_left_minus=92 max_left_plus=92 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=94 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.05 new_junction_frequency=1.000000e+00 new_junction_read_count=456 pos_hash_score=149 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=431 JC 1020 . NC_007779 3748105 -1 NC_007779 3748643 1 0 alignment_overlap=0 coverage_minus=224 coverage_plus=224 flanking_left=101 flanking_right=101 frequency=9.977876e-01 junction_possible_overlap_registers=90 key=NC_007779__3748105__-1__NC_007779__3748643__1__0____101__101__1__0 max_left=95 max_left_minus=94 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=49 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=94 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.03 new_junction_frequency=9.977876e-01 new_junction_read_count=451 pos_hash_score=160 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=1 side_2_redundant=0 total_non_overlap_reads=448 JC 1021 . NC_007779 3750590 -1 NC_007779 3751790 1 0 alignment_overlap=4 coverage_minus=256 coverage_plus=247 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=86 key=NC_007779__3750590__-1__NC_007779__3751786__1__4____101__101__0__0 max_left=91 max_left_minus=90 max_left_plus=91 max_min_left=48 max_min_left_minus=48 max_min_left_plus=48 max_min_right=48 max_min_right_minus=48 max_min_right_plus=48 max_pos_hash_score=172 max_right=91 max_right_minus=91 max_right_plus=91 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.21 new_junction_frequency=1.000000e+00 new_junction_read_count=504 pos_hash_score=168 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=4 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=86 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=503 JC 1022 . NC_007779 3903279 -1 NC_007779 4504190 -1 0 alignment_overlap=1 coverage_minus=228 coverage_plus=234 flanking_left=101 flanking_right=101 frequency=9.915291e-01 junction_possible_overlap_registers=89 key=NC_007779__3903279__-1__NC_007779__4504191__-1__1____101__101__0__1 max_left=94 max_left_minus=94 max_left_plus=94 max_min_left=49 max_min_left_minus=49 max_min_left_plus=48 max_min_right=50 max_min_right_minus=49 max_min_right_plus=50 max_pos_hash_score=178 max_right=94 max_right_minus=94 max_right_plus=94 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.07 new_junction_frequency=9.915291e-01 new_junction_read_count=463 pos_hash_score=160 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.01 side_1_overlap=1 side_1_possible_overlap_registers=90 side_1_read_count=4 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=462 JC 1023 . NC_007779 3958122 -1 NC_007779 3958157 1 0 alignment_overlap=2 coverage_minus=200 coverage_plus=226 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=88 key=NC_007779__3958122__-1__NC_007779__3958155__1__2____101__101__0__0 max_left=93 max_left_minus=93 max_left_plus=93 max_min_left=49 max_min_left_minus=49 max_min_left_plus=49 max_min_right=49 max_min_right_minus=49 max_min_right_plus=48 max_pos_hash_score=176 max_right=93 max_right_minus=93 max_right_plus=92 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.00 new_junction_frequency=1.000000e+00 new_junction_read_count=427 pos_hash_score=161 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=2 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=88 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=426 JC 1024 . NC_007779 3987186 1 NC_007779 4009203 -1 0 alignment_overlap=1 coverage_minus=245 coverage_plus=236 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=89 key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0 max_left=94 max_left_minus=94 max_left_plus=94 max_min_left=49 max_min_left_minus=49 max_min_left_plus=49 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=178 max_right=94 max_right_minus=94 max_right_plus=94 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.12 new_junction_frequency=1.000000e+00 new_junction_read_count=483 pos_hash_score=165 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=1 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=481 JC 1025 . NC_007779 3988379 -1 NC_007779 4009199 1 0 alignment_overlap=0 coverage_minus=222 coverage_plus=223 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__3988379__-1__NC_007779__4009199__1__0____101__101__1__0 