#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	05:11:26 06 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	3_D16_CTTGTA_L004_R2_001.fastq
SNP	1	71	NC_007779	66457	A	frequency=1
SNP	2	76	NC_007779	97880	T	frequency=1
SNP	3	86	NC_007779	167632	A	frequency=1
SNP	4	101	NC_007779	274547	G	frequency=1
DEL	5	809,824	NC_007779	274733	97240	frequency=1
SNP	6	134	NC_007779	547694	G	frequency=1
INS	7	135	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	137	NC_007779	556858	T	frequency=1
SNP	9	138	NC_007779	569996	C	frequency=1
SNP	10	166	NC_007779	749354	A	frequency=1
SNP	11	169	NC_007779	758440	A	frequency=1
SNP	12	177	NC_007779	887234	A	frequency=1
SNP	13	187	NC_007779	987574	T	frequency=1
SNP	14	199	NC_007779	1093686	C	frequency=1
SNP	15	200	NC_007779	1097580	T	frequency=1.784258e-01
SNP	16	212	NC_007779	1170573	T	frequency=1
SNP	17	215	NC_007779	1213001	C	frequency=2.658367e-02
SNP	18	216	NC_007779	1213013	C	frequency=2.224255e-02
DEL	19	811,837	NC_007779	1301041	1336	frequency=1
SNP	20	235	NC_007779	1318876	A	frequency=1
DEL	21	812,840	NC_007779	1413639	23060	frequency=1
SNP	22	256	NC_007779	1468443	A	frequency=2.368546e-02
SNP	23	257	NC_007779	1483588	A	frequency=1
DEL	24	260	NC_007779	1496775	1	frequency=1
SNP	25	290	NC_007779	1615814	A	frequency=1
DEL	26	294	NC_007779	1669599	1	frequency=1
DEL	27	842	NC_007779	1724327	3	frequency=1.236597e-01
SNP	28	312	NC_007779	1844073	A	frequency=1
SNP	29	322	NC_007779	1909041	A	frequency=2.548981e-02
SNP	30	325	NC_007779	1918872	A	frequency=1
SNP	31	330	NC_007779	1973476	A	frequency=1
SNP	32	335	NC_007779	2005401	T	frequency=1
SNP	33	349	NC_007779	2170094	A	frequency=1
DEL	34	814,848	NC_007779	2320795	1336	frequency=1
SNP	35	382	NC_007779	2406075	T	frequency=1
SNP	36	386	NC_007779	2416102	A	frequency=1
SNP	37	400	NC_007779	2538628	T	frequency=1
SNP	38	431	NC_007779	2827675	G	frequency=1.659966e-02
SNP	39	438	NC_007779	2865228	G	frequency=3.365898e-02
INS	40	855	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=6.028856e-01
INS	41	856	NC_007779	2865278	TTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGC	frequency=4.549975e-01
SNP	42	439	NC_007779	2866111	G	frequency=1
SNP	43	452	NC_007779	3003330	A	frequency=1
SNP	44	457	NC_007779	3049815	T	frequency=1
SNP	45	501	NC_007779	3397813	G	frequency=1
DEL	46	817,865	NC_007779	3742936	1336	frequency=1
DEL	47	622	NC_007779	3750122	1	frequency=9.543858e-01
SNP	48	623	NC_007779	3750123	T	frequency=4.553509e-02
DEL	49	818,870	NC_007779	3750591	1199	frequency=1
SNP	50	651	NC_007779	3898657	G	frequency=1
DEL	51	819,872	NC_007779	3958123	34	frequency=1
SNP	52	679	NC_007779	4090749	T	frequency=1
SNP	53	688	NC_007779	4165991	C	frequency=1
DEL	54	820,875	NC_007779	4310363	1199	frequency=1
SNP	55	754	NC_007779	4347517	C	frequency=2.155190e-01
DEL	56	756,757	NC_007779	4371271	2	frequency=1
SNP	57	795	NC_007779	4546535	A	frequency=1
RA	58	.	NC_007779	5595	0	G	T	bias_e_value=173.862	bias_p_value=3.74193e-05	fisher_strand_p_value=2.70774e-06	frequency=5.231571e-02	genotype_quality=795.9	ks_quality_p_value=1	log10_base_likelihood=-8.64547	log10_qual_likelihood_position_model=14.0382	log10_strand_likelihood_position_model=5.62218	new_cov=0/19	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=117/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/129
RA	59	.	NC_007779	6495	1	.	A	bias_e_value=2841480	bias_p_value=0.611554	fisher_strand_p_value=1	frequency=7.041931e-03	genotype_quality=1397.3	ks_quality_p_value=0.260977	log10_base_likelihood=-7.89432	log10_qual_likelihood_position_model=1.08412	log10_strand_likelihood_position_model=0.299584	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.89335e-08	ref_cov=143/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/140
RA	60	.	NC_007779	11143	0	G	T	bias_e_value=1.42131	bias_p_value=3.059e-07	fisher_strand_p_value=1.61498e-08	frequency=6.619406e-02	genotype_quality=847.8	ks_quality_p_value=1	log10_base_likelihood=-12.0499	log10_qual_likelihood_position_model=18.9262	log10_strand_likelihood_position_model=7.79183	new_cov=0/23	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=132/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/123
RA	61	.	NC_007779	15382	0	A	G	bias_e_value=2.28109e-06	bias_p_value=4.90944e-13	fisher_strand_p_value=1.49523e-14	frequency=9.814262e-02	genotype_quality=532.0	ks_quality_p_value=1	log10_base_likelihood=-10.6731	log10_qual_likelihood_position_model=21.141	log10_strand_likelihood_position_model=13.8253	new_cov=22/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=27/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/123
RA	62	.	NC_007779	29486	0	C	A	bias_e_value=2857.89	bias_p_value=0.000615085	fisher_strand_p_value=5.71079e-05	frequency=4.230118e-02	genotype_quality=721.7	ks_quality_p_value=1	log10_base_likelihood=-6.63691	log10_qual_likelihood_position_model=11.3559	log10_strand_likelihood_position_model=4.2433	new_cov=0/10	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=115/64	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/74
RA	63	.	NC_007779	29496	0	T	A	bias_e_value=0.131469	bias_p_value=2.82953e-08	fisher_strand_p_value=1.31937e-09	frequency=9.718943e-02	genotype_quality=736.6	ks_quality_p_value=1	log10_base_likelihood=-25.1446	log10_qual_likelihood_position_model=29.4971	log10_strand_likelihood_position_model=8.87963	new_cov=0/23	polymorphism_quality=19.9	quality=19.9	quality_position_model=Inf	ref_cov=127/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/100
RA	64	.	NC_007779	29503	0	T	C	bias_e_value=1.84607e-07	bias_p_value=3.97318e-14	fisher_strand_p_value=1.12161e-15	frequency=1.278062e-01	genotype_quality=663.1	ks_quality_p_value=1	log10_base_likelihood=-20.5107	log10_qual_likelihood_position_model=25.9867	log10_strand_likelihood_position_model=14.9502	new_cov=0/38	polymorphism_quality=15.2	quality=15.2	quality_position_model=Inf	ref_cov=135/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/111
RA	65	.	NC_007779	34111	1	.	T	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=1.438808e-02	genotype_quality=1333.1	ks_quality_p_value=0.99958	log10_base_likelihood=-16.5972	log10_qual_likelihood_position_model=2.82948	log10_strand_likelihood_position_model=0.427367	new_cov=2/2	polymorphism_quality=11.3	quality=11.3	quality_position_model=1.98776e-15	ref_cov=147/127	reject=INDEL_HOMOPOLYMER	tot_cov=149/129
RA	66	.	NC_007779	34112	0	T	.	bias_e_value=773286	bias_p_value=0.166429	fisher_strand_p_value=0.251959	frequency=1.070690e-02	genotype_quality=1113.4	ks_quality_p_value=0.155897	log10_base_likelihood=-8.12411	log10_qual_likelihood_position_model=1.91067	log10_strand_likelihood_position_model=0.808553	new_cov=3/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.63541e-07	ref_cov=148/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/129
RA	67	.	NC_007779	38106	0	C	G	bias_e_value=259.417	bias_p_value=5.58327e-05	fisher_strand_p_value=4.18151e-06	frequency=4.469681e-02	genotype_quality=628.3	ks_quality_p_value=0.997373	log10_base_likelihood=-6.7054	log10_qual_likelihood_position_model=11.4965	log10_strand_likelihood_position_model=5.37867	new_cov=0/9	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=124/37	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/46
RA	68	.	NC_007779	47305	0	G	T	bias_e_value=0.0363058	bias_p_value=7.81387e-09	fisher_strand_p_value=3.42806e-10	frequency=9.263897e-02	genotype_quality=738.2	ks_quality_p_value=1	log10_base_likelihood=-13.5088	log10_qual_likelihood_position_model=22.2126	log10_strand_likelihood_position_model=9.46495	new_cov=0/28	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=119/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/115
RA	69	.	NC_007779	48338	0	T	G	bias_e_value=3565.43	bias_p_value=0.000767364	fisher_strand_p_value=7.34203e-05	frequency=2.894115e-02	genotype_quality=510.2	ks_quality_p_value=0.992895	log10_base_likelihood=-6.12849	log10_qual_likelihood_position_model=4.97626	log10_strand_likelihood_position_model=4.13418	new_cov=4/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=10/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=14/122
RA	70	.	NC_007779	61542	0	C	G	bias_e_value=1102.22	bias_p_value=0.000237224	fisher_strand_p_value=2.00963e-05	frequency=5.375195e-02	genotype_quality=514.2	ks_quality_p_value=0.999019	log10_base_likelihood=-9.35415	log10_qual_likelihood_position_model=10.3369	log10_strand_likelihood_position_model=4.70695	new_cov=8/1	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=23/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=31/109
RA	71	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1052.9	new_cov=131/129	quality=1052.9	ref_cov=0/0	tot_cov=131/129
RA	72	.	NC_007779	70602	0	G	T	bias_e_value=0.102284	bias_p_value=2.20139e-08	fisher_strand_p_value=1.01403e-09	frequency=7.245111e-02	genotype_quality=730.3	ks_quality_p_value=1	log10_base_likelihood=-8.87288	log10_qual_likelihood_position_model=23.6166	log10_strand_likelihood_position_model=8.99395	new_cov=0/26	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=117/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/111
RA	73	.	NC_007779	75074	0	T	G	bias_e_value=6.04092e-37	bias_p_value=1.30015e-43	fisher_strand_p_value=1.24539e-45	frequency=2.861009e-01	genotype_quality=480.0	ks_quality_p_value=1	log10_base_likelihood=-66.1068	log10_qual_likelihood_position_model=56.8657	log10_strand_likelihood_position_model=44.9047	new_cov=82/0	polymorphism_quality=61.1	quality=61.1	quality_position_model=Inf	ref_cov=19/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/136
RA	74	.	NC_007779	75079	0	C	T	bias_e_value=0.00453161	bias_p_value=9.75308e-10	fisher_strand_p_value=3.90658e-11	frequency=7.416677e-02	genotype_quality=602.2	ks_quality_p_value=1	log10_base_likelihood=-15.6302	log10_qual_likelihood_position_model=15.5885	log10_strand_likelihood_position_model=10.4082	new_cov=14/0	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=23/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/137
RA	75	.	NC_007779	89555	0	G	T	bias_e_value=0.353377	bias_p_value=7.6055e-08	fisher_strand_p_value=4.11264e-09	frequency=6.654644e-02	genotype_quality=834.3	ks_quality_p_value=0.906176	log10_base_likelihood=-15.1668	log10_qual_likelihood_position_model=24.8783	log10_strand_likelihood_position_model=8.38588	new_cov=20/0	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=82/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/150
RA	76	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=988.2	new_cov=130/115	quality=988.2	ref_cov=0/0	tot_cov=130/115
RA	77	.	NC_007779	101246	0	T	G	bias_e_value=5471.9	bias_p_value=0.00117768	fisher_strand_p_value=0.000117159	frequency=3.812790e-02	genotype_quality=405.2	ks_quality_p_value=1	log10_base_likelihood=-9.79874	log10_qual_likelihood_position_model=8.08031	log10_strand_likelihood_position_model=3.93122	new_cov=6/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=21/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/86
RA	78	.	NC_007779	114328	0	G	T	bias_e_value=61318.1	bias_p_value=0.0131971	fisher_strand_p_value=0.00180335	frequency=2.646828e-02	genotype_quality=867.2	ks_quality_p_value=1	log10_base_likelihood=-6.04412	log10_qual_likelihood_position_model=12.4875	log10_strand_likelihood_position_model=2.87833	new_cov=0/10	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=117/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=117/130
RA	79	.	NC_007779	119384	0	T	G	bias_e_value=6.52883e-20	bias_p_value=1.40516e-26	fisher_strand_p_value=2.17191e-28	frequency=1.704626e-01	genotype_quality=533.1	ks_quality_p_value=1	log10_base_likelihood=-26.3782	log10_qual_likelihood_position_model=38.2474	log10_strand_likelihood_position_model=27.6632	new_cov=50/0	polymorphism_quality=21.2	quality=21.2	quality_position_model=Inf	ref_cov=28/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=78/131
RA	80	.	NC_007779	137009	0	G	T	bias_e_value=0.357423	bias_p_value=7.69258e-08	fisher_strand_p_value=4.29592e-09	frequency=6.301689e-02	genotype_quality=716.4	ks_quality_p_value=0.877964	log10_base_likelihood=-11.6826	log10_qual_likelihood_position_model=21.9005	log10_strand_likelihood_position_model=8.36694	new_cov=16/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=53/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=69/143
RA	81	.	NC_007779	149550	1	.	T	bias_e_value=2124240	bias_p_value=0.457186	fisher_strand_p_value=0.185585	frequency=7.781982e-03	genotype_quality=1245.3	ks_quality_p_value=0.873866	log10_base_likelihood=-8.03647	log10_qual_likelihood_position_model=1.28111	log10_strand_likelihood_position_model=0.731457	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=6.02301e-08	ref_cov=146/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/111
RA	82	.	NC_007779	151656	0	T	G	bias_e_value=4.70065e-10	bias_p_value=1.01169e-16	fisher_strand_p_value=2.43448e-18	frequency=1.269879e-01	genotype_quality=816.8	ks_quality_p_value=1	log10_base_likelihood=-24.8461	log10_qual_likelihood_position_model=41.4811	log10_strand_likelihood_position_model=17.6136	new_cov=44/0	polymorphism_quality=19.6	quality=19.6	quality_position_model=Inf	ref_cov=81/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/155
RA	83	.	NC_007779	151946	0	G	T	bias_e_value=28562.5	bias_p_value=0.00614733	fisher_strand_p_value=0.000750104	frequency=2.414417e-02	genotype_quality=1063.5	ks_quality_p_value=1	log10_base_likelihood=-5.76319	log10_qual_likelihood_position_model=10.0772	log10_strand_likelihood_position_model=3.12488	new_cov=9/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=120/153	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/153
RA	84	.	NC_007779	164576	0	A	G	bias_e_value=36.6497	bias_p_value=7.88788e-06	fisher_strand_p_value=5.09211e-07	frequency=5.625725e-02	genotype_quality=360.9	ks_quality_p_value=1	log10_base_likelihood=-6.74987	log10_qual_likelihood_position_model=9.9044	log10_strand_likelihood_position_model=6.2931	new_cov=0/8	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=99/15	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=99/23
RA	85	.	NC_007779	164601	0	T	C	bias_e_value=112240	bias_p_value=0.0241566	fisher_strand_p_value=0.00389753	frequency=4.768133e-02	genotype_quality=328.8	ks_quality_p_value=0.937362	log10_base_likelihood=-5.81818	log10_qual_likelihood_position_model=6.22163	log10_strand_likelihood_position_model=2.40921	new_cov=5/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=30/67	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=35/67
RA	86	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=906.8	new_cov=102/123	quality=906.8	ref_cov=0/0	tot_cov=102/123
RA	87	.	NC_007779	173073	0	A	C	bias_e_value=2.87391	bias_p_value=6.18534e-07	fisher_strand_p_value=3.39906e-08	frequency=3.645897e-02	genotype_quality=727.2	ks_quality_p_value=1	log10_base_likelihood=-5.73841	log10_qual_likelihood_position_model=16.6941	log10_strand_likelihood_position_model=7.46864	new_cov=0/15	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=137/56	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/71
RA	88	.	NC_007779	175694	0	T	G	bias_e_value=2.16763e-12	bias_p_value=4.66525e-19	fisher_strand_p_value=9.91332e-21	frequency=1.236668e-01	genotype_quality=533.2	ks_quality_p_value=1	log10_base_likelihood=-10.0848	log10_qual_likelihood_position_model=32.6336	log10_strand_likelihood_position_model=20.0038	new_cov=47/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=44/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/110
RA	89	.	NC_007779	193477	1	.	G	bias_e_value=1028860	bias_p_value=0.221434	fisher_strand_p_value=0.101815	frequency=1.315784e-02	genotype_quality=1106.3	ks_quality_p_value=0.563775	log10_base_likelihood=-12.8924	log10_qual_likelihood_position_model=1.97133	log10_strand_likelihood_position_model=0.99219	new_cov=3/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=5.91217e-12	ref_cov=104/121	reject=POLYMORPHISM_STRAND	tot_cov=107/121
RA	90	.	NC_007779	193480	0	C	G	bias_e_value=6.05619e-18	bias_p_value=1.30343e-24	fisher_strand_p_value=2.17603e-26	frequency=2.379274e-01	genotype_quality=537.0	ks_quality_p_value=0.996785	log10_base_likelihood=-69.5295	log10_qual_likelihood_position_model=33.5615	log10_strand_likelihood_position_model=25.6623	new_cov=50/0	polymorphism_quality=64.5	quality=64.5	quality_position_model=2.43858e-12	ref_cov=31/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=81/122
RA	91	.	NC_007779	193483	0	C	G	bias_e_value=2.65288e-08	bias_p_value=5.70962e-15	fisher_strand_p_value=1.52587e-16	frequency=1.176157e-01	genotype_quality=571.7	ks_quality_p_value=1	log10_base_likelihood=-12.9923	log10_qual_likelihood_position_model=23.1716	log10_strand_likelihood_position_model=15.8165	new_cov=27/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=30/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=57/123
RA	92	.	NC_007779	193489	0	G	T	bias_e_value=0.057514	bias_p_value=1.23784e-08	fisher_strand_p_value=5.54773e-10	frequency=9.538937e-02	genotype_quality=722.8	ks_quality_p_value=1	log10_base_likelihood=-14.6727	log10_qual_likelihood_position_model=19.138	log10_strand_likelihood_position_model=9.26396	new_cov=23/1	polymorphism_quality=9.3	quality=9.3	quality_position_model=Inf	ref_cov=59/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/132
RA	93	.	NC_007779	193496	0	A	T	bias_e_value=3.20122e-07	bias_p_value=6.88977e-14	fisher_strand_p_value=1.97656e-15	frequency=1.280732e-01	genotype_quality=715.9	ks_quality_p_value=1	log10_base_likelihood=-43.0125	log10_qual_likelihood_position_model=30.9782	log10_strand_likelihood_position_model=14.7041	new_cov=26/0	polymorphism_quality=37.9	quality=37.9	quality_position_model=Inf	ref_cov=38/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=64/136
RA	94	.	NC_007779	194839	1	.	T	bias_e_value=3950160	bias_p_value=0.850167	fisher_strand_p_value=0.576026	frequency=1.224518e-02	genotype_quality=1179.6	ks_quality_p_value=0.877084	log10_base_likelihood=-13.0961	log10_qual_likelihood_position_model=2.02608	log10_strand_likelihood_position_model=0.505951	new_cov=1/2	polymorphism_quality=7.7	quality=7.7	quality_position_model=1.32924e-12	ref_cov=140/102	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/104
RA	95	.	NC_007779	209042	0	G	A	bias_e_value=2861060	bias_p_value=0.615768	fisher_strand_p_value=0.341583	frequency=1.571560e-02	genotype_quality=1040.5	ks_quality_p_value=0.773248	log10_base_likelihood=-7.2491	log10_qual_likelihood_position_model=3.27853	log10_strand_likelihood_position_model=0.665215	new_cov=1/3	polymorphism_quality=1.7	quality=1.7	quality_position_model=4.15192e-05	ref_cov=134/115	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=135/118
RA	96	.	NC_007779	212548	0	T	G	bias_e_value=9.17742e-07	bias_p_value=1.9752e-13	fisher_strand_p_value=5.84852e-15	frequency=1.232362e-01	genotype_quality=557.5	ks_quality_p_value=1	log10_base_likelihood=-16.4627	log10_qual_likelihood_position_model=30.6529	log10_strand_likelihood_position_model=14.233	new_cov=33/0	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=51/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=84/114
RA	97	.	NC_007779	218827	1	.	A	bias_e_value=3847010	bias_p_value=0.827968	fisher_strand_p_value=1	frequency=9.346008e-03	genotype_quality=1039.1	ks_quality_p_value=0.47414	log10_base_likelihood=-8.48987	log10_qual_likelihood_position_model=1.87489	log10_strand_likelihood_position_model=0.300364	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.01637e-08	ref_cov=100/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=101/113
RA	98	.	NC_007779	233118	0	T	C	bias_e_value=4.63544	bias_p_value=9.97657e-07	fisher_strand_p_value=5.6444e-08	frequency=5.987072e-02	genotype_quality=555.5	ks_quality_p_value=0.999111	log10_base_likelihood=-9.21434	log10_qual_likelihood_position_model=13.7377	log10_strand_likelihood_position_model=7.24838	new_cov=0/10	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=122/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/33
RA	99	.	NC_007779	252970	0	A	C	bias_e_value=1.43544e-09	bias_p_value=3.08941e-16	fisher_strand_p_value=7.64468e-18	frequency=9.441996e-02	genotype_quality=572.3	ks_quality_p_value=1	log10_base_likelihood=-10.8284	log10_qual_likelihood_position_model=27.218	log10_strand_likelihood_position_model=17.1166	new_cov=0/43	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=118/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/102
RA	100	.	NC_007779	265564	0	T	G	bias_e_value=1.18305e-05	bias_p_value=2.5462e-12	fisher_strand_p_value=8.17799e-14	frequency=6.498957e-02	genotype_quality=674.0	ks_quality_p_value=1	log10_base_likelihood=-7.1119	log10_qual_likelihood_position_model=21.9079	log10_strand_likelihood_position_model=13.0874	new_cov=29/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=59/134	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=88/134
RA	101	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1080.9	new_cov=130/125	quality=1080.9	ref_cov=0/0	tot_cov=130/125
RA	102	.	NC_007779	289860	0	T	G	deleted=1	frequency=1	genotype_quality=-0.3	new_cov=1/0	quality=-0.3	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	103	.	NC_007779	289862	0	A	T	deleted=1	frequency=1	genotype_quality=-0.3	new_cov=1/0	quality=-0.3	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	104	.	NC_007779	289922	0	T	A	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	105	.	NC_007779	371962	0	C	G	deleted=1	frequency=1	genotype_quality=1.8	new_cov=1/0	quality=1.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	106	.	NC_007779	374799	0	T	G	bias_e_value=2.96099e-13	bias_p_value=6.37276e-20	fisher_strand_p_value=1.29809e-21	frequency=9.098768e-02	genotype_quality=586.2	ks_quality_p_value=1	log10_base_likelihood=-10.0023	log10_qual_likelihood_position_model=28.9581	log10_strand_likelihood_position_model=20.8867	new_cov=27/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=16/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=43/142
RA	107	.	NC_007779	379236	1	.	G	bias_e_value=159562	bias_p_value=0.0343415	fisher_strand_p_value=0.0843357	frequency=4.000092e-02	genotype_quality=662.9	ks_quality_p_value=0.0657285	log10_base_likelihood=-30.466	log10_qual_likelihood_position_model=3.36616	log10_strand_likelihood_position_model=1.2445	new_cov=6/0	polymorphism_quality=25.3	quality=25.3	quality_position_model=4.39459e-28	ref_cov=88/56	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=94/56
RA	108	.	NC_007779	379237	0	G	.	bias_e_value=4003490	bias_p_value=0.861645	fisher_strand_p_value=1	frequency=2.394485e-02	genotype_quality=677.8	ks_quality_p_value=0.522461	log10_base_likelihood=-12.3627	log10_qual_likelihood_position_model=2.13265	log10_strand_likelihood_position_model=0.451556	new_cov=2/2	polymorphism_quality=7.0	quality=7.0	quality_position_model=8.41994e-12	ref_cov=97/66	reject=INDEL_HOMOPOLYMER	tot_cov=99/68
RA	109	.	NC_007779	379266	0	G	C	bias_e_value=294.606	bias_p_value=6.34061e-05	fisher_strand_p_value=5.20189e-06	frequency=6.382704e-02	genotype_quality=578.6	ks_quality_p_value=0.919932	log10_base_likelihood=-7.42795	log10_qual_likelihood_position_model=18.0206	log10_strand_likelihood_position_model=5.28384	new_cov=14/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=62/96	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=76/97
RA	110	.	NC_007779	387900	1	.	G	bias_e_value=290998	bias_p_value=0.0626296	fisher_strand_p_value=0.0126944	frequency=1.449299e-02	genotype_quality=660.4	ks_quality_p_value=0.901988	log10_base_likelihood=-8.85672	log10_qual_likelihood_position_model=3.19742	log10_strand_likelihood_position_model=1.89639	new_cov=0/2	polymorphism_quality=3.4	quality=3.4	quality_position_model=1.36534e-05	ref_cov=122/14	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/16
RA	111	.	NC_007779	387917	0	T	G	bias_e_value=0.0613047	bias_p_value=1.31942e-08	fisher_strand_p_value=5.93114e-10	frequency=6.490660e-02	genotype_quality=418.1	ks_quality_p_value=1	log10_base_likelihood=-9.44559	log10_qual_likelihood_position_model=14.0592	log10_strand_likelihood_position_model=9.2305	new_cov=1/12	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=118/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/25
RA	112	.	NC_007779	387919	0	A	G	bias_e_value=1.56238e-07	bias_p_value=3.36261e-14	fisher_strand_p_value=9.51154e-16	frequency=1.076837e-01	genotype_quality=425.5	ks_quality_p_value=0.99318	log10_base_likelihood=-22.286	log10_qual_likelihood_position_model=16.2358	log10_strand_likelihood_position_model=15.0217	new_cov=0/16	polymorphism_quality=17.0	quality=17.0	quality_position_model=Inf	ref_cov=121/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/24
RA	113	.	NC_007779	414911	0	T	G	bias_e_value=2.32919e-06	bias_p_value=5.01296e-13	fisher_strand_p_value=1.52777e-14	frequency=8.237314e-02	genotype_quality=645.8	ks_quality_p_value=1	log10_base_likelihood=-8.27404	log10_qual_likelihood_position_model=26.7927	log10_strand_likelihood_position_model=13.8159	new_cov=39/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=73/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=112/116
RA	114	.	NC_007779	416826	0	A	G	bias_e_value=0.202492	bias_p_value=4.35811e-08	fisher_strand_p_value=2.076e-09	frequency=7.781601e-02	genotype_quality=576.4	ks_quality_p_value=1	log10_base_likelihood=-7.8959	log10_qual_likelihood_position_model=15.0922	log10_strand_likelihood_position_model=8.68277	new_cov=16/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=40/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=56/120
RA	115	.	NC_007779	429745	0	T	.	bias_e_value=4498890	bias_p_value=0.968266	fisher_strand_p_value=1	frequency=1.228619e-02	genotype_quality=970.6	ks_quality_p_value=0.758889	log10_base_likelihood=-8.0787	log10_qual_likelihood_position_model=1.3087	log10_strand_likelihood_position_model=0.389942	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.58185e-08	ref_cov=131/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/111
RA	116	.	NC_007779	432858	0	T	G	bias_e_value=1.59309e-11	bias_p_value=3.4287e-18	fisher_strand_p_value=7.6157e-20	frequency=1.605377e-01	genotype_quality=519.7	ks_quality_p_value=1	log10_base_likelihood=-17.506	log10_qual_likelihood_position_model=34.6069	log10_strand_likelihood_position_model=19.1461	new_cov=53/0	polymorphism_quality=12.2	quality=12.2	quality_position_model=Inf	ref_cov=56/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/105
RA	117	.	NC_007779	440767	0	G	T	bias_e_value=0.00316536	bias_p_value=6.81261e-10	fisher_strand_p_value=2.68854e-11	frequency=9.802580e-02	genotype_quality=768.4	ks_quality_p_value=1	log10_base_likelihood=-22.0239	log10_qual_likelihood_position_model=21.5953	log10_strand_likelihood_position_model=10.5705	new_cov=0/28	polymorphism_quality=16.8	quality=16.8	quality_position_model=Inf	ref_cov=133/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/111
RA	118	.	NC_007779	450484	0	G	T	bias_e_value=596.247	bias_p_value=0.000128326	fisher_strand_p_value=1.11055e-05	frequency=4.670477e-02	genotype_quality=651.2	ks_quality_p_value=0.925493	log10_base_likelihood=-6.70926	log10_qual_likelihood_position_model=13.8065	log10_strand_likelihood_position_model=4.95446	new_cov=11/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=60/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=71/120
RA	119	.	NC_007779	465801	0	C	A	bias_e_value=0.00309112	bias_p_value=6.65283e-10	fisher_strand_p_value=2.6271e-11	frequency=1.083250e-01	genotype_quality=556.2	ks_quality_p_value=0.998413	log10_base_likelihood=-22.639	log10_qual_likelihood_position_model=22.4381	log10_strand_likelihood_position_model=10.5805	new_cov=0/20	polymorphism_quality=17.4	quality=17.4	quality_position_model=Inf	ref_cov=112/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/57
RA	120	.	NC_007779	467487	1	.	T	bias_e_value=2223270	bias_p_value=0.478499	fisher_strand_p_value=0.568156	frequency=1.327419e-02	genotype_quality=1072.2	ks_quality_p_value=0.306481	log10_base_likelihood=-12.6058	log10_qual_likelihood_position_model=3.76784	log10_strand_likelihood_position_model=0.529484	new_cov=2/1	polymorphism_quality=7.2	quality=7.2	quality_position_model=2.68644e-10	ref_cov=90/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=92/134
RA	121	.	NC_007779	468401	0	C	A	bias_e_value=3394.08	bias_p_value=0.000730487	fisher_strand_p_value=6.90386e-05	frequency=4.103088e-02	genotype_quality=827.1	ks_quality_p_value=1	log10_base_likelihood=-5.66668	log10_qual_likelihood_position_model=14.2839	log10_strand_likelihood_position_model=4.19522	new_cov=15/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=116/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/112
RA	122	.	NC_007779	494823	0	T	G	bias_e_value=1.75364e-06	bias_p_value=3.77424e-13	fisher_strand_p_value=1.14008e-14	frequency=6.791544e-02	genotype_quality=578.3	ks_quality_p_value=1	log10_base_likelihood=-6.88805	log10_qual_likelihood_position_model=25.5188	log10_strand_likelihood_position_model=13.9431	new_cov=22/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=27/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=50/125
RA	123	.	NC_007779	497079	0	C	G	bias_e_value=397.449	bias_p_value=8.55404e-05	fisher_strand_p_value=6.61784e-06	frequency=4.775381e-02	genotype_quality=733.0	ks_quality_p_value=1	log10_base_likelihood=-8.18136	log10_qual_likelihood_position_model=13.2312	log10_strand_likelihood_position_model=5.17928	new_cov=0/11	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=127/59	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/70
RA	124	.	NC_007779	497096	0	T	G	bias_e_value=200.195	bias_p_value=4.30867e-05	fisher_strand_p_value=3.15254e-06	frequency=4.972029e-02	genotype_quality=633.6	ks_quality_p_value=1	log10_base_likelihood=-8.20425	log10_qual_likelihood_position_model=18.4433	log10_strand_likelihood_position_model=5.51561	new_cov=1/16	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=117/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/84
RA	125	.	NC_007779	497098	0	A	G	bias_e_value=386.172	bias_p_value=8.31133e-05	fisher_strand_p_value=6.41458e-06	frequency=5.555201e-02	genotype_quality=667.0	ks_quality_p_value=1	log10_base_likelihood=-11.6951	log10_qual_likelihood_position_model=16.3467	log10_strand_likelihood_position_model=5.19283	new_cov=0/13	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=119/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/85
RA	126	.	NC_007779	500799	0	A	C	bias_e_value=5.21464e-07	bias_p_value=1.12231e-13	fisher_strand_p_value=3.26682e-15	frequency=6.633759e-02	genotype_quality=576.5	ks_quality_p_value=1	log10_base_likelihood=-6.31069	log10_qual_likelihood_position_model=25.7892	log10_strand_likelihood_position_model=14.4859	new_cov=0/24	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=129/31	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/55
RA	127	.	NC_007779	503058	0	T	C	bias_e_value=0.00940796	bias_p_value=2.02481e-09	fisher_strand_p_value=8.36551e-11	frequency=9.882689e-02	genotype_quality=519.9	ks_quality_p_value=1	log10_base_likelihood=-8.68	log10_qual_likelihood_position_model=20.6725	log10_strand_likelihood_position_model=10.0775	new_cov=0/21	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=102/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/61
RA	128	.	NC_007779	513848	0	A	C	bias_e_value=3.50107e-15	bias_p_value=7.53513e-22	fisher_strand_p_value=1.4053e-23	frequency=1.339278e-01	genotype_quality=536.6	ks_quality_p_value=1	log10_base_likelihood=-13.1407	log10_qual_likelihood_position_model=34.3539	log10_strand_likelihood_position_model=22.8522	new_cov=0/43	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=120/30	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=120/73
RA	129	.	NC_007779	522431	0	T	.	bias_e_value=241424	bias_p_value=0.0519601	fisher_strand_p_value=1	frequency=1.715946e-02	genotype_quality=936.6	ks_quality_p_value=0.00912018	log10_base_likelihood=-11.6442	log10_qual_likelihood_position_model=2.51296	log10_strand_likelihood_position_model=0.452581	new_cov=2/2	polymorphism_quality=6.2	quality=6.2	quality_position_model=1.12192e-10	ref_cov=136/93	reject=INDEL_HOMOPOLYMER	tot_cov=138/95
RA	130	.	NC_007779	524490	0	T	G	bias_e_value=3.27358e-09	bias_p_value=7.04551e-16	fisher_strand_p_value=1.78065e-17	frequency=1.067691e-01	genotype_quality=629.7	ks_quality_p_value=1	log10_base_likelihood=-16.4164	log10_qual_likelihood_position_model=30.2218	log10_strand_likelihood_position_model=16.7494	new_cov=26/0	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=29/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=55/143
RA	131	.	NC_007779	527270	0	A	C	bias_e_value=0.0101278	bias_p_value=2.17975e-09	fisher_strand_p_value=9.03432e-11	frequency=6.412029e-02	genotype_quality=655.4	ks_quality_p_value=1	log10_base_likelihood=-6.07295	log10_qual_likelihood_position_model=21.5423	log10_strand_likelihood_position_model=10.0441	new_cov=0/20	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=131/50	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/70
RA	132	.	NC_007779	535125	0	T	G	bias_e_value=4.15354e-16	bias_p_value=8.93939e-23	fisher_strand_p_value=1.60231e-24	frequency=1.401730e-01	genotype_quality=565.4	ks_quality_p_value=1	log10_base_likelihood=-12.7844	log10_qual_likelihood_position_model=34.3904	log10_strand_likelihood_position_model=23.7953	new_cov=58/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=50/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=109/121
RA	133	.	NC_007779	535142	0	A	G	bias_e_value=7.84258e-05	bias_p_value=1.68791e-11	fisher_strand_p_value=5.78479e-13	frequency=1.051230e-01	genotype_quality=605.4	ks_quality_p_value=1	log10_base_likelihood=-13.8829	log10_qual_likelihood_position_model=19.0239	log10_strand_likelihood_position_model=12.2377	new_cov=26/0	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=51/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=77/125
RA	134	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=851.8	new_cov=90/114	quality=851.8	ref_cov=0/0	tot_cov=90/114
RA	135	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=950.1	new_cov=107/114	quality=950.1	ref_cov=2/0	tot_cov=109/114
RA	136	.	NC_007779	556653	0	A	C	bias_e_value=4.31912e-11	bias_p_value=9.29577e-18	fisher_strand_p_value=2.11262e-19	frequency=8.301497e-02	genotype_quality=655.6	ks_quality_p_value=1	log10_base_likelihood=-13.4839	log10_qual_likelihood_position_model=27.4236	log10_strand_likelihood_position_model=18.6752	new_cov=0/27	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=153/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/53
RA	137	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=1024.1	new_cov=130/125	quality=1024.1	ref_cov=0/0	tot_cov=130/125
RA	138	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1120.2	new_cov=128/130	quality=1120.2	ref_cov=0/0	tot_cov=128/130
RA	139	.	NC_007779	589153	0	A	G	bias_e_value=152.13	bias_p_value=3.27419e-05	fisher_strand_p_value=2.34486e-06	frequency=5.468798e-02	genotype_quality=611.4	ks_quality_p_value=1	log10_base_likelihood=-5.74022	log10_qual_likelihood_position_model=11.4977	log10_strand_likelihood_position_model=5.62988	new_cov=15/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=73/111	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=88/111
RA	140	.	NC_007779	589157	0	T	G	bias_e_value=3.62008e-10	bias_p_value=7.79126e-17	fisher_strand_p_value=1.86285e-18	frequency=1.303916e-01	genotype_quality=507.5	ks_quality_p_value=1	log10_base_likelihood=-16.4688	log10_qual_likelihood_position_model=35.4108	log10_strand_likelihood_position_model=17.7298	new_cov=37/0	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=37/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=74/110
RA	141	.	NC_007779	593216	0	T	G	bias_e_value=2.22546e-11	bias_p_value=4.78971e-18	fisher_strand_p_value=1.07201e-19	frequency=1.176910e-01	genotype_quality=527.9	ks_quality_p_value=1	log10_base_likelihood=-23.12	log10_qual_likelihood_position_model=26.812	log10_strand_likelihood_position_model=18.9698	new_cov=23/0	polymorphism_quality=17.9	quality=17.9	quality_position_model=Inf	ref_cov=12/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/130
RA	142	.	NC_007779	595481	0	T	G	bias_e_value=7.02795e-07	bias_p_value=1.51258e-13	fisher_strand_p_value=4.44255e-15	frequency=8.534813e-02	genotype_quality=581.4	ks_quality_p_value=1	log10_base_likelihood=-5.98134	log10_qual_likelihood_position_model=26.8409	log10_strand_likelihood_position_model=14.6222	new_cov=44/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=71/106	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/106
RA	143	.	NC_007779	598799	0	T	G	bias_e_value=2.12224e-09	bias_p_value=4.56756e-16	fisher_strand_p_value=1.14156e-17	frequency=1.284552e-01	genotype_quality=486.2	ks_quality_p_value=1	log10_base_likelihood=-17.7986	log10_qual_likelihood_position_model=27.1862	log10_strand_likelihood_position_model=16.9425	new_cov=26/0	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=20/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=46/113
