#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	07:27:53 04 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	4_D16_CTTGTA_L003_R1_001.fastq
SNP	1	100	NC_007779	66457	A	frequency=1
SNP	2	106	NC_007779	97880	T	frequency=1
SNP	3	114	NC_007779	167632	A	frequency=1
SNP	4	205	NC_007779	274547	G	frequency=1
DEL	5	1017,1033	NC_007779	274733	97240	frequency=1
SNP	6	250	NC_007779	547694	G	frequency=1
INS	7	251	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	253	NC_007779	556858	T	frequency=1
SNP	9	254	NC_007779	569996	C	frequency=1
DEL	10	1018,1039	NC_007779	654214	1199	frequency=1
SNP	11	279	NC_007779	707080	T	frequency=6.917858e-02
SNP	12	282	NC_007779	749354	A	frequency=1
SNP	13	284	NC_007779	758440	A	frequency=1
SNP	14	299	NC_007779	887234	A	frequency=1
SNP	15	312	NC_007779	987574	T	frequency=1
SNP	16	333	NC_007779	1093686	C	frequency=1
SNP	17	348	NC_007779	1170573	T	frequency=1
SNP	18	351	NC_007779	1197797	T	frequency=8.315706e-02
SNP	19	352	NC_007779	1197809	T	frequency=7.777882e-02
SNP	20	353	NC_007779	1197822	C	frequency=5.293655e-02
SNP	21	354	NC_007779	1197824	G	frequency=5.312443e-02
SNP	22	358	NC_007779	1213001	C	frequency=2.654648e-02
SNP	23	359	NC_007779	1213013	C	frequency=2.292061e-02
SNP	24	360	NC_007779	1213026	T	frequency=2.062607e-02
SNP	25	361	NC_007779	1213028	A	frequency=2.103806e-02
DEL	26	1020,1044	NC_007779	1301041	1336	frequency=1
SNP	27	371	NC_007779	1318876	A	frequency=1
DEL	28	1021,1047	NC_007779	1413639	23060	frequency=1
SNP	29	401	NC_007779	1483588	A	frequency=1
DEL	30	404	NC_007779	1496775	1	frequency=1
SNP	31	416	NC_007779	1615814	A	frequency=1
DEL	32	426	NC_007779	1669599	1	frequency=1
SNP	33	443	NC_007779	1740536	T	frequency=4.040718e-02
SNP	34	451	NC_007779	1844073	A	frequency=1
SNP	35	464	NC_007779	1918872	A	frequency=1
SNP	36	469	NC_007779	1973476	A	frequency=1
SNP	37	473	NC_007779	2005401	T	frequency=1
SNP	38	482	NC_007779	2170094	A	frequency=1
SNP	39	484	NC_007779	2178210	C	frequency=1.203060e-02
SNP	40	492	NC_007779	2262756	C	frequency=2.408123e-02
DEL	41	1023,1055	NC_007779	2320795	1336	frequency=1
SNP	42	501	NC_007779	2406075	T	frequency=1
SNP	43	505	NC_007779	2416102	A	frequency=1
SNP	44	521	NC_007779	2538628	T	frequency=1
SNP	45	559	NC_007779	2865228	G	frequency=2.429676e-02
INS	46	1064	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=6.641583e-01
INS	47	1065	NC_007779	2865278	TTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGC	frequency=4.777070e-01
SNP	48	560	NC_007779	2866111	G	frequency=1
DEL	49	1066	NC_007779	2941415	8	frequency=1.136388e-01
SNP	50	580	NC_007779	3003330	A	frequency=1
SNP	51	587	NC_007779	3049815	T	frequency=1
DEL	52	592	NC_007779	3124070	1	frequency=1.722813e-02
DEL	53	593	NC_007779	3124071	1	frequency=1.740932e-02
DEL	54	1068	NC_007779	3175000	3	frequency=1.175830e-01
SNP	55	629	NC_007779	3397813	G	frequency=1
SNP	56	643	NC_007779	3441358	G	frequency=1.344967e-02
SNP	57	648	NC_007779	3441388	C	frequency=1.943588e-02
SNP	58	649	NC_007779	3441391	G	frequency=1.906204e-02
SNP	59	650	NC_007779	3441401	A	frequency=1.937389e-02
SNP	60	651	NC_007779	3441402	A	frequency=1.859951e-02
SNP	61	652	NC_007779	3441403	G	frequency=1.848888e-02
SNP	62	653	NC_007779	3441404	G	frequency=1.890182e-02
SNP	63	654	NC_007779	3441406	C	frequency=1.894951e-02
SNP	64	659	NC_007779	3450031	T	frequency=2.476501e-02
SNP	65	660	NC_007779	3451585	G	frequency=1.170254e-02
SNP	66	663	NC_007779	3451602	G	frequency=1.119041e-02
SNP	67	665	NC_007779	3451615	C	frequency=1.104164e-02
SNP	68	674	NC_007779	3452916	T	frequency=2.062893e-02
DEL	69	1026,1075	NC_007779	3742936	1336	frequency=1
DEL	70	736	NC_007779	3750122	1	frequency=9.698629e-01
SNP	71	737	NC_007779	3750123	T	frequency=2.999878e-02
DEL	72	1027,1080	NC_007779	3750591	1199	frequency=1
SNP	73	765	NC_007779	3898657	G	frequency=1
DEL	74	1028,1082	NC_007779	3958123	34	frequency=1
DEL	75	1085	NC_007779	4080561	64	frequency=1.873699e-02
SNP	76	795	NC_007779	4090749	T	frequency=1
SNP	77	804	NC_007779	4153710	C	frequency=5.443907e-02
SNP	78	808	NC_007779	4165991	C	frequency=1
DEL	79	1029,1086	NC_007779	4310363	1199	frequency=1
DEL	80	983,984	NC_007779	4371271	2	frequency=1
SNP	81	996	NC_007779	4546535	A	frequency=1
RA	82	.	NC_007779	301	1	.	T	bias_e_value=2775090	bias_p_value=0.597265	fisher_strand_p_value=0.510289	frequency=7.601738e-03	genotype_quality=1256.5	ks_quality_p_value=0.490897	log10_base_likelihood=-6.59801	log10_qual_likelihood_position_model=3.09007	log10_strand_likelihood_position_model=0.477437	new_cov=0/2	polymorphism_quality=1.1	quality=1.1	quality_position_model=8.12817e-05	ref_cov=111/150	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/152
RA	83	.	NC_007779	5595	0	G	T	bias_e_value=2.39327	bias_p_value=5.15089e-07	fisher_strand_p_value=2.8008e-08	frequency=4.207802e-02	genotype_quality=1127.2	ks_quality_p_value=1	log10_base_likelihood=-9.07149	log10_qual_likelihood_position_model=21.238	log10_strand_likelihood_position_model=7.75874	new_cov=0/29	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=159/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/202
RA	84	.	NC_007779	11143	0	G	T	bias_e_value=3.65053e-07	bias_p_value=7.8568e-14	fisher_strand_p_value=2.26276e-15	frequency=7.445621e-02	genotype_quality=1124.4	ks_quality_p_value=1	log10_base_likelihood=-19.4467	log10_qual_likelihood_position_model=25.2693	log10_strand_likelihood_position_model=14.6454	new_cov=0/41	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=188/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=188/169
RA	85	.	NC_007779	13293	0	T	G	bias_e_value=3280390	bias_p_value=0.706017	fisher_strand_p_value=0.619742	frequency=8.324623e-03	genotype_quality=1381.7	ks_quality_p_value=0.547451	log10_base_likelihood=-5.73793	log10_qual_likelihood_position_model=3.59127	log10_strand_likelihood_position_model=0.429737	new_cov=2/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.00214425	ref_cov=174/179	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=176/180
RA	86	.	NC_007779	13317	0	C	G	bias_e_value=3353540	bias_p_value=0.72176	fisher_strand_p_value=0.35414	frequency=9.037971e-03	genotype_quality=1460.7	ks_quality_p_value=1	log10_base_likelihood=-6.13565	log10_qual_likelihood_position_model=4.19386	log10_strand_likelihood_position_model=0.638105	new_cov=3/1	polymorphism_quality=0.6	quality=0.6	quality_position_model=0.00624461	ref_cov=167/183	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=170/184
RA	87	.	NC_007779	13320	0	A	C	bias_e_value=3962910	bias_p_value=0.852912	fisher_strand_p_value=0.604281	frequency=8.661270e-03	genotype_quality=1348.5	ks_quality_p_value=0.842767	log10_base_likelihood=-6.00855	log10_qual_likelihood_position_model=3.5833	log10_strand_likelihood_position_model=0.450776	new_cov=2/1	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.00111592	ref_cov=161/181	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=163/183
RA	88	.	NC_007779	13338	0	G	C	bias_e_value=4139800	bias_p_value=0.890982	fisher_strand_p_value=0.609618	frequency=9.683609e-03	genotype_quality=1287.1	ks_quality_p_value=0.936689	log10_base_likelihood=-6.26878	log10_qual_likelihood_position_model=1.93383	log10_strand_likelihood_position_model=0.44259	new_cov=2/1	polymorphism_quality=0.7	quality=0.7	quality_position_model=9.97962e-06	ref_cov=146/159	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=148/162
RA	89	.	NC_007779	15382	0	A	G	bias_e_value=0.000664297	bias_p_value=1.42972e-10	fisher_strand_p_value=5.30258e-12	frequency=6.397867e-02	genotype_quality=784.2	ks_quality_p_value=1	log10_base_likelihood=-10.9993	log10_qual_likelihood_position_model=18.9576	log10_strand_likelihood_position_model=11.2755	new_cov=23/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=72/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/175
RA	90	.	NC_007779	17050	0	A	C	bias_e_value=7.48791e-11	bias_p_value=1.61158e-17	fisher_strand_p_value=3.71005e-19	frequency=1.233516e-01	genotype_quality=600.6	ks_quality_p_value=1	log10_base_likelihood=-14.2394	log10_qual_likelihood_position_model=29.8076	log10_strand_likelihood_position_model=18.4306	new_cov=0/41	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=119/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/87
RA	91	.	NC_007779	29486	0	C	A	bias_e_value=203.783	bias_p_value=4.38588e-05	fisher_strand_p_value=3.21354e-06	frequency=4.195118e-02	genotype_quality=1083.9	ks_quality_p_value=1	log10_base_likelihood=-8.51216	log10_qual_likelihood_position_model=16.1659	log10_strand_likelihood_position_model=5.50672	new_cov=1/14	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=182/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=183/102