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.02 new_junction_frequency=1.000000e+00 new_junction_read_count=447 pos_hash_score=166 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=445 JC 1026 . NC_007779 4310362 -1 NC_007779 4311562 1 0 alignment_overlap=4 coverage_minus=242 coverage_plus=230 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=86 key=NC_007779__4310362__-1__NC_007779__4311558__1__4____101__101__0__0 max_left=91 max_left_minus=91 max_left_plus=91 max_min_left=48 max_min_left_minus=48 max_min_left_plus=48 max_min_right=48 max_min_right_minus=47 max_min_right_plus=48 max_pos_hash_score=172 max_right=91 max_right_minus=91 max_right_plus=91 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.14 new_junction_frequency=1.000000e+00 new_junction_read_count=475 pos_hash_score=157 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=4 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=86 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=472 JC 1027 . NC_007779 4310363 1 NC_007779 4353540 1 0 alignment_overlap=0 coverage_minus=248 coverage_plus=218 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__4310363__1__NC_007779__4353540__1__0____101__101__1__0 max_left=94 max_left_minus=94 max_left_plus=94 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=94 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.08 new_junction_frequency=1.000000e+00 new_junction_read_count=471 pos_hash_score=155 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=466 JC 1028 . NC_007779 4311557 -1 NC_007779 4353543 -1 0 alignment_overlap=0 coverage_minus=197 coverage_plus=252 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__4311557__-1__NC_007779__4353543__-1__0____101__101__1__0 max_left=93 max_left_minus=93 max_left_plus=93 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=95 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.08 new_junction_frequency=1.000000e+00 new_junction_read_count=469 pos_hash_score=160 side_1_annotate_key=repeat side_1_continuation=0 side_1_coverage=NA side_1_overlap=0 side_1_read_count=NA side_1_redundant=1 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.00 side_2_overlap=0 side_2_possible_overlap_registers=90 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=449 JC 1029 . NC_007779 4355060 1 NC_007779 4502861 1 0 alignment_overlap=0 coverage_minus=226 coverage_plus=315 flanking_left=101 flanking_right=101 frequency=1.000000e+00 junction_possible_overlap_registers=90 key=NC_007779__4355060__1__NC_007779__4502861__1__0____101__101__0__1 max_left=95 max_left_minus=95 max_left_plus=95 max_min_left=50 max_min_left_minus=50 max_min_left_plus=50 max_min_right=50 max_min_right_minus=50 max_min_right_plus=50 max_pos_hash_score=180 max_right=95 max_right_minus=94 max_right_plus=95 neg_log10_pos_hash_p_value=NT new_junction_coverage=1.25 new_junction_frequency=1.000000e+00 new_junction_read_count=545 pos_hash_score=166 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=0 side_1_possible_overlap_registers=90 side_1_read_count=0 side_1_redundant=0 side_2_annotate_key=repeat side_2_continuation=0 side_2_coverage=NA side_2_overlap=0 side_2_possible_overlap_registers=NA side_2_read_count=NA side_2_redundant=1 total_non_overlap_reads=541 JC 1030 . 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NC_007779 4547362 1 NC_007779 4547676 1 0 alignment_overlap=9 coverage_minus=38 coverage_plus=25 flanking_left=101 flanking_right=101 frequency=1.636364e-01 junction_possible_overlap_registers=81 key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0 max_left=85 max_left_minus=81 max_left_plus=85 max_min_left=45 max_min_left_minus=45 max_min_left_plus=45 max_min_right=45 max_min_right_minus=43 max_min_right_plus=45 max_pos_hash_score=162 max_right=85 max_right_minus=83 max_right_plus=85 neg_log10_pos_hash_p_value=NT new_junction_coverage=0.16 new_junction_frequency=1.636364e-01 new_junction_read_count=63 pos_hash_score=51 side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.78 side_1_overlap=9 side_1_possible_overlap_registers=90 side_1_read_count=340 side_1_redundant=0 side_2_annotate_key=gene side_2_continuation=0 side_2_coverage=0.86 side_2_overlap=0 side_2_possible_overlap_registers=81 side_2_read_count=338 side_2_redundant=0 total_non_overlap_reads=63 JC 1032 . 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