RA	144	.	NC_007779	598802	0	T	G	bias_e_value=0.000984559	bias_p_value=2.119e-10	fisher_strand_p_value=7.97995e-12	frequency=7.431650e-02	genotype_quality=513.4	ks_quality_p_value=1	log10_base_likelihood=-6.14065	log10_qual_likelihood_position_model=18.3748	log10_strand_likelihood_position_model=11.098	new_cov=18/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=27/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=45/113
RA	145	.	NC_007779	606911	1	.	G	bias_e_value=134462	bias_p_value=0.0289395	fisher_strand_p_value=0.00585975	frequency=2.272701e-02	genotype_quality=1061.0	ks_quality_p_value=0.771834	log10_base_likelihood=-24.1475	log10_qual_likelihood_position_model=2.26006	log10_strand_likelihood_position_model=2.23212	new_cov=5/0	polymorphism_quality=18.9	quality=18.9	quality_position_model=7.96833e-22	ref_cov=75/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=80/140
RA	146	.	NC_007779	606915	0	T	G	bias_e_value=8.36702e-08	bias_p_value=1.80078e-14	fisher_strand_p_value=4.99104e-16	frequency=8.052397e-02	genotype_quality=546.8	ks_quality_p_value=0.995645	log10_base_likelihood=-29.7416	log10_qual_likelihood_position_model=14.8491	log10_strand_likelihood_position_model=15.3018	new_cov=13/0	polymorphism_quality=24.5	quality=24.5	quality_position_model=Inf	ref_cov=4/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=17/144
RA	147	.	NC_007779	612991	0	C	G	bias_e_value=0.000179148	bias_p_value=3.85568e-11	fisher_strand_p_value=1.36327e-12	frequency=9.281826e-02	genotype_quality=562.6	ks_quality_p_value=0.998589	log10_base_likelihood=-22.7311	log10_qual_likelihood_position_model=18.0885	log10_strand_likelihood_position_model=11.8654	new_cov=0/14	polymorphism_quality=17.5	quality=17.5	quality_position_model=Inf	ref_cov=121/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/27
RA	148	.	NC_007779	616029	0	C	A	bias_e_value=2.23822	bias_p_value=4.81717e-07	fisher_strand_p_value=2.61696e-08	frequency=4.980087e-02	genotype_quality=674.1	ks_quality_p_value=0.997071	log10_base_likelihood=-5.98363	log10_qual_likelihood_position_model=17.4252	log10_strand_likelihood_position_model=7.5822	new_cov=0/12	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=139/36	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/48
RA	149	.	NC_007779	617601	0	C	A	bias_e_value=89.7738	bias_p_value=1.93214e-05	fisher_strand_p_value=1.32971e-06	frequency=4.745150e-02	genotype_quality=666.9	ks_quality_p_value=1	log10_base_likelihood=-8.56499	log10_qual_likelihood_position_model=11.5634	log10_strand_likelihood_position_model=5.87624	new_cov=9/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=32/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=41/129
RA	150	.	NC_007779	645484	0	A	C	bias_e_value=9.96621e-08	bias_p_value=2.14496e-14	fisher_strand_p_value=5.94861e-16	frequency=9.597397e-02	genotype_quality=746.6	ks_quality_p_value=1	log10_base_likelihood=-12.5047	log10_qual_likelihood_position_model=30.0327	log10_strand_likelihood_position_model=15.2256	new_cov=0/33	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=150/63	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/96
RA	151	.	NC_007779	645970	0	T	G	bias_e_value=1.22318e-14	bias_p_value=2.63257e-21	fisher_strand_p_value=5.02935e-23	frequency=1.567054e-01	genotype_quality=453.4	ks_quality_p_value=1	log10_base_likelihood=-36.7039	log10_qual_likelihood_position_model=28.6721	log10_strand_likelihood_position_model=22.2985	new_cov=28/0	polymorphism_quality=31.5	quality=31.5	quality_position_model=Inf	ref_cov=10/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=38/120
RA	152	.	NC_007779	646440	0	C	A	bias_e_value=5.20638e-15	bias_p_value=1.12054e-21	fisher_strand_p_value=2.11992e-23	frequency=1.271291e-01	genotype_quality=630.8	ks_quality_p_value=0.993285	log10_base_likelihood=-67.072	log10_qual_likelihood_position_model=19.8792	log10_strand_likelihood_position_model=22.6737	new_cov=0/22	polymorphism_quality=62.0	quality=62.0	quality_position_model=9.78261e-27	ref_cov=146/5	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/27
RA	153	.	NC_007779	649677	0	T	G	bias_e_value=2.59008e-13	bias_p_value=5.57446e-20	fisher_strand_p_value=1.13233e-21	frequency=1.279411e-01	genotype_quality=531.5	ks_quality_p_value=1	log10_base_likelihood=-15.9533	log10_qual_likelihood_position_model=29.2473	log10_strand_likelihood_position_model=20.946	new_cov=35/0	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=25/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/123
RA	154	.	NC_007779	650004	0	C	T	bias_e_value=79.2958	bias_p_value=1.70663e-05	fisher_strand_p_value=1.16384e-06	frequency=5.170059e-02	genotype_quality=880.3	ks_quality_p_value=1	log10_base_likelihood=-9.23111	log10_qual_likelihood_position_model=16.8007	log10_strand_likelihood_position_model=5.93411	new_cov=15/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=89/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/144
RA	155	.	NC_007779	660356	0	T	G	bias_e_value=1.41308e-17	bias_p_value=3.04127e-24	fisher_strand_p_value=5.13458e-26	frequency=1.457882e-01	genotype_quality=517.7	ks_quality_p_value=1	log10_base_likelihood=-21.2506	log10_qual_likelihood_position_model=32.6554	log10_strand_likelihood_position_model=25.2895	new_cov=42/0	polymorphism_quality=16.0	quality=16.0	quality_position_model=Inf	ref_cov=23/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=65/127
RA	156	.	NC_007779	665062	0	C	A	bias_e_value=0.00403715	bias_p_value=8.6889e-10	fisher_strand_p_value=3.52444e-11	frequency=1.355705e-01	genotype_quality=539.1	ks_quality_p_value=0.982745	log10_base_likelihood=-31.5485	log10_qual_likelihood_position_model=26.3748	log10_strand_likelihood_position_model=10.4529	new_cov=0/24	polymorphism_quality=26.4	quality=26.4	quality_position_model=Inf	ref_cov=100/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=100/70
RA	157	.	NC_007779	685600	0	T	.	bias_e_value=1702430	bias_p_value=0.366402	fisher_strand_p_value=0.596604	frequency=4.735947e-03	genotype_quality=2513.6	ks_quality_p_value=0.194838	log10_base_likelihood=-6.71863	log10_qual_likelihood_position_model=2.88413	log10_strand_likelihood_position_model=0.464849	new_cov=2/1	polymorphism_quality=1.2	quality=1.2	quality_position_model=3.54966e-05	ref_cov=288/340	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=290/342
RA	158	.	NC_007779	686495	0	A	C	bias_e_value=3.74741e-32	bias_p_value=8.0653e-39	fisher_strand_p_value=8.64925e-41	frequency=1.186309e-01	genotype_quality=1330.4	ks_quality_p_value=1	log10_base_likelihood=-59.1636	log10_qual_likelihood_position_model=65.392	log10_strand_likelihood_position_model=40.063	new_cov=0/57	polymorphism_quality=54.1	quality=54.1	quality_position_model=Inf	ref_cov=311/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=311/107
RA	159	.	NC_007779	687133	0	A	C	bias_e_value=1.26837e-16	bias_p_value=2.72983e-23	fisher_strand_p_value=4.78931e-25	frequency=4.914427e-02	genotype_quality=1807.5	ks_quality_p_value=1	log10_base_likelihood=-21.3108	log10_qual_likelihood_position_model=55.8159	log10_strand_likelihood_position_model=24.3197	new_cov=0/51	polymorphism_quality=16.0	quality=16.0	quality_position_model=Inf	ref_cov=342/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=342/198
RA	160	.	NC_007779	688155	0	T	G	bias_e_value=2.63479e-17	bias_p_value=5.67068e-24	fisher_strand_p_value=9.67736e-26	frequency=4.838896e-02	genotype_quality=1925.1	ks_quality_p_value=1	log10_base_likelihood=-15.9913	log10_qual_likelihood_position_model=78.2142	log10_strand_likelihood_position_model=25.0142	new_cov=66/0	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=208/335	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=274/335
RA	161	.	NC_007779	704593	0	T	G	bias_e_value=2.53715e-11	bias_p_value=5.46055e-18	fisher_strand_p_value=1.22584e-19	frequency=8.241940e-02	genotype_quality=614.2	ks_quality_p_value=1	log10_base_likelihood=-8.87332	log10_qual_likelihood_position_model=29.2621	log10_strand_likelihood_position_model=18.9116	new_cov=31/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=30/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/138
RA	162	.	NC_007779	704668	0	T	G	bias_e_value=1.76907e-11	bias_p_value=3.80746e-18	fisher_strand_p_value=8.47716e-20	frequency=8.604479e-02	genotype_quality=527.1	ks_quality_p_value=1	log10_base_likelihood=-7.82395	log10_qual_likelihood_position_model=29.515	log10_strand_likelihood_position_model=19.0717	new_cov=26/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=16/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=42/125
RA	163	.	NC_007779	706282	0	T	G	bias_e_value=120.413	bias_p_value=2.59156e-05	fisher_strand_p_value=1.82381e-06	frequency=2.588654e-02	genotype_quality=569.6	ks_quality_p_value=0.999625	log10_base_likelihood=-6.08107	log10_qual_likelihood_position_model=6.20391	log10_strand_likelihood_position_model=5.73902	new_cov=4/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=3/141	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=7/141
RA	164	.	NC_007779	706385	1	.	T	bias_e_value=3748250	bias_p_value=0.806711	fisher_strand_p_value=0.606196	frequency=1.115227e-02	genotype_quality=1292.9	ks_quality_p_value=0.736951	log10_base_likelihood=-12.5578	log10_qual_likelihood_position_model=2.78858	log10_strand_likelihood_position_model=0.447044	new_cov=1/2	polymorphism_quality=7.2	quality=7.2	quality_position_model=2.46365e-11	ref_cov=140/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/128
RA	165	.	NC_007779	706386	0	T	.	bias_e_value=2654510	bias_p_value=0.571314	fisher_strand_p_value=0.248954	frequency=1.106071e-02	genotype_quality=1079.3	ks_quality_p_value=0.932881	log10_base_likelihood=-7.92234	log10_qual_likelihood_position_model=1.90869	log10_strand_likelihood_position_model=0.84645	new_cov=3/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.65194e-07	ref_cov=139/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/129
RA	166	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=1184.8	new_cov=161/131	quality=1184.8	ref_cov=0/0	tot_cov=161/131
RA	167	.	NC_007779	752693	0	A	C	bias_e_value=1.0702e-20	bias_p_value=2.30333e-27	fisher_strand_p_value=3.46193e-29	frequency=1.704712e-01	genotype_quality=649.0	ks_quality_p_value=1	log10_base_likelihood=-34.6287	log10_qual_likelihood_position_model=43.0752	log10_strand_likelihood_position_model=28.4607	new_cov=0/47	polymorphism_quality=29.5	quality=29.5	quality_position_model=Inf	ref_cov=157/30	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/77
RA	168	.	NC_007779	753547	0	T	A	bias_e_value=1629.99	bias_p_value=0.000350812	fisher_strand_p_value=3.08059e-05	frequency=3.768158e-02	genotype_quality=751.0	ks_quality_p_value=1	log10_base_likelihood=-5.86604	log10_qual_likelihood_position_model=14.5658	log10_strand_likelihood_position_model=4.51137	new_cov=0/9	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=141/60	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/69
RA	169	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=1027.9	new_cov=126/130	quality=1027.9	ref_cov=0/0	tot_cov=126/130
RA	170	.	NC_007779	759019	0	C	G	bias_e_value=2.35841e-09	bias_p_value=5.07584e-16	fisher_strand_p_value=1.28775e-17	frequency=9.601164e-02	genotype_quality=611.7	ks_quality_p_value=0.9878	log10_base_likelihood=-37.6267	log10_qual_likelihood_position_model=15.998	log10_strand_likelihood_position_model=16.8902	new_cov=0/15	polymorphism_quality=32.5	quality=32.5	quality_position_model=1.29929e-06	ref_cov=137/4	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/19
RA	171	.	NC_007779	827921	0	T	G	bias_e_value=5.75799e-13	bias_p_value=1.23926e-19	fisher_strand_p_value=2.55968e-21	frequency=1.499782e-01	genotype_quality=488.2	ks_quality_p_value=1	log10_base_likelihood=-13.5738	log10_qual_likelihood_position_model=31.8164	log10_strand_likelihood_position_model=20.5918	new_cov=46/0	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=40/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/111
RA	172	.	NC_007779	829585	0	G	T	bias_e_value=0.018309	bias_p_value=3.94053e-09	fisher_strand_p_value=1.67798e-10	frequency=8.699274e-02	genotype_quality=654.7	ks_quality_p_value=0.998911	log10_base_likelihood=-21.3352	log10_qual_likelihood_position_model=20.612	log10_strand_likelihood_position_model=9.77521	new_cov=18/0	polymorphism_quality=16.1	quality=16.1	quality_position_model=Inf	ref_cov=43/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/130
RA	173	.	NC_007779	837857	0	A	.	bias_e_value=3723360	bias_p_value=0.801355	fisher_strand_p_value=0.648467	frequency=1.531696e-02	genotype_quality=1041.7	ks_quality_p_value=0.678755	log10_base_likelihood=-11.3205	log10_qual_likelihood_position_model=2.00131	log10_strand_likelihood_position_model=0.466624	new_cov=1/3	polymorphism_quality=5.9	quality=5.9	quality_position_model=7.44618e-11	ref_cov=105/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/155
RA	174	.	NC_007779	853114	0	C	G	bias_e_value=9.39823e-06	bias_p_value=2.02272e-12	fisher_strand_p_value=6.44743e-14	frequency=1.107812e-01	genotype_quality=597.2	ks_quality_p_value=1	log10_base_likelihood=-31.9286	log10_qual_likelihood_position_model=19.0474	log10_strand_likelihood_position_model=13.1906	new_cov=0/19	polymorphism_quality=26.7	quality=26.7	quality_position_model=Inf	ref_cov=124/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/41
RA	175	.	NC_007779	868836	1	.	C	bias_e_value=2500450	bias_p_value=0.538155	fisher_strand_p_value=0.246753	frequency=8.657455e-03	genotype_quality=1116.9	ks_quality_p_value=0.852141	log10_base_likelihood=-7.96169	log10_qual_likelihood_position_model=0.994881	log10_strand_likelihood_position_model=0.607737	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.71391e-08	ref_cov=116/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/115
RA	176	.	NC_007779	881118	0	T	.	bias_e_value=1978760	bias_p_value=0.425875	fisher_strand_p_value=0.361255	frequency=1.319122e-02	genotype_quality=1192.4	ks_quality_p_value=0.402637	log10_base_likelihood=-10.8062	log10_qual_likelihood_position_model=2.79233	log10_strand_likelihood_position_model=0.622814	new_cov=3/1	polymorphism_quality=5.4	quality=5.4	quality_position_model=2.34831e-09	ref_cov=145/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/155
RA	177	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=812.9	new_cov=134/86	quality=812.9	ref_cov=1/0	tot_cov=135/86
RA	178	.	NC_007779	894943	0	T	G	bias_e_value=1.49644e-06	bias_p_value=3.22068e-13	fisher_strand_p_value=9.68084e-15	frequency=8.628321e-02	genotype_quality=587.9	ks_quality_p_value=1	log10_base_likelihood=-11.5014	log10_qual_likelihood_position_model=23.204	log10_strand_likelihood_position_model=14.0141	new_cov=22/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=29/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=51/133
RA	179	.	NC_007779	901814	0	A	C	bias_e_value=1.01805	bias_p_value=2.19108e-07	fisher_strand_p_value=1.13566e-08	frequency=7.980013e-02	genotype_quality=625.4	ks_quality_p_value=1	log10_base_likelihood=-7.11747	log10_qual_likelihood_position_model=22.2338	log10_strand_likelihood_position_model=7.94475	new_cov=0/24	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=103/78	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=103/102
RA	180	.	NC_007779	904838	0	C	A	bias_e_value=0.00564739	bias_p_value=1.21545e-09	fisher_strand_p_value=5.22687e-11	frequency=8.591986e-02	genotype_quality=817.5	ks_quality_p_value=0.940066	log10_base_likelihood=-17.7292	log10_qual_likelihood_position_model=24.6948	log10_strand_likelihood_position_model=10.2818	new_cov=29/0	polymorphism_quality=12.4	quality=12.4	quality_position_model=Inf	ref_cov=94/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/137
RA	181	.	NC_007779	929059	0	T	C	bias_e_value=2495330	bias_p_value=0.537053	fisher_strand_p_value=0.248135	frequency=1.345921e-02	genotype_quality=863.5	ks_quality_p_value=0.844551	log10_base_likelihood=-5.99765	log10_qual_likelihood_position_model=2.23907	log10_strand_likelihood_position_model=0.851107	new_cov=0/3	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.000109912	ref_cov=106/113	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=107/116
RA	182	.	NC_007779	954820	0	A	C	bias_e_value=1.05552e-17	bias_p_value=2.27173e-24	fisher_strand_p_value=3.81625e-26	frequency=1.431913e-01	genotype_quality=555.8	ks_quality_p_value=1	log10_base_likelihood=-13.7432	log10_qual_likelihood_position_model=38.2584	log10_strand_likelihood_position_model=25.4184	new_cov=0/50	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=127/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/84
RA	183	.	NC_007779	969494	0	C	A	bias_e_value=115.965	bias_p_value=2.49584e-05	fisher_strand_p_value=1.7508e-06	frequency=6.094980e-02	genotype_quality=652.1	ks_quality_p_value=1	log10_base_likelihood=-7.60419	log10_qual_likelihood_position_model=15.5496	log10_strand_likelihood_position_model=5.89424	new_cov=19/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=89/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/103
RA	184	.	NC_007779	975142	0	T	G	bias_e_value=757.057	bias_p_value=0.000162937	fisher_strand_p_value=1.33274e-05	frequency=3.314590e-02	genotype_quality=540.5	ks_quality_p_value=1	log10_base_likelihood=-7.8885	log10_qual_likelihood_position_model=6.2654	log10_strand_likelihood_position_model=4.87525	new_cov=5/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=12/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=17/126
RA	185	.	NC_007779	987422	1	.	T	bias_e_value=2846570	bias_p_value=0.612649	fisher_strand_p_value=0.499163	frequency=8.333206e-03	genotype_quality=1129.5	ks_quality_p_value=0.524464	log10_base_likelihood=-8.09616	log10_qual_likelihood_position_model=1.9261	log10_strand_likelihood_position_model=0.561329	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.61996e-07	ref_cov=114/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/126
RA	186	.	NC_007779	987436	0	A	C	bias_e_value=9.3299e-05	bias_p_value=2.00801e-11	fisher_strand_p_value=6.92454e-13	frequency=1.028318e-01	genotype_quality=657.0	ks_quality_p_value=1	log10_base_likelihood=-11.1502	log10_qual_likelihood_position_model=33.706	log10_strand_likelihood_position_model=12.3378	new_cov=0/41	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=111/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/132
RA	187	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=906.1	new_cov=102/120	quality=906.1	ref_cov=0/0	tot_cov=102/120
RA	188	.	NC_007779	987916	0	T	G	bias_e_value=0.200691	bias_p_value=4.31934e-08	fisher_strand_p_value=2.05661e-09	frequency=6.055450e-02	genotype_quality=472.9	ks_quality_p_value=1	log10_base_likelihood=-17.0943	log10_qual_likelihood_position_model=11.2945	log10_strand_likelihood_position_model=8.68685	new_cov=9/0	polymorphism_quality=11.8	quality=11.8	quality_position_model=Inf	ref_cov=9/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=18/113
RA	189	.	NC_007779	991407	0	G	T	bias_e_value=172.947	bias_p_value=3.72223e-05	fisher_strand_p_value=3.43152e-06	frequency=5.768538e-02	genotype_quality=825.9	ks_quality_p_value=0.784602	log10_base_likelihood=-13.6189	log10_qual_likelihood_position_model=18.8039	log10_strand_likelihood_position_model=5.49808	new_cov=0/19	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=122/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/140
RA	190	.	NC_007779	1002413	0	T	G	bias_e_value=7.14653e-14	bias_p_value=1.5381e-20	fisher_strand_p_value=3.04309e-22	frequency=1.102767e-01	genotype_quality=757.2	ks_quality_p_value=1	log10_base_likelihood=-14.8443	log10_qual_likelihood_position_model=37.1999	log10_strand_likelihood_position_model=21.5167	new_cov=50/0	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=67/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/154
RA	191	.	NC_007779	1004576	0	G	.	bias_e_value=4068500	bias_p_value=0.875637	fisher_strand_p_value=0.557467	frequency=1.420784e-02	genotype_quality=894.6	ks_quality_p_value=0.977161	log10_base_likelihood=-8.21261	log10_qual_likelihood_position_model=2.06155	log10_strand_likelihood_position_model=0.579231	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.76909e-07	ref_cov=131/77	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/79
RA	192	.	NC_007779	1013042	0	G	C	bias_e_value=0.000140895	bias_p_value=3.0324e-11	fisher_strand_p_value=1.06134e-12	frequency=9.362793e-02	genotype_quality=541.2	ks_quality_p_value=1	log10_base_likelihood=-18.7554	log10_qual_likelihood_position_model=15.1314	log10_strand_likelihood_position_model=11.9741	new_cov=0/15	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=119/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/30
RA	193	.	NC_007779	1019391	0	A	.	bias_e_value=2214360	bias_p_value=0.476582	fisher_strand_p_value=0.363403	frequency=1.442623e-02	genotype_quality=1108.5	ks_quality_p_value=0.47615	log10_base_likelihood=-10.5182	log10_qual_likelihood_position_model=3.79356	log10_strand_likelihood_position_model=0.618216	new_cov=3/1	polymorphism_quality=5.1	quality=5.1	quality_position_model=4.94903e-08	ref_cov=133/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/141
RA	194	.	NC_007779	1028521	0	G	C	bias_e_value=1992790	bias_p_value=0.428895	fisher_strand_p_value=0.571971	frequency=1.151657e-02	genotype_quality=1087.7	ks_quality_p_value=0.25705	log10_base_likelihood=-6.8015	log10_qual_likelihood_position_model=2.6154	log10_strand_likelihood_position_model=0.51812	new_cov=2/1	polymorphism_quality=1.3	quality=1.3	quality_position_model=1.71877e-05	ref_cov=106/151	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=108/152
RA	195	.	NC_007779	1036813	0	G	A	bias_e_value=1185210	bias_p_value=0.255085	fisher_strand_p_value=0.0696965	frequency=1.804733e-02	genotype_quality=1047.0	ks_quality_p_value=0.998622	log10_base_likelihood=-5.7795	log10_qual_likelihood_position_model=6.64728	log10_strand_likelihood_position_model=1.26459	new_cov=5/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=140/113	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=145/113
RA	196	.	NC_007779	1037529	0	T	G	bias_e_value=736.309	bias_p_value=0.000158471	fisher_strand_p_value=1.29354e-05	frequency=2.779579e-02	genotype_quality=539.3	ks_quality_p_value=0.999592	log10_base_likelihood=-6.36009	log10_qual_likelihood_position_model=4.59978	log10_strand_likelihood_position_model=4.88822	new_cov=4/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=6/132	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=10/132
RA	197	.	NC_007779	1037604	0	C	G	bias_e_value=9.25371e-09	bias_p_value=1.99162e-15	fisher_strand_p_value=5.17296e-17	frequency=1.095543e-01	genotype_quality=562.2	ks_quality_p_value=1	log10_base_likelihood=-20.4217	log10_qual_likelihood_position_model=22.179	log10_strand_likelihood_position_model=16.2863	new_cov=18/0	polymorphism_quality=15.1	quality=15.1	quality_position_model=Inf	ref_cov=9/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=27/124
RA	198	.	NC_007779	1086017	0	A	C	bias_e_value=8.26372e-15	bias_p_value=1.77855e-21	fisher_strand_p_value=3.37204e-23	frequency=1.332889e-01	genotype_quality=642.3	ks_quality_p_value=1	log10_base_likelihood=-23.3078	log10_qual_likelihood_position_model=33.7006	log10_strand_likelihood_position_model=22.4721	new_cov=0/47	polymorphism_quality=18.1	quality=18.1	quality_position_model=Inf	ref_cov=141/48	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/95
RA	199	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1241.8	new_cov=132/153	quality=1241.8	ref_cov=0/0	tot_cov=132/153
RA	200	.	NC_007779	1097580	0	C	T	bias_e_value=51080.8	bias_p_value=0.0109938	fisher_strand_p_value=0.251337	frequency=1.784258e-01	genotype_quality=814.2	ks_quality_p_value=0.00580952	log10_base_likelihood=-158.289	log10_qual_likelihood_position_model=20.1625	log10_strand_likelihood_position_model=1.22965	new_cov=30/29	polymorphism_quality=153.5	quality=153.5	quality_position_model=1.74736e-139	ref_cov=115/155	tot_cov=145/184
RA	201	.	NC_007779	1097583	1	.	A	bias_e_value=3892560	bias_p_value=0.837771	fisher_strand_p_value=0.504697	frequency=6.622314e-03	genotype_quality=1109.2	ks_quality_p_value=0.965979	log10_base_likelihood=-7.84012	log10_qual_likelihood_position_model=3.27733	log10_strand_likelihood_position_model=0.510548	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=6.78038e-06	ref_cov=134/166	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/168
RA	202	.	NC_007779	1097764	1	.	A	bias_e_value=2081700	bias_p_value=0.448032	fisher_strand_p_value=0.634531	frequency=7.812500e-03	genotype_quality=2082.5	ks_quality_p_value=0.247721	log10_base_likelihood=-16.3826	log10_qual_likelihood_position_model=2.3208	log10_strand_likelihood_position_model=0.508644	new_cov=1/3	polymorphism_quality=11.1	quality=11.1	quality_position_model=1.20843e-15	ref_cov=224/284	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=225/287
RA	203	.	NC_007779	1105181	1	.	T	bias_e_value=3521460	bias_p_value=0.757902	fisher_strand_p_value=0.498812	frequency=7.692337e-03	genotype_quality=1269.4	ks_quality_p_value=0.783295	log10_base_likelihood=-8.3668	log10_qual_likelihood_position_model=1.26717	log10_strand_likelihood_position_model=0.570835	new_cov=0/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.81337e-08	ref_cov=125/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/135
RA	204	.	NC_007779	1115091	0	C	A	bias_e_value=504.312	bias_p_value=0.00010854	fisher_strand_p_value=8.58764e-06	frequency=4.074574e-02	genotype_quality=661.7	ks_quality_p_value=0.99776	log10_base_likelihood=-6.47545	log10_qual_likelihood_position_model=9.67122	log10_strand_likelihood_position_model=5.06613	new_cov=0/8	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=130/35	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/43
RA	205	.	NC_007779	1116582	0	G	C	bias_e_value=8.61228e-16	bias_p_value=1.85357e-22	fisher_strand_p_value=3.37542e-24	frequency=1.438613e-01	genotype_quality=459.3	ks_quality_p_value=0.997559	log10_base_likelihood=-40.7869	log10_qual_likelihood_position_model=17.9533	log10_strand_likelihood_position_model=23.4717	new_cov=0/21	polymorphism_quality=35.7	quality=35.7	quality_position_model=Inf	ref_cov=120/1	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/22
RA	206	.	NC_007779	1150586	0	C	T	bias_e_value=2317830	bias_p_value=0.498851	fisher_strand_p_value=1	frequency=1.721573e-02	genotype_quality=952.6	ks_quality_p_value=0.185998	log10_base_likelihood=-7.26698	log10_qual_likelihood_position_model=4.06359	log10_strand_likelihood_position_model=0.4222	new_cov=2/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=0.000149932	ref_cov=113/114	reject=EVALUE	tot_cov=115/116
RA	207	.	NC_007779	1155150	0	T	G	bias_e_value=1978.57	bias_p_value=0.000425835	fisher_strand_p_value=3.81055e-05	frequency=2.159119e-02	genotype_quality=553.1	ks_quality_p_value=1	log10_base_likelihood=-6.6144	log10_qual_likelihood_position_model=7.42653	log10_strand_likelihood_position_model=4.41901	new_cov=5/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=16/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=21/127
RA	208	.	NC_007779	1158848	0	T	G	bias_e_value=2.20111e-19	bias_p_value=4.7373e-26	fisher_strand_p_value=7.46476e-28	frequency=1.960292e-01	genotype_quality=538.3	ks_quality_p_value=1	log10_base_likelihood=-32.8225	log10_qual_likelihood_position_model=40.2458	log10_strand_likelihood_position_model=27.127	new_cov=58/0	polymorphism_quality=27.6	quality=27.6	quality_position_model=Inf	ref_cov=37/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/123
RA	209	.	NC_007779	1163018	0	T	G	bias_e_value=7.32854e-08	bias_p_value=1.57727e-14	fisher_strand_p_value=4.33623e-16	frequency=1.647243e-01	genotype_quality=612.8	ks_quality_p_value=1	log10_base_likelihood=-34.2654	log10_qual_likelihood_position_model=34.0646	log10_strand_likelihood_position_model=15.4217	new_cov=45/0	polymorphism_quality=29.1	quality=29.1	quality_position_model=Inf	ref_cov=74/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/115
RA	210	.	NC_007779	1164942	0	A	G	bias_e_value=0.346043	bias_p_value=7.44767e-08	fisher_strand_p_value=3.6455e-09	frequency=8.373070e-02	genotype_quality=427.6	ks_quality_p_value=1	log10_base_likelihood=-12.172	log10_qual_likelihood_position_model=14.694	log10_strand_likelihood_position_model=8.43824	new_cov=12/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=18/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=30/98
RA	211	.	NC_007779	1164944	0	T	G	bias_e_value=0.00149387	bias_p_value=3.21516e-10	fisher_strand_p_value=1.23088e-11	frequency=9.522009e-02	genotype_quality=441.9	ks_quality_p_value=1	log10_base_likelihood=-12.8019	log10_qual_likelihood_position_model=17.9977	log10_strand_likelihood_position_model=10.9098	new_cov=16/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=18/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=34/99
RA	212	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1149.0	new_cov=179/100	quality=1149.0	ref_cov=0/0	tot_cov=179/100
RA	213	.	NC_007779	1177683	0	A	G	bias_e_value=1.27876e-07	bias_p_value=2.7522e-14	fisher_strand_p_value=7.68732e-16	frequency=1.235929e-01	genotype_quality=530.6	ks_quality_p_value=1	log10_base_likelihood=-38.149	log10_qual_likelihood_position_model=21.5309	log10_strand_likelihood_position_model=15.1142	new_cov=23/0	polymorphism_quality=33.0	quality=33.0	quality_position_model=0.00370573	ref_cov=26/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/132
RA	214	.	NC_007779	1182809	0	T	G	bias_e_value=1.69757e-12	bias_p_value=3.65358e-19	fisher_strand_p_value=7.72261e-21	frequency=8.249807e-02	genotype_quality=699.6	ks_quality_p_value=1	log10_base_likelihood=-7.38565	log10_qual_likelihood_position_model=40.9697	log10_strand_likelihood_position_model=20.1122	new_cov=42/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=49/139	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/139
RA	215	.	NC_007779	1213001	0	T	C	bias_e_value=2809500	bias_p_value=0.604671	fisher_strand_p_value=0.457466	frequency=2.658367e-02	genotype_quality=1027.3	ks_quality_p_value=0.559366	log10_base_likelihood=-17.1878	log10_qual_likelihood_position_model=3.61038	log10_strand_likelihood_position_model=0.690008	new_cov=5/2	polymorphism_quality=11.9	quality=11.9	quality_position_model=5.73556e-15	ref_cov=137/119	tot_cov=142/121
RA	216	.	NC_007779	1213013	0	T	C	bias_e_value=4390990	bias_p_value=0.945045	fisher_strand_p_value=0.687822	frequency=2.224255e-02	genotype_quality=1052.8	ks_quality_p_value=0.999311	log10_base_likelihood=-11.9525	log10_qual_likelihood_position_model=5.16105	log10_strand_likelihood_position_model=0.577426	new_cov=4/2	polymorphism_quality=6.6	quality=6.6	quality_position_model=3.83138e-08	ref_cov=138/123	tot_cov=143/125
RA	217	.	NC_007779	1213026	0	C	T	bias_e_value=4217570	bias_p_value=0.907719	fisher_strand_p_value=0.624884	frequency=1.485157e-02	genotype_quality=1138.2	ks_quality_p_value=0.964028	log10_base_likelihood=-7.58009	log10_qual_likelihood_position_model=1.87089	log10_strand_likelihood_position_model=0.552708	new_cov=3/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=4.77259e-07	ref_cov=139/125	reject=POLYMORPHISM_STRAND	tot_cov=142/126
RA	218	.	NC_007779	1213028	0	G	A	bias_e_value=4215860	bias_p_value=0.907352	fisher_strand_p_value=0.623962	frequency=1.475620e-02	genotype_quality=1140.2	ks_quality_p_value=0.964292	log10_base_likelihood=-6.83758	log10_qual_likelihood_position_model=2.75928	log10_strand_likelihood_position_model=0.561648	new_cov=3/1	polymorphism_quality=1.3	quality=1.3	quality_position_model=2.4821e-05	ref_cov=138/127	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=141/128
RA	219	.	NC_007779	1215933	0	C	A	bias_e_value=0.193085	bias_p_value=4.15565e-08	fisher_strand_p_value=2.04342e-09	frequency=6.945610e-02	genotype_quality=664.2	ks_quality_p_value=0.966447	log10_base_likelihood=-11.8413	log10_qual_likelihood_position_model=17.4787	log10_strand_likelihood_position_model=8.68964	new_cov=0/14	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=131/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/48
RA	220	.	NC_007779	1224173	0	G	A	bias_e_value=12.2735	bias_p_value=2.64154e-06	fisher_strand_p_value=1.58585e-07	frequency=5.925655e-02	genotype_quality=725.5	ks_quality_p_value=1	log10_base_likelihood=-9.09283	log10_qual_likelihood_position_model=16.3964	log10_strand_likelihood_position_model=6.79974	new_cov=0/15	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=134/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/80
RA	221	.	NC_007779	1225577	1	.	G	bias_e_value=3682120	bias_p_value=0.792478	fisher_strand_p_value=0.499616	frequency=6.919861e-03	genotype_quality=1427.7	ks_quality_p_value=0.859644	log10_base_likelihood=-8.03409	log10_qual_likelihood_position_model=1.01666	log10_strand_likelihood_position_model=0.55947	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.14561e-08	ref_cov=150/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/137
RA	222	.	NC_007779	1229345	1	.	A	bias_e_value=2261080	bias_p_value=0.486638	fisher_strand_p_value=1	frequency=7.967949e-03	genotype_quality=1226.8	ks_quality_p_value=0.178821	log10_base_likelihood=-8.00201	log10_qual_likelihood_position_model=1.26359	log10_strand_likelihood_position_model=0.317607	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.34356e-08	ref_cov=150/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/100
RA	223	.	NC_007779	1236439	0	T	A	bias_e_value=4218630	bias_p_value=0.907948	fisher_strand_p_value=0.610162	frequency=1.209736e-02	genotype_quality=998.4	ks_quality_p_value=0.988026	log10_base_likelihood=-6.22047	log10_qual_likelihood_position_model=3.76219	log10_strand_likelihood_position_model=0.441038	new_cov=2/1	polymorphism_quality=0.7	quality=0.7	quality_position_model=0.00100194	ref_cov=117/127	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=119/128
RA	224	.	NC_007779	1250117	0	T	.	bias_e_value=2712730	bias_p_value=0.583844	fisher_strand_p_value=1	frequency=1.189613e-02	genotype_quality=981.6	ks_quality_p_value=0.240938	log10_base_likelihood=-8.08303	log10_qual_likelihood_position_model=2.99729	log10_strand_likelihood_position_model=0.372779	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.38162e-06	ref_cov=106/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/145
RA	225	.	NC_007779	1262472	0	A	C	bias_e_value=2.36276e-11	bias_p_value=5.08521e-18	fisher_strand_p_value=1.13971e-19	frequency=1.068268e-01	genotype_quality=676.4	ks_quality_p_value=1	log10_base_likelihood=-11.7612	log10_qual_likelihood_position_model=30.9525	log10_strand_likelihood_position_model=18.9432	new_cov=0/47	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=137/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/114
RA	226	.	NC_007779	1273399	0	T	G	bias_e_value=3.15988e-24	bias_p_value=6.8008e-31	fisher_strand_p_value=9.09471e-33	frequency=2.169404e-01	genotype_quality=538.6	ks_quality_p_value=1	log10_base_likelihood=-47.4125	log10_qual_likelihood_position_model=43.1724	log10_strand_likelihood_position_model=32.0412	new_cov=59/0	polymorphism_quality=42.3	quality=42.3	quality_position_model=Inf	ref_cov=28/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=87/136
RA	227	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=74.0	new_cov=11/13	quality=74.0	ref_cov=0/0	tot_cov=11/13
RA	228	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=42.6	new_cov=9/5	quality=42.6	ref_cov=0/0	tot_cov=9/5
RA	229	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=18.3	new_cov=9/4	quality=18.3	ref_cov=0/0	tot_cov=9/4
RA	230	.	NC_007779	1288911	0	T	G	bias_e_value=542.976	bias_p_value=0.000116861	fisher_strand_p_value=9.28413e-06	frequency=2.249146e-02	genotype_quality=796.3	ks_quality_p_value=1	log10_base_likelihood=-5.69717	log10_qual_likelihood_position_model=13.2535	log10_strand_likelihood_position_model=5.03226	new_cov=14/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=92/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/128
RA	231	.	NC_007779	1290902	0	A	.	bias_e_value=969272	bias_p_value=0.20861	fisher_strand_p_value=0.249287	frequency=1.153088e-02	genotype_quality=1047.7	ks_quality_p_value=0.212503	log10_base_likelihood=-8.19986	log10_qual_likelihood_position_model=1.56295	log10_strand_likelihood_position_model=0.8393	new_cov=0/3	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.03252e-07	ref_cov=123/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/137
RA	232	.	NC_007779	1292264	0	A	C	bias_e_value=0.00412646	bias_p_value=8.88111e-10	fisher_strand_p_value=3.54347e-11	frequency=3.976631e-02	genotype_quality=825.1	ks_quality_p_value=1	log10_base_likelihood=-6.15152	log10_qual_likelihood_position_model=32.2236	log10_strand_likelihood_position_model=10.4506	new_cov=0/25	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=145/77	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/102
RA	233	.	NC_007779	1294035	0	T	A	bias_e_value=1390.38	bias_p_value=0.000299243	fisher_strand_p_value=2.58817e-05	frequency=4.769564e-02	genotype_quality=837.3	ks_quality_p_value=1	log10_base_likelihood=-9.66677	log10_qual_likelihood_position_model=19.4723	log10_strand_likelihood_position_model=4.58701	new_cov=0/13	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=134/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/113