RA	92	.	NC_007779	29496	0	T	A	bias_e_value=9.36606	bias_p_value=2.0158e-06	fisher_strand_p_value=1.18965e-07	frequency=4.839277e-02	genotype_quality=897.1	ks_quality_p_value=1	log10_base_likelihood=-9.84428	log10_qual_likelihood_position_model=26.8569	log10_strand_likelihood_position_model=6.92458	new_cov=0/17	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=177/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=177/122
RA	93	.	NC_007779	34111	1	.	T	bias_e_value=710190	bias_p_value=0.15285	fisher_strand_p_value=0.151289	frequency=1.159382e-02	genotype_quality=1657.7	ks_quality_p_value=0.232362	log10_base_likelihood=-16.9757	log10_qual_likelihood_position_model=2.742	log10_strand_likelihood_position_model=0.90095	new_cov=4/0	polymorphism_quality=11.7	quality=11.7	quality_position_model=2.02341e-15	ref_cov=202/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=206/139
RA	94	.	NC_007779	34112	0	T	.	bias_e_value=172284	bias_p_value=0.0370795	fisher_strand_p_value=0.650935	frequency=1.141834e-02	genotype_quality=1346.0	ks_quality_p_value=0.00933281	log10_base_likelihood=-10.4181	log10_qual_likelihood_position_model=3.08446	log10_strand_likelihood_position_model=0.463343	new_cov=3/1	polymorphism_quality=5.0	quality=5.0	quality_position_model=8.06366e-09	ref_cov=206/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=209/141
RA	95	.	NC_007779	39910	0	G	T	bias_e_value=134817	bias_p_value=0.0290158	fisher_strand_p_value=0.00453944	frequency=3.247261e-02	genotype_quality=780.0	ks_quality_p_value=0.999441	log10_base_likelihood=-7.27291	log10_qual_likelihood_position_model=12.8018	log10_strand_likelihood_position_model=2.51591	new_cov=0/18	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=70/175	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=70/193
RA	96	.	NC_007779	47305	0	G	T	bias_e_value=1.84772e-10	bias_p_value=3.97673e-17	fisher_strand_p_value=9.35408e-19	frequency=8.041525e-02	genotype_quality=1197.2	ks_quality_p_value=1	log10_base_likelihood=-20.0506	log10_qual_likelihood_position_model=31.0069	log10_strand_likelihood_position_model=18.029	new_cov=0/46	polymorphism_quality=14.8	quality=14.8	quality_position_model=Inf	ref_cov=212/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=212/168
RA	97	.	NC_007779	48338	0	T	G	bias_e_value=292.394	bias_p_value=6.293e-05	fisher_strand_p_value=4.74654e-06	frequency=2.844810e-02	genotype_quality=575.6	ks_quality_p_value=1	log10_base_likelihood=-6.60375	log10_qual_likelihood_position_model=6.94385	log10_strand_likelihood_position_model=5.32362	new_cov=5/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=10/137	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=15/137
RA	98	.	NC_007779	57100	1	.	T	bias_e_value=4545620	bias_p_value=0.978325	fisher_strand_p_value=1	frequency=7.041931e-03	genotype_quality=1382.3	ks_quality_p_value=0.799153	log10_base_likelihood=-7.86967	log10_qual_likelihood_position_model=1.70207	log10_strand_likelihood_position_model=0.300274	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=8.74489e-08	ref_cov=147/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/136
RA	99	.	NC_007779	63418	1	.	T	bias_e_value=4497640	bias_p_value=0.967998	fisher_strand_p_value=1	frequency=8.522034e-03	genotype_quality=1712.0	ks_quality_p_value=0.75792	log10_base_likelihood=-11.6785	log10_qual_likelihood_position_model=2.90614	log10_strand_likelihood_position_model=0.404091	new_cov=1/2	polymorphism_quality=6.3	quality=6.3	quality_position_model=2.33289e-10	ref_cov=166/183	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=167/185
RA	100	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1279.1	new_cov=184/142	quality=1279.1	ref_cov=0/1	tot_cov=184/143
RA	101	.	NC_007779	70602	0	G	T	bias_e_value=5.72684e-07	bias_p_value=1.23255e-13	fisher_strand_p_value=3.5978e-15	frequency=6.478024e-02	genotype_quality=1012.2	ks_quality_p_value=1	log10_base_likelihood=-10.3902	log10_qual_likelihood_position_model=31.3549	log10_strand_likelihood_position_model=14.444	new_cov=0/39	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=170/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/147
RA	102	.	NC_007779	72039	0	T	G	bias_e_value=0.00676771	bias_p_value=1.45657e-09	fisher_strand_p_value=5.93361e-11	frequency=6.227446e-02	genotype_quality=743.0	ks_quality_p_value=1	log10_base_likelihood=-9.58654	log10_qual_likelihood_position_model=23.6748	log10_strand_likelihood_position_model=10.2267	new_cov=22/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=64/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/144
RA	103	.	NC_007779	75070	1	.	G	bias_e_value=1519480	bias_p_value=0.327027	fisher_strand_p_value=0.151044	frequency=5.813599e-03	genotype_quality=1686.0	ks_quality_p_value=0.652795	log10_base_likelihood=-7.30731	log10_qual_likelihood_position_model=2.39061	log10_strand_likelihood_position_model=0.820896	new_cov=2/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=6.10336e-06	ref_cov=132/210	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/210
RA	104	.	NC_007779	75074	0	T	G	bias_e_value=4.41834e-29	bias_p_value=9.5093e-36	fisher_strand_p_value=1.1045e-37	frequency=1.246405e-01	genotype_quality=948.8	ks_quality_p_value=1	log10_base_likelihood=-22.3048	log10_qual_likelihood_position_model=52.689	log10_strand_likelihood_position_model=36.9568	new_cov=55/0	polymorphism_quality=17.0	quality=17.0	quality_position_model=Inf	ref_cov=32/212	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=87/213
RA	105	.	NC_007779	84005	1	.	T	bias_e_value=1828740	bias_p_value=0.393588	fisher_strand_p_value=0.157275	frequency=1.094723e-02	genotype_quality=1337.8	ks_quality_p_value=0.821471	log10_base_likelihood=-11.2644	log10_qual_likelihood_position_model=2.90708	log10_strand_likelihood_position_model=0.848249	new_cov=2/1	polymorphism_quality=5.9	quality=5.9	quality_position_model=1.77615e-09	ref_cov=67/204	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=69/205
RA	106	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=1203.3	new_cov=152/151	quality=1203.3	ref_cov=0/0	tot_cov=152/151
RA	107	.	NC_007779	119384	0	T	G	bias_e_value=8.95002e-14	bias_p_value=1.92625e-20	fisher_strand_p_value=3.82843e-22	frequency=1.242237e-01	genotype_quality=818.1	ks_quality_p_value=1	log10_base_likelihood=-22.343	log10_qual_likelihood_position_model=39.3617	log10_strand_likelihood_position_model=21.417	new_cov=54/0	polymorphism_quality=17.1	quality=17.1	quality_position_model=Inf	ref_cov=78/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/156
RA	108	.	NC_007779	123396	1	.	C	bias_e_value=2375120	bias_p_value=0.511181	fisher_strand_p_value=0.19536	frequency=5.865097e-03	genotype_quality=1690.8	ks_quality_p_value=0.99005	log10_base_likelihood=-7.32358	log10_qual_likelihood_position_model=2.91811	log10_strand_likelihood_position_model=0.709165	new_cov=0/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=1.6046e-05	ref_cov=190/149	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=190/151
RA	109	.	NC_007779	136449	1	.	T	bias_e_value=2768510	bias_p_value=0.595848	fisher_strand_p_value=0.629921	frequency=1.269817e-02	genotype_quality=1517.4	ks_quality_p_value=0.396044	log10_base_likelihood=-17.0586	log10_qual_likelihood_position_model=3.06692	log10_strand_likelihood_position_model=0.52402	new_cov=3/1	polymorphism_quality=11.7	quality=11.7	quality_position_model=1.47591e-15	ref_cov=170/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=173/142
RA	110	.	NC_007779	150535	0	G	A	bias_e_value=7339.6	bias_p_value=0.00157966	fisher_strand_p_value=0.000162428	frequency=3.294563e-02	genotype_quality=1155.8	ks_quality_p_value=1	log10_base_likelihood=-11.3363	log10_qual_likelihood_position_model=14.2886	log10_strand_likelihood_position_model=3.78934	new_cov=12/0	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=132/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/148
RA	111	.	NC_007779	161004	0	A	T	bias_e_value=2248880	bias_p_value=0.484012	fisher_strand_p_value=0.24758	frequency=1.016426e-02	genotype_quality=1132.8	ks_quality_p_value=0.716129	log10_base_likelihood=-5.87356	log10_qual_likelihood_position_model=2.30648	log10_strand_likelihood_position_model=0.889832	new_cov=0/3	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.000193707	ref_cov=145/146	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=145/149