RA	234	.	NC_007779	1294042	0	T	C	bias_e_value=6.32883	bias_p_value=1.36211e-06	fisher_strand_p_value=7.84596e-08	frequency=4.898739e-02	genotype_quality=774.6	ks_quality_p_value=1	log10_base_likelihood=-5.8123	log10_qual_likelihood_position_model=15.9203	log10_strand_likelihood_position_model=7.10535	new_cov=0/21	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=133/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/124
RA	235	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=946.5	new_cov=121/115	quality=946.5	ref_cov=0/0	tot_cov=121/115
RA	236	.	NC_007779	1324190	0	T	C	bias_e_value=0.829467	bias_p_value=1.78521e-07	fisher_strand_p_value=9.15047e-09	frequency=5.666161e-02	genotype_quality=618.0	ks_quality_p_value=1	log10_base_likelihood=-5.9367	log10_qual_likelihood_position_model=15.6147	log10_strand_likelihood_position_model=8.03856	new_cov=0/16	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=127/50	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/66
RA	237	.	NC_007779	1330179	0	T	G	bias_e_value=0.113016	bias_p_value=2.43236e-08	fisher_strand_p_value=1.12585e-09	frequency=4.828501e-02	genotype_quality=742.7	ks_quality_p_value=1	log10_base_likelihood=-6.70475	log10_qual_likelihood_position_model=23.482	log10_strand_likelihood_position_model=8.94852	new_cov=26/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=87/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/121
RA	238	.	NC_007779	1336531	0	G	T	bias_e_value=0.0168121	bias_p_value=3.61835e-09	fisher_strand_p_value=1.5333e-10	frequency=9.499359e-02	genotype_quality=862.7	ks_quality_p_value=1	log10_base_likelihood=-21.201	log10_qual_likelihood_position_model=22.1497	log10_strand_likelihood_position_model=9.9155	new_cov=0/31	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=129/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/134
RA	239	.	NC_007779	1348546	1	.	T	bias_e_value=3566570	bias_p_value=0.76761	fisher_strand_p_value=1	frequency=1.224518e-02	genotype_quality=1166.4	ks_quality_p_value=0.401195	log10_base_likelihood=-12.9976	log10_qual_likelihood_position_model=2.05735	log10_strand_likelihood_position_model=0.422416	new_cov=1/2	polymorphism_quality=7.6	quality=7.6	quality_position_model=1.48169e-12	ref_cov=121/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/123
RA	240	.	NC_007779	1371749	1	.	T	bias_e_value=3334620	bias_p_value=0.717688	fisher_strand_p_value=0.444885	frequency=2.325630e-02	genotype_quality=1201.9	ks_quality_p_value=0.787255	log10_base_likelihood=-27.5806	log10_qual_likelihood_position_model=3.3887	log10_strand_likelihood_position_model=0.635369	new_cov=4/2	polymorphism_quality=22.4	quality=22.4	quality_position_model=9.15385e-26	ref_cov=124/128	reject=INDEL_HOMOPOLYMER	tot_cov=128/130
RA	241	.	NC_007779	1374996	0	A	C	bias_e_value=8.01118	bias_p_value=1.72419e-06	fisher_strand_p_value=1.00769e-07	frequency=3.772068e-02	genotype_quality=603.1	ks_quality_p_value=1	log10_base_likelihood=-8.85228	log10_qual_likelihood_position_model=11.8418	log10_strand_likelihood_position_model=6.99667	new_cov=9/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=22/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=31/134
RA	242	.	NC_007779	1377000	0	C	T	bias_e_value=896954	bias_p_value=0.193046	fisher_strand_p_value=0.0743776	frequency=1.389980e-02	genotype_quality=873.9	ks_quality_p_value=0.642219	log10_base_likelihood=-5.84567	log10_qual_likelihood_position_model=1.36613	log10_strand_likelihood_position_model=1.12856	new_cov=3/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=3.71484e-05	ref_cov=88/124	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=91/124
RA	243	.	NC_007779	1378219	0	A	C	bias_e_value=1.08734e-12	bias_p_value=2.34022e-19	fisher_strand_p_value=4.89942e-21	frequency=1.379471e-01	genotype_quality=552.7	ks_quality_p_value=1	log10_base_likelihood=-11.8861	log10_qual_likelihood_position_model=42.6457	log10_strand_likelihood_position_model=20.3099	new_cov=0/42	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=114/36	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/78
RA	244	.	NC_007779	1386502	0	T	G	bias_e_value=0.0295795	bias_p_value=6.36621e-09	fisher_strand_p_value=2.76694e-10	frequency=6.966496e-02	genotype_quality=625.6	ks_quality_p_value=1	log10_base_likelihood=-7.51835	log10_qual_likelihood_position_model=26.0542	log10_strand_likelihood_position_model=9.558	new_cov=27/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=77/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/114
RA	245	.	NC_007779	1405508	0	G	T	bias_e_value=3.91428e-09	bias_p_value=8.42445e-16	fisher_strand_p_value=2.14478e-17	frequency=1.561904e-01	genotype_quality=474.6	ks_quality_p_value=0.99734	log10_base_likelihood=-52.226	log10_qual_likelihood_position_model=21.4342	log10_strand_likelihood_position_model=16.6686	new_cov=22/0	polymorphism_quality=47.1	quality=47.1	quality_position_model=3.18782e-16	ref_cov=12/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=34/107
RA	246	.	NC_007779	1409137	0	G	T	bias_e_value=0.000108372	bias_p_value=2.33243e-11	fisher_strand_p_value=8.0962e-13	frequency=1.108079e-01	genotype_quality=789.9	ks_quality_p_value=0.998805	log10_base_likelihood=-24.8456	log10_qual_likelihood_position_model=20.466	log10_strand_likelihood_position_model=12.3927	new_cov=0/37	polymorphism_quality=19.6	quality=19.6	quality_position_model=Inf	ref_cov=134/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/134
RA	247	.	NC_007779	1412694	0	C	A	bias_e_value=5.78909	bias_p_value=1.24595e-06	fisher_strand_p_value=7.13795e-08	frequency=5.296087e-02	genotype_quality=809.1	ks_quality_p_value=1	log10_base_likelihood=-8.98116	log10_qual_likelihood_position_model=17.7587	log10_strand_likelihood_position_model=7.14643	new_cov=22/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=102/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/126
RA	248	.	NC_007779	1413639	0	T	A	deleted=1	frequency=1	genotype_quality=1.4	new_cov=0/1	quality=1.4	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	249	.	NC_007779	1413640	0	G	C	deleted=1	frequency=1	genotype_quality=1.4	new_cov=0/1	quality=1.4	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	250	.	NC_007779	1429737	0	A	C	deleted=1	frequency=1	genotype_quality=0.8	new_cov=0/1	quality=0.8	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	251	.	NC_007779	1435377	0	A	G	deleted=1	frequency=1	genotype_quality=1.9	new_cov=0/1	quality=1.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	252	.	NC_007779	1437441	0	G	A	bias_e_value=75.935	bias_p_value=1.6343e-05	fisher_strand_p_value=1.11099e-06	frequency=3.938961e-02	genotype_quality=749.6	ks_quality_p_value=1	log10_base_likelihood=-7.77338	log10_qual_likelihood_position_model=13.0638	log10_strand_likelihood_position_model=5.95429	new_cov=0/8	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=152/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=152/37
RA	253	.	NC_007779	1437447	0	G	C	bias_e_value=3.54809e-10	bias_p_value=7.63632e-17	fisher_strand_p_value=1.82491e-18	frequency=1.176066e-01	genotype_quality=726.0	ks_quality_p_value=1	log10_base_likelihood=-18.3781	log10_qual_likelihood_position_model=27.9667	log10_strand_likelihood_position_model=17.7388	new_cov=0/34	polymorphism_quality=13.1	quality=13.1	quality_position_model=Inf	ref_cov=150/48	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/82
RA	254	.	NC_007779	1438937	0	T	.	bias_e_value=1206270	bias_p_value=0.259618	fisher_strand_p_value=0.0869543	frequency=1.259613e-02	genotype_quality=950.1	ks_quality_p_value=0.820079	log10_base_likelihood=-8.13886	log10_qual_likelihood_position_model=1.72234	log10_strand_likelihood_position_model=1.06071	new_cov=3/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.96329e-07	ref_cov=103/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/132
RA	255	.	NC_007779	1442205	0	G	C	bias_e_value=0.0867098	bias_p_value=1.8662e-08	fisher_strand_p_value=8.52829e-10	frequency=6.401157e-02	genotype_quality=603.6	ks_quality_p_value=1	log10_base_likelihood=-10.2566	log10_qual_likelihood_position_model=12.7795	log10_strand_likelihood_position_model=9.06914	new_cov=0/12	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=128/21	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/33
RA	256	.	NC_007779	1468443	0	G	A	bias_e_value=2880890	bias_p_value=0.620036	fisher_strand_p_value=0.267621	frequency=2.368546e-02	genotype_quality=907.3	ks_quality_p_value=0.998982	log10_base_likelihood=-7.59396	log10_qual_likelihood_position_model=7.33972	log10_strand_likelihood_position_model=0.833659	new_cov=2/5	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=121/110	tot_cov=123/115
RA	257	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=665.5	new_cov=118/52	quality=665.5	ref_cov=0/0	tot_cov=118/52
RA	258	.	NC_007779	1483616	0	C	G	bias_e_value=0.00135816	bias_p_value=2.92309e-10	fisher_strand_p_value=1.11484e-11	frequency=7.585430e-02	genotype_quality=532.6	ks_quality_p_value=1	log10_base_likelihood=-16.8746	log10_qual_likelihood_position_model=13.877	log10_strand_likelihood_position_model=10.9528	new_cov=0/11	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=121/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/19
RA	259	.	NC_007779	1493621	0	T	C	bias_e_value=6492.3	bias_p_value=0.0013973	fisher_strand_p_value=0.000141686	frequency=4.181290e-02	genotype_quality=799.2	ks_quality_p_value=1	log10_base_likelihood=-9.3574	log10_qual_likelihood_position_model=13.1934	log10_strand_likelihood_position_model=3.86796	new_cov=1/11	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=144/79	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/90
RA	260	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1323.3	new_cov=122/147	quality=1323.3	ref_cov=0/1	tot_cov=123/148
RA	261	.	NC_007779	1504851	0	C	A	bias_e_value=457840	bias_p_value=0.098538	fisher_strand_p_value=0.0203859	frequency=3.223038e-02	genotype_quality=723.6	ks_quality_p_value=0.984805	log10_base_likelihood=-5.86655	log10_qual_likelihood_position_model=11.885	log10_strand_likelihood_position_model=1.7829	new_cov=11/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=151/71	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=162/71
RA	262	.	NC_007779	1505667	0	T	.	bias_e_value=3385410	bias_p_value=0.728621	fisher_strand_p_value=0.605228	frequency=1.029682e-02	genotype_quality=1158.7	ks_quality_p_value=0.596156	log10_base_likelihood=-7.51047	log10_qual_likelihood_position_model=3.63591	log10_strand_likelihood_position_model=0.448776	new_cov=1/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=3.09617e-05	ref_cov=152/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/138
RA	263	.	NC_007779	1507742	0	A	C	bias_e_value=8.0486e-07	bias_p_value=1.73225e-13	fisher_strand_p_value=5.1087e-15	frequency=6.917715e-02	genotype_quality=582.7	ks_quality_p_value=1	log10_base_likelihood=-5.94218	log10_qual_likelihood_position_model=28.5564	log10_strand_likelihood_position_model=14.2917	new_cov=0/30	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=117/44	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/74
RA	264	.	NC_007779	1512930	0	T	C	bias_e_value=1.56627e-08	bias_p_value=3.37098e-15	fisher_strand_p_value=8.88032e-17	frequency=1.576018e-01	genotype_quality=530.6	ks_quality_p_value=1	log10_base_likelihood=-19.5606	log10_qual_likelihood_position_model=25.4509	log10_strand_likelihood_position_model=16.0516	new_cov=0/38	polymorphism_quality=14.3	quality=14.3	quality_position_model=Inf	ref_cov=114/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/89
RA	265	.	NC_007779	1515709	0	A	G	bias_e_value=7.8824e-16	bias_p_value=1.69648e-22	fisher_strand_p_value=3.07678e-24	frequency=1.938043e-01	genotype_quality=548.8	ks_quality_p_value=1	log10_base_likelihood=-48.4314	log10_qual_likelihood_position_model=39.1015	log10_strand_likelihood_position_model=23.5119	new_cov=46/0	polymorphism_quality=43.3	quality=43.3	quality_position_model=Inf	ref_cov=39/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/136
RA	266	.	NC_007779	1515714	0	A	T	bias_e_value=0.0232234	bias_p_value=4.99822e-09	fisher_strand_p_value=2.14876e-10	frequency=9.262800e-02	genotype_quality=647.7	ks_quality_p_value=1	log10_base_likelihood=-15.8937	log10_qual_likelihood_position_model=24.446	log10_strand_likelihood_position_model=9.66781	new_cov=20/0	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=52/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=72/127
RA	267	.	NC_007779	1527466	0	T	A	bias_e_value=852.251	bias_p_value=0.000183425	fisher_strand_p_value=1.51633e-05	frequency=4.463863e-02	genotype_quality=751.7	ks_quality_p_value=1	log10_base_likelihood=-7.39939	log10_qual_likelihood_position_model=13.8071	log10_strand_likelihood_position_model=4.81921	new_cov=0/11	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=134/71	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/82
RA	268	.	NC_007779	1527474	0	G	A	bias_e_value=1.2312e-10	bias_p_value=2.64984e-17	fisher_strand_p_value=6.1726e-19	frequency=1.649160e-01	genotype_quality=686.8	ks_quality_p_value=1	log10_base_likelihood=-52.2701	log10_qual_likelihood_position_model=41.1207	log10_strand_likelihood_position_model=18.2095	new_cov=0/42	polymorphism_quality=47.2	quality=47.2	quality_position_model=Inf	ref_cov=141/62	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/104
RA	269	.	NC_007779	1527479	0	C	A	bias_e_value=0.0157859	bias_p_value=3.3975e-09	fisher_strand_p_value=1.72237e-10	frequency=1.086230e-01	genotype_quality=794.0	ks_quality_p_value=0.83357	log10_base_likelihood=-33.0678	log10_qual_likelihood_position_model=33.616	log10_strand_likelihood_position_model=9.77241	new_cov=1/28	polymorphism_quality=27.9	quality=27.9	quality_position_model=Inf	ref_cov=138/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/108
RA	270	.	NC_007779	1537499	0	A	G	bias_e_value=1.50627e-07	bias_p_value=3.24185e-14	fisher_strand_p_value=9.0978e-16	frequency=1.613345e-01	genotype_quality=553.3	ks_quality_p_value=1	log10_base_likelihood=-24.7246	log10_qual_likelihood_position_model=27.4996	log10_strand_likelihood_position_model=15.0411	new_cov=40/0	polymorphism_quality=19.5	quality=19.5	quality_position_model=Inf	ref_cov=62/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/112
RA	271	.	NC_007779	1552377	0	A	C	bias_e_value=2.55209e-14	bias_p_value=5.4927e-21	fisher_strand_p_value=1.06459e-22	frequency=1.171155e-01	genotype_quality=641.6	ks_quality_p_value=1	log10_base_likelihood=-17.6985	log10_qual_likelihood_position_model=32.9064	log10_strand_likelihood_position_model=21.9728	new_cov=0/38	polymorphism_quality=12.4	quality=12.4	quality_position_model=Inf	ref_cov=145/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/72
RA	272	.	NC_007779	1562465	0	T	G	bias_e_value=0.000217741	bias_p_value=4.68631e-11	fisher_strand_p_value=1.66652e-12	frequency=1.651087e-01	genotype_quality=458.8	ks_quality_p_value=1	log10_base_likelihood=-21.8666	log10_qual_likelihood_position_model=29.5277	log10_strand_likelihood_position_model=11.8418	new_cov=37/0	polymorphism_quality=16.6	quality=16.6	quality_position_model=Inf	ref_cov=61/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/87
RA	273	.	NC_007779	1562518	0	A	C	bias_e_value=0.000218869	bias_p_value=4.71058e-11	fisher_strand_p_value=1.67547e-12	frequency=9.724712e-02	genotype_quality=326.8	ks_quality_p_value=1	log10_base_likelihood=-5.81671	log10_qual_likelihood_position_model=18.1325	log10_strand_likelihood_position_model=11.7759	new_cov=0/21	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=77/19	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=77/40
RA	274	.	NC_007779	1564550	0	G	T	bias_e_value=11.1772	bias_p_value=2.40559e-06	fisher_strand_p_value=1.45531e-07	frequency=6.301546e-02	genotype_quality=621.0	ks_quality_p_value=0.98647	log10_base_likelihood=-13.9468	log10_qual_likelihood_position_model=15.9374	log10_strand_likelihood_position_model=6.83704	new_cov=12/0	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=39/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=51/123
RA	275	.	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	276	.	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	277	.	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	278	.	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	279	.	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	280	.	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	281	.	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	282	.	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	283	.	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	284	.	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	285	.	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	286	.	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	287	.	NC_007779	1572963	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	288	.	NC_007779	1578837	0	A	C	bias_e_value=4.65072e-06	bias_p_value=1.00095e-12	fisher_strand_p_value=3.11832e-14	frequency=4.531384e-02	genotype_quality=710.4	ks_quality_p_value=1	log10_base_likelihood=-5.89924	log10_qual_likelihood_position_model=26.9107	log10_strand_likelihood_position_model=13.5061	new_cov=0/37	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=132/82	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/119
RA	289	.	NC_007779	1581577	1	.	T	bias_e_value=4573670	bias_p_value=0.984362	fisher_strand_p_value=1	frequency=7.326126e-03	genotype_quality=1330.9	ks_quality_p_value=0.828445	log10_base_likelihood=-8.25579	log10_qual_likelihood_position_model=1.37491	log10_strand_likelihood_position_model=0.299582	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.60082e-08	ref_cov=133/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/139
RA	290	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=825.2	new_cov=107/111	quality=825.2	ref_cov=0/0	tot_cov=107/111
RA	291	.	NC_007779	1624530	1	.	A	bias_e_value=4568770	bias_p_value=0.983308	fisher_strand_p_value=1	frequency=8.968353e-03	genotype_quality=1032.5	ks_quality_p_value=0.822938	log10_base_likelihood=-8.0079	log10_qual_likelihood_position_model=2.43939	log10_strand_likelihood_position_model=0.299506	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=3.64654e-07	ref_cov=114/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/108
RA	292	.	NC_007779	1628027	0	G	T	bias_e_value=26.592	bias_p_value=5.72323e-06	fisher_strand_p_value=3.64447e-07	frequency=2.213755e-01	genotype_quality=210.3	ks_quality_p_value=0.991839	log10_base_likelihood=-35.4934	log10_qual_likelihood_position_model=13.8241	log10_strand_likelihood_position_model=6.43837	new_cov=16/0	polymorphism_quality=30.3	quality=30.3	quality_position_model=2.39795e-17	ref_cov=17/38	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=33/38
RA	293	.	NC_007779	1651009	0	T	G	bias_e_value=4.94716e-07	bias_p_value=1.06475e-13	fisher_strand_p_value=3.09436e-15	frequency=1.110969e-01	genotype_quality=459.0	ks_quality_p_value=1	log10_base_likelihood=-24.6867	log10_qual_likelihood_position_model=19.686	log10_strand_likelihood_position_model=14.5094	new_cov=18/0	polymorphism_quality=19.4	quality=19.4	quality_position_model=Inf	ref_cov=12/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=30/112
RA	294	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=931.6	new_cov=94/94	quality=931.6	ref_cov=0/0	tot_cov=94/94
RA	295	.	NC_007779	1681026	0	A	C	bias_e_value=1.51355e-08	bias_p_value=3.25751e-15	fisher_strand_p_value=8.57346e-17	frequency=8.206558e-02	genotype_quality=648.9	ks_quality_p_value=1	log10_base_likelihood=-11.2996	log10_qual_likelihood_position_model=28.1162	log10_strand_likelihood_position_model=16.0668	new_cov=0/37	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=134/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/98
RA	296	.	NC_007779	1681402	0	T	G	bias_e_value=0.0142459	bias_p_value=3.06606e-09	fisher_strand_p_value=1.28981e-10	frequency=8.152342e-02	genotype_quality=568.8	ks_quality_p_value=1	log10_base_likelihood=-14.7598	log10_qual_likelihood_position_model=21.4825	log10_strand_likelihood_position_model=9.88947	new_cov=22/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=49/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=71/110
RA	297	.	NC_007779	1686463	0	A	C	bias_e_value=7.29653e-09	bias_p_value=1.57038e-15	fisher_strand_p_value=4.05319e-17	frequency=1.124630e-01	genotype_quality=467.7	ks_quality_p_value=1	log10_base_likelihood=-7.64318	log10_qual_likelihood_position_model=28.7945	log10_strand_likelihood_position_model=16.3922	new_cov=0/38	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=97/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=97/77
RA	298	.	NC_007779	1703024	0	A	C	bias_e_value=4.81824e-05	bias_p_value=1.037e-11	fisher_strand_p_value=3.49361e-13	frequency=5.839205e-02	genotype_quality=651.6	ks_quality_p_value=1	log10_base_likelihood=-6.75392	log10_qual_likelihood_position_model=25.0686	log10_strand_likelihood_position_model=12.4567	new_cov=0/32	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=123/69	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/101
RA	299	.	NC_007779	1703335	0	G	C	bias_e_value=4.31417e-12	bias_p_value=9.28512e-19	fisher_strand_p_value=2.14587e-20	frequency=1.339884e-01	genotype_quality=573.8	ks_quality_p_value=0.933401	log10_base_likelihood=-43.2072	log10_qual_likelihood_position_model=23.6665	log10_strand_likelihood_position_model=19.6684	new_cov=22/0	polymorphism_quality=38.1	quality=38.1	quality_position_model=Inf	ref_cov=9/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=31/132
RA	300	.	NC_007779	1704412	0	T	.	bias_e_value=4646260	bias_p_value=0.999984	fisher_strand_p_value=1	frequency=1.308441e-02	genotype_quality=907.2	ks_quality_p_value=0.994335	log10_base_likelihood=-7.54596	log10_qual_likelihood_position_model=3.42936	log10_strand_likelihood_position_model=0.398146	new_cov=2/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.5207e-05	ref_cov=120/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/107
RA	301	.	NC_007779	1713510	0	A	C	bias_e_value=8.99941e-06	bias_p_value=1.93688e-12	fisher_strand_p_value=6.16503e-14	frequency=1.358485e-01	genotype_quality=656.2	ks_quality_p_value=1	log10_base_likelihood=-21.764	log10_qual_likelihood_position_model=41.4832	log10_strand_likelihood_position_model=13.4331	new_cov=1/43	polymorphism_quality=16.5	quality=16.5	quality_position_model=Inf	ref_cov=118/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/120
RA	302	.	NC_007779	1716031	1	.	T	bias_e_value=13375.5	bias_p_value=0.00287872	fisher_strand_p_value=0.379633	frequency=1.984119e-02	genotype_quality=1177.2	ks_quality_p_value=0.000837558	log10_base_likelihood=-22.4562	log10_qual_likelihood_position_model=4.41522	log10_strand_likelihood_position_model=0.702299	new_cov=4/1	polymorphism_quality=17.2	quality=17.2	quality_position_model=1.75643e-19	ref_cov=133/114	reject=POLYMORPHISM_STRAND,KS_QUALITY_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=137/115
RA	303	.	NC_007779	1732516	0	T	G	bias_e_value=5.34826e-07	bias_p_value=1.15107e-13	fisher_strand_p_value=3.35307e-15	frequency=8.380842e-02	genotype_quality=435.8	ks_quality_p_value=1	log10_base_likelihood=-5.76835	log10_qual_likelihood_position_model=21.064	log10_strand_likelihood_position_model=14.4746	new_cov=27/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=28/100	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=55/100
RA	304	.	NC_007779	1746048	0	C	A	bias_e_value=1108.32	bias_p_value=0.000238536	fisher_strand_p_value=2.01979e-05	frequency=4.520512e-02	genotype_quality=732.1	ks_quality_p_value=1	log10_base_likelihood=-6.19786	log10_qual_likelihood_position_model=15.2077	log10_strand_likelihood_position_model=4.8051	new_cov=16/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=99/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/107
RA	305	.	NC_007779	1759411	1	.	T	bias_e_value=3139920	bias_p_value=0.675786	fisher_strand_p_value=1	frequency=7.843018e-03	genotype_quality=1227.9	ks_quality_p_value=0.312329	log10_base_likelihood=-8.24791	log10_qual_likelihood_position_model=1.95404	log10_strand_likelihood_position_model=0.299865	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.46735e-08	ref_cov=131/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/123
RA	306	.	NC_007779	1777181	0	A	C	bias_e_value=5.4449e-05	bias_p_value=1.17187e-11	fisher_strand_p_value=3.9649e-13	frequency=9.111929e-02	genotype_quality=597.5	ks_quality_p_value=1	log10_base_likelihood=-8.62741	log10_qual_likelihood_position_model=45.7685	log10_strand_likelihood_position_model=12.5917	new_cov=2/46	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=119/84	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/133
RA	307	.	NC_007779	1801443	0	A	C	bias_e_value=1.45184e-10	bias_p_value=3.1247e-17	fisher_strand_p_value=7.3075e-19	frequency=1.076388e-01	genotype_quality=668.8	ks_quality_p_value=1	log10_base_likelihood=-18.3468	log10_qual_likelihood_position_model=35.9099	log10_strand_likelihood_position_model=18.1362	new_cov=0/41	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=134/56	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/97
RA	308	.	NC_007779	1801456	0	C	G	bias_e_value=0.000428515	bias_p_value=9.22265e-11	fisher_strand_p_value=3.45909e-12	frequency=1.159630e-01	genotype_quality=787.9	ks_quality_p_value=0.972431	log10_base_likelihood=-30.33	log10_qual_likelihood_position_model=25.5087	log10_strand_likelihood_position_model=11.461	new_cov=0/33	polymorphism_quality=25.1	quality=25.1	quality_position_model=Inf	ref_cov=134/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/126
RA	309	.	NC_007779	1808686	0	G	T	bias_e_value=5675.22	bias_p_value=0.00122144	fisher_strand_p_value=0.000122004	frequency=3.060722e-02	genotype_quality=775.4	ks_quality_p_value=1	log10_base_likelihood=-5.91045	log10_qual_likelihood_position_model=11.5408	log10_strand_likelihood_position_model=3.91362	new_cov=0/12	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=137/116	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/128
RA	310	.	NC_007779	1820099	0	A	C	bias_e_value=2.11301e-10	bias_p_value=4.54768e-17	fisher_strand_p_value=1.07318e-18	frequency=1.442108e-01	genotype_quality=683.9	ks_quality_p_value=1	log10_base_likelihood=-30.5937	log10_qual_likelihood_position_model=30.9355	log10_strand_likelihood_position_model=17.9693	new_cov=0/43	polymorphism_quality=25.4	quality=25.4	quality_position_model=Inf	ref_cov=142/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/110
RA	311	.	NC_007779	1837206	0	G	T	bias_e_value=0.000326715	bias_p_value=7.03168e-11	fisher_strand_p_value=2.55088e-12	frequency=8.707762e-02	genotype_quality=655.0	ks_quality_p_value=0.995173	log10_base_likelihood=-18.6235	log10_qual_likelihood_position_model=22.8116	log10_strand_likelihood_position_model=11.5933	new_cov=19/0	polymorphism_quality=13.3	quality=13.3	quality_position_model=Inf	ref_cov=34/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=53/134
RA	312	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=1081.2	new_cov=123/144	quality=1081.2	ref_cov=1/0	tot_cov=124/144
RA	313	.	NC_007779	1861399	0	A	C	bias_e_value=9.70269e-05	bias_p_value=2.08825e-11	fisher_strand_p_value=7.21131e-13	frequency=6.610012e-02	genotype_quality=550.3	ks_quality_p_value=1	log10_base_likelihood=-9.87079	log10_qual_likelihood_position_model=21.6114	log10_strand_likelihood_position_model=12.142	new_cov=0/18	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=123/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/43
RA	314	.	NC_007779	1864105	1	.	T	bias_e_value=1974430	bias_p_value=0.424945	fisher_strand_p_value=0.230838	frequency=9.174347e-03	genotype_quality=1061.3	ks_quality_p_value=0.628027	log10_base_likelihood=-8.42205	log10_qual_likelihood_position_model=1.13085	log10_strand_likelihood_position_model=0.636694	new_cov=0/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.34545e-08	ref_cov=113/103	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/105
RA	315	.	NC_007779	1879404	0	A	C	bias_e_value=6.10029e-13	bias_p_value=1.31293e-19	fisher_strand_p_value=2.71516e-21	frequency=9.271765e-02	genotype_quality=592.9	ks_quality_p_value=1	log10_base_likelihood=-20.3864	log10_qual_likelihood_position_model=27.0925	log10_strand_likelihood_position_model=20.5662	new_cov=0/22	polymorphism_quality=15.1	quality=15.1	quality_position_model=Inf	ref_cov=147/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/31
RA	316	.	NC_007779	1879996	0	G	T	bias_e_value=612.807	bias_p_value=0.00013189	fisher_strand_p_value=1.05887e-05	frequency=4.386425e-02	genotype_quality=772.2	ks_quality_p_value=1	log10_base_likelihood=-5.87528	log10_qual_likelihood_position_model=9.96525	log10_strand_likelihood_position_model=4.97516	new_cov=11/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=71/141	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/141
RA	317	.	NC_007779	1881068	1	.	T	bias_e_value=4644620	bias_p_value=0.999631	fisher_strand_p_value=1	frequency=1.185703e-02	genotype_quality=1192.3	ks_quality_p_value=0.972957	log10_base_likelihood=-12.1069	log10_qual_likelihood_position_model=2.93749	log10_strand_likelihood_position_model=0.422529	new_cov=2/1	polymorphism_quality=6.7	quality=6.7	quality_position_model=9.55243e-11	ref_cov=125/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/126
RA	318	.	NC_007779	1896055	1	.	A	bias_e_value=2136340	bias_p_value=0.459791	fisher_strand_p_value=0.187524	frequency=6.944656e-03	genotype_quality=1409.0	ks_quality_p_value=0.872483	log10_base_likelihood=-8.26628	log10_qual_likelihood_position_model=1.29818	log10_strand_likelihood_position_model=0.726943	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=3.59198e-08	ref_cov=123/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/163
RA	319	.	NC_007779	1905959	0	T	G	bias_e_value=1622.23	bias_p_value=0.000349143	fisher_strand_p_value=3.06453e-05	frequency=2.948666e-02	genotype_quality=844.0	ks_quality_p_value=1	log10_base_likelihood=-5.61155	log10_qual_likelihood_position_model=16.5304	log10_strand_likelihood_position_model=4.53151	new_cov=14/1	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=92/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=106/146
RA	320	.	NC_007779	1906475	1	.	C	bias_e_value=647716	bias_p_value=0.139404	fisher_strand_p_value=0.0793455	frequency=1.200008e-02	genotype_quality=1194.1	ks_quality_p_value=0.3933	log10_base_likelihood=-13.5233	log10_qual_likelihood_position_model=2.2548	log10_strand_likelihood_position_model=1.10048	new_cov=3/0	polymorphism_quality=8.2	quality=8.2	quality_position_model=3.37005e-12	ref_cov=105/142	reject=POLYMORPHISM_STRAND	tot_cov=108/142
RA	321	.	NC_007779	1906477	1	.	G	bias_e_value=222354	bias_p_value=0.0478559	fisher_strand_p_value=0.00833685	frequency=2.212334e-02	genotype_quality=1062.3	ks_quality_p_value=0.990237	log10_base_likelihood=-20.7709	log10_qual_likelihood_position_model=6.29289	log10_strand_likelihood_position_model=2.079	new_cov=5/0	polymorphism_quality=15.5	quality=15.5	quality_position_model=1.79928e-14	ref_cov=83/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=88/138
RA	322	.	NC_007779	1909041	0	G	A	bias_e_value=4421870	bias_p_value=0.951691	fisher_strand_p_value=0.716832	frequency=2.548981e-02	genotype_quality=1126.1	ks_quality_p_value=0.984505	log10_base_likelihood=-13.5328	log10_qual_likelihood_position_model=5.13394	log10_strand_likelihood_position_model=0.570733	new_cov=4/3	polymorphism_quality=8.2	quality=8.2	quality_position_model=8.35289e-10	ref_cov=129/137	tot_cov=133/140
RA	323	.	NC_007779	1910325	1	.	A	bias_e_value=3955500	bias_p_value=0.851317	fisher_strand_p_value=0.508406	frequency=6.756783e-03	genotype_quality=1463.3	ks_quality_p_value=0.997063	log10_base_likelihood=-7.8576	log10_qual_likelihood_position_model=3.38481	log10_strand_likelihood_position_model=0.487918	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=7.979e-06	ref_cov=127/167	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/169
RA	324	.	NC_007779	1913464	0	T	G	bias_e_value=0.000551589	bias_p_value=1.18715e-10	fisher_strand_p_value=4.37161e-12	frequency=9.885645e-02	genotype_quality=524.8	ks_quality_p_value=1	log10_base_likelihood=-8.14602	log10_qual_likelihood_position_model=23.3206	log10_strand_likelihood_position_model=11.3854	new_cov=42/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=80/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/87
RA	325	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=982.9	new_cov=141/116	quality=982.9	ref_cov=0/0	tot_cov=141/116
RA	326	.	NC_007779	1941891	0	T	.	bias_e_value=2887890	bias_p_value=0.621541	fisher_strand_p_value=1	frequency=1.784706e-02	genotype_quality=896.7	ks_quality_p_value=0.268492	log10_base_likelihood=-11.3144	log10_qual_likelihood_position_model=2.53721	log10_strand_likelihood_position_model=0.422135	new_cov=2/2	polymorphism_quality=5.9	quality=5.9	quality_position_model=2.40678e-10	ref_cov=111/109	reject=INDEL_HOMOPOLYMER	tot_cov=113/111
RA	327	.	NC_007779	1949857	0	A	C	bias_e_value=5.90415e-05	bias_p_value=1.27071e-11	fisher_strand_p_value=4.31154e-13	frequency=7.946634e-02	genotype_quality=750.8	ks_quality_p_value=1	log10_base_likelihood=-9.24702	log10_qual_likelihood_position_model=31.8667	log10_strand_likelihood_position_model=12.3654	new_cov=0/30	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=136/71	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/101
RA	328	.	NC_007779	1956118	0	C	A	bias_e_value=10.2793	bias_p_value=2.21236e-06	fisher_strand_p_value=1.33504e-07	frequency=6.182241e-02	genotype_quality=497.8	ks_quality_p_value=0.983733	log10_base_likelihood=-20.0796	log10_qual_likelihood_position_model=8.22021	log10_strand_likelihood_position_model=6.87451	new_cov=0/8	polymorphism_quality=14.8	quality=14.8	quality_position_model=7.1976e-07	ref_cov=108/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/21
RA	329	.	NC_007779	1971508	0	A	C	bias_e_value=0.000923059	bias_p_value=1.98664e-10	fisher_strand_p_value=7.47111e-12	frequency=6.678343e-02	genotype_quality=496.9	ks_quality_p_value=0.998868	log10_base_likelihood=-12.6455	log10_qual_likelihood_position_model=14.1477	log10_strand_likelihood_position_model=11.1266	new_cov=0/11	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=126/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/19
RA	330	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=854.9	new_cov=115/104	quality=854.9	ref_cov=0/0	tot_cov=115/104
RA	331	.	NC_007779	1993894	0	A	C	bias_e_value=0.00115593	bias_p_value=2.48782e-10	fisher_strand_p_value=9.42811e-12	frequency=7.663774e-02	genotype_quality=817.8	ks_quality_p_value=1	log10_base_likelihood=-18.7781	log10_qual_likelihood_position_model=25.5298	log10_strand_likelihood_position_model=11.0256	new_cov=0/27	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=146/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/107
RA	332	.	NC_007779	1999234	0	T	G	bias_e_value=0.000641316	bias_p_value=1.38026e-10	fisher_strand_p_value=5.1122e-12	frequency=6.864834e-02	genotype_quality=496.1	ks_quality_p_value=1	log10_base_likelihood=-5.93084	log10_qual_likelihood_position_model=24.1134	log10_strand_likelihood_position_model=11.2914	new_cov=28/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=47/93	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=75/93
RA	333	.	NC_007779	1999251	0	T	G	bias_e_value=0.00948425	bias_p_value=2.04123e-09	fisher_strand_p_value=8.43628e-11	frequency=7.851744e-02	genotype_quality=572.0	ks_quality_p_value=1	log10_base_likelihood=-7.59915	log10_qual_likelihood_position_model=25.8142	log10_strand_likelihood_position_model=10.0738	new_cov=29/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=64/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/96
RA	334	.	NC_007779	2004055	0	A	C	bias_e_value=1.92342e-26	bias_p_value=4.13966e-33	fisher_strand_p_value=5.17807e-35	frequency=2.305903e-01	genotype_quality=572.6	ks_quality_p_value=1	log10_base_likelihood=-50.7276	log10_qual_likelihood_position_model=49.5775	log10_strand_likelihood_position_model=34.2858	new_cov=0/71	polymorphism_quality=45.6	quality=45.6	quality_position_model=Inf	ref_cov=145/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/111
RA	335	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=1092.4	new_cov=117/150	quality=1092.4	ref_cov=0/0	tot_cov=117/150
RA	336	.	NC_007779	2014007	1	.	T	bias_e_value=2499390	bias_p_value=0.537927	fisher_strand_p_value=0.210433	frequency=7.662773e-03	genotype_quality=1285.5	ks_quality_p_value=0.998522	log10_base_likelihood=-8.04908	log10_qual_likelihood_position_model=2.97428	log10_strand_likelihood_position_model=0.676886	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.94636e-06	ref_cov=141/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/120
RA	337	.	NC_007779	2014008	0	T	.	bias_e_value=4628760	bias_p_value=0.996218	fisher_strand_p_value=1	frequency=1.081848e-02	genotype_quality=1121.6	ks_quality_p_value=0.914294	log10_base_likelihood=-7.6824	log10_qual_likelihood_position_model=2.68453	log10_strand_likelihood_position_model=0.394942	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.79953e-06	ref_cov=147/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/128
RA	338	.	NC_007779	2022921	0	A	C	bias_e_value=0.00290703	bias_p_value=6.25661e-10	fisher_strand_p_value=2.46051e-11	frequency=5.515480e-02	genotype_quality=641.1	ks_quality_p_value=1	log10_base_likelihood=-8.06777	log10_qual_likelihood_position_model=16.9457	log10_strand_likelihood_position_model=10.609	new_cov=0/18	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=136/38	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/56
RA	339	.	NC_007779	2032185	0	G	C	bias_e_value=3.27755	bias_p_value=7.05405e-07	fisher_strand_p_value=3.9094e-08	frequency=4.323578e-02	genotype_quality=461.4	ks_quality_p_value=0.99921	log10_base_likelihood=-9.73849	log10_qual_likelihood_position_model=5.98192	log10_strand_likelihood_position_model=7.40789	new_cov=5/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=1/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=6/109
RA	340	.	NC_007779	2047442	0	A	.	bias_e_value=4020890	bias_p_value=0.865389	fisher_strand_p_value=0.613399	frequency=1.175404e-02	genotype_quality=1019.1	ks_quality_p_value=0.861231	log10_base_likelihood=-7.88465	log10_qual_likelihood_position_model=1.54639	log10_strand_likelihood_position_model=0.436775	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=8.06147e-08	ref_cov=130/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/124
RA	341	.	NC_007779	2060392	0	T	G	bias_e_value=1.42188e-06	bias_p_value=3.06021e-13	fisher_strand_p_value=9.18395e-15	frequency=8.882666e-02	genotype_quality=607.9	ks_quality_p_value=1	log10_base_likelihood=-9.27125	log10_qual_likelihood_position_model=49.6041	log10_strand_likelihood_position_model=14.2969	new_cov=49/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=86/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/105
RA	342	.	NC_007779	2076214	0	A	C	bias_e_value=0.0038994	bias_p_value=8.39243e-10	fisher_strand_p_value=3.34063e-11	frequency=8.280420e-02	genotype_quality=538.2	ks_quality_p_value=1	log10_base_likelihood=-13.1392	log10_qual_likelihood_position_model=19.6375	log10_strand_likelihood_position_model=10.4762	new_cov=0/21	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=111/41	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/62
RA	343	.	NC_007779	2082880	1	.	A	bias_e_value=3605070	bias_p_value=0.775897	fisher_strand_p_value=0.499171	frequency=8.474350e-03	genotype_quality=1145.3	ks_quality_p_value=0.82213	log10_base_likelihood=-8.63939	log10_qual_likelihood_position_model=2.21506	log10_strand_likelihood_position_model=0.560653	new_cov=2/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=8.82127e-08	ref_cov=122/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/112
RA	344	.	NC_007779	2089250	1	.	T	bias_e_value=2426960	bias_p_value=0.522338	fisher_strand_p_value=0.20768	frequency=8.620262e-03	genotype_quality=1130.7	ks_quality_p_value=0.964368	log10_base_likelihood=-8.04253	log10_qual_likelihood_position_model=2.82601	log10_strand_likelihood_position_model=0.682605	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.1242e-06	ref_cov=104/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/126
RA	345	.	NC_007779	2089543	0	A	C	bias_e_value=6.37652e-05	bias_p_value=1.37238e-11	fisher_strand_p_value=4.66912e-13	frequency=7.367563e-02	genotype_quality=842.1	ks_quality_p_value=1	log10_base_likelihood=-12.5365	log10_qual_likelihood_position_model=26.7022	log10_strand_likelihood_position_model=12.3308	new_cov=0/27	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=163/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/101
RA	346	.	NC_007779	2098223	0	T	G	bias_e_value=6.78181e-10	bias_p_value=1.45961e-16	fisher_strand_p_value=3.54435e-18	frequency=1.280370e-01	genotype_quality=589.8	ks_quality_p_value=1	log10_base_likelihood=-14.9033	log10_qual_likelihood_position_model=32.3258	log10_strand_likelihood_position_model=17.4505	new_cov=44/0	polymorphism_quality=9.6	quality=9.6	quality_position_model=Inf	ref_cov=58/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=102/118
RA	347	.	NC_007779	2107010	1	.	A	bias_e_value=1752620	bias_p_value=0.377205	fisher_strand_p_value=0.320638	frequency=1.646137e-02	genotype_quality=1152.2	ks_quality_p_value=0.378344	log10_base_likelihood=-17.9684	log10_qual_likelihood_position_model=2.46334	log10_strand_likelihood_position_model=0.729341	new_cov=1/3	polymorphism_quality=12.7	quality=12.7	quality_position_model=6.94142e-17	ref_cov=136/103	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/106
RA	348	.	NC_007779	2107011	0	A	.	bias_e_value=3718830	bias_p_value=0.800381	fisher_strand_p_value=0.593091	frequency=1.157475e-02	genotype_quality=1042.7	ks_quality_p_value=0.740132	log10_base_likelihood=-8.08206	log10_qual_likelihood_position_model=1.72957	log10_strand_likelihood_position_model=0.468444	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=8.40331e-08	ref_cov=140/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/118
RA	349	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1141.4	new_cov=121/158	quality=1141.4	ref_cov=0/1	tot_cov=121/159
RA	350	.	NC_007779	2170678	0	C	T	bias_e_value=1889950	bias_p_value=0.406762	fisher_strand_p_value=0.263649	frequency=1.166725e-02	genotype_quality=1072.0	ks_quality_p_value=0.514751	log10_base_likelihood=-5.76376	log10_qual_likelihood_position_model=1.45831	log10_strand_likelihood_position_model=0.726576	new_cov=3/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=2.13381e-05	ref_cov=144/109	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=147/109
RA	351	.	NC_007779	2174678	0	C	G	bias_e_value=1.39809e-14	bias_p_value=3.00903e-21	fisher_strand_p_value=5.76355e-23	frequency=1.393590e-01	genotype_quality=726.2	ks_quality_p_value=1	log10_base_likelihood=-47.2269	log10_qual_likelihood_position_model=28.9051	log10_strand_likelihood_position_model=22.2393	new_cov=0/30	polymorphism_quality=42.1	quality=42.1	quality_position_model=Inf	ref_cov=159/21	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=159/51
RA	352	.	NC_007779	2184751	0	T	G	bias_e_value=0.416152	bias_p_value=8.95657e-08	fisher_strand_p_value=4.42611e-09	frequency=6.499481e-02	genotype_quality=773.2	ks_quality_p_value=1	log10_base_likelihood=-7.83285	log10_qual_likelihood_position_model=21.6128	log10_strand_likelihood_position_model=8.35398	new_cov=23/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=90/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/133
RA	353	.	NC_007779	2199432	0	G	C	bias_e_value=3.38065e-11	bias_p_value=7.27596e-18	fisher_strand_p_value=1.64421e-19	frequency=1.346984e-01	genotype_quality=601.5	ks_quality_p_value=1	log10_base_likelihood=-45.5545	log10_qual_likelihood_position_model=23.5123	log10_strand_likelihood_position_model=18.784	new_cov=0/23	polymorphism_quality=40.4	quality=40.4	quality_position_model=4.65879e-05	ref_cov=133/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/36
RA	354	.	NC_007779	2200801	1	.	A	bias_e_value=2408940	bias_p_value=0.51846	fisher_strand_p_value=1	frequency=1.619434e-02	genotype_quality=1187.8	ks_quality_p_value=0.197877	log10_base_likelihood=-17.5164	log10_qual_likelihood_position_model=1.84773	log10_strand_likelihood_position_model=0.427628	new_cov=2/2	polymorphism_quality=12.2	quality=12.2	quality_position_model=2.34194e-17	ref_cov=112/131	reject=INDEL_HOMOPOLYMER	tot_cov=114/133
RA	355	.	NC_007779	2211749	0	G	C	bias_e_value=3.984	bias_p_value=8.57451e-07	fisher_strand_p_value=4.81891e-08	frequency=5.978251e-02	genotype_quality=635.0	ks_quality_p_value=0.996756	log10_base_likelihood=-12.0916	log10_qual_likelihood_position_model=13.0306	log10_strand_likelihood_position_model=7.31705	new_cov=12/0	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=36/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=48/130
RA	356	.	NC_007779	2212417	0	G	T	bias_e_value=1.29708e-05	bias_p_value=2.79162e-12	fisher_strand_p_value=8.99373e-14	frequency=9.693289e-02	genotype_quality=615.9	ks_quality_p_value=1	log10_base_likelihood=-33.9843	log10_qual_likelihood_position_model=19.0089	log10_strand_likelihood_position_model=13.048	new_cov=15/1	polymorphism_quality=28.8	quality=28.8	quality_position_model=0.00125694	ref_cov=10/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=25/137
RA	357	.	NC_007779	2213136	0	G	T	bias_e_value=2.3275e-13	bias_p_value=5.00932e-20	fisher_strand_p_value=1.10203e-21	frequency=2.081509e-01	genotype_quality=506.5	ks_quality_p_value=0.921288	log10_base_likelihood=-86.0809	log10_qual_likelihood_position_model=27.4481	log10_strand_likelihood_position_model=20.9578	new_cov=34/0	polymorphism_quality=81.1	quality=81.1	quality_position_model=5.52873e-40	ref_cov=19/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=53/109
RA	358	.	NC_007779	2222886	0	T	G	bias_e_value=3.95915	bias_p_value=8.52102e-07	fisher_strand_p_value=4.77438e-08	frequency=4.340267e-02	genotype_quality=594.4	ks_quality_p_value=0.999406	log10_base_likelihood=-11.9045	log10_qual_likelihood_position_model=10.6557	log10_strand_likelihood_position_model=7.32108	new_cov=7/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=10/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=17/140
RA	359	.	NC_007779	2225700	0	T	G	bias_e_value=697.859	bias_p_value=0.000150196	fisher_strand_p_value=1.22302e-05	frequency=2.593803e-02	genotype_quality=690.2	ks_quality_p_value=0.997271	log10_base_likelihood=-6.42544	log10_qual_likelihood_position_model=7.66481	log10_strand_likelihood_position_model=4.91257	new_cov=5/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=16/163	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=21/163
RA	360	.	NC_007779	2226744	0	T	G	bias_e_value=1.09098e-06	bias_p_value=2.34805e-13	fisher_strand_p_value=6.98942e-15	frequency=1.095848e-01	genotype_quality=703.2	ks_quality_p_value=1	log10_base_likelihood=-17.4775	log10_qual_likelihood_position_model=30.8223	log10_strand_likelihood_position_model=14.1556	new_cov=36/0	polymorphism_quality=12.2	quality=12.2	quality_position_model=Inf	ref_cov=76/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=112/138
RA	361	.	NC_007779	2231556	0	T	G	bias_e_value=182.725	bias_p_value=3.93267e-05	fisher_strand_p_value=2.85684e-06	frequency=6.428099e-02	genotype_quality=532.7	ks_quality_p_value=1	log10_base_likelihood=-9.60744	log10_qual_likelihood_position_model=14.5672	log10_strand_likelihood_position_model=5.54411	new_cov=15/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=60/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=76/91
RA	362	.	NC_007779	2245262	0	G	C	bias_e_value=4.02166	bias_p_value=8.65556e-07	fisher_strand_p_value=4.90934e-08	frequency=7.597828e-02	genotype_quality=497.0	ks_quality_p_value=0.988195	log10_base_likelihood=-12.2827	log10_qual_likelihood_position_model=10.6725	log10_strand_likelihood_position_model=7.30898	new_cov=0/12	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=102/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=102/39
RA	363	.	NC_007779	2249963	0	T	G	bias_e_value=1.68392e-15	bias_p_value=3.6242e-22	fisher_strand_p_value=6.66642e-24	frequency=2.057652e-01	genotype_quality=539.8	ks_quality_p_value=1	log10_base_likelihood=-32.6785	log10_qual_likelihood_position_model=44.8399	log10_strand_likelihood_position_model=23.1761	new_cov=56/0	polymorphism_quality=27.5	quality=27.5	quality_position_model=Inf	ref_cov=48/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/118
RA	364	.	NC_007779	2249972	0	A	T	bias_e_value=6525.35	bias_p_value=0.00140441	fisher_strand_p_value=0.000142489	frequency=4.449177e-02	genotype_quality=720.5	ks_quality_p_value=1	log10_base_likelihood=-6.56544	log10_qual_likelihood_position_model=10.4295	log10_strand_likelihood_position_model=3.84622	new_cov=12/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=98/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/114
RA	365	.	NC_007779	2264335	0	A	C	bias_e_value=0.00113816	bias_p_value=2.44959e-10	fisher_strand_p_value=9.27755e-12	frequency=1.043420e-01	genotype_quality=579.9	ks_quality_p_value=1	log10_base_likelihood=-15.277	log10_qual_likelihood_position_model=22.5038	log10_strand_likelihood_position_model=11.0326	new_cov=0/30	polymorphism_quality=9.9	quality=9.9	quality_position_model=Inf	ref_cov=105/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/94
RA	366	.	NC_007779	2264339	0	A	C	bias_e_value=0.493334	bias_p_value=1.06177e-07	fisher_strand_p_value=5.29384e-09	frequency=9.325361e-02	genotype_quality=617.5	ks_quality_p_value=1	log10_base_likelihood=-11.9162	log10_qual_likelihood_position_model=23.9047	log10_strand_likelihood_position_model=8.42783	new_cov=0/26	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=101/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=101/104
RA	367	.	NC_007779	2278884	0	T	G	bias_e_value=1.10793e-09	bias_p_value=2.38453e-16	fisher_strand_p_value=5.86196e-18	frequency=8.501101e-02	genotype_quality=641.7	ks_quality_p_value=1	log10_base_likelihood=-11.7317	log10_qual_likelihood_position_model=34.921	log10_strand_likelihood_position_model=17.232	new_cov=34/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=45/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/136
RA	368	.	NC_007779	2287114	0	C	A	bias_e_value=0.0289687	bias_p_value=6.23475e-09	fisher_strand_p_value=3.04542e-10	frequency=7.920742e-02	genotype_quality=814.4	ks_quality_p_value=0.888954	log10_base_likelihood=-20.3466	log10_qual_likelihood_position_model=26.9192	log10_strand_likelihood_position_model=9.51635	new_cov=0/23	polymorphism_quality=15.1	quality=15.1	quality_position_model=Inf	ref_cov=146/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/103
RA	369	.	NC_007779	2307309	0	T	C	bias_e_value=2.99564e-05	bias_p_value=6.44732e-12	fisher_strand_p_value=2.13669e-13	frequency=8.120680e-02	genotype_quality=544.8	ks_quality_p_value=1	log10_base_likelihood=-12.0706	log10_qual_likelihood_position_model=15.9744	log10_strand_likelihood_position_model=12.6703	new_cov=0/15	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=135/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/30
RA	370	.	NC_007779	2308002	0	G	A	bias_e_value=2406430	bias_p_value=0.517921	fisher_strand_p_value=0.454545	frequency=1.667299e-01	genotype_quality=22.4	ks_quality_p_value=0.434598	log10_base_likelihood=-5.9133	log10_qual_likelihood_position_model=0.740363	log10_strand_likelihood_position_model=0.643453	new_cov=0/2	polymorphism_quality=0.4	quality=0.4	quality_position_model=2.14695e-06	ref_cov=6/4	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=6/6
RA	371	.	NC_007779	2331120	0	T	G	bias_e_value=1.80573e-22	bias_p_value=3.88635e-29	fisher_strand_p_value=5.49885e-31	frequency=2.484312e-01	genotype_quality=469.4	ks_quality_p_value=1	log10_base_likelihood=-39.9688	log10_qual_likelihood_position_model=46.3139	log10_strand_likelihood_position_model=30.2597	new_cov=71/0	polymorphism_quality=34.8	quality=34.8	quality_position_model=Inf	ref_cov=36/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/113
RA	372	.	NC_007779	2332580	0	A	C	bias_e_value=5.84257e-16	bias_p_value=1.25746e-22	fisher_strand_p_value=2.26802e-24	frequency=1.540184e-01	genotype_quality=487.2	ks_quality_p_value=1	log10_base_likelihood=-15.1206	log10_qual_likelihood_position_model=32.1288	log10_strand_likelihood_position_model=23.6444	new_cov=0/48	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=112/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/79
RA	373	.	NC_007779	2341298	0	T	.	bias_e_value=1034410	bias_p_value=0.222628	fisher_strand_p_value=0.273805	frequency=1.204014e-02	genotype_quality=999.1	ks_quality_p_value=0.211169	log10_base_likelihood=-8.25648	log10_qual_likelihood_position_model=1.66184	log10_strand_likelihood_position_model=0.681416	new_cov=3/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.83922e-08	ref_cov=145/101	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/101
RA	374	.	NC_007779	2342393	0	A	C	bias_e_value=3.05246e-09	bias_p_value=6.5696e-16	fisher_strand_p_value=1.65737e-17	frequency=1.308899e-01	genotype_quality=612.0	ks_quality_p_value=1	log10_base_likelihood=-15.8175	log10_qual_likelihood_position_model=30.0531	log10_strand_likelihood_position_model=16.7806	new_cov=0/39	polymorphism_quality=10.5	quality=10.5	quality_position_model=Inf	ref_cov=125/55	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/96
RA	375	.	NC_007779	2344586	0	C	A	bias_e_value=181.131	bias_p_value=3.89837e-05	fisher_strand_p_value=2.82999e-06	frequency=3.922462e-02	genotype_quality=1012.6	ks_quality_p_value=1	log10_base_likelihood=-8.57704	log10_qual_likelihood_position_model=16.6523	log10_strand_likelihood_position_model=5.54822	new_cov=16/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=116/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/152
RA	376	.	NC_007779	2347976	0	A	C	bias_e_value=1.57495e-13	bias_p_value=3.38967e-20	fisher_strand_p_value=6.81508e-22	frequency=1.244402e-01	genotype_quality=630.1	ks_quality_p_value=1	log10_base_likelihood=-17.3004	log10_qual_likelihood_position_model=36.881	log10_strand_likelihood_position_model=21.1694	new_cov=1/45	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=138/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/88
RA	377	.	NC_007779	2353815	0	A	C	bias_e_value=4.86722	bias_p_value=1.04754e-06	fisher_strand_p_value=5.93871e-08	frequency=4.859352e-02	genotype_quality=477.2	ks_quality_p_value=1	log10_base_likelihood=-9.41142	log10_qual_likelihood_position_model=11.0331	log10_strand_likelihood_position_model=7.22631	new_cov=0/9	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=106/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/24
RA	378	.	NC_007779	2354291	0	A	C	bias_e_value=5.86186e-19	bias_p_value=1.26161e-25	fisher_strand_p_value=2.01965e-27	frequency=2.027650e-01	genotype_quality=613.9	ks_quality_p_value=1	log10_base_likelihood=-44.4244	log10_qual_likelihood_position_model=41.0266	log10_strand_likelihood_position_model=26.6947	new_cov=0/59	polymorphism_quality=39.3	quality=39.3	quality_position_model=Inf	ref_cov=144/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/111
RA	379	.	NC_007779	2374921	0	T	G	bias_e_value=0.00234945	bias_p_value=5.05656e-10	fisher_strand_p_value=1.97139e-11	frequency=8.145475e-02	genotype_quality=501.2	ks_quality_p_value=1	log10_base_likelihood=-7.01269	log10_qual_likelihood_position_model=17.4129	log10_strand_likelihood_position_model=10.7052	new_cov=16/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=23/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=39/114
RA	380	.	NC_007779	2374933	0	A	C	bias_e_value=3883.87	bias_p_value=0.0008359	fisher_strand_p_value=8.01825e-05	frequency=3.442860e-02	genotype_quality=556.6	ks_quality_p_value=0.999339	log10_base_likelihood=-6.13666	log10_qual_likelihood_position_model=10.7488	log10_strand_likelihood_position_model=4.09592	new_cov=7/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=34/108	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=41/108
RA	381	.	NC_007779	2381946	0	A	C	bias_e_value=0.00153151	bias_p_value=3.29618e-10	fisher_strand_p_value=1.26315e-11	frequency=6.019163e-02	genotype_quality=678.1	ks_quality_p_value=1	log10_base_likelihood=-8.26138	log10_qual_likelihood_position_model=24.197	log10_strand_likelihood_position_model=10.8985	new_cov=0/22	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=130/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/72
RA	382	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=997.8	new_cov=120/129	quality=997.8	ref_cov=0/0	tot_cov=120/129
RA	383	.	NC_007779	2409404	0	A	C	bias_e_value=6.69553e-08	bias_p_value=1.44104e-14	fisher_strand_p_value=3.95159e-16	frequency=1.569867e-01	genotype_quality=514.5	ks_quality_p_value=1	log10_base_likelihood=-25.23	log10_qual_likelihood_position_model=29.0676	log10_strand_likelihood_position_model=15.4032	new_cov=0/36	polymorphism_quality=20.0	quality=20.0	quality_position_model=Inf	ref_cov=108/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/83
RA	384	.	NC_007779	2410289	0	T	A	bias_e_value=1042.73	bias_p_value=0.000224421	fisher_strand_p_value=1.88961e-05	frequency=5.284595e-02	genotype_quality=966.2	ks_quality_p_value=1	log10_base_likelihood=-14.2113	log10_qual_likelihood_position_model=22.4037	log10_strand_likelihood_position_model=4.72363	new_cov=0/15	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=133/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/132
RA	385	.	NC_007779	2410316	0	A	C	bias_e_value=5.48151e-11	bias_p_value=1.17975e-17	fisher_strand_p_value=2.69612e-19	frequency=1.464643e-01	genotype_quality=654.5	ks_quality_p_value=1	log10_base_likelihood=-39.6841	log10_qual_likelihood_position_model=34.7074	log10_strand_likelihood_position_model=18.5693	new_cov=0/52	polymorphism_quality=34.5	quality=34.5	quality_position_model=Inf	ref_cov=130/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=130/129
RA	386	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=965.9	new_cov=106/139	quality=965.9	ref_cov=1/0	tot_cov=107/139
RA	387	.	NC_007779	2416329	0	G	.	bias_e_value=2741780	bias_p_value=0.590096	fisher_strand_p_value=0.252025	frequency=1.560020e-02	genotype_quality=780.8	ks_quality_p_value=0.973547	log10_base_likelihood=-7.36012	log10_qual_likelihood_position_model=4.20077	log10_strand_likelihood_position_model=0.797778	new_cov=3/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=0.000423412	ref_cov=101/87	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=104/88
RA	388	.	NC_007779	2417605	0	C	A	bias_e_value=34.8252	bias_p_value=7.49521e-06	fisher_strand_p_value=7.18344e-07	frequency=6.244326e-02	genotype_quality=823.8	ks_quality_p_value=0.671214	log10_base_likelihood=-10.7661	log10_qual_likelihood_position_model=26.6757	log10_strand_likelihood_position_model=6.25886	new_cov=26/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=138/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/112
RA	389	.	NC_007779	2420902	0	G	C	bias_e_value=0.203461	bias_p_value=4.37896e-08	fisher_strand_p_value=2.21807e-09	frequency=6.352568e-02	genotype_quality=778.1	ks_quality_p_value=0.940653	log10_base_likelihood=-11.6384	log10_qual_likelihood_position_model=20.0851	log10_strand_likelihood_position_model=8.65403	new_cov=19/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=69/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=88/147
RA	390	.	NC_007779	2426889	0	A	C	bias_e_value=0.295533	bias_p_value=6.36057e-08	fisher_strand_p_value=3.08831e-09	frequency=5.627155e-02	genotype_quality=482.1	ks_quality_p_value=1	log10_base_likelihood=-13.6856	log10_qual_likelihood_position_model=9.84171	log10_strand_likelihood_position_model=8.51028	new_cov=0/8	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=119/7	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/15
RA	391	.	NC_007779	2446456	0	C	A	bias_e_value=256.389	bias_p_value=5.5181e-05	fisher_strand_p_value=4.27032e-06	frequency=5.022335e-02	genotype_quality=634.6	ks_quality_p_value=0.964316	log10_base_likelihood=-6.0325	log10_qual_likelihood_position_model=16.5971	log10_strand_likelihood_position_model=5.36954	new_cov=0/12	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=116/58	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/70
RA	392	.	NC_007779	2458860	0	T	G	bias_e_value=9.81095	bias_p_value=2.11155e-06	fisher_strand_p_value=1.2498e-07	frequency=2.371502e-02	genotype_quality=538.1	ks_quality_p_value=1	log10_base_likelihood=-6.46755	log10_qual_likelihood_position_model=6.31689	log10_strand_likelihood_position_model=6.90316	new_cov=5/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=3/134	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=8/134
RA	393	.	NC_007779	2461194	0	T	G	bias_e_value=3213360	bias_p_value=0.691591	fisher_strand_p_value=0.511767	frequency=1.333427e-02	genotype_quality=588.9	ks_quality_p_value=0.637341	log10_base_likelihood=-5.94468	log10_qual_likelihood_position_model=1.69607	log10_strand_likelihood_position_model=0.465276	new_cov=2/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=1.29941e-05	ref_cov=86/62	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=88/62
RA	394	.	NC_007779	2465370	0	C	A	bias_e_value=1.31733e-05	bias_p_value=2.8352e-12	fisher_strand_p_value=9.19449e-14	frequency=9.744406e-02	genotype_quality=536.5	ks_quality_p_value=0.993947	log10_base_likelihood=-30.1486	log10_qual_likelihood_position_model=17.2676	log10_strand_likelihood_position_model=13.0365	new_cov=0/14	polymorphism_quality=25.0	quality=25.0	quality_position_model=Inf	ref_cov=120/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/23
RA	395	.	NC_007779	2468327	0	C	.	bias_e_value=4149250	bias_p_value=0.893016	fisher_strand_p_value=0.735738	frequency=3.829098e-02	genotype_quality=953.4	ks_quality_p_value=0.781084	log10_base_likelihood=-29.6073	log10_qual_likelihood_position_model=3.55541	log10_strand_likelihood_position_model=0.634693	new_cov=3/6	polymorphism_quality=24.4	quality=24.4	quality_position_model=1.21537e-27	ref_cov=98/128	reject=INDEL_HOMOPOLYMER	tot_cov=101/134
RA	396	.	NC_007779	2484034	0	G	T	bias_e_value=302.025	bias_p_value=6.5003e-05	fisher_strand_p_value=4.92536e-06	frequency=4.404831e-02	genotype_quality=924.9	ks_quality_p_value=0.998077	log10_base_likelihood=-8.86652	log10_qual_likelihood_position_model=17.8178	log10_strand_likelihood_position_model=5.30756	new_cov=0/16	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=138/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/129
RA	397	.	NC_007779	2517218	0	A	C	bias_e_value=2.28528e-11	bias_p_value=4.91846e-18	fisher_strand_p_value=1.1015e-19	frequency=8.822680e-02	genotype_quality=537.9	ks_quality_p_value=1	log10_base_likelihood=-9.54305	log10_qual_likelihood_position_model=30.2814	log10_strand_likelihood_position_model=18.958	new_cov=0/26	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=128/17	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/43
RA	398	.	NC_007779	2522930	0	T	G	bias_e_value=15.3549	bias_p_value=3.30473e-06	fisher_strand_p_value=2.0128e-07	frequency=6.626701e-02	genotype_quality=755.0	ks_quality_p_value=1	log10_base_likelihood=-9.52718	log10_qual_likelihood_position_model=22.7312	log10_strand_likelihood_position_model=6.86602	new_cov=24/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=109/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/113
RA	399	.	NC_007779	2536601	0	T	G	bias_e_value=3.88388e-06	bias_p_value=8.35903e-13	fisher_strand_p_value=2.58915e-14	frequency=1.234384e-01	genotype_quality=622.5	ks_quality_p_value=1	log10_base_likelihood=-21.7455	log10_qual_likelihood_position_model=27.1816	log10_strand_likelihood_position_model=13.5868	new_cov=33/0	polymorphism_quality=16.5	quality=16.5	quality_position_model=Inf	ref_cov=61/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/122
RA	400	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=1130.4	new_cov=141/143	quality=1130.4	ref_cov=0/0	tot_cov=141/143
RA	401	.	NC_007779	2556426	0	G	T	bias_e_value=0.181649	bias_p_value=3.90951e-08	fisher_strand_p_value=2.10178e-09	frequency=7.083225e-02	genotype_quality=908.4	ks_quality_p_value=0.881272	log10_base_likelihood=-17.0612	log10_qual_likelihood_position_model=27.3893	log10_strand_likelihood_position_model=8.78277	new_cov=0/28	polymorphism_quality=11.7	quality=11.7	quality_position_model=Inf	ref_cov=141/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/147
RA	402	.	NC_007779	2559232	0	G	T	bias_e_value=33173.2	bias_p_value=0.00713966	fisher_strand_p_value=0.000889722	frequency=3.710842e-02	genotype_quality=727.1	ks_quality_p_value=1	log10_base_likelihood=-6.10756	log10_qual_likelihood_position_model=9.20265	log10_strand_likelihood_position_model=3.15689	new_cov=11/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=103/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/102
RA	403	.	NC_007779	2574652	1	.	T	bias_e_value=4587040	bias_p_value=0.98724	fisher_strand_p_value=1	frequency=8.439064e-03	genotype_quality=1162.7	ks_quality_p_value=0.844561	log10_base_likelihood=-8.27572	log10_qual_likelihood_position_model=1.05746	log10_strand_likelihood_position_model=0.299573	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.18967e-09	ref_cov=121/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/115
RA	404	.	NC_007779	2600440	0	A	G	bias_e_value=0.000148581	bias_p_value=3.19781e-11	fisher_strand_p_value=1.12139e-12	frequency=8.558941e-02	genotype_quality=699.7	ks_quality_p_value=1	log10_base_likelihood=-11.0395	log10_qual_likelihood_position_model=19.6842	log10_strand_likelihood_position_model=11.9502	new_cov=26/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=63/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=89/143
RA	405	.	NC_007779	2601998	0	A	C	bias_e_value=2.62546	bias_p_value=5.65061e-07	fisher_strand_p_value=3.09124e-08	frequency=5.151415e-02	genotype_quality=622.0	ks_quality_p_value=0.999265	log10_base_likelihood=-11.4467	log10_qual_likelihood_position_model=12.8794	log10_strand_likelihood_position_model=7.50987	new_cov=0/10	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=136/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/34
RA	406	.	NC_007779	2606900	0	T	G	bias_e_value=0.0516668	bias_p_value=1.11199e-08	fisher_strand_p_value=4.95878e-10	frequency=7.161570e-02	genotype_quality=541.3	ks_quality_p_value=1	log10_base_likelihood=-7.48395	log10_qual_likelihood_position_model=21.8605	log10_strand_likelihood_position_model=9.30463	new_cov=27/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=65/95	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=93/95
RA	407	.	NC_007779	2610583	0	G	C	bias_e_value=188.606	bias_p_value=4.05925e-05	fisher_strand_p_value=2.96379e-06	frequency=4.917955e-02	genotype_quality=667.3	ks_quality_p_value=0.997419	log10_base_likelihood=-7.45459	log10_qual_likelihood_position_model=11.0286	log10_strand_likelihood_position_model=5.52815	new_cov=0/10	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=127/44	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/54
RA	408	.	NC_007779	2619555	1	.	A	bias_e_value=4498800	bias_p_value=0.968247	fisher_strand_p_value=1	frequency=9.174347e-03	genotype_quality=1057.9	ks_quality_p_value=0.758818	log10_base_likelihood=-8.46154	log10_qual_likelihood_position_model=1.19925	log10_strand_likelihood_position_model=0.300351	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=6.48887e-09	ref_cov=102/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=103/115
RA	409	.	NC_007779	2623159	0	T	G	bias_e_value=9.63781e-26	bias_p_value=2.07428e-32	fisher_strand_p_value=2.64868e-34	frequency=2.352896e-01	genotype_quality=473.2	ks_quality_p_value=1	log10_base_likelihood=-38.3793	log10_qual_likelihood_position_model=44.3318	log10_strand_likelihood_position_model=33.577	new_cov=57/0	polymorphism_quality=33.2	quality=33.2	quality_position_model=Inf	ref_cov=18/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=75/124
RA	410	.	NC_007779	2623173	0	G	T	bias_e_value=12.8852	bias_p_value=2.7732e-06	fisher_strand_p_value=1.67008e-07	frequency=7.522249e-02	genotype_quality=701.1	ks_quality_p_value=1	log10_base_likelihood=-14.6302	log10_qual_likelihood_position_model=16.3341	log10_strand_likelihood_position_model=6.77726	new_cov=17/0	polymorphism_quality=9.3	quality=9.3	quality_position_model=Inf	ref_cov=69/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=88/117
RA	411	.	NC_007779	2640922	0	T	G	bias_e_value=1.09068e-07	bias_p_value=2.3474e-14	fisher_strand_p_value=6.52682e-16	frequency=9.856462e-02	genotype_quality=653.1	ks_quality_p_value=1	log10_base_likelihood=-17.3376	log10_qual_likelihood_position_model=34.3407	log10_strand_likelihood_position_model=15.1853	new_cov=35/0	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=61/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=97/134
RA	412	.	NC_007779	2641345	0	T	G	bias_e_value=29.4915	bias_p_value=6.34727e-06	fisher_strand_p_value=4.05055e-07	frequency=5.155468e-02	genotype_quality=484.5	ks_quality_p_value=0.996664	log10_base_likelihood=-10.7399	log10_qual_likelihood_position_model=10.3167	log10_strand_likelihood_position_model=6.39249	new_cov=7/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=12/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=19/114
RA	413	.	NC_007779	2646804	0	A	C	bias_e_value=4.05064e-09	bias_p_value=8.71793e-16	fisher_strand_p_value=2.21557e-17	frequency=9.864426e-02	genotype_quality=629.5	ks_quality_p_value=1	log10_base_likelihood=-14.8952	log10_qual_likelihood_position_model=35.3161	log10_strand_likelihood_position_model=16.6545	new_cov=0/37	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=129/53	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/92
RA	414	.	NC_007779	2648595	0	A	C	bias_e_value=5.32833e-05	bias_p_value=1.14678e-11	fisher_strand_p_value=3.87708e-13	frequency=8.920288e-02	genotype_quality=516.6	ks_quality_p_value=1	log10_base_likelihood=-16.8295	log10_qual_likelihood_position_model=18.2112	log10_strand_likelihood_position_model=12.4115	new_cov=0/15	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=123/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/29
RA	415	.	NC_007779	2672817	0	A	C	bias_e_value=2.86049e-08	bias_p_value=6.15646e-15	fisher_strand_p_value=1.6487e-16	frequency=1.107540e-01	genotype_quality=489.0	ks_quality_p_value=1	log10_base_likelihood=-15.4094	log10_qual_likelihood_position_model=25.5001	log10_strand_likelihood_position_model=15.7829	new_cov=0/29	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=110/30	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/59
RA	416	.	NC_007779	2700681	0	T	G	bias_e_value=0.000340007	bias_p_value=7.31776e-11	fisher_strand_p_value=2.6458e-12	frequency=1.101494e-01	genotype_quality=661.2	ks_quality_p_value=1	log10_base_likelihood=-12.3686	log10_qual_likelihood_position_model=30.2813	log10_strand_likelihood_position_model=11.6001	new_cov=36/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=85/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/113
RA	417	.	NC_007779	2708923	0	A	C	bias_e_value=27.8957	bias_p_value=6.00381e-06	fisher_strand_p_value=3.80422e-07	frequency=6.576157e-02	genotype_quality=632.9	ks_quality_p_value=1	log10_base_likelihood=-8.88386	log10_qual_likelihood_position_model=15.4864	log10_strand_likelihood_position_model=6.43619	new_cov=0/22	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=105/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/120
RA	418	.	NC_007779	2708932	0	T	C	bias_e_value=6.33415	bias_p_value=1.36326e-06	fisher_strand_p_value=7.85297e-08	frequency=6.301022e-02	genotype_quality=655.5	ks_quality_p_value=1	log10_base_likelihood=-6.68218	log10_qual_likelihood_position_model=19.9509	log10_strand_likelihood_position_model=7.25675	new_cov=0/23	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=115/96	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/119
RA	419	.	NC_007779	2708935	0	A	C	bias_e_value=1.18333e-11	bias_p_value=2.5468e-18	fisher_strand_p_value=5.61891e-20	frequency=2.059402e-01	genotype_quality=535.6	ks_quality_p_value=1	log10_base_likelihood=-38.8262	log10_qual_likelihood_position_model=37.4185	log10_strand_likelihood_position_model=19.391	new_cov=0/56	polymorphism_quality=33.7	quality=33.7	quality_position_model=Inf	ref_cov=114/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/123
RA	420	.	NC_007779	2714668	1	.	A	bias_e_value=4592840	bias_p_value=0.988487	fisher_strand_p_value=1	frequency=6.873131e-03	genotype_quality=1426.8	ks_quality_p_value=0.852142	log10_base_likelihood=-8.33111	log10_qual_likelihood_position_model=1.51266	log10_strand_likelihood_position_model=0.299786	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.85751e-08	ref_cov=148/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/142
RA	421	.	NC_007779	2756638	1	.	T	bias_e_value=1631460	bias_p_value=0.351128	fisher_strand_p_value=0.497781	frequency=9.216309e-03	genotype_quality=1066.8	ks_quality_p_value=0.219461	log10_base_likelihood=-8.30506	log10_qual_likelihood_position_model=1.14873	log10_strand_likelihood_position_model=0.592094	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.66701e-08	ref_cov=108/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/107
RA	422	.	NC_007779	2767290	0	A	T	bias_e_value=29226.1	bias_p_value=0.00629015	fisher_strand_p_value=0.00076999	frequency=3.536892e-02	genotype_quality=850.3	ks_quality_p_value=1	log10_base_likelihood=-7.25656	log10_qual_likelihood_position_model=10.0822	log10_strand_likelihood_position_model=3.11351	new_cov=10/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=110/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=120/121
RA	423	.	NC_007779	2771144	0	G	T	bias_e_value=135.241	bias_p_value=2.9107e-05	fisher_strand_p_value=2.35277e-06	frequency=5.063248e-02	genotype_quality=744.3	ks_quality_p_value=0.878025	log10_base_likelihood=-9.83869	log10_qual_likelihood_position_model=17.9729	log10_strand_likelihood_position_model=5.62842	new_cov=0/17	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=121/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/114
RA	424	.	NC_007779	2774179	0	A	T	bias_e_value=264415	bias_p_value=0.0569083	fisher_strand_p_value=0.0101864	frequency=3.417778e-02	genotype_quality=785.9	ks_quality_p_value=1	log10_base_likelihood=-7.56564	log10_qual_likelihood_position_model=12.5988	log10_strand_likelihood_position_model=2.04264	new_cov=8/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=113/94	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=121/94