RA	112	.	NC_007779	164569	0	C	G	bias_e_value=3.86389	bias_p_value=8.316e-07	fisher_strand_p_value=4.65002e-08	frequency=4.571724e-02	genotype_quality=559.8	ks_quality_p_value=1	log10_base_likelihood=-8.08354	log10_qual_likelihood_position_model=11.1561	log10_strand_likelihood_position_model=7.33255	new_cov=0/8	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=133/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/22
RA	113	.	NC_007779	164597	1	.	C	bias_e_value=561332	bias_p_value=0.120812	fisher_strand_p_value=0.027559	frequency=1.554394e-02	genotype_quality=848.7	ks_quality_p_value=0.942643	log10_base_likelihood=-12.4235	log10_qual_likelihood_position_model=4.33935	log10_strand_likelihood_position_model=1.55974	new_cov=3/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=1.83232e-08	ref_cov=56/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=59/134
RA	114	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=1212.7	new_cov=139/170	quality=1212.7	ref_cov=0/0	tot_cov=139/170
RA	115	.	NC_007779	175694	0	T	G	bias_e_value=3.15643e-12	bias_p_value=6.79339e-19	fisher_strand_p_value=1.45542e-20	frequency=8.205366e-02	genotype_quality=887.9	ks_quality_p_value=1	log10_base_likelihood=-14.4961	log10_qual_likelihood_position_model=37.8165	log10_strand_likelihood_position_model=19.837	new_cov=51/0	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=94/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/172
RA	116	.	NC_007779	179256	1	.	A	bias_e_value=4520230	bias_p_value=0.972859	fisher_strand_p_value=1	frequency=6.514549e-03	genotype_quality=1505.9	ks_quality_p_value=0.776249	log10_base_likelihood=-8.02476	log10_qual_likelihood_position_model=1.19427	log10_strand_likelihood_position_model=0.300947	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.81017e-08	ref_cov=161/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/145
RA	117	.	NC_007779	184944	0	A	.	bias_e_value=4603290	bias_p_value=0.990736	fisher_strand_p_value=1	frequency=8.709908e-03	genotype_quality=1353.8	ks_quality_p_value=0.867007	log10_base_likelihood=-7.48888	log10_qual_likelihood_position_model=2.83895	log10_strand_likelihood_position_model=0.390474	new_cov=2/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=4.11262e-06	ref_cov=185/155	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=187/157
RA	118	.	NC_007779	207536	0	G	T	bias_e_value=9.60671e-10	bias_p_value=2.06759e-16	fisher_strand_p_value=5.06461e-18	frequency=1.310320e-01	genotype_quality=857.6	ks_quality_p_value=1	log10_base_likelihood=-36.8081	log10_qual_likelihood_position_model=31.1587	log10_strand_likelihood_position_model=17.4598	new_cov=0/54	polymorphism_quality=31.7	quality=31.7	quality_position_model=Inf	ref_cov=155/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/169
RA	119	.	NC_007779	212548	0	T	G	bias_e_value=9.83277	bias_p_value=2.11624e-06	fisher_strand_p_value=1.25275e-07	frequency=3.969669e-02	genotype_quality=875.0	ks_quality_p_value=1	log10_base_likelihood=-6.19157	log10_qual_likelihood_position_model=23.8165	log10_strand_likelihood_position_model=6.90213	new_cov=20/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=110/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=130/146
RA	120	.	NC_007779	223884	0	T	G	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	121	.	NC_007779	224686	0	T	G	bias_e_value=687651	bias_p_value=0.147999	fisher_strand_p_value=0.27792	frequency=9.757423e-02	genotype_quality=128.9	ks_quality_p_value=0.121308	log10_base_likelihood=-13.8466	log10_qual_likelihood_position_model=1.88491	log10_strand_likelihood_position_model=0.83084	new_cov=4/0	polymorphism_quality=8.5	quality=8.5	quality_position_model=3.51471e-13	ref_cov=22/15	reject=POLYMORPHISM_STRAND	tot_cov=26/15
RA	122	.	NC_007779	224713	0	T	C	bias_e_value=357666	bias_p_value=0.0769781	fisher_strand_p_value=0.138609	frequency=3.043365e-02	genotype_quality=455.4	ks_quality_p_value=0.106474	log10_base_likelihood=-9.51592	log10_qual_likelihood_position_model=3.15004	log10_strand_likelihood_position_model=0.960585	new_cov=4/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=2.63286e-07	ref_cov=72/55	reject=POLYMORPHISM_STRAND	tot_cov=77/55
RA	123	.	NC_007779	224725	0	T	A	bias_e_value=1799900	bias_p_value=0.38738	fisher_strand_p_value=0.137366	frequency=2.385616e-02	genotype_quality=612.3	ks_quality_p_value=0.918573	log10_base_likelihood=-8.02893	log10_qual_likelihood_position_model=3.08713	log10_strand_likelihood_position_model=0.973547	new_cov=4/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=8.30596e-06	ref_cov=92/71	reject=POLYMORPHISM_STRAND	tot_cov=96/71
RA	124	.	NC_007779	224759	0	T	G	bias_e_value=1766780	bias_p_value=0.380253	fisher_strand_p_value=0.134428	frequency=1.360226e-02	genotype_quality=1086.2	ks_quality_p_value=0.913208	log10_base_likelihood=-8.51487	log10_qual_likelihood_position_model=4.04249	log10_strand_likelihood_position_model=1.00451	new_cov=4/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.79474e-05	ref_cov=161/128	reject=POLYMORPHISM_STRAND	tot_cov=165/128
RA	125	.	NC_007779	224768	0	C	A	bias_e_value=1764980	bias_p_value=0.379864	fisher_strand_p_value=0.134514	frequency=1.188183e-02	genotype_quality=1394.7	ks_quality_p_value=0.911245	log10_base_likelihood=-8.8204	log10_qual_likelihood_position_model=2.46581	log10_strand_likelihood_position_model=1.0056	new_cov=4/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=3.01201e-07	ref_cov=185/147	reject=POLYMORPHISM_STRAND	tot_cov=189/147
RA	126	.	NC_007779	224769	0	C	T	bias_e_value=1846930	bias_p_value=0.397503	fisher_strand_p_value=0.135805	frequency=1.178455e-02	genotype_quality=1395.9	ks_quality_p_value=0.96548	log10_base_likelihood=-5.63386	log10_qual_likelihood_position_model=3.84066	log10_strand_likelihood_position_model=0.995183	new_cov=4/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=0.0246756	ref_cov=185/145	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=189/145
RA	127	.	NC_007779	224902	1	.	A	bias_e_value=912683	bias_p_value=0.196431	fisher_strand_p_value=0.503517	frequency=7.721901e-03	genotype_quality=940.5	ks_quality_p_value=0.0970852	log10_base_likelihood=-7.94688	log10_qual_likelihood_position_model=1.65701	log10_strand_likelihood_position_model=0.517295	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.09601e-07	ref_cov=141/116	reject=POLYMORPHISM_STRAND	tot_cov=143/116
RA	128	.	NC_007779	224910	0	C	G	bias_e_value=623293	bias_p_value=0.134147	fisher_strand_p_value=0.507454	frequency=8.942604e-03	genotype_quality=762.6	ks_quality_p_value=0.0585298	log10_base_likelihood=-5.58304	log10_qual_likelihood_position_model=1.59429	log10_strand_likelihood_position_model=0.490484	new_cov=2/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=2.59558e-05	ref_cov=125/96	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=128/96
RA	129	.	NC_007779	227991	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	130	.	NC_007779	227992	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	131	.	NC_007779	227993	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	132	.	NC_007779	227994	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	133	.	NC_007779	227995	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	134	.	NC_007779	227996	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	135	.	NC_007779	227997	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	136	.	NC_007779	227998	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	137	.	NC_007779	228000	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	138	.	NC_007779	228001	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	139	.	NC_007779	228002	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	140	.	NC_007779	228003	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	141	.	NC_007779	228004	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=2/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	142	.	NC_007779	228006	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	143	.	NC_007779	228007	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	144	.	NC_007779	228008	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	145	.	NC_007779	228009	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	146	.	NC_007779	228010	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	147	.	NC_007779	228011	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	148	.	NC_007779	228012	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	149	.	NC_007779	228013	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	150	.	NC_007779	228014	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	151	.	NC_007779	228015	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	152	.	NC_007779	228016	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	153	.	