RA	425	.	NC_007779	2783853	0	A	.	bias_e_value=4137330	bias_p_value=0.89045	fisher_strand_p_value=0.575888	frequency=1.114368e-02	genotype_quality=1101.6	ks_quality_p_value=0.989905	log10_base_likelihood=-7.99835	log10_qual_likelihood_position_model=1.44418	log10_strand_likelihood_position_model=0.506962	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.69805e-08	ref_cov=154/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=155/114
RA	426	.	NC_007779	2791635	0	C	T	bias_e_value=4.54348e-05	bias_p_value=9.77864e-12	fisher_strand_p_value=3.28766e-13	frequency=9.486151e-02	genotype_quality=549.6	ks_quality_p_value=1	log10_base_likelihood=-11.9875	log10_qual_likelihood_position_model=18.547	log10_strand_likelihood_position_model=12.4831	new_cov=0/19	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=122/25	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/45
RA	427	.	NC_007779	2791639	0	C	G	bias_e_value=4.87532	bias_p_value=1.04928e-06	fisher_strand_p_value=5.95396e-08	frequency=5.830479e-02	genotype_quality=658.7	ks_quality_p_value=0.999197	log10_base_likelihood=-8.96521	log10_qual_likelihood_position_model=12.9803	log10_strand_likelihood_position_model=7.22519	new_cov=0/12	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=130/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/49
RA	428	.	NC_007779	2797644	0	C	A	bias_e_value=0.642968	bias_p_value=1.38382e-07	fisher_strand_p_value=7.01789e-09	frequency=7.432461e-02	genotype_quality=773.4	ks_quality_p_value=0.996997	log10_base_likelihood=-17.3566	log10_qual_likelihood_position_model=15.0539	log10_strand_likelihood_position_model=8.15379	new_cov=0/18	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=142/68	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/86
RA	429	.	NC_007779	2816615	0	G	C	bias_e_value=8.02513e-18	bias_p_value=1.7272e-24	fisher_strand_p_value=3.5362e-26	frequency=2.106824e-01	genotype_quality=622.8	ks_quality_p_value=0.816686	log10_base_likelihood=-74.1732	log10_qual_likelihood_position_model=37.7814	log10_strand_likelihood_position_model=25.4515	new_cov=49/0	polymorphism_quality=69.2	quality=69.2	quality_position_model=5.49535e-13	ref_cov=37/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/138
RA	430	.	NC_007779	2817030	0	G	C	bias_e_value=3.49688e-21	bias_p_value=7.5261e-28	fisher_strand_p_value=1.20606e-29	frequency=2.512093e-01	genotype_quality=568.4	ks_quality_p_value=0.922177	log10_base_likelihood=-83.15	log10_qual_likelihood_position_model=41.6273	log10_strand_likelihood_position_model=28.9186	new_cov=56/0	polymorphism_quality=78.2	quality=78.2	quality_position_model=1.11329e-14	ref_cov=31/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=88/129
RA	431	.	NC_007779	2827675	0	T	G	bias_e_value=4108900	bias_p_value=0.884332	fisher_strand_p_value=0.66426	frequency=1.659966e-02	genotype_quality=1190.5	ks_quality_p_value=0.842093	log10_base_likelihood=-12.1243	log10_qual_likelihood_position_model=4.78785	log10_strand_likelihood_position_model=0.544577	new_cov=2/3	polymorphism_quality=6.7	quality=6.7	quality_position_model=9.71204e-09	ref_cov=160/135	tot_cov=162/138
RA	432	.	NC_007779	2833904	0	A	C	bias_e_value=1.88512e-05	bias_p_value=4.05721e-12	fisher_strand_p_value=1.32358e-13	frequency=1.107726e-01	genotype_quality=534.9	ks_quality_p_value=1	log10_base_likelihood=-14.3227	log10_qual_likelihood_position_model=23.6977	log10_strand_likelihood_position_model=12.8782	new_cov=0/36	polymorphism_quality=9.0	quality=9.0	quality_position_model=Inf	ref_cov=103/63	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=104/99
RA	433	.	NC_007779	2833989	0	A	C	bias_e_value=0.000774814	bias_p_value=1.66758e-10	fisher_strand_p_value=6.22163e-12	frequency=7.241821e-02	genotype_quality=515.4	ks_quality_p_value=1	log10_base_likelihood=-15.3233	log10_qual_likelihood_position_model=15.6669	log10_strand_likelihood_position_model=11.2061	new_cov=0/13	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=123/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/26
RA	434	.	NC_007779	2839296	0	A	G	bias_e_value=1.09812e-05	bias_p_value=2.3634e-12	fisher_strand_p_value=7.57217e-14	frequency=9.158850e-02	genotype_quality=558.7	ks_quality_p_value=1	log10_base_likelihood=-18.3297	log10_qual_likelihood_position_model=20.376	log10_strand_likelihood_position_model=13.1208	new_cov=18/0	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=22/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=40/136
RA	435	.	NC_007779	2841626	0	T	.	bias_e_value=4364620	bias_p_value=0.939368	fisher_strand_p_value=1	frequency=1.297569e-02	genotype_quality=869.7	ks_quality_p_value=0.67263	log10_base_likelihood=-7.9427	log10_qual_likelihood_position_model=1.87785	log10_strand_likelihood_position_model=0.398365	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.41148e-07	ref_cov=107/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/123
RA	436	.	NC_007779	2847445	0	G	T	bias_e_value=102.401	bias_p_value=2.2039e-05	fisher_strand_p_value=1.53164e-06	frequency=4.174614e-02	genotype_quality=867.2	ks_quality_p_value=1	log10_base_likelihood=-6.8487	log10_qual_likelihood_position_model=14.261	log10_strand_likelihood_position_model=5.81484	new_cov=0/17	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=140/108	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/126
RA	437	.	NC_007779	2864518	0	T	G	bias_e_value=3.238e-08	bias_p_value=6.96894e-15	fisher_strand_p_value=1.87267e-16	frequency=1.055832e-01	genotype_quality=428.6	ks_quality_p_value=1	log10_base_likelihood=-15.0028	log10_qual_likelihood_position_model=21.0813	log10_strand_likelihood_position_model=15.7275	new_cov=22/0	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=15/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/107
RA	438	.	NC_007779	2865228	0	A	G	bias_e_value=4646320	bias_p_value=0.999998	fisher_strand_p_value=1	frequency=3.365898e-02	genotype_quality=1093.8	ks_quality_p_value=0.997861	log10_base_likelihood=-20.4227	log10_qual_likelihood_position_model=7.11965	log10_strand_likelihood_position_model=0.608849	new_cov=5/5	polymorphism_quality=15.1	quality=15.1	quality_position_model=9.01496e-15	ref_cov=134/151	tot_cov=140/156
RA	439	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1090.3	new_cov=118/135	quality=1090.3	ref_cov=0/0	tot_cov=118/135
RA	440	.	NC_007779	2872916	0	T	G	bias_e_value=0.000242538	bias_p_value=5.21999e-11	fisher_strand_p_value=1.86372e-12	frequency=6.531000e-02	genotype_quality=780.6	ks_quality_p_value=1	log10_base_likelihood=-9.47532	log10_qual_likelihood_position_model=36.3646	log10_strand_likelihood_position_model=11.7296	new_cov=31/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=81/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/134
RA	441	.	NC_007779	2895131	0	A	C	bias_e_value=2.83427e-06	bias_p_value=6.10001e-13	fisher_strand_p_value=1.8706e-14	frequency=1.041183e-01	genotype_quality=486.6	ks_quality_p_value=1	log10_base_likelihood=-10.793	log10_qual_likelihood_position_model=25.3521	log10_strand_likelihood_position_model=13.728	new_cov=0/22	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=105/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/44
RA	442	.	NC_007779	2895144	0	G	C	bias_e_value=0.326943	bias_p_value=7.03659e-08	fisher_strand_p_value=3.43425e-09	frequency=1.086183e-01	genotype_quality=481.4	ks_quality_p_value=1	log10_base_likelihood=-12.7166	log10_qual_likelihood_position_model=18.0454	log10_strand_likelihood_position_model=8.47101	new_cov=1/17	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=97/28	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/45
RA	443	.	NC_007779	2898954	0	A	.	bias_e_value=3287480	bias_p_value=0.707542	fisher_strand_p_value=0.451796	frequency=2.844334e-02	genotype_quality=974.0	ks_quality_p_value=0.754086	log10_base_likelihood=-20.89	log10_qual_likelihood_position_model=3.18748	log10_strand_likelihood_position_model=0.715849	new_cov=2/5	polymorphism_quality=15.6	quality=15.6	quality_position_model=3.99018e-19	ref_cov=114/125	reject=INDEL_HOMOPOLYMER	tot_cov=116/130
RA	444	.	NC_007779	2905194	1	.	G	bias_e_value=863981	bias_p_value=0.185949	fisher_strand_p_value=0.0495364	frequency=1.324463e-02	genotype_quality=726.4	ks_quality_p_value=0.91755	log10_base_likelihood=-8.30852	log10_qual_likelihood_position_model=1.58422	log10_strand_likelihood_position_model=1.30508	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.54668e-07	ref_cov=32/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=34/117
RA	445	.	NC_007779	2915479	0	C	G	bias_e_value=0.0290767	bias_p_value=6.258e-09	fisher_strand_p_value=2.72017e-10	frequency=6.512499e-02	genotype_quality=668.0	ks_quality_p_value=0.999125	log10_base_likelihood=-14.539	log10_qual_likelihood_position_model=15.7885	log10_strand_likelihood_position_model=9.5654	new_cov=0/13	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=141/25	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/38
RA	446	.	NC_007779	2926157	0	T	G	bias_e_value=2.91052e-07	bias_p_value=6.26412e-14	fisher_strand_p_value=1.79203e-15	frequency=6.978273e-02	genotype_quality=489.8	ks_quality_p_value=1	log10_base_likelihood=-10.3431	log10_qual_likelihood_position_model=18.0754	log10_strand_likelihood_position_model=14.7467	new_cov=15/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=7/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=23/123
RA	447	.	NC_007779	2939008	0	A	C	bias_e_value=1.07329e-05	bias_p_value=2.30998e-12	fisher_strand_p_value=7.39542e-14	frequency=1.153555e-01	genotype_quality=595.5	ks_quality_p_value=1	log10_base_likelihood=-11.5252	log10_qual_likelihood_position_model=29.5584	log10_strand_likelihood_position_model=13.131	new_cov=0/31	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=116/55	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=117/86
RA	448	.	NC_007779	2983097	0	A	C	bias_e_value=4.17003e-16	bias_p_value=8.97488e-23	fisher_strand_p_value=1.60879e-24	frequency=1.573606e-01	genotype_quality=521.8	ks_quality_p_value=1	log10_base_likelihood=-15.4088	log10_qual_likelihood_position_model=43.4218	log10_strand_likelihood_position_model=23.7935	new_cov=0/46	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=115/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/75
RA	449	.	NC_007779	2987535	0	A	C	bias_e_value=1.03724e-26	bias_p_value=2.23238e-33	fisher_strand_p_value=2.77068e-35	frequency=2.918420e-01	genotype_quality=489.9	ks_quality_p_value=1	log10_base_likelihood=-80.2454	log10_qual_likelihood_position_model=62.4998	log10_strand_likelihood_position_model=34.6904	new_cov=0/87	polymorphism_quality=75.3	quality=75.3	quality_position_model=Inf	ref_cov=126/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/132
RA	450	.	NC_007779	2994664	0	T	.	bias_e_value=3288700	bias_p_value=0.707806	fisher_strand_p_value=1	frequency=1.249218e-02	genotype_quality=970.9	ks_quality_p_value=0.340938	log10_base_likelihood=-8.29845	log10_qual_likelihood_position_model=1.45169	log10_strand_likelihood_position_model=0.417038	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.29447e-08	ref_cov=120/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/118
RA	451	.	NC_007779	2999826	0	A	C	bias_e_value=4.30771e-10	bias_p_value=9.27121e-17	fisher_strand_p_value=2.22618e-18	frequency=9.462261e-02	genotype_quality=509.2	ks_quality_p_value=1	log10_base_likelihood=-9.70211	log10_qual_likelihood_position_model=27.9531	log10_strand_likelihood_position_model=17.6524	new_cov=0/30	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=116/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/56
RA	452	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=1062.7	new_cov=128/135	quality=1062.7	ref_cov=0/0	tot_cov=129/135
RA	453	.	NC_007779	3029385	0	C	A	bias_e_value=1.35927e-11	bias_p_value=2.92547e-18	fisher_strand_p_value=6.48196e-20	frequency=9.828186e-02	genotype_quality=726.9	ks_quality_p_value=0.998866	log10_base_likelihood=-40.1842	log10_qual_likelihood_position_model=21.7816	log10_strand_likelihood_position_model=19.1883	new_cov=0/20	polymorphism_quality=35.0	quality=35.0	quality_position_model=Inf	ref_cov=167/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=168/31
RA	454	.	NC_007779	3034413	0	A	C	bias_e_value=1.25808e-15	bias_p_value=2.70768e-22	fisher_strand_p_value=4.95351e-24	frequency=9.913063e-02	genotype_quality=607.1	ks_quality_p_value=1	log10_base_likelihood=-13.691	log10_qual_likelihood_position_model=32.0171	log10_strand_likelihood_position_model=23.3051	new_cov=0/35	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=147/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/60
RA	455	.	NC_007779	3035390	0	T	C	bias_e_value=8.34302e-09	bias_p_value=1.79561e-15	fisher_strand_p_value=4.65102e-17	frequency=1.470094e-01	genotype_quality=368.5	ks_quality_p_value=1	log10_base_likelihood=-38.533	log10_qual_likelihood_position_model=16.0029	log10_strand_likelihood_position_model=16.3325	new_cov=0/22	polymorphism_quality=33.4	quality=33.4	quality_position_model=3.98348e-08	ref_cov=111/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/36
RA	456	.	NC_007779	3044714	0	A	C	bias_e_value=105.769	bias_p_value=2.27639e-05	fisher_strand_p_value=1.58585e-06	frequency=4.133797e-02	genotype_quality=432.6	ks_quality_p_value=1	log10_base_likelihood=-8.70273	log10_qual_likelihood_position_model=11.7826	log10_strand_likelihood_position_model=5.80736	new_cov=7/2	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=9/127	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/129
RA	457	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=986.4	new_cov=120/126	quality=986.4	ref_cov=0/0	tot_cov=120/126
RA	458	.	NC_007779	3059421	0	T	.	bias_e_value=4645930	bias_p_value=0.999913	fisher_strand_p_value=1	frequency=1.998901e-02	genotype_quality=972.2	ks_quality_p_value=0.986863	log10_base_likelihood=-14.2783	log10_qual_likelihood_position_model=3.51392	log10_strand_likelihood_position_model=0.494874	new_cov=2/3	polymorphism_quality=8.9	quality=8.9	quality_position_model=2.65507e-12	ref_cov=121/124	reject=INDEL_HOMOPOLYMER	tot_cov=123/127
RA	459	.	NC_007779	3074129	0	G	T	bias_e_value=17.7282	bias_p_value=3.81552e-06	fisher_strand_p_value=2.34578e-07	frequency=5.133629e-02	genotype_quality=907.2	ks_quality_p_value=1	log10_base_likelihood=-6.63722	log10_qual_likelihood_position_model=18.7718	log10_strand_likelihood_position_model=6.79536	new_cov=0/24	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=128/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/151
RA	460	.	NC_007779	3081543	0	T	C	bias_e_value=4435950	bias_p_value=0.954722	fisher_strand_p_value=1	frequency=1.379013e-02	genotype_quality=845.5	ks_quality_p_value=0.71458	log10_base_likelihood=-6.44814	log10_qual_likelihood_position_model=1.36516	log10_strand_likelihood_position_model=0.406901	new_cov=1/2	polymorphism_quality=0.9	quality=0.9	quality_position_model=1.50955e-06	ref_cov=103/111	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=104/113
RA	461	.	NC_007779	3089270	0	C	A	bias_e_value=15.217	bias_p_value=3.27506e-06	fisher_strand_p_value=1.99356e-07	frequency=5.689383e-02	genotype_quality=885.9	ks_quality_p_value=1	log10_base_likelihood=-9.72965	log10_qual_likelihood_position_model=15.5751	log10_strand_likelihood_position_model=6.87422	new_cov=22/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=115/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/133
RA	462	.	NC_007779	3090796	0	A	C	bias_e_value=40.9316	bias_p_value=8.80945e-06	fisher_strand_p_value=5.73075e-07	frequency=3.818035e-02	genotype_quality=770.5	ks_quality_p_value=1	log10_base_likelihood=-5.68843	log10_qual_likelihood_position_model=13.8333	log10_strand_likelihood_position_model=6.24179	new_cov=0/17	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=134/92	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/111
RA	463	.	NC_007779	3091181	0	C	G	bias_e_value=115130	bias_p_value=0.0247786	fisher_strand_p_value=0.00459316	frequency=1.055107e-01	genotype_quality=320.6	ks_quality_p_value=0.819593	log10_base_likelihood=-10.1297	log10_qual_likelihood_position_model=15.7626	log10_strand_likelihood_position_model=2.48484	new_cov=0/14	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=36/64	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=36/79
RA	464	.	NC_007779	3110532	0	C	A	bias_e_value=5.12979e-06	bias_p_value=1.10405e-12	fisher_strand_p_value=3.50316e-14	frequency=1.064172e-01	genotype_quality=531.9	ks_quality_p_value=0.984941	log10_base_likelihood=-34.479	log10_qual_likelihood_position_model=14.9171	log10_strand_likelihood_position_model=13.4555	new_cov=0/16	polymorphism_quality=29.3	quality=29.3	quality_position_model=4.94978e-08	ref_cov=118/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/28
RA	465	.	NC_007779	3125196	0	A	G	bias_e_value=4190210	bias_p_value=0.901832	fisher_strand_p_value=0.623245	frequency=1.437950e-02	genotype_quality=1052.7	ks_quality_p_value=0.948269	log10_base_likelihood=-6.34309	log10_qual_likelihood_position_model=4.6645	log10_strand_likelihood_position_model=0.570961	new_cov=1/3	polymorphism_quality=0.8	quality=0.8	quality_position_model=0.010512	ref_cov=130/138	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=131/141
RA	466	.	NC_007779	3152854	1	.	A	bias_e_value=1163320	bias_p_value=0.250375	fisher_strand_p_value=0.225666	frequency=7.379532e-03	genotype_quality=1317.4	ks_quality_p_value=0.300628	log10_base_likelihood=-8.25379	log10_qual_likelihood_position_model=2.24316	log10_strand_likelihood_position_model=0.646533	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.90518e-07	ref_cov=127/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/142
RA	467	.	NC_007779	3152855	0	A	.	bias_e_value=3055080	bias_p_value=0.657524	fisher_strand_p_value=1	frequency=2.489948e-02	genotype_quality=1102.1	ks_quality_p_value=0.296967	log10_base_likelihood=-20.5438	log10_qual_likelihood_position_model=4.51643	log10_strand_likelihood_position_model=0.543457	new_cov=3/4	polymorphism_quality=15.3	quality=15.3	quality_position_model=1.32849e-17	ref_cov=132/142	reject=INDEL_HOMOPOLYMER	tot_cov=135/146
RA	468	.	NC_007779	3160153	0	G	C	bias_e_value=4.07387e-10	bias_p_value=8.76792e-17	fisher_strand_p_value=2.10989e-18	frequency=1.734099e-01	genotype_quality=360.3	ks_quality_p_value=0.996471	log10_base_likelihood=-51.9016	log10_qual_likelihood_position_model=15.0442	log10_strand_likelihood_position_model=17.6757	new_cov=21/0	polymorphism_quality=46.8	quality=46.8	quality_position_model=2.40002e-21	ref_cov=6/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/94
RA	469	.	NC_007779	3162929	0	G	C	bias_e_value=0.368662	bias_p_value=7.93448e-08	fisher_strand_p_value=4.97867e-09	frequency=8.584642e-02	genotype_quality=712.7	ks_quality_p_value=0.782635	log10_base_likelihood=-19.5066	log10_qual_likelihood_position_model=24.9367	log10_strand_likelihood_position_model=8.30289	new_cov=23/0	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=84/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=107/124
RA	470	.	NC_007779	3212355	0	G	C	bias_e_value=4.35289e-08	bias_p_value=9.36844e-15	fisher_strand_p_value=2.8169e-16	frequency=1.330619e-01	genotype_quality=643.1	ks_quality_p_value=0.901058	log10_base_likelihood=-34.9371	log10_qual_likelihood_position_model=25.2423	log10_strand_likelihood_position_model=15.5502	new_cov=28/0	polymorphism_quality=29.8	quality=29.8	quality_position_model=Inf	ref_cov=38/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=66/134
RA	471	.	NC_007779	3212363	0	T	A	bias_e_value=148.584	bias_p_value=3.19787e-05	fisher_strand_p_value=2.28604e-06	frequency=3.860855e-02	genotype_quality=658.5	ks_quality_p_value=1	log10_base_likelihood=-5.90147	log10_qual_likelihood_position_model=12.1709	log10_strand_likelihood_position_model=5.64092	new_cov=9/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=39/142	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=48/142
RA	472	.	NC_007779	3220025	0	C	A	bias_e_value=35.5457	bias_p_value=7.65028e-06	fisher_strand_p_value=4.92832e-07	frequency=4.646158e-02	genotype_quality=958.9	ks_quality_p_value=1	log10_base_likelihood=-9.61934	log10_qual_likelihood_position_model=17.4377	log10_strand_likelihood_position_model=6.3073	new_cov=19/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=120/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/150
RA	473	.	NC_007779	3226067	0	A	C	bias_e_value=4.96946e-05	bias_p_value=1.06954e-11	fisher_strand_p_value=3.60715e-13	frequency=6.057405e-02	genotype_quality=681.9	ks_quality_p_value=1	log10_base_likelihood=-5.68024	log10_qual_likelihood_position_model=31.6866	log10_strand_likelihood_position_model=12.4428	new_cov=0/25	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=134/50	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/75
RA	474	.	NC_007779	3228280	0	C	A	bias_e_value=496981	bias_p_value=0.106962	fisher_strand_p_value=0.0226148	frequency=2.793121e-02	genotype_quality=895.3	ks_quality_p_value=0.984353	log10_base_likelihood=-8.20584	log10_qual_likelihood_position_model=11.009	log10_strand_likelihood_position_model=1.84316	new_cov=0/8	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=92/127	reject=POLYMORPHISM_STRAND	tot_cov=92/135
RA	475	.	NC_007779	3231302	0	C	G	bias_e_value=10.9178	bias_p_value=2.34976e-06	fisher_strand_p_value=1.42329e-07	frequency=4.934645e-02	genotype_quality=674.6	ks_quality_p_value=0.983784	log10_base_likelihood=-11.029	log10_qual_likelihood_position_model=12.6757	log10_strand_likelihood_position_model=6.84671	new_cov=0/11	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=140/38	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/49
RA	476	.	NC_007779	3233618	0	T	G	bias_e_value=55.2898	bias_p_value=1.18997e-05	fisher_strand_p_value=7.90654e-07	frequency=2.166748e-02	genotype_quality=740.0	ks_quality_p_value=1	log10_base_likelihood=-5.58739	log10_qual_likelihood_position_model=13.2656	log10_strand_likelihood_position_model=6.10201	new_cov=12/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=57/141	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=69/141
RA	477	.	NC_007779	3235914	0	A	.	bias_e_value=833910	bias_p_value=0.179477	fisher_strand_p_value=1	frequency=1.118565e-02	genotype_quality=1069.2	ks_quality_p_value=0.043374	log10_base_likelihood=-8.04782	log10_qual_likelihood_position_model=2.01482	log10_strand_likelihood_position_model=0.384392	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.47294e-07	ref_cov=118/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/148
RA	478	.	NC_007779	3238322	0	T	C	bias_e_value=235.753	bias_p_value=5.07396e-05	fisher_strand_p_value=3.76105e-06	frequency=8.185005e-02	genotype_quality=388.7	ks_quality_p_value=1	log10_base_likelihood=-12.5579	log10_qual_likelihood_position_model=15.1903	log10_strand_likelihood_position_model=5.42469	new_cov=13/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=44/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=57/82
RA	479	.	NC_007779	3238324	0	A	C	bias_e_value=38826.5	bias_p_value=0.00835638	fisher_strand_p_value=0.00129135	frequency=3.164291e-02	genotype_quality=386.8	ks_quality_p_value=0.82491	log10_base_likelihood=-6.23133	log10_qual_likelihood_position_model=8.05701	log10_strand_likelihood_position_model=2.88896	new_cov=7/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=49/84	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=56/84
RA	480	.	NC_007779	3239641	0	T	G	bias_e_value=0.00682065	bias_p_value=1.46796e-09	fisher_strand_p_value=5.98201e-11	frequency=7.578278e-02	genotype_quality=577.3	ks_quality_p_value=1	log10_base_likelihood=-7.89076	log10_qual_likelihood_position_model=19.0047	log10_strand_likelihood_position_model=10.2232	new_cov=24/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=54/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=78/110
RA	481	.	NC_007779	3256890	1	.	A	bias_e_value=3659380	bias_p_value=0.787585	fisher_strand_p_value=1	frequency=9.132385e-03	genotype_quality=1062.4	ks_quality_p_value=0.423748	log10_base_likelihood=-8.44241	log10_qual_likelihood_position_model=1.65524	log10_strand_likelihood_position_model=0.300575	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.00452e-08	ref_cov=115/102	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/103
RA	482	.	NC_007779	3259711	0	A	C	bias_e_value=1.71714e-12	bias_p_value=3.69568e-19	fisher_strand_p_value=7.81354e-21	frequency=9.603071e-02	genotype_quality=616.7	ks_quality_p_value=1	log10_base_likelihood=-11.9658	log10_qual_likelihood_position_model=30.3815	log10_strand_likelihood_position_model=20.1072	new_cov=0/36	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=142/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/73
RA	483	.	NC_007779	3266843	0	C	G	bias_e_value=0.00308421	bias_p_value=6.63794e-10	fisher_strand_p_value=2.6409e-11	frequency=7.367802e-02	genotype_quality=642.5	ks_quality_p_value=0.990881	log10_base_likelihood=-14.2787	log10_qual_likelihood_position_model=14.434	log10_strand_likelihood_position_model=10.5782	new_cov=0/14	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=137/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/36
RA	484	.	NC_007779	3270336	1	.	C	bias_e_value=4238680	bias_p_value=0.912264	fisher_strand_p_value=1	frequency=8.620262e-03	genotype_quality=1103.8	ks_quality_p_value=0.611507	log10_base_likelihood=-8.39983	log10_qual_likelihood_position_model=1.77486	log10_strand_likelihood_position_model=0.300317	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.94524e-08	ref_cov=121/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/110
RA	485	.	NC_007779	3280326	0	A	C	bias_e_value=6.28101e-18	bias_p_value=1.35182e-24	fisher_strand_p_value=2.25094e-26	frequency=1.371436e-01	genotype_quality=594.6	ks_quality_p_value=1	log10_base_likelihood=-23.9433	log10_qual_likelihood_position_model=34.4196	log10_strand_likelihood_position_model=25.6476	new_cov=0/45	polymorphism_quality=18.7	quality=18.7	quality_position_model=Inf	ref_cov=141/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/76
RA	486	.	NC_007779	3300073	0	T	G	bias_e_value=1.08062e-06	bias_p_value=2.32576e-13	fisher_strand_p_value=6.92103e-15	frequency=1.308122e-01	genotype_quality=506.3	ks_quality_p_value=1	log10_base_likelihood=-18.2594	log10_qual_likelihood_position_model=29.9485	log10_strand_likelihood_position_model=14.1598	new_cov=38/0	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=56/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/101
RA	487	.	NC_007779	3300100	0	A	C	bias_e_value=0.698563	bias_p_value=1.50347e-07	fisher_strand_p_value=7.63554e-09	frequency=4.288006e-02	genotype_quality=638.1	ks_quality_p_value=1	log10_base_likelihood=-5.99122	log10_qual_likelihood_position_model=17.8613	log10_strand_likelihood_position_model=8.11716	new_cov=0/18	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=119/56	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/74
RA	488	.	NC_007779	3310088	0	G	C	bias_e_value=0.056738	bias_p_value=1.22114e-08	fisher_strand_p_value=5.4694e-10	frequency=5.136061e-02	genotype_quality=629.3	ks_quality_p_value=1	log10_base_likelihood=-10.3456	log10_qual_likelihood_position_model=11.7682	log10_strand_likelihood_position_model=9.26206	new_cov=0/9	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=143/10	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=143/19
RA	489	.	NC_007779	3333608	1	.	G	bias_e_value=3921620	bias_p_value=0.844024	fisher_strand_p_value=0.498127	frequency=7.462502e-03	genotype_quality=1323.5	ks_quality_p_value=0.996415	log10_base_likelihood=-7.8077	log10_qual_likelihood_position_model=2.09422	log10_strand_likelihood_position_model=0.60369	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=5.33702e-07	ref_cov=132/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/134
RA	490	.	NC_007779	3333612	0	T	G	bias_e_value=1.2928e-06	bias_p_value=2.7824e-13	fisher_strand_p_value=8.32571e-15	frequency=9.540844e-02	genotype_quality=523.3	ks_quality_p_value=1	log10_base_likelihood=-30.1669	log10_qual_likelihood_position_model=18.5293	log10_strand_likelihood_position_model=14.0796	new_cov=16/0	polymorphism_quality=25.0	quality=25.0	quality_position_model=Inf	ref_cov=12/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=28/131
RA	491	.	NC_007779	3341957	0	G	.	bias_e_value=822877	bias_p_value=0.177102	fisher_strand_p_value=0.166553	frequency=9.518623e-03	genotype_quality=887.2	ks_quality_p_value=0.255891	log10_base_likelihood=-5.59728	log10_qual_likelihood_position_model=1.22573	log10_strand_likelihood_position_model=0.778448	new_cov=0/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=2.06131e-05	ref_cov=124/84	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/86
RA	492	.	NC_007779	3342857	0	G	T	bias_e_value=1640820	bias_p_value=0.353144	fisher_strand_p_value=0.598813	frequency=1.058292e-02	genotype_quality=1197.2	ks_quality_p_value=0.183957	log10_base_likelihood=-5.79521	log10_qual_likelihood_position_model=2.32681	log10_strand_likelihood_position_model=0.458801	new_cov=1/2	polymorphism_quality=0.2	quality=0.2	quality_position_model=8.55547e-05	ref_cov=150/129	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=151/131
RA	493	.	NC_007779	3350708	0	A	C	bias_e_value=7.23419e-07	bias_p_value=1.55697e-13	fisher_strand_p_value=4.57693e-15	frequency=1.376238e-01	genotype_quality=584.4	ks_quality_p_value=1	log10_base_likelihood=-20.6433	log10_qual_likelihood_position_model=31.569	log10_strand_likelihood_position_model=14.5389	new_cov=0/46	polymorphism_quality=15.4	quality=15.4	quality_position_model=Inf	ref_cov=104/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/121
RA	494	.	NC_007779	3352509	0	T	C	bias_e_value=2649300	bias_p_value=0.570192	fisher_strand_p_value=1	frequency=1.467228e-02	genotype_quality=806.9	ks_quality_p_value=0.231478	log10_base_likelihood=-6.59278	log10_qual_likelihood_position_model=1.60848	log10_strand_likelihood_position_model=0.350034	new_cov=1/2	polymorphism_quality=1.1	quality=1.1	quality_position_model=1.66899e-06	ref_cov=63/138	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=64/140
RA	495	.	NC_007779	3377617	0	A	C	bias_e_value=0.369491	bias_p_value=7.95232e-08	fisher_strand_p_value=3.90569e-09	frequency=5.798960e-02	genotype_quality=828.6	ks_quality_p_value=1	log10_base_likelihood=-8.01784	log10_qual_likelihood_position_model=26.7088	log10_strand_likelihood_position_model=8.48999	new_cov=0/33	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=116/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/162
RA	496	.	NC_007779	3385700	1	.	T	bias_e_value=2754990	bias_p_value=0.592939	fisher_strand_p_value=0.249602	frequency=1.149368e-02	genotype_quality=1243.3	ks_quality_p_value=0.991129	log10_base_likelihood=-12.3313	log10_qual_likelihood_position_model=2.64446	log10_strand_likelihood_position_model=0.834775	new_cov=0/3	polymorphism_quality=6.9	quality=6.9	quality_position_model=7.45504e-11	ref_cov=123/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/138
RA	497	.	NC_007779	3387541	0	G	A	bias_e_value=1.9304	bias_p_value=4.15467e-07	fisher_strand_p_value=2.23371e-08	frequency=7.789850e-02	genotype_quality=677.7	ks_quality_p_value=0.999027	log10_base_likelihood=-9.00922	log10_qual_likelihood_position_model=17.5774	log10_strand_likelihood_position_model=7.65097	new_cov=0/20	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=119/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/94
RA	498	.	NC_007779	3389914	0	A	C	bias_e_value=1.26955e-10	bias_p_value=2.73237e-17	fisher_strand_p_value=6.36951e-19	frequency=1.141148e-01	genotype_quality=603.4	ks_quality_p_value=1	log10_base_likelihood=-15.9726	log10_qual_likelihood_position_model=29.6242	log10_strand_likelihood_position_model=18.1959	new_cov=0/44	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=121/55	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/99
RA	499	.	NC_007779	3392267	0	C	A	bias_e_value=15.518	bias_p_value=3.33984e-06	fisher_strand_p_value=2.03558e-07	frequency=5.415535e-02	genotype_quality=785.1	ks_quality_p_value=1	log10_base_likelihood=-10.9348	log10_qual_likelihood_position_model=14.8966	log10_strand_likelihood_position_model=6.69131	new_cov=18/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=86/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/130
RA	500	.	NC_007779	3397405	0	A	C	bias_e_value=3.84448e-21	bias_p_value=8.27422e-28	fisher_strand_p_value=1.2245e-29	frequency=1.385112e-01	genotype_quality=601.9	ks_quality_p_value=1	log10_base_likelihood=-14.8372	log10_qual_likelihood_position_model=40.0057	log10_strand_likelihood_position_model=28.912	new_cov=0/49	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=146/28	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/77
RA	501	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1006.8	new_cov=113/124	quality=1006.8	ref_cov=0/0	tot_cov=113/124
RA	502	.	NC_007779	3404070	0	T	G	bias_e_value=1.25765e-11	bias_p_value=2.70677e-18	fisher_strand_p_value=5.98005e-20	frequency=1.637883e-01	genotype_quality=493.0	ks_quality_p_value=1	log10_base_likelihood=-23.5906	log10_qual_likelihood_position_model=34.68	log10_strand_likelihood_position_model=19.2233	new_cov=40/0	polymorphism_quality=18.3	quality=18.3	quality_position_model=Inf	ref_cov=35/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=75/109
RA	503	.	NC_007779	3412753	0	C	T	bias_e_value=0.00854946	bias_p_value=1.84005e-09	fisher_strand_p_value=7.59796e-11	frequency=7.011986e-02	genotype_quality=727.6	ks_quality_p_value=0.996441	log10_base_likelihood=-10.2624	log10_qual_likelihood_position_model=23.415	log10_strand_likelihood_position_model=10.1193	new_cov=0/17	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=146/41	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/58
RA	504	.	NC_007779	3412756	0	G	T	bias_e_value=22.9258	bias_p_value=4.93418e-06	fisher_strand_p_value=3.08552e-07	frequency=3.830910e-02	genotype_quality=770.2	ks_quality_p_value=1	log10_base_likelihood=-7.51873	log10_qual_likelihood_position_model=13.9831	log10_strand_likelihood_position_model=6.51067	new_cov=0/11	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=145/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/55
RA	505	.	NC_007779	3412772	0	A	C	bias_e_value=2.84231e-05	bias_p_value=6.11732e-12	fisher_strand_p_value=2.02368e-13	frequency=5.712986e-02	genotype_quality=614.3	ks_quality_p_value=1	log10_base_likelihood=-6.37993	log10_qual_likelihood_position_model=18.3569	log10_strand_likelihood_position_model=12.6939	new_cov=0/16	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=141/19	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/35
RA	506	.	NC_007779	3421203	0	T	C	bias_e_value=2.98731e-05	bias_p_value=6.42939e-12	fisher_strand_p_value=2.13054e-13	frequency=9.145927e-02	genotype_quality=602.9	ks_quality_p_value=1	log10_base_likelihood=-12.12	log10_qual_likelihood_position_model=23.9434	log10_strand_likelihood_position_model=12.6715	new_cov=0/20	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=132/30	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/50
RA	507	.	NC_007779	3421217	0	C	G	bias_e_value=0.406023	bias_p_value=8.73856e-08	fisher_strand_p_value=5.40816e-09	frequency=7.512283e-02	genotype_quality=695.4	ks_quality_p_value=0.797471	log10_base_likelihood=-15.9444	log10_qual_likelihood_position_model=20.6521	log10_strand_likelihood_position_model=8.26695	new_cov=0/18	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=132/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=132/79
RA	508	.	NC_007779	3423145	0	A	C	bias_e_value=486136	bias_p_value=0.104628	fisher_strand_p_value=0.0216497	frequency=4.414940e-02	genotype_quality=392.2	ks_quality_p_value=1	log10_base_likelihood=-8.34795	log10_qual_likelihood_position_model=12.6415	log10_strand_likelihood_position_model=1.74088	new_cov=5/6	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=20/116	reject=SURROUNDING_HOMOPOLYMER	tot_cov=25/122
RA	509	.	NC_007779	3440600	0	A	C	bias_e_value=2.50254e-09	bias_p_value=5.38605e-16	fisher_strand_p_value=1.35184e-17	frequency=1.207361e-01	genotype_quality=507.1	ks_quality_p_value=1	log10_base_likelihood=-11.7863	log10_qual_likelihood_position_model=31.0459	log10_strand_likelihood_position_model=16.8691	new_cov=0/42	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=105/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/92
RA	510	.	NC_007779	3444231	0	T	G	bias_e_value=0.000976368	bias_p_value=2.10137e-10	fisher_strand_p_value=7.91097e-12	frequency=5.779171e-02	genotype_quality=618.8	ks_quality_p_value=1	log10_base_likelihood=-7.83097	log10_qual_likelihood_position_model=21.5334	log10_strand_likelihood_position_model=11.1018	new_cov=27/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=62/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=89/119
RA	511	.	NC_007779	3447052	0	T	C	bias_e_value=6.19627	bias_p_value=1.33358e-06	fisher_strand_p_value=7.6717e-08	frequency=6.092596e-02	genotype_quality=754.7	ks_quality_p_value=1	log10_base_likelihood=-7.29711	log10_qual_likelihood_position_model=16.1835	log10_strand_likelihood_position_model=7.37351	new_cov=0/23	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=122/100	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/124
RA	512	.	NC_007779	3447060	0	T	A	bias_e_value=13952.2	bias_p_value=0.00300284	fisher_strand_p_value=0.000333423	frequency=4.279709e-02	genotype_quality=927.2	ks_quality_p_value=1	log10_base_likelihood=-10.326	log10_qual_likelihood_position_model=21.072	log10_strand_likelihood_position_model=3.5084	new_cov=0/13	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=124/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/150
RA	513	.	NC_007779	3451707	0	G	A	bias_e_value=3269800	bias_p_value=0.703738	fisher_strand_p_value=0.360763	frequency=1.738930e-02	genotype_quality=872.4	ks_quality_p_value=0.934623	log10_base_likelihood=-5.75565	log10_qual_likelihood_position_model=5.06263	log10_strand_likelihood_position_model=0.622088	new_cov=1/3	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.364162	ref_cov=114/107	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=115/110
RA	514	.	NC_007779	3459841	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	515	.	NC_007779	3459843	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	516	.	NC_007779	3459844	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	517	.	NC_007779	3459845	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	518	.	NC_007779	3459846	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	519	.	NC_007779	3459847	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	520	.	NC_007779	3459848	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	521	.	NC_007779	3459849	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	522	.	NC_007779	3459850	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	523	.	NC_007779	3459851	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	524	.	NC_007779	3459852	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	525	.	NC_007779	3459853	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	526	.	NC_007779	3459854	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	527	.	NC_007779	3459855	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	528	.	NC_007779	3459857	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	529	.	NC_007779	3459858	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	530	.	NC_007779	3459859	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	531	.	NC_007779	3459861	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	532	.	NC_007779	3459862	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	533	.	NC_007779	3459864	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	534	.	NC_007779	3459865	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	535	.	NC_007779	3459866	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	536	.	NC_007779	3459867	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	537	.	NC_007779	3459869	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	538	.	NC_007779	3459870	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	539	.	NC_007779	3459872	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	540	.	NC_007779	3459873	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	541	.	NC_007779	3459874	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	542	.	NC_007779	3459875	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	543	.	NC_007779	3459876	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	544	.	NC_007779	3459877	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	545	.	NC_007779	3459879	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	546	.	NC_007779	3459880	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	547	.	NC_007779	3459881	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	548	.	NC_007779	3459882	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	549	.	NC_007779	3459883	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	550	.	NC_007779	3459884	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	551	.	NC_007779	3459885	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	552	.	NC_007779	3459887	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	553	.	NC_007779	3459888	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	554	.	NC_007779	3459889	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	555	.	NC_007779	3459890	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	556	.	NC_007779	3459891	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	557	.	NC_007779	3475527	0	T	G	bias_e_value=2.34717e-15	bias_p_value=5.05166e-22	fisher_strand_p_value=9.35032e-24	frequency=2.096491e-01	genotype_quality=560.7	ks_quality_p_value=1	log10_base_likelihood=-41.9513	log10_qual_likelihood_position_model=39.0121	log10_strand_likelihood_position_model=23.0602	new_cov=69/0	polymorphism_quality=36.8	quality=36.8	quality_position_model=Inf	ref_cov=68/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/116
RA	558	.	NC_007779	3475533	0	C	T	bias_e_value=2.48066e-13	bias_p_value=5.33895e-20	fisher_strand_p_value=1.08352e-21	frequency=2.446742e-01	genotype_quality=554.0	ks_quality_p_value=1	log10_base_likelihood=-89.9447	log10_qual_likelihood_position_model=58.2111	log10_strand_likelihood_position_model=21.0092	new_cov=65/0	polymorphism_quality=85.0	quality=85.0	quality_position_model=9.12317e-13	ref_cov=78/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/120
RA	559	.	NC_007779	3475539	0	G	T	bias_e_value=25.3185	bias_p_value=5.44913e-06	fisher_strand_p_value=3.43026e-07	frequency=8.111095e-02	genotype_quality=645.3	ks_quality_p_value=1	log10_base_likelihood=-17.8333	log10_qual_likelihood_position_model=14.0834	log10_strand_likelihood_position_model=6.46467	new_cov=16/0	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=64/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/111
RA	560	.	NC_007779	3478395	1	.	T	bias_e_value=4318460	bias_p_value=0.929434	fisher_strand_p_value=1	frequency=8.733749e-03	genotype_quality=1088.1	ks_quality_p_value=0.648668	log10_base_likelihood=-8.10271	log10_qual_likelihood_position_model=1.69411	log10_strand_likelihood_position_model=0.300997	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.93511e-08	ref_cov=106/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/122
RA	561	.	NC_007779	3481746	0	T	G	bias_e_value=0.41933	bias_p_value=9.02497e-08	fisher_strand_p_value=4.46168e-09	frequency=6.827259e-02	genotype_quality=709.9	ks_quality_p_value=1	log10_base_likelihood=-8.61185	log10_qual_likelihood_position_model=19.1604	log10_strand_likelihood_position_model=8.3505	new_cov=24/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=88/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=112/123
RA	562	.	NC_007779	3484372	0	A	C	bias_e_value=7.04635e-11	bias_p_value=1.51654e-17	fisher_strand_p_value=3.48628e-19	frequency=1.296649e-01	genotype_quality=562.0	ks_quality_p_value=1	log10_base_likelihood=-21.3988	log10_qual_likelihood_position_model=31.3443	log10_strand_likelihood_position_model=18.4576	new_cov=0/41	polymorphism_quality=16.1	quality=16.1	quality_position_model=Inf	ref_cov=123/48	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/90
RA	563	.	NC_007779	3499066	0	A	C	bias_e_value=0.0371993	bias_p_value=8.00615e-09	fisher_strand_p_value=3.51634e-10	frequency=7.304764e-02	genotype_quality=573.7	ks_quality_p_value=1	log10_base_likelihood=-10.3995	log10_qual_likelihood_position_model=19.3424	log10_strand_likelihood_position_model=9.45391	new_cov=0/14	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=124/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/40
RA	564	.	NC_007779	3520391	0	C	G	bias_e_value=1.59246e-05	bias_p_value=3.42735e-12	fisher_strand_p_value=1.11178e-13	frequency=8.413744e-02	genotype_quality=572.1	ks_quality_p_value=1	log10_base_likelihood=-20.9627	log10_qual_likelihood_position_model=15.7062	log10_strand_likelihood_position_model=12.954	new_cov=13/0	polymorphism_quality=15.7	quality=15.7	quality_position_model=Inf	ref_cov=8/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=21/129
RA	565	.	NC_007779	3523734	0	G	T	bias_e_value=19.2239	bias_p_value=4.13743e-06	fisher_strand_p_value=2.55726e-07	frequency=4.470062e-02	genotype_quality=984.1	ks_quality_p_value=1	log10_base_likelihood=-8.2727	log10_qual_likelihood_position_model=20.7678	log10_strand_likelihood_position_model=6.59222	new_cov=0/19	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=149/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/131
RA	566	.	NC_007779	3530294	0	A	.	bias_e_value=4602960	bias_p_value=0.990666	fisher_strand_p_value=1	frequency=1.314926e-02	genotype_quality=920.8	ks_quality_p_value=0.866516	log10_base_likelihood=-8.17953	log10_qual_likelihood_position_model=1.83442	log10_strand_likelihood_position_model=0.409487	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=7.43188e-08	ref_cov=116/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/110
RA	567	.	NC_007779	3543542	0	G	T	bias_e_value=0.0244049	bias_p_value=5.25251e-09	fisher_strand_p_value=2.26313e-10	frequency=7.987976e-02	genotype_quality=595.3	ks_quality_p_value=1	log10_base_likelihood=-9.92086	log10_qual_likelihood_position_model=19.6928	log10_strand_likelihood_position_model=9.64529	new_cov=0/22	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=110/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/74
RA	568	.	NC_007779	3543547	0	A	C	bias_e_value=2.06428e-25	bias_p_value=4.44283e-32	fisher_strand_p_value=5.72955e-34	frequency=3.171186e-01	genotype_quality=413.2	ks_quality_p_value=1	log10_base_likelihood=-85.1484	log10_qual_likelihood_position_model=56.7288	log10_strand_likelihood_position_model=33.3225	new_cov=0/84	polymorphism_quality=80.2	quality=80.2	quality_position_model=Inf	ref_cov=112/38	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/124
RA	569	.	NC_007779	3571074	0	A	G	bias_e_value=0.0121491	bias_p_value=2.61476e-09	fisher_strand_p_value=1.09233e-10	frequency=6.882811e-02	genotype_quality=691.6	ks_quality_p_value=1	log10_base_likelihood=-7.24755	log10_qual_likelihood_position_model=18.7197	log10_strand_likelihood_position_model=9.96165	new_cov=22/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=64/138	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/138
RA	570	.	NC_007779	3576400	1	.	A	bias_e_value=1539050	bias_p_value=0.331239	fisher_strand_p_value=0.158996	frequency=8.333206e-03	genotype_quality=1162.8	ks_quality_p_value=0.631629	log10_base_likelihood=-8.43661	log10_qual_likelihood_position_model=1.42738	log10_strand_likelihood_position_model=0.798614	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.86261e-08	ref_cov=94/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=96/144
RA	571	.	NC_007779	3576401	0	A	.	bias_e_value=4030950	bias_p_value=0.867556	fisher_strand_p_value=1	frequency=1.638412e-02	genotype_quality=983.7	ks_quality_p_value=0.53169	log10_base_likelihood=-11.324	log10_qual_likelihood_position_model=2.59224	log10_strand_likelihood_position_model=0.454085	new_cov=2/2	polymorphism_quality=5.9	quality=5.9	quality_position_model=2.88899e-10	ref_cov=97/143	reject=INDEL_HOMOPOLYMER	tot_cov=99/145
RA	572	.	NC_007779	3603950	0	A	C	bias_e_value=2.33334e-13	bias_p_value=5.0219e-20	fisher_strand_p_value=1.01789e-21	frequency=1.365557e-01	genotype_quality=584.9	ks_quality_p_value=1	log10_base_likelihood=-15.9272	log10_qual_likelihood_position_model=46.0496	log10_strand_likelihood_position_model=20.9923	new_cov=0/46	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=126/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/92
RA	573	.	NC_007779	3609441	0	T	G	bias_e_value=5.15274e-09	bias_p_value=1.10899e-15	fisher_strand_p_value=2.83619e-17	frequency=8.391428e-02	genotype_quality=647.1	ks_quality_p_value=1	log10_base_likelihood=-9.7024	log10_qual_likelihood_position_model=30.2665	log10_strand_likelihood_position_model=16.5473	new_cov=39/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=59/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/129
RA	574	.	NC_007779	3614261	0	T	.	bias_e_value=3825420	bias_p_value=0.82332	fisher_strand_p_value=0.607529	frequency=1.109886e-02	genotype_quality=1046.0	ks_quality_p_value=0.770275	log10_base_likelihood=-7.73004	log10_qual_likelihood_position_model=2.27547	log10_strand_likelihood_position_model=0.445111	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=6.78616e-07	ref_cov=127/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/141
RA	575	.	NC_007779	3648353	1	.	A	bias_e_value=1839240	bias_p_value=0.395848	fisher_strand_p_value=1	frequency=7.220268e-03	genotype_quality=1355.7	ks_quality_p_value=0.130304	log10_base_likelihood=-8.16558	log10_qual_likelihood_position_model=1.42672	log10_strand_likelihood_position_model=0.29951	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.2426e-08	ref_cov=136/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/140
RA	576	.	NC_007779	3654011	0	A	C	bias_e_value=20.4506	bias_p_value=4.40144e-06	fisher_strand_p_value=2.73157e-07	frequency=3.291225e-02	genotype_quality=923.0	ks_quality_p_value=1	log10_base_likelihood=-6.61957	log10_qual_likelihood_position_model=19.1604	log10_strand_likelihood_position_model=6.57446	new_cov=1/15	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=179/73	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=180/88
RA	577	.	NC_007779	3676780	0	A	C	bias_e_value=1.08831	bias_p_value=2.3423e-07	fisher_strand_p_value=1.21848e-08	frequency=8.485508e-02	genotype_quality=631.1	ks_quality_p_value=1	log10_base_likelihood=-11.6114	log10_qual_likelihood_position_model=18.5915	log10_strand_likelihood_position_model=8.21521	new_cov=0/25	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=107/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/108
RA	578	.	NC_007779	3677212	0	C	G	bias_e_value=1001.09	bias_p_value=0.000215459	fisher_strand_p_value=1.80738e-05	frequency=3.901958e-02	genotype_quality=541.6	ks_quality_p_value=1	log10_base_likelihood=-6.50426	log10_qual_likelihood_position_model=9.21302	log10_strand_likelihood_position_model=4.74295	new_cov=0/6	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=116/19	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/25
RA	579	.	NC_007779	3677217	0	T	G	bias_e_value=635.189	bias_p_value=0.000136708	fisher_strand_p_value=1.101e-05	frequency=8.097887e-02	genotype_quality=381.0	ks_quality_p_value=1	log10_base_likelihood=-11.4487	log10_qual_likelihood_position_model=12.3674	log10_strand_likelihood_position_model=4.98683	new_cov=6/10	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=108/13	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/23
RA	580	.	NC_007779	3688841	0	T	G	bias_e_value=0.373595	bias_p_value=8.04065e-08	fisher_strand_p_value=3.95133e-09	frequency=6.263065e-02	genotype_quality=689.1	ks_quality_p_value=1	log10_base_likelihood=-10.5095	log10_qual_likelihood_position_model=20.4915	log10_strand_likelihood_position_model=8.40326	new_cov=0/15	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=131/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/57
RA	581	.	NC_007779	3688858	0	A	C	bias_e_value=7.75543e-30	bias_p_value=1.66915e-36	fisher_strand_p_value=1.89986e-38	frequency=2.256188e-01	genotype_quality=471.9	ks_quality_p_value=1	log10_base_likelihood=-49.5696	log10_qual_likelihood_position_model=44.7662	log10_strand_likelihood_position_model=37.7213	new_cov=0/56	polymorphism_quality=44.5	quality=44.5	quality_position_model=Inf	ref_cov=134/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/68
RA	582	.	NC_007779	3689839	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	583	.	NC_007779	3689840	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	584	.	NC_007779	3689842	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	585	.	NC_007779	3689843	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	586	.	NC_007779	3689844	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	587	.	NC_007779	3689845	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	588	.	NC_007779	3689846	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	589	.	NC_007779	3689847	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	590	.	NC_007779	3689848	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	591	.	NC_007779	3689850	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	592	.	NC_007779	3689851	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	593	.	NC_007779	3689852	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	594	.	NC_007779	3689853	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	595	.	NC_007779	3689854	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	596	.	NC_007779	3689855	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	597	.	NC_007779	3689858	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	598	.	NC_007779	3689859	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	599	.	NC_007779	3689860	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	600	.	NC_007779	3689861	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	601	.	NC_007779	3689863	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	602	.	NC_007779	3689864	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	603	.	NC_007779	3689865	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	604	.	NC_007779	3689866	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	605	.	NC_007779	3689867	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	606	.	NC_007779	3689868	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	607	.	NC_007779	3689869	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	608	.	NC_007779	3689870	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	609	.	NC_007779	3689872	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	610	.	NC_007779	3689873	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	611	.	NC_007779	3689874	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	612	.	NC_007779	3689875	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	613	.	NC_007779	3689876	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	614	.	NC_007779	3689877	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	615	.	NC_007779	3689878	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	616	.	NC_007779	3701118	0	G	T	bias_e_value=109.42	bias_p_value=2.35498e-05	fisher_strand_p_value=1.659e-06	frequency=4.451752e-02	genotype_quality=828.1	ks_quality_p_value=0.991428	log10_base_likelihood=-11.2772	log10_qual_likelihood_position_model=13.6704	log10_strand_likelihood_position_model=5.78015	new_cov=0/16	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=138/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/114
RA	617	.	NC_007779	3717981	1	.	A	bias_e_value=4637040	bias_p_value=0.998001	fisher_strand_p_value=1	frequency=8.298874e-03	genotype_quality=1176.7	ks_quality_p_value=0.937441	log10_base_likelihood=-8.28951	log10_qual_likelihood_position_model=2.53692	log10_strand_likelihood_position_model=0.302534	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.3659e-07	ref_cov=109/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/131
RA	618	.	NC_007779	3721172	1	.	T	bias_e_value=4394100	bias_p_value=0.945714	fisher_strand_p_value=1	frequency=8.439064e-03	genotype_quality=1124.6	ks_quality_p_value=0.689138	log10_base_likelihood=-8.1949	log10_qual_likelihood_position_model=2.07741	log10_strand_likelihood_position_model=0.299387	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=9.83317e-08	ref_cov=120/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=121/116
RA	619	.	NC_007779	3727557	0	A	G	bias_e_value=0.00249156	bias_p_value=5.36241e-10	fisher_strand_p_value=2.09563e-11	frequency=8.017969e-02	genotype_quality=482.4	ks_quality_p_value=1	log10_base_likelihood=-12.0461	log10_qual_likelihood_position_model=15.2997	log10_strand_likelihood_position_model=10.6787	new_cov=13/0	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=14/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/116
RA	620	.	NC_007779	3732310	0	G	T	bias_e_value=0.00171675	bias_p_value=3.69485e-10	fisher_strand_p_value=1.45041e-11	frequency=7.592297e-02	genotype_quality=926.5	ks_quality_p_value=0.980694	log10_base_likelihood=-18.7235	log10_qual_likelihood_position_model=20.9811	log10_strand_likelihood_position_model=10.8385	new_cov=0/27	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=159/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/118
RA	621	.	NC_007779	3741461	0	A	T	bias_e_value=15749.3	bias_p_value=0.00338961	fisher_strand_p_value=0.000382158	frequency=4.171276e-02	genotype_quality=907.0	ks_quality_p_value=1	log10_base_likelihood=-9.59687	log10_qual_likelihood_position_model=17.7124	log10_strand_likelihood_position_model=3.64411	new_cov=12/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=122/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/130
RA	622	.	NC_007779	3750122	0	C	.	bias_e_value=38121.2	bias_p_value=0.00820458	fisher_strand_p_value=0.0880433	frequency=9.543858e-01	genotype_quality=1287.4	ks_quality_p_value=0.0118476	log10_base_likelihood=-65.2061	log10_qual_likelihood_position_model=9.08079	log10_strand_likelihood_position_model=1.36774	new_cov=134/138	polymorphism_quality=60.2	quality=60.2	quality_position_model=3.79844e-57	ref_cov=3/10	tot_cov=137/148
RA	623	.	NC_007779	3750123	0	C	T	bias_e_value=1174700	bias_p_value=0.252823	fisher_strand_p_value=0.0880433	frequency=4.553509e-02	genotype_quality=1082.8	ks_quality_p_value=0.780907	log10_base_likelihood=-29.2267	log10_qual_likelihood_position_model=9.99211	log10_strand_likelihood_position_model=1.36774	new_cov=3/10	polymorphism_quality=24.0	quality=24.0	quality_position_model=5.12978e-20	ref_cov=134/138	tot_cov=137/148
RA	624	.	NC_007779	3761469	0	A	C	bias_e_value=1.74981	bias_p_value=3.76601e-07	fisher_strand_p_value=2.01157e-08	frequency=3.478146e-02	genotype_quality=515.1	ks_quality_p_value=1	log10_base_likelihood=-6.35804	log10_qual_likelihood_position_model=9.62995	log10_strand_likelihood_position_model=7.69647	new_cov=0/7	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=125/7	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/14
RA	625	.	NC_007779	3762475	0	T	G	bias_e_value=9.16535e-12	bias_p_value=1.9726e-18	fisher_strand_p_value=4.32713e-20	frequency=1.456208e-01	genotype_quality=617.0	ks_quality_p_value=1	log10_base_likelihood=-24.144	log10_qual_likelihood_position_model=33.5386	log10_strand_likelihood_position_model=19.3638	new_cov=41/0	polymorphism_quality=18.9	quality=18.9	quality_position_model=Inf	ref_cov=50/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=92/137
RA	626	.	NC_007779	3788380	0	G	T	bias_e_value=0.376239	bias_p_value=8.09755e-08	fisher_strand_p_value=3.98075e-09	frequency=8.971786e-02	genotype_quality=781.8	ks_quality_p_value=1	log10_base_likelihood=-18.8174	log10_qual_likelihood_position_model=18.9914	log10_strand_likelihood_position_model=8.53961	new_cov=0/29	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=115/104	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/133
RA	627	.	NC_007779	3789663	0	T	.	bias_e_value=858290	bias_p_value=0.184724	fisher_strand_p_value=0.338137	frequency=1.525688e-02	genotype_quality=1008.5	ks_quality_p_value=0.133249	log10_base_likelihood=-11.0213	log10_qual_likelihood_position_model=4.07542	log10_strand_likelihood_position_model=0.674422	new_cov=1/3	polymorphism_quality=5.6	quality=5.6	quality_position_model=3.34231e-08	ref_cov=140/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/121
RA	628	.	NC_007779	3800772	0	T	G	bias_e_value=4.49075	bias_p_value=9.66515e-07	fisher_strand_p_value=5.45298e-08	frequency=5.943871e-02	genotype_quality=737.1	ks_quality_p_value=1	log10_base_likelihood=-7.0181	log10_qual_likelihood_position_model=22.2934	log10_strand_likelihood_position_model=7.30803	new_cov=24/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=101/115	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/115
RA	629	.	NC_007779	3812429	0	G	T	bias_e_value=2074.38	bias_p_value=0.000446455	fisher_strand_p_value=4.01373e-05	frequency=3.968620e-02	genotype_quality=796.3	ks_quality_p_value=1	log10_base_likelihood=-6.38162	log10_qual_likelihood_position_model=12.7298	log10_strand_likelihood_position_model=4.58736	new_cov=0/17	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=111/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/138
RA	630	.	NC_007779	3813810	0	T	G	bias_e_value=9.66126e-11	bias_p_value=2.07933e-17	fisher_strand_p_value=4.8158e-19	frequency=1.066351e-01	genotype_quality=562.8	ks_quality_p_value=1	log10_base_likelihood=-16.2298	log10_qual_likelihood_position_model=27.0489	log10_strand_likelihood_position_model=18.3173	new_cov=29/0	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=26/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=56/131
RA	631	.	NC_007779	3820146	0	T	G	bias_e_value=0.123754	bias_p_value=2.66347e-08	fisher_strand_p_value=1.23827e-09	frequency=8.236742e-02	genotype_quality=680.2	ks_quality_p_value=1	log10_base_likelihood=-13.0801	log10_qual_likelihood_position_model=21.9561	log10_strand_likelihood_position_model=8.90718	new_cov=25/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=81/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=106/119
RA	632	.	NC_007779	3824606	1	.	T	bias_e_value=1697400	bias_p_value=0.365321	fisher_strand_p_value=0.319953	frequency=1.777744e-02	genotype_quality=1050.3	ks_quality_p_value=0.361739	log10_base_likelihood=-17.6985	log10_qual_likelihood_position_model=2.78039	log10_strand_likelihood_position_model=0.730956	new_cov=3/1	polymorphism_quality=12.4	quality=12.4	quality_position_model=2.7453e-16	ref_cov=95/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=98/127
RA	633	.	NC_007779	3828029	0	G	T	bias_e_value=2.88958e-07	bias_p_value=6.21906e-14	fisher_strand_p_value=2.15685e-15	frequency=1.556659e-01	genotype_quality=735.7	ks_quality_p_value=0.824702	log10_base_likelihood=-57.7249	log10_qual_likelihood_position_model=40.2009	log10_strand_likelihood_position_model=14.6662	new_cov=40/0	polymorphism_quality=52.7	quality=52.7	quality_position_model=0.000124163	ref_cov=77/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=117/128
RA	634	.	NC_007779	3845596	0	G	T	bias_e_value=15.5952	bias_p_value=3.35645e-06	fisher_strand_p_value=2.04636e-07	frequency=4.035664e-02	genotype_quality=949.7	ks_quality_p_value=1	log10_base_likelihood=-8.1823	log10_qual_likelihood_position_model=16.087	log10_strand_likelihood_position_model=6.68902	new_cov=0/20	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=150/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/140
RA	635	.	NC_007779	3846240	0	G	C	bias_e_value=9.92532e-08	bias_p_value=2.13616e-14	fisher_strand_p_value=5.96019e-16	frequency=1.037745e-01	genotype_quality=535.0	ks_quality_p_value=0.993846	log10_base_likelihood=-19.8454	log10_qual_likelihood_position_model=15.627	log10_strand_likelihood_position_model=15.2247	new_cov=0/18	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=131/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/31
RA	636	.	NC_007779	3855255	0	C	A	bias_e_value=1752.75	bias_p_value=0.000377232	fisher_strand_p_value=3.62576e-05	frequency=2.679825e-02	genotype_quality=597.9	ks_quality_p_value=0.920062	log10_base_likelihood=-8.80143	log10_qual_likelihood_position_model=5.59594	log10_strand_likelihood_position_model=4.4406	new_cov=0/4	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=136/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/13
RA	637	.	NC_007779	3859254	1	.	T	bias_e_value=887790	bias_p_value=0.191073	fisher_strand_p_value=0.0507246	frequency=1.435375e-02	genotype_quality=999.8	ks_quality_p_value=0.92893	log10_base_likelihood=-13.159	log10_qual_likelihood_position_model=1.61612	log10_strand_likelihood_position_model=1.29478	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=2.79205e-12	ref_cov=75/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=78/131
RA	638	.	NC_007779	3859263	0	T	C	bias_e_value=3.44718e-06	bias_p_value=7.41915e-13	fisher_strand_p_value=2.2893e-14	frequency=1.088967e-01	genotype_quality=535.7	ks_quality_p_value=1	log10_base_likelihood=-28.9411	log10_qual_likelihood_position_model=19.5556	log10_strand_likelihood_position_model=13.6403	new_cov=22/0	polymorphism_quality=23.7	quality=23.7	quality_position_model=Inf	ref_cov=32/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=54/136
RA	639	.	NC_007779	3859265	0	A	C	bias_e_value=0.000213006	bias_p_value=4.58438e-11	fisher_strand_p_value=1.62896e-12	frequency=8.945131e-02	genotype_quality=488.6	ks_quality_p_value=1	log10_base_likelihood=-21.1948	log10_qual_likelihood_position_model=15.425	log10_strand_likelihood_position_model=11.7927	new_cov=21/1	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=32/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=53/135
RA	640	.	NC_007779	3859270	0	G	C	bias_e_value=0.000170217	bias_p_value=3.66347e-11	fisher_strand_p_value=1.29106e-12	frequency=8.565187e-02	genotype_quality=672.9	ks_quality_p_value=1	log10_base_likelihood=-29.9391	log10_qual_likelihood_position_model=14.8769	log10_strand_likelihood_position_model=11.8891	new_cov=16/0	polymorphism_quality=24.7	quality=24.7	quality_position_model=5.73323e-05	ref_cov=23/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=39/141
RA	641	.	NC_007779	3859271	0	G	C	bias_e_value=11779.2	bias_p_value=0.00253517	fisher_strand_p_value=0.000275673	frequency=2.562618e-02	genotype_quality=697.3	ks_quality_p_value=1	log10_base_likelihood=-8.23904	log10_qual_likelihood_position_model=5.35887	log10_strand_likelihood_position_model=3.55961	new_cov=5/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=31/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=36/141
RA	642	.	NC_007779	3859275	0	T	C	bias_e_value=0.00244675	bias_p_value=5.26599e-10	fisher_strand_p_value=2.05643e-11	frequency=6.381941e-02	genotype_quality=579.1	ks_quality_p_value=1	log10_base_likelihood=-12.7029	log10_qual_likelihood_position_model=14.8412	log10_strand_likelihood_position_model=10.6869	new_cov=14/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=22/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=36/140
RA	643	.	NC_007779	3859381	0	T	G	bias_e_value=1252.21	bias_p_value=0.000269504	fisher_strand_p_value=2.30809e-05	frequency=4.093933e-02	genotype_quality=525.2	ks_quality_p_value=1	log10_base_likelihood=-7.44204	log10_qual_likelihood_position_model=13.0727	log10_strand_likelihood_position_model=4.6495	new_cov=3/6	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=145/10	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=149/16
RA	644	.	NC_007779	3859383	0	A	G	bias_e_value=0.000453974	bias_p_value=9.77059e-11	fisher_strand_p_value=3.57387e-12	frequency=5.077791e-02	genotype_quality=560.4	ks_quality_p_value=0.999301	log10_base_likelihood=-9.67649	log10_qual_likelihood_position_model=12.2677	log10_strand_likelihood_position_model=11.4469	new_cov=0/9	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=152/4	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=152/13
RA	645	.	NC_007779	3871155	0	T	.	bias_e_value=1923520	bias_p_value=0.413988	fisher_strand_p_value=1	frequency=1.161861e-02	genotype_quality=1030.4	ks_quality_p_value=0.139356	log10_base_likelihood=-8.0397	log10_qual_likelihood_position_model=1.467	log10_strand_likelihood_position_model=0.358115	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.82629e-08	ref_cov=99/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=100/158
RA	646	.	NC_007779	3873374	1	.	T	bias_e_value=3041710	bias_p_value=0.654648	fisher_strand_p_value=1	frequency=8.402824e-03	genotype_quality=1155.6	ks_quality_p_value=0.294605	log10_base_likelihood=-8.31072	log10_qual_likelihood_position_model=1.62682	log10_strand_likelihood_position_model=0.301169	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.56554e-08	ref_cov=110/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/127
RA	647	.	NC_007779	3891224	0	G	C	bias_e_value=43113	bias_p_value=0.00927894	fisher_strand_p_value=0.0012038	frequency=3.120041e-02	genotype_quality=536.4	ks_quality_p_value=0.997886	log10_base_likelihood=-5.72509	log10_qual_likelihood_position_model=6.40262	log10_strand_likelihood_position_model=2.91945	new_cov=0/5	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=102/33	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=102/38
RA	648	.	NC_007779	3891907	0	T	.	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=2.064419e-02	genotype_quality=953.5	ks_quality_p_value=0.999824	log10_base_likelihood=-13.5959	log10_qual_likelihood_position_model=5.80931	log10_strand_likelihood_position_model=0.49971	new_cov=2/3	polymorphism_quality=8.2	quality=8.2	quality_position_model=3.00507e-09	ref_cov=118/118	reject=INDEL_HOMOPOLYMER	tot_cov=121/121
RA	649	.	NC_007779	3895373	0	T	G	bias_e_value=7.55814e-11	bias_p_value=1.62669e-17	fisher_strand_p_value=3.74567e-19	frequency=2.070284e-01	genotype_quality=391.9	ks_quality_p_value=1	log10_base_likelihood=-25.4739	log10_qual_likelihood_position_model=36.86	log10_strand_likelihood_position_model=18.4265	new_cov=48/0	polymorphism_quality=20.2	quality=20.2	quality_position_model=Inf	ref_cov=41/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/90
RA	650	.	NC_007779	3895414	0	A	C	bias_e_value=0.434306	bias_p_value=9.3473e-08	fisher_strand_p_value=4.62948e-09	frequency=6.565666e-02	genotype_quality=494.0	ks_quality_p_value=1	log10_base_likelihood=-8.91187	log10_qual_likelihood_position_model=17.5619	log10_strand_likelihood_position_model=8.35235	new_cov=0/27	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=94/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=94/105
RA	651	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1003.1	new_cov=113/124	quality=1003.1	ref_cov=0/0	tot_cov=113/124
RA	652	.	NC_007779	3898897	0	G	T	bias_e_value=56770.7	bias_p_value=0.0122184	fisher_strand_p_value=0.00172544	frequency=3.932953e-02	genotype_quality=572.8	ks_quality_p_value=0.955997	log10_base_likelihood=-11.1304	log10_qual_likelihood_position_model=7.34367	log10_strand_likelihood_position_model=2.77936	new_cov=5/1	polymorphism_quality=5.7	quality=5.7	quality_position_model=0.0137886	ref_cov=27/117	reject=POLYMORPHISM_STRAND	tot_cov=32/119
RA	653	.	NC_007779	3900676	1	.	G	bias_e_value=31730.2	bias_p_value=0.00682909	fisher_strand_p_value=0.000861543	frequency=2.985096e-02	genotype_quality=1271.2	ks_quality_p_value=0.981573	log10_base_likelihood=-36.8362	log10_qual_likelihood_position_model=5.27589	log10_strand_likelihood_position_model=3.06472	new_cov=8/0	polymorphism_quality=31.7	quality=31.7	quality_position_model=9.59124e-31	ref_cov=105/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=113/155
RA	654	.	NC_007779	3900680	0	T	G	bias_e_value=2.51623e-09	bias_p_value=5.41551e-16	fisher_strand_p_value=1.35942e-17	frequency=7.098866e-02	genotype_quality=644.6	ks_quality_p_value=1	log10_base_likelihood=-17.3152	log10_qual_likelihood_position_model=18.7896	log10_strand_likelihood_position_model=16.8666	new_cov=15/0	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=6/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=22/163
RA	655	.	NC_007779	3910746	0	C	A	bias_e_value=14.4978	bias_p_value=3.12026e-06	fisher_strand_p_value=1.89339e-07	frequency=5.533218e-02	genotype_quality=875.7	ks_quality_p_value=1	log10_base_likelihood=-7.78471	log10_qual_likelihood_position_model=24.9688	log10_strand_likelihood_position_model=6.98898	new_cov=26/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=128/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/121
RA	656	.	NC_007779	3930443	0	T	G	bias_e_value=6.39141e-12	bias_p_value=1.37558e-18	fisher_strand_p_value=2.9933e-20	frequency=9.558249e-02	genotype_quality=586.1	ks_quality_p_value=1	log10_base_likelihood=-10.0765	log10_qual_likelihood_position_model=29.0451	log10_strand_likelihood_position_model=19.5238	new_cov=27/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=20/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=47/141
RA	657	.	NC_007779	3932243	0	T	.	bias_e_value=1869770	bias_p_value=0.402419	fisher_strand_p_value=1	frequency=1.161957e-02	genotype_quality=1030.7	ks_quality_p_value=0.133548	log10_base_likelihood=-8.17335	log10_qual_likelihood_position_model=1.81447	log10_strand_likelihood_position_model=0.416007	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=7.30467e-08	ref_cov=129/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/126
RA	658	.	NC_007779	3952095	1	.	G	bias_e_value=1317.55	bias_p_value=0.000283568	fisher_strand_p_value=3.44503e-05	frequency=6.060648e-02	genotype_quality=717.4	ks_quality_p_value=0.708314	log10_base_likelihood=-49.6027	log10_qual_likelihood_position_model=4.86422	log10_strand_likelihood_position_model=4.46281	new_cov=10/0	polymorphism_quality=44.5	quality=44.5	quality_position_model=1.34153e-42	ref_cov=52/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=62/103
RA	659	.	NC_007779	3968988	0	C	G	bias_e_value=0.0903854	bias_p_value=1.94531e-08	fisher_strand_p_value=8.90751e-10	frequency=3.850937e-02	genotype_quality=549.5	ks_quality_p_value=1	log10_base_likelihood=-5.99334	log10_qual_likelihood_position_model=9.89534	log10_strand_likelihood_position_model=9.05024	new_cov=6/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=1/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=7/129