NC_007779	228017	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	154	.	NC_007779	228018	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	155	.	NC_007779	228019	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	156	.	NC_007779	228020	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	157	.	NC_007779	228021	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	158	.	NC_007779	228022	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	159	.	NC_007779	228023	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	160	.	NC_007779	228027	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	161	.	NC_007779	228029	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	162	.	NC_007779	228030	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	163	.	NC_007779	228033	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	164	.	NC_007779	228034	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	165	.	NC_007779	228035	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	166	.	NC_007779	228037	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	167	.	NC_007779	228038	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	168	.	NC_007779	228040	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	169	.	NC_007779	228041	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	170	.	NC_007779	228043	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	171	.	NC_007779	228044	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=2/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	172	.	NC_007779	228047	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	173	.	NC_007779	228048	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	174	.	NC_007779	228049	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	175	.	NC_007779	228050	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	176	.	NC_007779	228051	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	177	.	NC_007779	228052	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	178	.	NC_007779	228053	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	179	.	NC_007779	228054	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	180	.	NC_007779	228057	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	181	.	NC_007779	228058	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	182	.	NC_007779	228059	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	183	.	NC_007779	228060	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	184	.	NC_007779	228061	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	185	.	NC_007779	228062	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	186	.	NC_007779	228063	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	187	.	NC_007779	228064	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	188	.	NC_007779	228065	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	189	.	NC_007779	228066	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	190	.	NC_007779	228068	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=2/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	191	.	NC_007779	228070	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	192	.	NC_007779	228071	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	193	.	NC_007779	228073	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	194	.	NC_007779	228074	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	195	.	NC_007779	228076	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	196	.	NC_007779	228077	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	197	.	NC_007779	228078	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	198	.	NC_007779	228079	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	199	.	NC_007779	228081	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	200	.	NC_007779	228082	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	201	.	NC_007779	228083	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=2/0	reject=EVALUE	tot_cov=2/0
RA	202	.	NC_007779	228084	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	203	.	NC_007779	232552	0	A	.	bias_e_value=4084330	bias_p_value=0.879043	fisher_strand_p_value=0.580098	frequency=9.307861e-03	genotype_quality=1274.5	ks_quality_p_value=0.948787	log10_base_likelihood=-7.76739	log10_qual_likelihood_position_model=2.80005	log10_strand_likelihood_position_model=0.497045	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.47536e-06	ref_cov=182/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=183/139
RA	204	.	NC_007779	233118	0	T	C	bias_e_value=0.0897695	bias_p_value=1.93205e-08	fisher_strand_p_value=8.84391e-10	frequency=5.811930e-02	genotype_quality=653.7	ks_quality_p_value=1	log10_base_likelihood=-11.1856	log10_qual_likelihood_position_model=16.7072	log10_strand_likelihood_position_model=9.05336	new_cov=0/13	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=150/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/44
RA	205	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1395.5	new_cov=171/159	quality=1395.5	ref_cov=1/0	tot_cov=172/159
RA	206	.	NC_007779	279157	0	G	T	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	207	.	NC_007779	329646	0	G	A	deleted=1	frequency=1	genotype_quality=3.6	new_cov=1/0	quality=3.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	208	.	NC_007779	329647	0	C	A	deleted=1	frequency=1	genotype_quality=3.8	new_cov=1/0	quality=3.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	209	.	NC_007779	329654	0	T	A	deleted=1	frequency=1	genotype_quality=3.3	new_cov=1/0	quality=3.3	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	210	.	NC_007779	329661	0	A	C	deleted=1	frequency=1	genotype_quality=7.9	new_cov=1/1	quality=7.9	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	211	.	NC_007779	329668	0	G	A	deleted=1	frequency=1	genotype_quality=6.7	new_cov=1/1	quality=6.7	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	212	.	NC_007779	329670	0	G	T	deleted=1	frequency=1	genotype_quality=7.0	new_cov=1/1	quality=7.0	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	213	.	NC_007779	329671	0	G	T	deleted=1	frequency=1	genotype_quality=7.6	new_cov=1/1	quality=7.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	214	.	NC_007779	329673	0	A	C	deleted=1	frequency=1	genotype_quality=8.1	new_cov=1/1	quality=8.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	215	.	NC_007779	329691	0	C	T	deleted=1	frequency=1	genotype_quality=7.8	new_cov=1/1	quality=7.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	216	.	NC_007779	329692	0	T	A	deleted=1	frequency=1	genotype_quality=7.8	new_cov=1/1	quality=7.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	217	.	NC_007779	329698	0	C	A	deleted=1	frequency=1	genotype_quality=7.8	new_cov=1/1	quality=7.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	218	.	NC_007779	329700	0	G	C	deleted=1	frequency=1	genotype_quality=7.9	new_cov=1/1	quality=7.9	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	219	.	NC_007779	329703	0	G	A	deleted=1	frequency=1	genotype_quality=6.5	new_cov=1/1	quality=6.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	220	.	NC_007779	329709	0	C	T	deleted=1	frequency=1	genotype_quality=7.8	new_cov=1/1	quality=7.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	221	.	NC_007779	329712	0	G	T	deleted=1	frequency=1	genotype_quality=7.5	new_cov=1/1	quality=7.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	222	.	NC_007779	329715	0	T	C	deleted=1	frequency=1	genotype_quality=8.2	new_cov=1/1	quality=8.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	223	.	NC_007779	329718	0	G	C	deleted=1	frequency=1	genotype_quality=7.5	new_cov=1/1	quality=7.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	224	.	NC_007779	329724	0	C	T	deleted=1	frequency=1	genotype_quality=7.5	new_cov=1/1	quality=7.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	225	.	NC_007779	329727	0	T	C	deleted=1	frequency=1	genotype_quality=8.8	new_cov=1/1	quality=8.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	226	.	NC_007779	329730	0	C	T	deleted=1	frequency=1	genotype_quality=7.5	new_cov=1/1	quality=7.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	227	.	NC_007779	329731	0	C	G	deleted=1	frequency=1	genotype_quality=8.1	new_cov=1/1	quality=8.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	228	.	NC_007779	365514	0	C	T	deleted=1	frequency=1	genotype_quality=11.7	new_cov=2/1	quality=11.7	ref_cov=0/0	tot_cov=2/1
RA	229	.	NC_007779	365524	0	G	.	deleted=1	frequency=1	genotype_quality=9.4	new_cov=2/0	quality=9.4	ref_cov=0/0	reject=EVALUE	tot_cov=2/0