RA	660	.	NC_007779	3973640	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	661	.	NC_007779	3986830	0	T	.	bias_e_value=3119510	bias_p_value=0.671392	fisher_strand_p_value=1	frequency=1.586342e-02	genotype_quality=759.2	ks_quality_p_value=0.308573	log10_base_likelihood=-8.38018	log10_qual_likelihood_position_model=2.04723	log10_strand_likelihood_position_model=0.404236	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=7.5552e-08	ref_cov=89/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=90/99
RA	662	.	NC_007779	3996114	0	G	T	bias_e_value=2.99739	bias_p_value=6.45108e-07	fisher_strand_p_value=3.55379e-08	frequency=5.312061e-02	genotype_quality=869.9	ks_quality_p_value=1	log10_base_likelihood=-10.1979	log10_qual_likelihood_position_model=15.2891	log10_strand_likelihood_position_model=7.44931	new_cov=0/20	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=147/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/120
RA	663	.	NC_007779	4000222	0	C	G	bias_e_value=1.34377	bias_p_value=2.89211e-07	fisher_strand_p_value=1.64311e-08	frequency=7.461691e-02	genotype_quality=824.5	ks_quality_p_value=0.926361	log10_base_likelihood=-14.7121	log10_qual_likelihood_position_model=25.7264	log10_strand_likelihood_position_model=7.78433	new_cov=0/23	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=133/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/124
RA	664	.	NC_007779	4022073	0	A	C	bias_e_value=0.000234266	bias_p_value=5.04195e-11	fisher_strand_p_value=1.79784e-12	frequency=5.216312e-02	genotype_quality=550.5	ks_quality_p_value=1	log10_base_likelihood=-9.29328	log10_qual_likelihood_position_model=21.9633	log10_strand_likelihood_position_model=11.7452	new_cov=0/22	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=116/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/59
RA	665	.	NC_007779	4023068	0	T	G	bias_e_value=31.1073	bias_p_value=6.69502e-06	fisher_strand_p_value=4.27958e-07	frequency=4.896069e-02	genotype_quality=388.7	ks_quality_p_value=0.998627	log10_base_likelihood=-7.90087	log10_qual_likelihood_position_model=10.2458	log10_strand_likelihood_position_model=6.3686	new_cov=8/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=13/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=21/91
RA	666	.	NC_007779	4029622	1	.	G	bias_e_value=1130650	bias_p_value=0.243342	fisher_strand_p_value=0.0864657	frequency=1.499939e-02	genotype_quality=961.1	ks_quality_p_value=0.754595	log10_base_likelihood=-12.5288	log10_qual_likelihood_position_model=1.62258	log10_strand_likelihood_position_model=1.06316	new_cov=3/0	polymorphism_quality=7.1	quality=7.1	quality_position_model=7.23378e-12	ref_cov=86/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=89/111
RA	667	.	NC_007779	4029628	0	C	G	bias_e_value=17293.8	bias_p_value=0.00372203	fisher_strand_p_value=0.000425438	frequency=3.117847e-02	genotype_quality=587.0	ks_quality_p_value=0.998235	log10_base_likelihood=-6.38758	log10_qual_likelihood_position_model=6.62248	log10_strand_likelihood_position_model=3.37116	new_cov=5/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=29/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=34/119
RA	668	.	NC_007779	4029633	0	T	G	bias_e_value=300.788	bias_p_value=6.47366e-05	fisher_strand_p_value=4.8941e-06	frequency=3.768921e-02	genotype_quality=570.7	ks_quality_p_value=1	log10_base_likelihood=-5.85749	log10_qual_likelihood_position_model=11.712	log10_strand_likelihood_position_model=5.31033	new_cov=8/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=28/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=36/117
RA	669	.	NC_007779	4031691	1	.	T	bias_e_value=1026030	bias_p_value=0.220826	fisher_strand_p_value=0.0613208	frequency=1.249981e-02	genotype_quality=770.6	ks_quality_p_value=0.9326	log10_base_likelihood=-8.61185	log10_qual_likelihood_position_model=1.68288	log10_strand_likelihood_position_model=1.21239	new_cov=2/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=1.25255e-07	ref_cov=38/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=40/120
RA	670	.	NC_007779	4034219	0	A	C	bias_e_value=737610	bias_p_value=0.158751	fisher_strand_p_value=0.502451	frequency=7.791519e-03	genotype_quality=961.6	ks_quality_p_value=0.0734991	log10_base_likelihood=-5.63867	log10_qual_likelihood_position_model=2.4382	log10_strand_likelihood_position_model=0.525637	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=0.000194868	ref_cov=138/116	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=141/116
RA	671	.	NC_007779	4055100	0	G	T	bias_e_value=5.26365e-07	bias_p_value=1.13286e-13	fisher_strand_p_value=3.41779e-15	frequency=1.428018e-01	genotype_quality=603.2	ks_quality_p_value=0.965082	log10_base_likelihood=-40.4723	log10_qual_likelihood_position_model=32.7106	log10_strand_likelihood_position_model=14.4663	new_cov=29/0	polymorphism_quality=35.3	quality=35.3	quality_position_model=Inf	ref_cov=42/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=71/121
RA	672	.	NC_007779	4055329	0	T	G	bias_e_value=1.18384e-13	bias_p_value=2.5479e-20	fisher_strand_p_value=5.09285e-22	frequency=1.172080e-01	genotype_quality=566.6	ks_quality_p_value=1	log10_base_likelihood=-28.2206	log10_qual_likelihood_position_model=26.2563	log10_strand_likelihood_position_model=21.293	new_cov=25/0	polymorphism_quality=23.0	quality=23.0	quality_position_model=Inf	ref_cov=12/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/146
RA	673	.	NC_007779	4059485	0	T	.	bias_e_value=3871370	bias_p_value=0.833211	fisher_strand_p_value=0.613714	frequency=1.303482e-02	genotype_quality=916.6	ks_quality_p_value=0.784137	log10_base_likelihood=-8.19725	log10_qual_likelihood_position_model=1.29173	log10_strand_likelihood_position_model=0.435954	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.08725e-08	ref_cov=117/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/112
RA	674	.	NC_007779	4062114	0	T	G	bias_e_value=1.01295e-16	bias_p_value=2.1801e-23	fisher_strand_p_value=3.80956e-25	frequency=1.937428e-01	genotype_quality=459.3	ks_quality_p_value=1	log10_base_likelihood=-33.3543	log10_qual_likelihood_position_model=33.8869	log10_strand_likelihood_position_model=24.4191	new_cov=47/0	polymorphism_quality=28.2	quality=28.2	quality_position_model=Inf	ref_cov=27/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/112
RA	675	.	NC_007779	4065564	0	C	G	bias_e_value=6443.86	bias_p_value=0.00138687	fisher_strand_p_value=0.00014051	frequency=4.362583e-02	genotype_quality=711.2	ks_quality_p_value=1	log10_base_likelihood=-6.69856	log10_qual_likelihood_position_model=9.23493	log10_strand_likelihood_position_model=3.85229	new_cov=11/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=82/109	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=93/109
RA	676	.	NC_007779	4074542	0	C	A	bias_e_value=247.159	bias_p_value=5.31945e-05	fisher_strand_p_value=3.95799e-06	frequency=5.771255e-02	genotype_quality=680.3	ks_quality_p_value=1	log10_base_likelihood=-12.6677	log10_qual_likelihood_position_model=16.7535	log10_strand_likelihood_position_model=5.4146	new_cov=1/12	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=130/48	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/60
RA	677	.	NC_007779	4076934	0	A	C	bias_e_value=1.33032e-05	bias_p_value=2.86317e-12	fisher_strand_p_value=9.232e-14	frequency=1.361270e-01	genotype_quality=552.3	ks_quality_p_value=1	log10_base_likelihood=-24.941	log10_qual_likelihood_position_model=24.5895	log10_strand_likelihood_position_model=13.0347	new_cov=0/32	polymorphism_quality=19.7	quality=19.7	quality_position_model=Inf	ref_cov=113/57	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/89
RA	678	.	NC_007779	4084209	0	A	G	bias_e_value=0.0108584	bias_p_value=2.33698e-09	fisher_strand_p_value=9.71526e-11	frequency=6.369448e-02	genotype_quality=713.2	ks_quality_p_value=1	log10_base_likelihood=-6.30197	log10_qual_likelihood_position_model=19.8398	log10_strand_likelihood_position_model=10.0125	new_cov=22/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=65/141	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=87/141
RA	679	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=901.2	new_cov=100/126	quality=901.2	ref_cov=0/0	tot_cov=100/126
RA	680	.	NC_007779	4098730	0	G	T	bias_e_value=30.794	bias_p_value=6.6276e-06	fisher_strand_p_value=4.22775e-07	frequency=5.080986e-02	genotype_quality=742.4	ks_quality_p_value=1	log10_base_likelihood=-10.6614	log10_qual_likelihood_position_model=13.154	log10_strand_likelihood_position_model=6.37389	new_cov=0/17	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=130/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/104
RA	681	.	NC_007779	4115400	1	.	C	bias_e_value=182827	bias_p_value=0.0393488	fisher_strand_p_value=0.00652286	frequency=2.648067e-02	genotype_quality=690.4	ks_quality_p_value=1	log10_base_likelihood=-12.7404	log10_qual_likelihood_position_model=6.14221	log10_strand_likelihood_position_model=2.18556	new_cov=0/4	polymorphism_quality=7.4	quality=7.4	quality_position_model=2.84385e-06	ref_cov=107/40	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/44
RA	682	.	NC_007779	4124974	0	G	T	bias_e_value=16563.8	bias_p_value=0.00356492	fisher_strand_p_value=0.000404515	frequency=2.595806e-02	genotype_quality=976.8	ks_quality_p_value=1	log10_base_likelihood=-9.41157	log10_qual_likelihood_position_model=8.70721	log10_strand_likelihood_position_model=3.39306	new_cov=0/9	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=152/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/114
RA	683	.	NC_007779	4135559	1	.	A	bias_e_value=643496	bias_p_value=0.138496	fisher_strand_p_value=0.030973	frequency=1.492405e-02	genotype_quality=608.0	ks_quality_p_value=0.999096	log10_base_likelihood=-6.95233	log10_qual_likelihood_position_model=2.56972	log10_strand_likelihood_position_model=1.50902	new_cov=0/2	polymorphism_quality=1.4	quality=1.4	quality_position_model=0.000119449	ref_cov=110/22	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=110/24
RA	684	.	NC_007779	4148399	0	A	C	bias_e_value=3.10923e-12	bias_p_value=6.69178e-19	fisher_strand_p_value=1.43318e-20	frequency=1.664567e-01	genotype_quality=539.2	ks_quality_p_value=1	log10_base_likelihood=-24.2104	log10_qual_likelihood_position_model=33.5023	log10_strand_likelihood_position_model=19.8437	new_cov=0/47	polymorphism_quality=19.0	quality=19.0	quality_position_model=Inf	ref_cov=112/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/94
RA	685	.	NC_007779	4148399	1	.	C	bias_e_value=2399800	bias_p_value=0.516493	fisher_strand_p_value=0.201714	frequency=9.897232e-03	genotype_quality=925.0	ks_quality_p_value=0.974972	log10_base_likelihood=-5.85823	log10_qual_likelihood_position_model=2.89254	log10_strand_likelihood_position_model=0.695264	new_cov=0/2	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.000531349	ref_cov=111/89	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/91
RA	686	.	NC_007779	4159514	0	T	G	bias_e_value=1.58199e-12	bias_p_value=3.40482e-19	fisher_strand_p_value=7.18587e-21	frequency=1.023755e-01	genotype_quality=554.6	ks_quality_p_value=1	log10_base_likelihood=-9.10668	log10_qual_likelihood_position_model=33.59	log10_strand_likelihood_position_model=20.1435	new_cov=43/0	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=41/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=85/119
RA	687	.	NC_007779	4163966	1	.	T	bias_e_value=1387880	bias_p_value=0.298704	fisher_strand_p_value=0.629456	frequency=1.762104e-02	genotype_quality=1065.9	ks_quality_p_value=0.137736	log10_base_likelihood=-17.9241	log10_qual_likelihood_position_model=3.08512	log10_strand_likelihood_position_model=0.521668	new_cov=3/1	polymorphism_quality=12.6	quality=12.6	quality_position_model=2.02535e-16	ref_cov=122/101	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/102
RA	688	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1156.6	new_cov=155/116	quality=1156.6	ref_cov=0/0	tot_cov=155/116
RA	689	.	NC_007779	4169820	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	4169821	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	4169822	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	692	.	NC_007779	4169823	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	693	.	NC_007779	4169824	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	4169825	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	695	.	NC_007779	4169826	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	4169827	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	4169829	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	698	.	NC_007779	4169830	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	699	.	NC_007779	4169834	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	700	.	NC_007779	4169836	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	4169838	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	702	.	NC_007779	4169839	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	703	.	NC_007779	4169840	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	704	.	NC_007779	4169842	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	4169845	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	706	.	NC_007779	4169846	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	707	.	NC_007779	4169847	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	708	.	NC_007779	4169848	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	709	.	NC_007779	4169850	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	710	.	NC_007779	4169851	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	711	.	NC_007779	4169852	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	712	.	NC_007779	4169853	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	4169854	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	714	.	NC_007779	4169856	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	715	.	NC_007779	4169857	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	716	.	NC_007779	4169858	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	717	.	NC_007779	4169859	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	718	.	NC_007779	4169860	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	719	.	NC_007779	4169861	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	720	.	NC_007779	4169862	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	721	.	NC_007779	4169863	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	722	.	NC_007779	4169864	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	723	.	NC_007779	4169868	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	724	.	NC_007779	4169869	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	725	.	NC_007779	4169870	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	726	.	NC_007779	4169871	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	727	.	NC_007779	4169872	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	728	.	NC_007779	4169873	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	729	.	NC_007779	4169874	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	730	.	NC_007779	4169875	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	731	.	NC_007779	4174729	1	.	T	bias_e_value=3888750	bias_p_value=0.836951	fisher_strand_p_value=1	frequency=1.036263e-02	genotype_quality=933.9	ks_quality_p_value=0.486387	log10_base_likelihood=-8.50445	log10_qual_likelihood_position_model=1.32089	log10_strand_likelihood_position_model=0.298879	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=7.79323e-09	ref_cov=94/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/98
RA	732	.	NC_007779	4174730	0	T	.	bias_e_value=4036130	bias_p_value=0.86867	fisher_strand_p_value=1	frequency=2.576447e-02	genotype_quality=755.8	ks_quality_p_value=0.533458	log10_base_likelihood=-15.1767	log10_qual_likelihood_position_model=3.03983	log10_strand_likelihood_position_model=0.491963	new_cov=2/3	polymorphism_quality=9.8	quality=9.8	quality_position_model=1.05287e-13	ref_cov=93/96	reject=INDEL_HOMOPOLYMER	tot_cov=95/99
RA	733	.	NC_007779	4194164	0	T	G	bias_e_value=2316.59	bias_p_value=0.000498586	fisher_strand_p_value=4.53186e-05	frequency=2.196407e-02	genotype_quality=533.6	ks_quality_p_value=1	log10_base_likelihood=-6.31235	log10_qual_likelihood_position_model=5.57478	log10_strand_likelihood_position_model=4.34372	new_cov=4/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=9/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=13/128
RA	734	.	NC_007779	4197139	0	T	G	bias_e_value=0.000419695	bias_p_value=9.03282e-11	fisher_strand_p_value=3.30275e-12	frequency=5.830193e-02	genotype_quality=570.6	ks_quality_p_value=0.996715	log10_base_likelihood=-19.2845	log10_qual_likelihood_position_model=13.5096	log10_strand_likelihood_position_model=11.4811	new_cov=10/0	polymorphism_quality=14.0	quality=14.0	quality_position_model=Inf	ref_cov=6/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=16/145
RA	735	.	NC_007779	4211631	0	A	C	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	736	.	NC_007779	4211639	0	G	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	737	.	NC_007779	4213497	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	738	.	NC_007779	4213498	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	739	.	NC_007779	4213499	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	740	.	NC_007779	4213500	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	741	.	NC_007779	4213501	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	742	.	NC_007779	4220019	0	A	C	bias_e_value=1.25759e-09	bias_p_value=2.70662e-16	fisher_strand_p_value=6.67508e-18	frequency=6.173897e-02	genotype_quality=791.9	ks_quality_p_value=1	log10_base_likelihood=-5.89774	log10_qual_likelihood_position_model=49.8821	log10_strand_likelihood_position_model=17.1755	new_cov=0/46	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=149/87	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/133
RA	743	.	NC_007779	4224824	1	.	T	bias_e_value=2722250	bias_p_value=0.585892	fisher_strand_p_value=1	frequency=6.779671e-03	genotype_quality=1454.5	ks_quality_p_value=0.24238	log10_base_likelihood=-7.8612	log10_qual_likelihood_position_model=1.08277	log10_strand_likelihood_position_model=0.3004	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.04573e-08	ref_cov=153/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/141
RA	744	.	NC_007779	4225629	0	T	G	bias_e_value=4439530	bias_p_value=0.955492	fisher_strand_p_value=1	frequency=6.956100e-03	genotype_quality=1161.7	ks_quality_p_value=0.716882	log10_base_likelihood=-5.76532	log10_qual_likelihood_position_model=0.868847	log10_strand_likelihood_position_model=0.306793	new_cov=1/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=1.85773e-06	ref_cov=124/161	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=125/163
RA	745	.	NC_007779	4227183	0	T	G	bias_e_value=2.18041e-13	bias_p_value=4.69275e-20	fisher_strand_p_value=9.4984e-22	frequency=1.079068e-01	genotype_quality=640.5	ks_quality_p_value=1	log10_base_likelihood=-12.19	log10_qual_likelihood_position_model=39.1006	log10_strand_likelihood_position_model=21.0223	new_cov=45/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=49/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/136
RA	746	.	NC_007779	4227210	0	T	G	bias_e_value=0.000232038	bias_p_value=4.99401e-11	fisher_strand_p_value=1.78012e-12	frequency=6.585073e-02	genotype_quality=724.1	ks_quality_p_value=1	log10_base_likelihood=-5.7957	log10_qual_likelihood_position_model=23.658	log10_strand_likelihood_position_model=11.7496	new_cov=24/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=56/142	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/142
RA	747	.	NC_007779	4244592	0	G	C	bias_e_value=5.65544e-06	bias_p_value=1.21718e-12	fisher_strand_p_value=3.83923e-14	frequency=8.600092e-02	genotype_quality=479.1	ks_quality_p_value=0.993945	log10_base_likelihood=-19.329	log10_qual_likelihood_position_model=13.0825	log10_strand_likelihood_position_model=13.4158	new_cov=0/11	polymorphism_quality=14.0	quality=14.0	quality_position_model=Inf	ref_cov=113/2	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/13
RA	748	.	NC_007779	4283054	1	.	G	bias_e_value=1005810	bias_p_value=0.216475	fisher_strand_p_value=0.0576567	frequency=1.428413e-02	genotype_quality=661.8	ks_quality_p_value=0.965615	log10_base_likelihood=-7.00512	log10_qual_likelihood_position_model=2.34466	log10_strand_likelihood_position_model=1.23915	new_cov=2/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=3.13007e-05	ref_cov=32/106	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=34/106
RA	749	.	NC_007779	4296690	0	G	.	bias_e_value=3199300	bias_p_value=0.688565	fisher_strand_p_value=0.653651	frequency=2.163887e-02	genotype_quality=967.8	ks_quality_p_value=0.494882	log10_base_likelihood=-15.3982	log10_qual_likelihood_position_model=2.73256	log10_strand_likelihood_position_model=0.587658	new_cov=3/2	polymorphism_quality=10.1	quality=10.1	quality_position_model=3.81625e-14	ref_cov=96/130	reject=INDEL_HOMOPOLYMER	tot_cov=99/132
RA	750	.	NC_007779	4309615	0	C	G	bias_e_value=602.082	bias_p_value=0.000129582	fisher_strand_p_value=1.05547e-05	frequency=4.642248e-02	genotype_quality=634.0	ks_quality_p_value=0.984154	log10_base_likelihood=-5.96298	log10_qual_likelihood_position_model=9.6905	log10_strand_likelihood_position_model=4.97656	new_cov=10/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=51/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/122
RA	751	.	NC_007779	4312218	0	T	G	bias_e_value=0.000797506	bias_p_value=1.71642e-10	fisher_strand_p_value=6.41101e-12	frequency=7.199240e-02	genotype_quality=648.7	ks_quality_p_value=1	log10_base_likelihood=-8.26497	log10_qual_likelihood_position_model=28.0225	log10_strand_likelihood_position_model=11.1931	new_cov=29/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=68/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=97/118
RA	752	.	NC_007779	4322023	0	T	.	bias_e_value=1546510	bias_p_value=0.332846	fisher_strand_p_value=0.248218	frequency=1.148510e-02	genotype_quality=996.4	ks_quality_p_value=0.40741	log10_base_likelihood=-8.02234	log10_qual_likelihood_position_model=3.39916	log10_strand_likelihood_position_model=0.858603	new_cov=3/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.35985e-05	ref_cov=132/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/126
RA	753	.	NC_007779	4337469	0	A	C	bias_e_value=2.94622e-11	bias_p_value=6.34095e-18	fisher_strand_p_value=1.42838e-19	frequency=1.474156e-01	genotype_quality=499.3	ks_quality_p_value=1	log10_base_likelihood=-30.1049	log10_qual_likelihood_position_model=28.9833	log10_strand_likelihood_position_model=18.8452	new_cov=0/30	polymorphism_quality=24.9	quality=24.9	quality_position_model=Inf	ref_cov=121/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/54
RA	754	.	NC_007779	4347517	0	T	C	bias_e_value=1066420	bias_p_value=0.229519	fisher_strand_p_value=0.424984	frequency=2.155190e-01	genotype_quality=508.6	ks_quality_p_value=0.141779	log10_base_likelihood=-158.439	log10_qual_likelihood_position_model=12.5397	log10_strand_likelihood_position_model=1.07666	new_cov=27/23	polymorphism_quality=153.6	quality=153.6	quality_position_model=2.01558e-147	ref_cov=85/97	tot_cov=112/120
RA	755	.	NC_007779	4351353	0	T	G	bias_e_value=2.21215e-08	bias_p_value=4.76107e-15	fisher_strand_p_value=1.26606e-16	frequency=5.631208e-02	genotype_quality=760.6	ks_quality_p_value=1	log10_base_likelihood=-8.42493	log10_qual_likelihood_position_model=32.5976	log10_strand_likelihood_position_model=15.8975	new_cov=26/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=39/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=65/160
RA	756	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=985.2	new_cov=93/104	quality=985.2	ref_cov=0/0	tot_cov=93/104
RA	757	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=985.2	new_cov=93/104	quality=985.2	ref_cov=0/0	tot_cov=93/104
RA	758	.	NC_007779	4375240	1	.	T	bias_e_value=3678740	bias_p_value=0.791752	fisher_strand_p_value=0.498024	frequency=7.873535e-03	genotype_quality=1239.4	ks_quality_p_value=0.86067	log10_base_likelihood=-8.56392	log10_qual_likelihood_position_model=1.88783	log10_strand_likelihood_position_model=0.60378	new_cov=0/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=5.36755e-08	ref_cov=127/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/127
RA	759	.	NC_007779	4404554	0	A	T	bias_e_value=1524600	bias_p_value=0.32813	fisher_strand_p_value=0.10927	frequency=1.187801e-02	genotype_quality=1000.9	ks_quality_p_value=0.906726	log10_base_likelihood=-6.64985	log10_qual_likelihood_position_model=2.18939	log10_strand_likelihood_position_model=0.961501	new_cov=3/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=2.59125e-05	ref_cov=118/131	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=121/131
RA	760	.	NC_007779	4414724	1	.	T	bias_e_value=2924740	bias_p_value=0.629473	fisher_strand_p_value=0.525295	frequency=9.009361e-03	genotype_quality=1079.0	ks_quality_p_value=0.522709	log10_base_likelihood=-8.42773	log10_qual_likelihood_position_model=1.92732	log10_strand_likelihood_position_model=0.420486	new_cov=0/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=5.27112e-08	ref_cov=85/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=85/137
RA	761	.	NC_007779	4419586	0	T	G	bias_e_value=5.11221e-16	bias_p_value=1.10027e-22	fisher_strand_p_value=1.97964e-24	frequency=2.667031e-01	genotype_quality=441.0	ks_quality_p_value=1	log10_base_likelihood=-52.2688	log10_qual_likelihood_position_model=36.5207	log10_strand_likelihood_position_model=23.8334	new_cov=64/0	polymorphism_quality=47.2	quality=47.2	quality_position_model=Inf	ref_cov=48/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=112/105
RA	762	.	NC_007779	4423038	0	C	G	bias_e_value=0.175145	bias_p_value=3.76952e-08	fisher_strand_p_value=1.78511e-09	frequency=7.645035e-02	genotype_quality=539.3	ks_quality_p_value=0.998647	log10_base_likelihood=-10.7436	log10_qual_likelihood_position_model=13.4134	log10_strand_likelihood_position_model=8.74834	new_cov=14/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=27/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=41/110
RA	763	.	NC_007779	4455463	0	T	G	bias_e_value=8.95654e-14	bias_p_value=1.92766e-20	fisher_strand_p_value=3.83128e-22	frequency=1.470561e-01	genotype_quality=577.9	ks_quality_p_value=1	log10_base_likelihood=-29.5787	log10_qual_likelihood_position_model=32.0153	log10_strand_likelihood_position_model=21.4167	new_cov=35/0	polymorphism_quality=24.4	quality=24.4	quality_position_model=Inf	ref_cov=29/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=64/141
RA	764	.	NC_007779	4490145	0	T	G	bias_e_value=0.0273912	bias_p_value=5.89524e-09	fisher_strand_p_value=2.55333e-10	frequency=6.616688e-02	genotype_quality=531.0	ks_quality_p_value=1	log10_base_likelihood=-11.5378	log10_qual_likelihood_position_model=16.9496	log10_strand_likelihood_position_model=9.59289	new_cov=21/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=49/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=70/111
RA	765	.	NC_007779	4494104	0	C	A	bias_e_value=306.291	bias_p_value=6.5921e-05	fisher_strand_p_value=4.99104e-06	frequency=5.908632e-02	genotype_quality=760.6	ks_quality_p_value=1	log10_base_likelihood=-8.79881	log10_qual_likelihood_position_model=15.8877	log10_strand_likelihood_position_model=5.37062	new_cov=18/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=98/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/106
RA	766	.	NC_007779	4509629	1	.	T	bias_e_value=4525280	bias_p_value=0.973946	fisher_strand_p_value=1	frequency=9.174347e-03	genotype_quality=1069.4	ks_quality_p_value=0.780589	log10_base_likelihood=-8.39814	log10_qual_likelihood_position_model=0.990071	log10_strand_likelihood_position_model=0.309728	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=4.69662e-09	ref_cov=91/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=92/126
RA	767	.	NC_007779	4513015	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	768	.	NC_007779	4513016	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	769	.	NC_007779	4513017	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	770	.	NC_007779	4513018	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	771	.	NC_007779	4513020	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	772	.	NC_007779	4513021	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	773	.	NC_007779	4513022	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	774	.	NC_007779	4513023	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	775	.	NC_007779	4513025	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	776	.	NC_007779	4513027	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	777	.	NC_007779	4513028	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	778	.	NC_007779	4513029	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	779	.	NC_007779	4513030	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	780	.	NC_007779	4513031	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	781	.	NC_007779	4513032	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	782	.	NC_007779	4513035	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	783	.	NC_007779	4513036	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	784	.	NC_007779	4513038	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	785	.	NC_007779	4513039	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	786	.	NC_007779	4513040	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	787	.	NC_007779	4513041	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	788	.	NC_007779	4513042	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	789	.	NC_007779	4515413	0	T	G	bias_e_value=0.000152908	bias_p_value=3.29093e-11	fisher_strand_p_value=1.15525e-12	frequency=5.771589e-02	genotype_quality=655.8	ks_quality_p_value=1	log10_base_likelihood=-6.62487	log10_qual_likelihood_position_model=22.39	log10_strand_likelihood_position_model=11.9417	new_cov=20/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=31/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=51/146
RA	790	.	NC_007779	4516697	0	T	G	bias_e_value=35864.7	bias_p_value=0.00771894	fisher_strand_p_value=0.00097272	frequency=6.331062e-02	genotype_quality=542.9	ks_quality_p_value=1	log10_base_likelihood=-8.46157	log10_qual_likelihood_position_model=14.0297	log10_strand_likelihood_position_model=3.23639	new_cov=15/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=87/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=103/84
RA	791	.	NC_007779	4540870	0	T	G	bias_e_value=1.76075e-30	bias_p_value=3.78955e-37	fisher_strand_p_value=4.24095e-39	frequency=1.795926e-01	genotype_quality=599.6	ks_quality_p_value=1	log10_base_likelihood=-33.1912	log10_qual_likelihood_position_model=48.3019	log10_strand_likelihood_position_model=38.3725	new_cov=56/0	polymorphism_quality=28.0	quality=28.0	quality_position_model=Inf	ref_cov=16/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=72/156
RA	792	.	NC_007779	4540877	0	A	T	bias_e_value=1.11413e-09	bias_p_value=2.39786e-16	fisher_strand_p_value=5.89555e-18	frequency=1.197801e-01	genotype_quality=707.3	ks_quality_p_value=1	log10_base_likelihood=-24.6051	log10_qual_likelihood_position_model=24.5465	log10_strand_likelihood_position_model=17.2295	new_cov=26/0	polymorphism_quality=19.4	quality=19.4	quality_position_model=Inf	ref_cov=29/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=55/150
RA	793	.	NC_007779	4541066	0	C	G	bias_e_value=446.096	bias_p_value=9.60104e-05	fisher_strand_p_value=7.53454e-06	frequency=6.971312e-02	genotype_quality=519.3	ks_quality_p_value=0.995481	log10_base_likelihood=-10.6077	log10_qual_likelihood_position_model=13.4487	log10_strand_likelihood_position_model=5.12294	new_cov=0/11	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=92/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=92/53
RA	794	.	NC_007779	4542789	0	A	C	bias_e_value=7.66183e-07	bias_p_value=1.64901e-13	fisher_strand_p_value=4.85593e-15	frequency=9.067965e-02	genotype_quality=782.2	ks_quality_p_value=1	log10_base_likelihood=-7.83775	log10_qual_likelihood_position_model=31.37	log10_strand_likelihood_position_model=14.3137	new_cov=0/39	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=145/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/130
RA	795	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=887.4	new_cov=118/96	quality=887.4	ref_cov=0/0	tot_cov=118/96
RA	796	.	NC_007779	4554527	1	.	C	bias_e_value=2073180	bias_p_value=0.446197	fisher_strand_p_value=0.158537	frequency=1.212025e-02	genotype_quality=753.1	ks_quality_p_value=0.985237	log10_base_likelihood=-7.66583	log10_qual_likelihood_position_model=3.35315	log10_strand_likelihood_position_model=0.799871	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=2.5054e-05	ref_cov=64/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=66/99
RA	797	.	NC_007779	4554532	0	T	C	bias_e_value=5456.91	bias_p_value=0.00117446	fisher_strand_p_value=0.000116803	frequency=5.404615e-02	genotype_quality=491.4	ks_quality_p_value=1	log10_base_likelihood=-9.37109	log10_qual_likelihood_position_model=12.3147	log10_strand_likelihood_position_model=3.94951	new_cov=10/1	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=46/104	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=56/105
RA	798	.	NC_007779	4561441	0	T	.	bias_e_value=4310290	bias_p_value=0.927675	fisher_strand_p_value=1	frequency=1.320744e-02	genotype_quality=883.5	ks_quality_p_value=0.644634	log10_base_likelihood=-8.30883	log10_qual_likelihood_position_model=1.62999	log10_strand_likelihood_position_model=0.362281	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=3.00247e-08	ref_cov=134/90	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/91
RA	799	.	NC_007779	4571391	0	T	.	bias_e_value=2129830	bias_p_value=0.458389	fisher_strand_p_value=0.615439	frequency=1.101589e-02	genotype_quality=1063.3	ks_quality_p_value=0.264589	log10_base_likelihood=-7.52791	log10_qual_likelihood_position_model=3.04017	log10_strand_likelihood_position_model=0.43434	new_cov=1/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=6.7614e-06	ref_cov=138/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/133
RA	800	.	NC_007779	4573184	0	T	G	bias_e_value=1.08319e-11	bias_p_value=2.33127e-18	fisher_strand_p_value=5.13316e-20	frequency=1.275406e-01	genotype_quality=657.7	ks_quality_p_value=1	log10_base_likelihood=-15.7381	log10_qual_likelihood_position_model=35.6131	log10_strand_likelihood_position_model=19.4292	new_cov=63/0	polymorphism_quality=10.4	quality=10.4	quality_position_model=Inf	ref_cov=89/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/123
RA	801	.	NC_007779	4583431	0	T	.	bias_e_value=4030400	bias_p_value=0.867436	fisher_strand_p_value=0.654692	frequency=2.099895e-02	genotype_quality=933.4	ks_quality_p_value=0.811833	log10_base_likelihood=-14.528	log10_qual_likelihood_position_model=2.79308	log10_strand_likelihood_position_model=0.581324	new_cov=3/2	polymorphism_quality=9.2	quality=9.2	quality_position_model=3.33214e-13	ref_cov=100/133	reject=INDEL_HOMOPOLYMER	tot_cov=103/135
RA	802	.	NC_007779	4584556	0	C	A	bias_e_value=498.827	bias_p_value=0.000107359	fisher_strand_p_value=8.46729e-06	frequency=3.580189e-02	genotype_quality=937.7	ks_quality_p_value=1	log10_base_likelihood=-6.82981	log10_qual_likelihood_position_model=18.1401	log10_strand_likelihood_position_model=5.07226	new_cov=15/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=116/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/146
RA	803	.	NC_007779	4610781	0	A	C	bias_e_value=6.26847e-05	bias_p_value=1.34912e-11	fisher_strand_p_value=4.58724e-13	frequency=7.341862e-02	genotype_quality=760.0	ks_quality_p_value=1	log10_base_likelihood=-15.4579	log10_qual_likelihood_position_model=26.8535	log10_strand_likelihood_position_model=12.3384	new_cov=0/34	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=133/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/119
RA	804	.	NC_007779	4613456	0	C	A	bias_e_value=2013.54	bias_p_value=0.000433361	fisher_strand_p_value=3.88458e-05	frequency=3.814220e-02	genotype_quality=776.0	ks_quality_p_value=1	log10_base_likelihood=-6.63792	log10_qual_likelihood_position_model=14.208	log10_strand_likelihood_position_model=4.43258	new_cov=16/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=116/111	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/111
RA	805	.	NC_007779	4636470	0	C	G	bias_e_value=1.53115e-20	bias_p_value=3.29538e-27	fisher_strand_p_value=4.98022e-29	frequency=3.010483e-01	genotype_quality=407.9	ks_quality_p_value=1	log10_base_likelihood=-97.6228	log10_qual_likelihood_position_model=36.0169	log10_strand_likelihood_position_model=28.3028	new_cov=55/0	polymorphism_quality=92.7	quality=92.7	quality_position_model=1.38343e-35	ref_cov=21/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=76/103
RA	806	.	NC_007779	4636473	0	A	G	bias_e_value=1.3142	bias_p_value=2.82847e-07	fisher_strand_p_value=1.48679e-08	frequency=6.678343e-02	genotype_quality=435.2	ks_quality_p_value=1	log10_base_likelihood=-9.14597	log10_qual_likelihood_position_model=12.7519	log10_strand_likelihood_position_model=7.82775	new_cov=9/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=11/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=20/101