RA	230	.	NC_007779	374799	0	T	G	bias_e_value=3.84772e-12	bias_p_value=8.2812e-19	fisher_strand_p_value=1.7819e-20	frequency=6.994152e-02	genotype_quality=776.0	ks_quality_p_value=1	log10_base_likelihood=-8.02834	log10_qual_likelihood_position_model=30.8131	log10_strand_likelihood_position_model=19.7491	new_cov=36/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=48/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=84/166
RA	231	.	NC_007779	379236	1	.	G	bias_e_value=841023	bias_p_value=0.181008	fisher_strand_p_value=0.0514139	frequency=3.535271e-02	genotype_quality=898.0	ks_quality_p_value=0.85313	log10_base_likelihood=-31.5201	log10_qual_likelihood_position_model=5.80447	log10_strand_likelihood_position_model=1.36017	new_cov=2/5	polymorphism_quality=26.3	quality=26.3	quality_position_model=1.43074e-26	ref_cov=127/64	reject=INDEL_HOMOPOLYMER	tot_cov=129/69
RA	232	.	NC_007779	379237	0	G	.	bias_e_value=4135230	bias_p_value=0.889998	fisher_strand_p_value=1	frequency=3.110313e-02	genotype_quality=893.6	ks_quality_p_value=0.569273	log10_base_likelihood=-22.1937	log10_qual_likelihood_position_model=3.61954	log10_strand_likelihood_position_model=0.528804	new_cov=4/3	polymorphism_quality=16.9	quality=16.9	quality_position_model=3.38439e-20	ref_cov=130/88	reject=INDEL_HOMOPOLYMER	tot_cov=134/91
RA	233	.	NC_007779	379266	0	G	C	bias_e_value=35.9066	bias_p_value=7.72795e-06	fisher_strand_p_value=6.00805e-07	frequency=5.285931e-02	genotype_quality=722.9	ks_quality_p_value=0.82919	log10_base_likelihood=-9.55428	log10_qual_likelihood_position_model=22.6441	log10_strand_likelihood_position_model=6.22127	new_cov=18/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=91/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/122
RA	234	.	NC_007779	387917	0	T	G	bias_e_value=0.0201686	bias_p_value=4.34076e-09	fisher_strand_p_value=2.2056e-10	frequency=5.635214e-02	genotype_quality=480.2	ks_quality_p_value=0.840754	log10_base_likelihood=-18.4059	log10_qual_likelihood_position_model=9.1882	log10_strand_likelihood_position_model=9.65647	new_cov=0/10	polymorphism_quality=13.1	quality=13.1	quality_position_model=Inf	ref_cov=142/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/23
RA	235	.	NC_007779	387919	0	A	G	bias_e_value=1.49149e-07	bias_p_value=3.21004e-14	fisher_strand_p_value=9.00598e-16	frequency=8.916426e-02	genotype_quality=498.6	ks_quality_p_value=1	log10_base_likelihood=-25.7548	log10_qual_likelihood_position_model=14.9244	log10_strand_likelihood_position_model=15.0455	new_cov=0/15	polymorphism_quality=20.5	quality=20.5	quality_position_model=Inf	ref_cov=139/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/23
RA	236	.	NC_007779	407306	0	C	A	bias_e_value=3.35872	bias_p_value=7.22875e-07	fisher_strand_p_value=4.0088e-08	frequency=5.286503e-02	genotype_quality=816.7	ks_quality_p_value=1	log10_base_likelihood=-8.31772	log10_qual_likelihood_position_model=17.9938	log10_strand_likelihood_position_model=7.40893	new_cov=24/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=99/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/142
RA	237	.	NC_007779	418000	1	.	A	bias_e_value=1227620	bias_p_value=0.264213	fisher_strand_p_value=1	frequency=6.249428e-03	genotype_quality=1581.0	ks_quality_p_value=0.0730574	log10_base_likelihood=-7.98295	log10_qual_likelihood_position_model=1.43122	log10_strand_likelihood_position_model=0.304036	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=3.53656e-08	ref_cov=175/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=176/144
RA	238	.	NC_007779	440767	0	G	T	bias_e_value=0.00235349	bias_p_value=5.06526e-10	fisher_strand_p_value=1.97492e-11	frequency=8.083391e-02	genotype_quality=939.2	ks_quality_p_value=1	log10_base_likelihood=-16.3289	log10_qual_likelihood_position_model=23.666	log10_strand_likelihood_position_model=10.7192	new_cov=2/33	polymorphism_quality=11.0	quality=11.0	quality_position_model=Inf	ref_cov=172/100	reject=FISHER_STRAND_P_VALUE	tot_cov=174/133
RA	239	.	NC_007779	468498	0	T	G	bias_e_value=0.496532	bias_p_value=1.06865e-07	fisher_strand_p_value=5.32996e-09	frequency=3.329086e-02	genotype_quality=968.6	ks_quality_p_value=1	log10_base_likelihood=-5.83427	log10_qual_likelihood_position_model=22.9152	log10_strand_likelihood_position_model=8.27328	new_cov=22/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=110/167	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=132/167
RA	240	.	NC_007779	468787	1	.	A	bias_e_value=2302440	bias_p_value=0.49554	fisher_strand_p_value=0.245869	frequency=6.622314e-03	genotype_quality=1466.6	ks_quality_p_value=0.748511	log10_base_likelihood=-7.70578	log10_qual_likelihood_position_model=2.27733	log10_strand_likelihood_position_model=0.609296	new_cov=0/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.07084e-06	ref_cov=152/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/150
RA	241	.	NC_007779	474686	0	G	T	bias_e_value=0.535814	bias_p_value=1.1532e-07	fisher_strand_p_value=5.77795e-09	frequency=4.624081e-02	genotype_quality=961.3	ks_quality_p_value=0.999439	log10_base_likelihood=-8.24808	log10_qual_likelihood_position_model=23.1589	log10_strand_likelihood_position_model=8.32941	new_cov=0/27	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=158/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/167
RA	242	.	NC_007779	492774	0	C	A	bias_e_value=24057.3	bias_p_value=0.00517769	fisher_strand_p_value=0.00061709	frequency=2.492809e-02	genotype_quality=988.5	ks_quality_p_value=1	log10_base_likelihood=-6.05433	log10_qual_likelihood_position_model=9.72057	log10_strand_likelihood_position_model=3.20965	new_cov=0/7	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=163/83	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/90
RA	243	.	NC_007779	500804	0	A	C	bias_e_value=1.37277e-10	bias_p_value=2.95453e-17	fisher_strand_p_value=6.90029e-19	frequency=4.131508e-02	genotype_quality=924.8	ks_quality_p_value=1	log10_base_likelihood=-6.28465	log10_qual_likelihood_position_model=29.1476	log10_strand_likelihood_position_model=18.1611	new_cov=0/34	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=193/63	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=193/97
RA	244	.	NC_007779	513848	0	A	C	bias_e_value=6.28012e-18	bias_p_value=1.35163e-24	fisher_strand_p_value=2.25062e-26	frequency=1.221647e-01	genotype_quality=723.1	ks_quality_p_value=1	log10_base_likelihood=-23.7311	log10_qual_likelihood_position_model=34.8549	log10_strand_likelihood_position_model=25.6477	new_cov=0/41	polymorphism_quality=18.5	quality=18.5	quality_position_model=Inf	ref_cov=162/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=162/73
RA	245	.	NC_007779	522430	1	.	T	bias_e_value=3015490	bias_p_value=0.649004	fisher_strand_p_value=0.316149	frequency=1.526737e-02	genotype_quality=1266.3	ks_quality_p_value=0.91734	log10_base_likelihood=-16.9813	log10_qual_likelihood_position_model=3.05325	log10_strand_likelihood_position_model=0.74913	new_cov=1/3	polymorphism_quality=11.7	quality=11.7	quality_position_model=2.89974e-15	ref_cov=149/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/112
RA	246	.	NC_007779	522431	0	T	.	bias_e_value=1257140	bias_p_value=0.270566	fisher_strand_p_value=0.0766717	frequency=3.052521e-02	genotype_quality=1025.0	ks_quality_p_value=0.98473	log10_base_likelihood=-24.6836	log10_qual_likelihood_position_model=4.19606	log10_strand_likelihood_position_model=1.26694	new_cov=2/6	polymorphism_quality=19.4	quality=19.4	quality_position_model=2.19202e-21	ref_cov=148/106	reject=INDEL_HOMOPOLYMER	tot_cov=150/112
RA	247	.	NC_007779	524490	0	T	G	bias_e_value=0.00279426	bias_p_value=6.0139e-10	fisher_strand_p_value=2.36124e-11	frequency=4.792547e-02	genotype_quality=1004.8	ks_quality_p_value=1	log10_base_likelihood=-7.03674	log10_qual_likelihood_position_model=27.7226	log10_strand_likelihood_position_model=10.6269	new_cov=21/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=79/198	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/198
RA	248	.	NC_007779	528272	0	T	.	bias_e_value=3331940	bias_p_value=0.717113	fisher_strand_p_value=0.684163	frequency=2.229500e-02	genotype_quality=1053.1	ks_quality_p_value=0.511121	log10_base_likelihood=-17.6161	log10_qual_likelihood_position_model=2.50281	log10_strand_likelihood_position_model=0.615568	new_cov=4/2	polymorphism_quality=12.3	quality=12.3	quality_position_model=1.32879e-16	ref_cov=132/130	reject=INDEL_HOMOPOLYMER	tot_cov=137/132
RA	249	.	NC_007779	535125	0	T	G	bias_e_value=3.22474e-05	bias_p_value=6.9404e-12	fisher_strand_p_value=2.30592e-13	frequency=7.124329e-02	genotype_quality=767.3	ks_quality_p_value=1	log10_base_likelihood=-6.3355	log10_qual_likelihood_position_model=31.539	log10_strand_likelihood_position_model=12.6765	new_cov=43/1	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=98/133	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/134
RA	250	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=1272.2	new_cov=141/170	quality=1272.2	ref_cov=0/0	tot_cov=141/171
RA	251	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=989.6	new_cov=122/116	quality=989.6	ref_cov=1/1	tot_cov=123/117
RA	252	.	NC_007779	556653	0	A	C	bias_e_value=4.47803e-13	bias_p_value=9.63776e-20	fisher_strand_p_value=1.98018e-21	frequency=7.827616e-02	genotype_quality=821.2	ks_quality_p_value=1	log10_base_likelihood=-9.27625	log10_qual_likelihood_position_model=31.3211	log10_strand_likelihood_position_model=20.7033	new_cov=0/35	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=177/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=177/79
RA	253	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=1347.3	new_cov=178/165	quality=1347.3	ref_cov=0/0	tot_cov=178/165
RA	254	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1343.8	new_cov=154/160	quality=1343.8	ref_cov=0/0	tot_cov=154/160
RA	255	.	NC_007779	589157	0	T	G	bias_e_value=6.38427e-10	bias_p_value=1.37404e-16	fisher_strand_p_value=3.33157e-18	frequency=8.303452e-02	genotype_quality=800.8	ks_quality_p_value=1	log10_base_likelihood=-12.8558	log10_qual_likelihood_position_model=41.4756	log10_strand_likelihood_position_model=17.4774	new_cov=39/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=69/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=109/159
RA	256	.	NC_007779	596918	0	G	T	bias_e_value=0.825624	bias_p_value=1.77694e-07	fisher_strand_p_value=1.06093e-08	frequency=4.559994e-02	genotype_quality=1078.8	ks_quality_p_value=0.858281	log10_base_likelihood=-11.6072	log10_qual_likelihood_position_model=23.1714	log10_strand_likelihood_position_model=7.97431	new_cov=0/23	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=172/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/152
RA	257	.	NC_007779	598799	0	T	G	bias_e_value=3.1173e-24	bias_p_value=6.70916e-31	fisher_strand_p_value=8.9705e-33	frequency=1.691132e-01	genotype_quality=706.0	ks_quality_p_value=1	log10_base_likelihood=-34.8095	log10_qual_likelihood_position_model=43.3613	log10_strand_likelihood_position_model=32.0472	new_cov=51/0	polymorphism_quality=29.6	quality=29.6	quality_position_model=Inf	ref_cov=28/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=79/167
RA	258	.	NC_007779	606687	1	.	T	bias_e_value=4645890	bias_p_value=0.999905	fisher_strand_p_value=1	frequency=9.553909e-03	genotype_quality=1523.7	ks_quality_p_value=0.986271	log10_base_likelihood=-12.293	log10_qual_likelihood_position_model=2.9189	log10_strand_likelihood_position_model=0.384784	new_cov=2/1	polymorphism_quality=6.9	quality=6.9	quality_position_model=5.39506e-11	ref_cov=172/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=174/140
RA	259	.	NC_007779	606911	1	.	G	bias_e_value=460752	bias_p_value=0.0991646	fisher_strand_p_value=0.0579999	frequency=1.071453e-02	genotype_quality=1380.4	ks_quality_p_value=0.348908	log10_base_likelihood=-12.6751	log10_qual_likelihood_position_model=1.35619	log10_strand_likelihood_position_model=1.23657	new_cov=3/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=4.12185e-12	ref_cov=106/171	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/171
RA	260	.	NC_007779	606915	0	T	G	bias_e_value=93.0127	bias_p_value=2.00185e-05	fisher_strand_p_value=1.3813e-06	frequency=2.093315e-02	genotype_quality=745.9	ks_quality_p_value=1	log10_base_likelihood=-5.85591	log10_qual_likelihood_position_model=8.55911	log10_strand_likelihood_position_model=5.85971	new_cov=5/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=10/179	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=15/179
RA	261	.	NC_007779	612991	0	C	G	bias_e_value=15.1749	bias_p_value=3.26599e-06	fisher_strand_p_value=1.98852e-07	frequency=3.345680e-02	genotype_quality=773.1	ks_quality_p_value=0.999579	log10_base_likelihood=-8.42701	log10_qual_likelihood_position_model=11.4012	log10_strand_likelihood_position_model=6.70147	new_cov=0/8	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=167/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=167/32
RA	262	.	NC_007779	616029	0	C	A	bias_e_value=40325.6	bias_p_value=0.00867902	fisher_strand_p_value=0.00111603	frequency=3.004932e-02	genotype_quality=850.9	ks_quality_p_value=0.996874	log10_base_likelihood=-6.37842	log10_qual_likelihood_position_model=13.3604	log10_strand_likelihood_position_model=2.97505	new_cov=1/8	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=150/73	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=151/81
RA	263	.	NC_007779	617621	0	G	T	bias_e_value=4038.51	bias_p_value=0.000869182	fisher_strand_p_value=8.36663e-05	frequency=4.276180e-02	genotype_quality=742.7	ks_quality_p_value=1	log10_base_likelihood=-6.65444	log10_qual_likelihood_position_model=10.8245	log10_strand_likelihood_position_model=4.07745	new_cov=10/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=71/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=81/119
RA	264	.	NC_007779	645970	0	T	G	bias_e_value=9.97329e-20	bias_p_value=2.14649e-26	fisher_strand_p_value=3.33998e-28	frequency=1.700363e-01	genotype_quality=694.2	ks_quality_p_value=1	log10_base_likelihood=-44.6357	log10_qual_likelihood_position_model=43.0963	log10_strand_likelihood_position_model=27.4763	new_cov=47/0	polymorphism_quality=39.5	quality=39.5	quality_position_model=Inf	ref_cov=33/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=80/158
RA	265	.	NC_007779	646433	0	A	C	bias_e_value=0.095913	bias_p_value=2.06427e-08	fisher_strand_p_value=9.47926e-10	frequency=2.831650e-02	genotype_quality=906.0	ks_quality_p_value=1	log10_base_likelihood=-6.44935	log10_qual_likelihood_position_model=15.7307	log10_strand_likelihood_position_model=9.02323	new_cov=0/10	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=212/25	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=212/35
RA	266	.	NC_007779	646440	0	C	A	bias_e_value=1.99317	bias_p_value=4.28978e-07	fisher_strand_p_value=2.3321e-08	frequency=3.283596e-02	genotype_quality=958.3	ks_quality_p_value=0.989795	log10_base_likelihood=-12.9539	log10_qual_likelihood_position_model=10.1689	log10_strand_likelihood_position_model=7.63225	new_cov=0/8	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=211/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=211/30
RA	267	.	NC_007779	647588	0	C	A	bias_e_value=30.7689	bias_p_value=6.62218e-06	fisher_strand_p_value=4.22406e-07	frequency=3.499031e-02	genotype_quality=1085.0	ks_quality_p_value=1	log10_base_likelihood=-7.67202	log10_qual_likelihood_position_model=16.9377	log10_strand_likelihood_position_model=6.40629	new_cov=22/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=152/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/157
RA	268	.	NC_007779	657963	1	.	T	bias_e_value=4169470	bias_p_value=0.897368	fisher_strand_p_value=1	frequency=7.041931e-03	genotype_quality=1364.9	ks_quality_p_value=0.582628	log10_base_likelihood=-7.76379	log10_qual_likelihood_position_model=2.04297	log10_strand_likelihood_position_model=0.299692	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.53517e-07	ref_cov=144/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/139
RA	269	.	NC_007779	660356	0	T	G	bias_e_value=1.34552e-10	bias_p_value=2.89588e-17	fisher_strand_p_value=6.76007e-19	frequency=6.247330e-02	genotype_quality=796.4	ks_quality_p_value=1	log10_base_likelihood=-7.54002	log10_qual_likelihood_position_model=29.5334	log10_strand_likelihood_position_model=18.17	new_cov=36/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=58/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/166
RA	270	.	NC_007779	665062	0	C	A	bias_e_value=756.207	bias_p_value=0.000162754	fisher_strand_p_value=1.41275e-05	frequency=4.221916e-02	genotype_quality=956.1	ks_quality_p_value=0.942212	log10_base_likelihood=-8.90688	log10_qual_likelihood_position_model=21.19	log10_strand_likelihood_position_model=4.86627	new_cov=1/14	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=166/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=167/110
RA	271	.	NC_007779	667452	0	G	T	bias_e_value=16124.6	bias_p_value=0.0034704	fisher_strand_p_value=0.0003955	frequency=4.011631e-02	genotype_quality=1112.3	ks_quality_p_value=0.992263	log10_base_likelihood=-17.9976	log10_qual_likelihood_position_model=15.511	log10_strand_likelihood_position_model=3.60421	new_cov=12/0	polymorphism_quality=12.7	quality=12.7	quality_position_model=Inf	ref_cov=133/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/139