RA	807	.	NC_007779	4640524	0	C	A	bias_e_value=7410.14	bias_p_value=0.00159484	fisher_strand_p_value=0.000164169	frequency=3.361225e-02	genotype_quality=880.9	ks_quality_p_value=1	log10_base_likelihood=-8.9072	log10_qual_likelihood_position_model=11.123	log10_strand_likelihood_position_model=3.78471	new_cov=12/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=121/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/136
RA	808	.	NC_007779	4644244	1	.	T	bias_e_value=2292790	bias_p_value=0.493462	fisher_strand_p_value=0.183201	frequency=7.660866e-03	genotype_quality=1250.4	ks_quality_p_value=0.997872	log10_base_likelihood=-6.62516	log10_qual_likelihood_position_model=3.92852	log10_strand_likelihood_position_model=0.737073	new_cov=0/2	polymorphism_quality=1.1	quality=1.1	quality_position_model=0.00115868	ref_cov=149/110	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/112
MC	809	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=239	right_inside_cov=3	right_outside_cov=238
MC	810	.	NC_007779	1288312	1288518	83	59	left_inside_cov=182	left_outside_cov=185	right_inside_cov=180	right_outside_cov=186
MC	811	.	NC_007779	1301041	1302376	1326	0	left_inside_cov=1	left_outside_cov=250	right_inside_cov=0	right_outside_cov=247
MC	812	.	NC_007779	1413639	1436698	0	0	left_inside_cov=2	left_outside_cov=285	right_inside_cov=0	right_outside_cov=283
MC	813	.	NC_007779	2176983	2178208	0	0	left_inside_cov=0	left_outside_cov=276	right_inside_cov=0	right_outside_cov=213
MC	814	.	NC_007779	2320795	2322130	1327	0	left_inside_cov=0	left_outside_cov=248	right_inside_cov=1	right_outside_cov=248
MC	815	.	NC_007779	3128830	3147473	1172	0	left_inside_cov=181	left_outside_cov=183	right_inside_cov=0	right_outside_cov=260
MC	816	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=273	right_inside_cov=0	right_outside_cov=253
MC	817	.	NC_007779	3742936	3744271	1325	0	left_inside_cov=0	left_outside_cov=302	right_inside_cov=1	right_outside_cov=299
MC	818	.	NC_007779	3750591	3751789	1195	0	left_inside_cov=0	left_outside_cov=255	right_inside_cov=0	right_outside_cov=257
MC	819	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=253	right_inside_cov=0	right_outside_cov=252
MC	820	.	NC_007779	4310363	4311561	0	1197	left_inside_cov=0	left_outside_cov=267	right_inside_cov=1	right_outside_cov=266
JC	821	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=119	coverage_plus=116	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=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=236	pos_hash_score=133	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=235
JC	822	.	NC_007779	273179	1	NC_007779	657877	1	0	alignment_overlap=0	coverage_minus=90	coverage_plus=94	flanking_left=101	flanking_right=101	frequency=6.751825e-01	junction_possible_overlap_registers=90	key=NC_007779__273179__1__NC_007779__657877__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=49	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=0.77	new_junction_frequency=6.751825e-01	new_junction_read_count=185	pos_hash_score=108	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=0.37	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=89	side_2_redundant=0	total_non_overlap_reads=184
JC	823	.	NC_007779	274373	-1	NC_007779	657880	-1	0	alignment_overlap=0	coverage_minus=70	coverage_plus=68	flanking_left=101	flanking_right=101	frequency=6.133333e-01	junction_possible_overlap_registers=90	key=NC_007779__274373__-1__NC_007779__657880__-1__0____101__101__1__0	max_left=83	max_left_minus=81	max_left_plus=83	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	max_pos_hash_score=180	max_right=94	max_right_minus=94	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.58	new_junction_frequency=6.133333e-01	new_junction_read_count=138	pos_hash_score=86	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=0.36	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=87	side_2_redundant=0	total_non_overlap_reads=138
JC	824	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=8	coverage_minus=76	coverage_plus=107	flanking_left=101	flanking_right=101	frequency=9.972452e-01	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371965__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=87	max_min_left=45	max_min_left_minus=43	max_min_left_plus=45	max_min_right=46	max_min_right_minus=46	max_min_right_plus=46	max_pos_hash_score=160	max_right=86	max_right_minus=84	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.85	new_junction_frequency=9.972452e-01	new_junction_read_count=181	pos_hash_score=108	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=2	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=80	side_2_read_count=1	side_2_redundant=0	total_non_overlap_reads=183
JC	825	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=95	coverage_plus=77	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=33	max_min_right_minus=33	max_min_right_plus=33	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=1.13	new_junction_frequency=1.000000e+00	new_junction_read_count=172	pos_hash_score=86	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=172	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	826	.	NC_007779	290625	-1	NC_007779	678240	1	0	alignment_overlap=0	coverage_minus=140	coverage_plus=206	flanking_left=101	flanking_right=101	frequency=5.690789e-01	junction_possible_overlap_registers=90	key=NC_007779__290625__-1__NC_007779__678240__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=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.44	new_junction_frequency=5.690789e-01	new_junction_read_count=346	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=gene	side_2_continuation=0	side_2_coverage=1.09	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=262	side_2_redundant=0	total_non_overlap_reads=346
JC	827	.	NC_007779	290625	-1	NC_007779	771432	1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=1	flanking_left=101	flanking_right=101	frequency=2.083333e-02	junction_possible_overlap_registers=90	key=NC_007779__290625__-1__NC_007779__771432__1__0____101__101__1__0	max_left=62	max_left_minus=54	max_left_plus=62	max_min_left=37	max_min_left_minus=37	max_min_left_plus=0	max_min_right=47	max_min_right_minus=47	max_min_right_plus=39	max_pos_hash_score=180	max_right=72	max_right_minus=72	max_right_plus=39	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=2.083333e-02	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=0.78	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=188	side_2_redundant=0	total_non_overlap_reads=4
JC	828	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=154	coverage_plus=91	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=89	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=49	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=1.03	new_junction_frequency=NA	new_junction_read_count=246	pos_hash_score=126	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=245
JC	829	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=111	coverage_plus=119	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=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=47	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=92	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=NA	new_junction_read_count=230	pos_hash_score=130	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=230
JC	830	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=95	coverage_plus=112	flanking_left=101	flanking_right=101	frequency=8.600965e-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=48	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=91	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=8.600965e-01	new_junction_read_count=208	pos_hash_score=115	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=0.15	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=35	side_2_redundant=0	total_non_overlap_reads=207
JC	831	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=110	coverage_plus=97	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=45	max_min_left_plus=47	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=170	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=207	pos_hash_score=112	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=207
JC	832	.	NC_007779	693388	-1	NC_007779	1050967	-1	0	alignment_overlap=0	coverage_minus=153	coverage_plus=198	flanking_left=101	flanking_right=101	frequency=5.993209e-01	junction_possible_overlap_registers=90	key=NC_007779__693388__-1__NC_007779__1050967__-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=1.47	new_junction_frequency=5.993209e-01	new_junction_read_count=353	pos_hash_score=148	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.99	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=236	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=351
JC	833	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=40	coverage_plus=47	flanking_left=101	flanking_right=101	frequency=4.323339e-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=79	max_left_plus=78	max_min_left=41	max_min_left_minus=38	max_min_left_plus=41	max_min_right=42	max_min_right_minus=42	max_min_right_plus=40	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=0.44	new_junction_frequency=4.323339e-01	new_junction_read_count=87	pos_hash_score=67	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.58	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=138	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.58	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=115	side_2_redundant=0	total_non_overlap_reads=87
JC	834	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=33	coverage_plus=34	flanking_left=101	flanking_right=101	frequency=3.748392e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=76	max_left_minus=76	max_left_plus=75	max_min_left=42	max_min_left_minus=39	max_min_left_plus=42	max_min_right=42	max_min_right_minus=42	max_min_right_plus=42	max_pos_hash_score=148	max_right=77	max_right_minus=76	max_right_plus=77	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.35	new_junction_frequency=3.748392e-01	new_junction_read_count=68	pos_hash_score=54	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.57	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=136	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.58	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=115	side_2_redundant=0	total_non_overlap_reads=67
JC	835	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=91	coverage_plus=130	flanking_left=101	flanking_right=101	frequency=9.912681e-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=93	max_left_plus=93	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=176	max_right=88	max_right_minus=85	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=9.912681e-01	new_junction_read_count=222	pos_hash_score=116	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=2	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=221
JC	836	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=123	coverage_plus=75	flanking_left=101	flanking_right=101	frequency=9.949749e-01	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=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=89	max_right_minus=89	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.83	new_junction_frequency=9.949749e-01	new_junction_read_count=198	pos_hash_score=110	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=198
JC	837	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=107	coverage_plus=94	flanking_left=101	flanking_right=101	frequency=9.977225e-01	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=86	max_left_plus=88	max_min_left=46	max_min_left_minus=42	max_min_left_plus=46	max_min_right=47	max_min_right_minus=46	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=0.91	new_junction_frequency=9.977225e-01	new_junction_read_count=202	pos_hash_score=114	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=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=83	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=201
JC	838	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=74	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=8.415477e-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=47	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=0.89	new_junction_frequency=8.415477e-01	new_junction_read_count=203	pos_hash_score=112	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.17	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=40	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=203
JC	839	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=109	coverage_plus=107	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=95	max_left_minus=95	max_left_plus=92	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=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=1.000000e+00	new_junction_read_count=216	pos_hash_score=125	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=216
JC	840	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=87	coverage_plus=78	flanking_left=101	flanking_right=101	frequency=9.957345e-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=36	max_min_left_plus=37	max_min_right=36	max_min_right_minus=35	max_min_right_plus=36	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=0.97	new_junction_frequency=9.957345e-01	new_junction_read_count=166	pos_hash_score=97	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=26	side_1_possible_overlap_registers=90	side_1_read_count=2	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=0	side_2_redundant=0	total_non_overlap_reads=165
JC	841	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=97	coverage_plus=119	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=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=86	max_right_minus=83	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=218	pos_hash_score=109	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=216
JC	842	.	NC_007779	1724326	-1	NC_007779	1724330	1	0	alignment_overlap=0	coverage_minus=2	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.236597e-01	junction_possible_overlap_registers=90	key=NC_007779__1724326__-1__NC_007779__1724330__1__0____101__101__0__0	max_left=62	max_left_minus=62	max_left_plus=30	max_min_left=30	max_min_left_minus=28	max_min_left_plus=30	max_min_right=39	max_min_right_minus=39	max_min_right_plus=0	max_pos_hash_score=158	max_right=74	max_right_minus=73	max_right_plus=74	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.13	new_junction_frequency=1.236597e-01	new_junction_read_count=30	pos_hash_score=4	side_1_annotate_key=gene	side_1_continuation=11	side_1_coverage=0.86	side_1_overlap=0	side_1_possible_overlap_registers=79	side_1_read_count=181	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.91	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=219	side_2_redundant=0	total_non_overlap_reads=4
JC	843	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=111	coverage_plus=90	flanking_left=101	flanking_right=101	frequency=9.663462e-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=49	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=91	max_right_minus=86	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.84	new_junction_frequency=9.663462e-01	new_junction_read_count=201	pos_hash_score=116	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.03	side_1_overlap=0	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=201
JC	844	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=121	coverage_plus=116	flanking_left=101	flanking_right=101	frequency=9.525692e-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=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=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=9.525692e-01	new_junction_read_count=241	pos_hash_score=122	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.05	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=12	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=237
JC	845	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=118	coverage_plus=36	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=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=38	max_min_right=50	max_min_right_minus=50	max_min_right_plus=47	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=0.65	new_junction_frequency=1.000000e+00	new_junction_read_count=155	pos_hash_score=95	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=154
JC	846	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=115	coverage_plus=98	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=46	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=178	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=1.000000e+00	new_junction_read_count=213	pos_hash_score=116	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=213
JC	847	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=97	coverage_plus=99	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=94	max_left_minus=94	max_left_plus=94	max_min_left=50	max_min_left_minus=50	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=89	max_right_minus=89	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=1.000000e+00	new_junction_read_count=197	pos_hash_score=114	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=196
JC	848	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=98	coverage_plus=101	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=88	max_min_left=47	max_min_left_minus=47	max_min_left_plus=46	max_min_right=46	max_min_right_minus=46	max_min_right_plus=46	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=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=199	pos_hash_score=111	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=199
JC	849	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=68	coverage_plus=118	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=85	max_left_minus=85	max_left_plus=84	max_min_left=50	max_min_left_minus=50	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=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.79	new_junction_frequency=1.000000e+00	new_junction_read_count=189	pos_hash_score=108	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=186
JC	850	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=112	coverage_plus=114	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=89	max_left_minus=85	max_left_plus=89	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	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=93	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=227	pos_hash_score=119	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=226
JC	851	.	NC_007779	2411458	1	NC_007779	2941499	-1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.736111e-02	junction_possible_overlap_registers=90	key=NC_007779__2411458__1__NC_007779__2941499__-1__0____101__101__1__0	max_left=88	max_left_minus=69	max_left_plus=88	max_min_left=35	max_min_left_minus=35	max_min_left_plus=0	max_min_right=37	max_min_right_minus=32	max_min_right_plus=37	max_pos_hash_score=180	max_right=79	max_right_minus=79	max_right_plus=37	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=1.736111e-02	new_junction_read_count=5	pos_hash_score=5	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=1.18	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=283	side_2_redundant=0	total_non_overlap_reads=5
JC	852	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=135	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=9.708029e-01	junction_possible_overlap_registers=90	key=NC_007779__2411458__1__NC_007779__2985055__-1__0____101__101__1__0	max_left=91	max_left_minus=89	max_left_plus=91	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=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=9.708029e-01	new_junction_read_count=266	pos_hash_score=122	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=0.03	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=8	side_2_redundant=0	total_non_overlap_reads=264
JC	853	.	NC_007779	2412225	-1	NC_007779	2941491	1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.805054e-02	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2941491__1__0____101__101__1__0	max_left=70	max_left_minus=70	max_left_plus=30	max_min_left=30	max_min_left_minus=0	max_min_left_plus=30	max_min_right=46	max_min_right_minus=46	max_min_right_plus=0	max_pos_hash_score=180	max_right=84	max_right_minus=46	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=1.805054e-02	new_junction_read_count=5	pos_hash_score=5	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=1.14	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=272	side_2_redundant=0	total_non_overlap_reads=5
JC	854	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=121	coverage_plus=126	flanking_left=101	flanking_right=101	frequency=9.652510e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__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=1.04	new_junction_frequency=9.652510e-01	new_junction_read_count=250	pos_hash_score=135	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=9	side_2_redundant=0	total_non_overlap_reads=247
JC	855	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=76	coverage_plus=85	flanking_left=101	flanking_right=101	frequency=6.028856e-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=90	max_min_left=46	max_min_left_minus=45	max_min_left_plus=46	max_min_right=46	max_min_right_minus=46	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=0.85	new_junction_frequency=6.028856e-01	new_junction_read_count=195	pos_hash_score=98	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.67	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=160	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.45	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=104	side_2_redundant=0	total_non_overlap_reads=161
JC	856	.	NC_007779	2865229	1	NC_007779	2865278	-1	-42	alignment_overlap=-42	coverage_minus=30	coverage_plus=31	flanking_left=101	flanking_right=101	frequency=4.549975e-01	junction_possible_overlap_registers=48	key=NC_007779__2865229__1__NC_007779__2865278__-1__-42__CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA__101__101__0__0	max_left=42	max_left_minus=42	max_left_plus=41	max_min_left=29	max_min_left_minus=29	max_min_left_plus=28	max_min_right=28	max_min_right_minus=28	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=0.48	new_junction_frequency=4.549975e-01	new_junction_read_count=61	pos_hash_score=38	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.67	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=160	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.48	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=114	side_2_redundant=0	total_non_overlap_reads=61	unique_read_sequence=CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA
JC	857	.	NC_007779	2941317	1	NC_007779	3129996	-1	0	alignment_overlap=0	coverage_minus=1	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.041667e-02	junction_possible_overlap_registers=90	key=NC_007779__2941317__1__NC_007779__3129996__-1__0____101__101__0__1	max_left=89	max_left_minus=64	max_left_plus=89	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=37	max_min_right_minus=37	max_min_right_plus=34	max_pos_hash_score=180	max_right=37	max_right_minus=37	max_right_plus=34	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.01	new_junction_frequency=1.041667e-02	new_junction_read_count=3	pos_hash_score=3	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.19	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=285	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=3
JC	858	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=110	coverage_plus=117	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=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=88	max_right_minus=86	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=229	pos_hash_score=118	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=227
JC	859	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=130	coverage_plus=125	flanking_left=101	flanking_right=101	frequency=9.884998e-01	junction_possible_overlap_registers=89	key=NC_007779__3186082__-1__NC_007779__3512753__1__1____101__101__1__0	max_left=94	max_left_minus=93	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=1.08	new_junction_frequency=9.884998e-01	new_junction_read_count=255	pos_hash_score=133	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=0.01	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=3	side_2_redundant=0	total_non_overlap_reads=255
JC	860	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=140	coverage_plus=99	flanking_left=101	flanking_right=101	frequency=1.000000e+00	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=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=47	max_min_right_minus=45	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=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=239	pos_hash_score=124	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=239	unique_read_sequence=CTTTGC
JC	861	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=113	coverage_plus=90	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=85	max_left_minus=85	max_left_plus=82	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=0.86	new_junction_frequency=1.000000e+00	new_junction_read_count=205	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=203
JC	862	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=110	coverage_plus=106	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=94	max_left_minus=92	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=47	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=216	pos_hash_score=122	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=216
JC	863	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=147	coverage_plus=123	flanking_left=101	flanking_right=101	frequency=9.963100e-01	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=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=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.13	new_junction_frequency=9.963100e-01	new_junction_read_count=270	pos_hash_score=133	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=270
JC	864	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=126	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=9.848999e-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=93	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=48	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=1.09	new_junction_frequency=9.848999e-01	new_junction_read_count=258	pos_hash_score=140	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=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=258
JC	865	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=135	coverage_plus=104	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=84	max_min_left=46	max_min_left_minus=46	max_min_left_plus=45	max_min_right=46	max_min_right_minus=45	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=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=239	pos_hash_score=122	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=239
JC	866	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=124	coverage_plus=95	flanking_left=101	flanking_right=101	frequency=9.910314e-01	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=0.92	new_junction_frequency=9.910314e-01	new_junction_read_count=221	pos_hash_score=119	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=0.01	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=2	side_2_redundant=0	total_non_overlap_reads=219
JC	867	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=106	coverage_plus=117	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3746910__-1__NC_007779__3748106__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=90	max_min_left=48	max_min_left_minus=47	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=46	max_pos_hash_score=172	max_right=91	max_right_minus=90	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=1.000000e+00	new_junction_read_count=223	pos_hash_score=130	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=223
JC	868	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=103	coverage_plus=125	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=90	max_left_plus=92	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=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=1.000000e+00	new_junction_read_count=265	pos_hash_score=120	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=228
JC	869	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=135	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=1.000000e+00	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=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=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=250	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=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=250
JC	870	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=111	coverage_plus=108	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=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=47	max_min_right_minus=47	max_min_right_plus=46	max_pos_hash_score=172	max_right=90	max_right_minus=89	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=219	pos_hash_score=122	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=219
JC	871	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=112	coverage_plus=116	flanking_left=101	flanking_right=101	frequency=9.956815e-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=48	max_min_left_plus=49	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=0.96	new_junction_frequency=9.956815e-01	new_junction_read_count=228	pos_hash_score=123	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=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=228
JC	872	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=107	coverage_plus=102	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=90	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=176	max_right=93	max_right_minus=92	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=1.000000e+00	new_junction_read_count=210	pos_hash_score=118	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=209
JC	873	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=108	coverage_plus=126	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=93	max_left_minus=90	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=47	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=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=234	pos_hash_score=122	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=234
JC	874	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=127	coverage_plus=153	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=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=280	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=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=280
JC	875	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=122	coverage_plus=110	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=90	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=90	max_right_minus=90	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=232	pos_hash_score=118	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=232
JC	876	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=110	coverage_plus=112	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=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=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=227	pos_hash_score=127	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=222
JC	877	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=140	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=49	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=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=278	pos_hash_score=127	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=262
JC	878	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=127	coverage_plus=145	flanking_left=101	flanking_right=101	frequency=9.963370e-01	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=49	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=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.14	new_junction_frequency=9.963370e-01	new_junction_read_count=272	pos_hash_score=135	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=272
JC	879	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=105	coverage_plus=119	flanking_left=101	flanking_right=101	frequency=9.870740e-01	junction_possible_overlap_registers=88	key=NC_007779__4355066__-1__NC_007779__4504191__-1__2____101__101__0__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=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=9.870740e-01	new_junction_read_count=224	pos_hash_score=121	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=3	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=224
UN	880	.	NC_007779	15482	16634
UN	881	.	NC_007779	19894	20468
UN	882	.	NC_007779	223637	223642
UN	883	.	NC_007779	223840	224673
UN	884	.	NC_007779	224990	225488
UN	885	.	NC_007779	225835	225923
UN	886	.	NC_007779	226120	226202
UN	887	.	NC_007779	226399	226505
UN	888	.	NC_007779	226701	226870
UN	889	.	NC_007779	227085	228591
UN	890	.	NC_007779	228787	228911
UN	891	.	NC_007779	269859	270420
UN	892	.	NC_007779	270706	270712
UN	893	.	NC_007779	273275	274275
UN	894	.	NC_007779	274733	371972
UN	895	.	NC_007779	380574	381719
UN	896	.	NC_007779	391029	392101
UN	897	.	NC_007779	525192	525848
UN	898	.	NC_007779	566089	567161
UN	899	.	NC_007779	573905	574918
UN	900	.	NC_007779	580439	580490
UN	901	.	NC_007779	607325	608476
UN	902	.	NC_007779	654214	655412
UN	903	.	NC_007779	688367	689374
UN	904	.	NC_007779	730322	730468
UN	905	.	NC_007779	730824	730860
UN	906	.	NC_007779	732510	732614
UN	907	.	NC_007779	733124	733151
UN	908	.	NC_007779	734994	735022
UN	909	.	NC_007779	1050344	1050401
UN	910	.	NC_007779	1050560	1050736
UN	911	.	NC_007779	1094763	1095829
UN	912	.	NC_007779	1105713	1106860
UN	913	.	NC_007779	1270760	1270799
UN	914	.	NC_007779	1271821	1271870
UN	915	.	NC_007779	1288372	1288460
UN	916	.	NC_007779	1301041	1302376
UN	917	.	NC_007779	1397851	1398858
UN	918	.	NC_007779	1413639	1436698
UN	919	.	NC_007779	1469721	1470864
UN	920	.	NC_007779	1471108	1472133
UN	921	.	NC_007779	1530138	1530792
UN	922	.	NC_007779	1533980	1534024
UN	923	.	NC_007779	1572480	1572486
UN	924	.	NC_007779	1572677	1572963
UN	925	.	NC_007779	1573217	1573420
UN	926	.	NC_007779	1634762	1634840
UN	927	.	NC_007779	1635034	1635244
UN	928	.	NC_007779	1635440	1635540
UN	929	.	NC_007779	1635907	1636254
UN	930	.	NC_007779	1636451	1636639
UN	931	.	NC_007779	1637648	1637699
UN	932	.	NC_007779	1652653	1653166
UN	933	.	NC_007779	1980302	1981309
UN	934	.	NC_007779	2068409	2068504
UN	935	.	NC_007779	2068701	2068747
UN	936	.	NC_007779	2068959	2069339
UN	937	.	NC_007779	2071174	2072316
UN	938	.	NC_007779	2103980	2104987
UN	939	.	NC_007779	2172403	2173469
UN	940	.	NC_007779	2176983	2178208
UN	941	.	NC_007779	2292349	2293349
UN	942	.	NC_007779	2308005	2308023
UN	943	.	NC_007779	2308230	2308249
UN	944	.	NC_007779	2320795	2322130
UN	945	.	NC_007779	2411554	2412131
UN	946	.	NC_007779	2519817	2520965
UN	947	.	NC_007779	2724817	2727806
UN	948	.	NC_007779	2728091	2728121
UN	949	.	NC_007779	2728321	2729507
UN	950	.	NC_007779	2729833	2729930
UN	951	.	NC_007779	2995113	2996257
UN	952	.	NC_007779	3128896	3147473
UN	953	.	NC_007779	3184842	3185986
UN	954	.	NC_007779	3261134	3262337
UN	955	.	NC_007779	3365505	3366515
UN	956	.	NC_007779	3423611	3424411
UN	957	.	NC_007779	3424606	3426562
UN	958	.	NC_007779	3426758	3426848
UN	959	.	NC_007779	3427044	3428592
UN	960	.	NC_007779	3459669	3460042
UN	961	.	NC_007779	3460235	3460348
UN	962	.	NC_007779	3465132	3468011
UN	963	.	NC_007779	3468301	3468330
UN	964	.	NC_007779	3468559	3470290
UN	965	.	NC_007779	3596172	3597194
UN	966	.	NC_007779	3597394	3597857
UN	967	.	NC_007779	3598088	3598748
UN	968	.	NC_007779	3598944	3599186
UN	969	.	NC_007779	3599298	3599491
UN	970	.	NC_007779	3599687	3600847
UN	971	.	NC_007779	3601043	3601421
UN	972	.	NC_007779	3689826	3689895
UN	973	.	NC_007779	3690160	3690355
UN	974	.	NC_007779	3690552	3690668
UN	975	.	NC_007779	3690872	3691015
UN	976	.	NC_007779	3691208	3692523
UN	977	.	NC_007779	3692789	3693186
UN	978	.	NC_007779	3693384	3694550
UN	979	.	NC_007779	3694746	3694931
UN	980	.	NC_007779	3742936	3744271
UN	981	.	NC_007779	3746911	3748109
UN	982	.	NC_007779	3750591	3751789
UN	983	.	NC_007779	3874863	3874904
UN	984	.	NC_007779	3875223	3876242
UN	985	.	NC_007779	3876439	3878053
UN	986	.	NC_007779	3958123	3958156
UN	987	.	NC_007779	3973174	3973377
UN	988	.	NC_007779	3973628	3973917
UN	989	.	NC_007779	3974108	3974116
UN	990	.	NC_007779	3987277	3988288
UN	991	.	NC_007779	4015543	4015587
UN	992	.	NC_007779	4017854	4017897
UN	993	.	NC_007779	4018214	4019232
UN	994	.	NC_007779	4019430	4021044
UN	995	.	NC_007779	4056314	4056890
UN	996	.	NC_007779	4169476	4169587
UN	997	.	NC_007779	4169782	4170155
UN	998	.	NC_007779	4211518	4211762
UN	999	.	NC_007779	4211960	4213506
UN	1000	.	NC_007779	4213667	4215789
UN	1001	.	NC_007779	4215988	4216660
UN	1002	.	NC_007779	4299521	4299550
UN	1003	.	NC_007779	4299747	4299777
UN	1004	.	NC_007779	4310363	4311561
UN	1005	.	NC_007779	4502953	4504095
UN	1006	.	NC_007779	4512231	4513265