RA	272	.	NC_007779	668290	0	G	C	bias_e_value=455007	bias_p_value=0.0979282	fisher_strand_p_value=0.248704	frequency=9.485245e-03	genotype_quality=1323.4	ks_quality_p_value=0.0800961	log10_base_likelihood=-7.21254	log10_qual_likelihood_position_model=1.97744	log10_strand_likelihood_position_model=0.858381	new_cov=3/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=3.10059e-06	ref_cov=161/152	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=164/152
RA	273	.	NC_007779	686495	0	A	C	bias_e_value=2.98304e-22	bias_p_value=6.42021e-29	fisher_strand_p_value=9.14997e-31	frequency=1.307569e-01	genotype_quality=844.7	ks_quality_p_value=1	log10_base_likelihood=-33.1656	log10_qual_likelihood_position_model=41.9798	log10_strand_likelihood_position_model=30.0386	new_cov=0/44	polymorphism_quality=28.0	quality=28.0	quality_position_model=Inf	ref_cov=189/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=189/73
RA	274	.	NC_007779	697558	1	.	T	bias_e_value=3866150	bias_p_value=0.832087	fisher_strand_p_value=0.501044	frequency=7.167816e-03	genotype_quality=1356.9	ks_quality_p_value=0.957405	log10_base_likelihood=-7.68014	log10_qual_likelihood_position_model=2.44249	log10_strand_likelihood_position_model=0.540371	new_cov=0/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.43463e-06	ref_cov=129/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/150
RA	275	.	NC_007779	704668	0	T	G	bias_e_value=1.19235e-09	bias_p_value=2.56622e-16	fisher_strand_p_value=6.32032e-18	frequency=5.570602e-02	genotype_quality=759.1	ks_quality_p_value=1	log10_base_likelihood=-6.13988	log10_qual_likelihood_position_model=26.9805	log10_strand_likelihood_position_model=17.1993	new_cov=27/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=38/171	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=65/172
RA	276	.	NC_007779	706278	1	.	G	bias_e_value=969415	bias_p_value=0.208641	fisher_strand_p_value=0.0591642	frequency=7.193565e-03	genotype_quality=1362.7	ks_quality_p_value=0.895555	log10_base_likelihood=-7.8817	log10_qual_likelihood_position_model=2.1246	log10_strand_likelihood_position_model=1.22794	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.14861e-06	ref_cov=66/210	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=68/210
RA	277	.	NC_007779	706385	1	.	T	bias_e_value=3278310	bias_p_value=0.70557	fisher_strand_p_value=0.685059	frequency=1.550388e-02	genotype_quality=1842.2	ks_quality_p_value=0.494652	log10_base_likelihood=-26.3762	log10_qual_likelihood_position_model=3.1901	log10_strand_likelihood_position_model=0.626709	new_cov=4/2	polymorphism_quality=21.2	quality=21.2	quality_position_model=9.28883e-25	ref_cov=190/191	reject=INDEL_HOMOPOLYMER	tot_cov=194/193
RA	278	.	NC_007779	706386	0	T	.	bias_e_value=4646230	bias_p_value=0.999979	fisher_strand_p_value=1	frequency=1.264286e-02	genotype_quality=1546.9	ks_quality_p_value=0.99353	log10_base_likelihood=-12.9789	log10_qual_likelihood_position_model=3.69614	log10_strand_likelihood_position_model=0.501839	new_cov=2/3	polymorphism_quality=7.6	quality=7.6	quality_position_model=8.81579e-11	ref_cov=195/195	reject=INDEL_HOMOPOLYMER	tot_cov=197/198
RA	279	.	NC_007779	707080	0	C	T	bias_e_value=4548270	bias_p_value=0.978894	fisher_strand_p_value=0.82638	frequency=6.917858e-02	genotype_quality=1152.4	ks_quality_p_value=0.970144	log10_base_likelihood=-51.4897	log10_qual_likelihood_position_model=6.9865	log10_strand_likelihood_position_model=0.783465	new_cov=10/12	polymorphism_quality=46.4	quality=46.4	quality_position_model=4.63339e-46	ref_cov=145/149	tot_cov=156/162
RA	280	.	NC_007779	730404	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	281	.	NC_007779	730413	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	282	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=1122.8	new_cov=119/163	quality=1122.8	ref_cov=0/0	tot_cov=119/163
RA	283	.	NC_007779	752693	0	A	C	bias_e_value=1.92763e-08	bias_p_value=4.14871e-15	fisher_strand_p_value=1.09909e-16	frequency=5.102205e-02	genotype_quality=1007.3	ks_quality_p_value=1	log10_base_likelihood=-5.81281	log10_qual_likelihood_position_model=36.3698	log10_strand_likelihood_position_model=15.959	new_cov=0/32	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=200/77	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=200/110
RA	284	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=1303.7	new_cov=140/188	quality=1303.7	ref_cov=0/0	tot_cov=140/188
RA	285	.	NC_007779	759019	0	C	G	bias_e_value=4.03992e-14	bias_p_value=8.69486e-21	fisher_strand_p_value=1.70068e-22	frequency=9.137535e-02	genotype_quality=738.5	ks_quality_p_value=1	log10_base_likelihood=-32.7838	log10_qual_likelihood_position_model=20.9567	log10_strand_likelihood_position_model=21.7694	new_cov=0/18	polymorphism_quality=27.6	quality=27.6	quality_position_model=Inf	ref_cov=170/3	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=170/21
RA	286	.	NC_007779	780786	0	C	A	bias_e_value=37.1645	bias_p_value=7.99868e-06	fisher_strand_p_value=5.16861e-07	frequency=3.823090e-02	genotype_quality=1110.4	ks_quality_p_value=1	log10_base_likelihood=-8.54707	log10_qual_likelihood_position_model=18.4413	log10_strand_likelihood_position_model=6.46705	new_cov=21/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=150/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/166
RA	287	.	NC_007779	804021	0	A	.	bias_e_value=4646330	bias_p_value=0.999999	fisher_strand_p_value=1	frequency=1.230049e-02	genotype_quality=1596.8	ks_quality_p_value=0.998466	log10_base_likelihood=-12.7235	log10_qual_likelihood_position_model=4.22303	log10_strand_likelihood_position_model=0.469238	new_cov=2/3	polymorphism_quality=7.3	quality=7.3	quality_position_model=5.16939e-10	ref_cov=180/221	reject=INDEL_HOMOPOLYMER	tot_cov=182/224
RA	288	.	NC_007779	815450	0	A	C	bias_e_value=4492230	bias_p_value=0.966834	fisher_strand_p_value=1	frequency=9.238243e-03	genotype_quality=1231.7	ks_quality_p_value=0.75376	log10_base_likelihood=-6.59225	log10_qual_likelihood_position_model=1.96849	log10_strand_likelihood_position_model=0.402346	new_cov=2/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=4.50762e-06	ref_cov=169/152	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=171/153
RA	289	.	NC_007779	817515	0	G	T	bias_e_value=5.564e-05	bias_p_value=1.1975e-11	fisher_strand_p_value=4.0547e-13	frequency=8.449173e-02	genotype_quality=951.1	ks_quality_p_value=1	log10_base_likelihood=-19.2057	log10_qual_likelihood_position_model=27.3373	log10_strand_likelihood_position_model=12.5581	new_cov=0/41	polymorphism_quality=13.9	quality=13.9	quality_position_model=Inf	ref_cov=155/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/172
RA	290	.	NC_007779	824398	0	A	C	bias_e_value=0.000829335	bias_p_value=1.78492e-10	fisher_strand_p_value=6.67702e-12	frequency=6.238651e-02	genotype_quality=850.3	ks_quality_p_value=1	log10_base_likelihood=-11.5472	log10_qual_likelihood_position_model=25.1355	log10_strand_likelihood_position_model=11.1754	new_cov=0/31	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=152/102	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=152/133
RA	291	.	NC_007779	827921	0	T	G	bias_e_value=6.69382e-14	bias_p_value=1.44067e-20	fisher_strand_p_value=2.84656e-22	frequency=1.087976e-01	genotype_quality=781.8	ks_quality_p_value=1	log10_base_likelihood=-16.3728	log10_qual_likelihood_position_model=32.5602	log10_strand_likelihood_position_model=21.5457	new_cov=53/0	polymorphism_quality=11.0	quality=11.0	quality_position_model=Inf	ref_cov=74/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/154
RA	292	.	NC_007779	827929	0	T	G	bias_e_value=7.85571e-06	bias_p_value=1.69073e-12	fisher_strand_p_value=5.3576e-14	frequency=6.070137e-02	genotype_quality=810.6	ks_quality_p_value=1	log10_base_likelihood=-6.78686	log10_qual_likelihood_position_model=29.8783	log10_strand_likelihood_position_model=13.271	new_cov=33/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=84/153	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/153
RA	293	.	NC_007779	835703	0	C	A	bias_e_value=19.4515	bias_p_value=4.18641e-06	fisher_strand_p_value=2.58954e-07	frequency=3.550339e-02	genotype_quality=952.3	ks_quality_p_value=1	log10_base_likelihood=-6.79793	log10_qual_likelihood_position_model=18.0274	log10_strand_likelihood_position_model=6.77835	new_cov=24/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=146/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/145
RA	294	.	NC_007779	847635	0	A	C	bias_e_value=0.0007702	bias_p_value=1.65765e-10	fisher_strand_p_value=6.18314e-12	frequency=4.186058e-02	genotype_quality=821.4	ks_quality_p_value=1	log10_base_likelihood=-5.86571	log10_qual_likelihood_position_model=28.0624	log10_strand_likelihood_position_model=11.2088	new_cov=19/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=55/187	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/187
RA	295	.	NC_007779	848585	0	C	A	bias_e_value=0.0747919	bias_p_value=1.6097e-08	fisher_strand_p_value=7.44816e-10	frequency=4.354858e-02	genotype_quality=1041.0	ks_quality_p_value=0.980699	log10_base_likelihood=-7.14972	log10_qual_likelihood_position_model=27.7577	log10_strand_likelihood_position_model=9.12795	new_cov=24/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=112/174	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/174
RA	296	.	NC_007779	853114	0	C	G	bias_e_value=176.104	bias_p_value=3.79018e-05	fisher_strand_p_value=2.7454e-06	frequency=3.453445e-02	genotype_quality=749.9	ks_quality_p_value=1	log10_base_likelihood=-7.90952	log10_qual_likelihood_position_model=9.95651	log10_strand_likelihood_position_model=5.56139	new_cov=0/8	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=152/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=153/42
RA	297	.	NC_007779	868836	1	.	C	bias_e_value=2589080	bias_p_value=0.557232	fisher_strand_p_value=1	frequency=1.034451e-02	genotype_quality=1399.8	ks_quality_p_value=0.222735	log10_base_likelihood=-12.806	log10_qual_likelihood_position_model=2.35473	log10_strand_likelihood_position_model=0.372837	new_cov=2/1	polymorphism_quality=7.4	quality=7.4	quality_position_model=4.15978e-12	ref_cov=165/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=167/123
RA	298	.	NC_007779	884191	1	.	T	bias_e_value=1752240	bias_p_value=0.377124	fisher_strand_p_value=0.121344	frequency=9.801865e-03	genotype_quality=1488.6	ks_quality_p_value=0.999418	log10_base_likelihood=-9.91544	log10_qual_likelihood_position_model=6.19762	log10_strand_likelihood_position_model=0.915983	new_cov=0/3	polymorphism_quality=4.5	quality=4.5	quality_position_model=0.000142502	ref_cov=154/149	reject=POLYMORPHISM_STRAND	tot_cov=154/152
RA	299	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=969.8	new_cov=148/110	quality=969.8	ref_cov=0/0	tot_cov=148/110
RA	300	.	NC_007779	889983	1	.	A	bias_e_value=3833500	bias_p_value=0.825059	fisher_strand_p_value=0.498683	frequency=6.191254e-03	genotype_quality=1577.2	ks_quality_p_value=0.94301	log10_base_likelihood=-7.75308	log10_qual_likelihood_position_model=2.35809	log10_strand_likelihood_position_model=0.584731	new_cov=0/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.09393e-06	ref_cov=158/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=158/165
RA	301	.	NC_007779	894943	0	T	G	bias_e_value=2.46126e-07	bias_p_value=5.29721e-14	fisher_strand_p_value=1.50797e-15	frequency=7.009983e-02	genotype_quality=751.1	ks_quality_p_value=1	log10_base_likelihood=-11.009	log10_qual_likelihood_position_model=32.6051	log10_strand_likelihood_position_model=14.8216	new_cov=32/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=64/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=96/152
RA	302	.	NC_007779	895911	0	C	A	bias_e_value=0.00105381	bias_p_value=2.26806e-10	fisher_strand_p_value=8.56405e-12	frequency=6.407213e-02	genotype_quality=802.5	ks_quality_p_value=1	log10_base_likelihood=-8.92441	log10_qual_likelihood_position_model=19.1651	log10_strand_likelihood_position_model=11.0673	new_cov=28/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=89/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/153
RA	303	.	NC_007779	904838	0	C	A	bias_e_value=2.3181e-12	bias_p_value=4.98911e-19	fisher_strand_p_value=1.25481e-20	frequency=1.339788e-01	genotype_quality=861.3	ks_quality_p_value=0.8461	log10_base_likelihood=-27.4086	log10_qual_likelihood_position_model=42.7304	log10_strand_likelihood_position_model=19.9014	new_cov=49/0	polymorphism_quality=22.2	quality=22.2	quality_position_model=Inf	ref_cov=81/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/162
RA	304	.	NC_007779	911333	0	T	G	bias_e_value=0.024015	bias_p_value=5.1686e-09	fisher_strand_p_value=2.22536e-10	frequency=4.178715e-02	genotype_quality=627.1	ks_quality_p_value=1	log10_base_likelihood=-6.87431	log10_qual_likelihood_position_model=17.2915	log10_strand_likelihood_position_model=9.6526	new_cov=14/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=29/141	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=43/141
RA	305	.	NC_007779	917407	0	C	A	bias_e_value=2.35563	bias_p_value=5.06986e-07	fisher_strand_p_value=3.0903e-08	frequency=4.414558e-02	genotype_quality=980.0	ks_quality_p_value=0.891249	log10_base_likelihood=-8.36925	log10_qual_likelihood_position_model=25.4171	log10_strand_likelihood_position_model=7.61011	new_cov=27/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=145/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/145
RA	306	.	NC_007779	932754	1	.	A	bias_e_value=4023830	bias_p_value=0.866023	fisher_strand_p_value=1	frequency=1.060104e-02	genotype_quality=1380.9	ks_quality_p_value=0.529272	log10_base_likelihood=-12.6519	log10_qual_likelihood_position_model=1.49562	log10_strand_likelihood_position_model=0.416907	new_cov=2/1	polymorphism_quality=7.3	quality=7.3	quality_position_model=8.80762e-13	ref_cov=142/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/139
RA	307	.	NC_007779	947970	0	C	A	bias_e_value=0.336674	bias_p_value=7.24601e-08	fisher_strand_p_value=3.54179e-09	frequency=4.857397e-02	genotype_quality=996.3	ks_quality_p_value=1	log10_base_likelihood=-10.3844	log10_qual_likelihood_position_model=14.9365	log10_strand_likelihood_position_model=8.45078	new_cov=24/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=119/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/164
RA	308	.	NC_007779	954820	0	A	C	bias_e_value=0.0134698	bias_p_value=2.89903e-09	fisher_strand_p_value=1.21655e-10	frequency=8.215380e-02	genotype_quality=680.2	ks_quality_p_value=1	log10_base_likelihood=-10.687	log10_qual_likelihood_position_model=21.7561	log10_strand_likelihood_position_model=10.1691	new_cov=0/33	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=113/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/127
RA	309	.	NC_007779	964577	0	T	G	bias_e_value=11.0443	bias_p_value=2.37699e-06	fisher_strand_p_value=1.41747e-07	frequency=3.156948e-02	genotype_quality=1114.8	ks_quality_p_value=1	log10_base_likelihood=-5.88863	log10_qual_likelihood_position_model=26.8571	log10_strand_likelihood_position_model=6.84848	new_cov=21/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=142/171	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=164/171
RA	310	.	NC_007779	969494	0	C	A	bias_e_value=2.59117e-07	bias_p_value=5.57681e-14	fisher_strand_p_value=1.58996e-15	frequency=1.412554e-01	genotype_quality=712.8	ks_quality_p_value=1	log10_base_likelihood=-34.4798	log10_qual_likelihood_position_model=24.0393	log10_strand_likelihood_position_model=14.8508	new_cov=49/0	polymorphism_quality=29.3	quality=29.3	quality_position_model=Inf	ref_cov=102/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/127
RA	311	.	NC_007779	986260	1	.	A	bias_e_value=2636110	bias_p_value=0.567354	fisher_strand_p_value=1	frequency=6.535530e-03	genotype_quality=1505.1	ks_quality_p_value=0.229543	log10_base_likelihood=-7.87335	log10_qual_likelihood_position_model=1.46732	log10_strand_likelihood_position_model=0.301114	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.96682e-08	ref_cov=161/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/144
RA	312	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=1061.3	new_cov=91/173	quality=1061.3	ref_cov=0/0	tot_cov=91/174
RA	313	.	NC_007779	987916	0	T	G	bias_e_value=3.87546e-09	bias_p_value=8.3409e-16	fisher_strand_p_value=2.11731e-17	frequency=8.117056e-02	genotype_quality=698.3	ks_quality_p_value=1	log10_base_likelihood=-14.2327	log10_qual_likelihood_position_model=24.5626	log10_strand_likelihood_position_model=16.6742	new_cov=19/0	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=15/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=34/159
RA	314	.	NC_007779	991407	0	G	T	bias_e_value=7.29772	bias_p_value=1.57064e-06	fisher_strand_p_value=1.03558e-07	frequency=4.177094e-02	genotype_quality=1029.3	ks_quality_p_value=0.881302	log10_base_likelihood=-8.93901	log10_qual_likelihood_position_model=27.1957	log10_strand_likelihood_position_model=7.19588	new_cov=0/23	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=157/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/160
RA	315	.	NC_007779	994634	0	G	T	bias_e_value=879.385	bias_p_value=0.000189264	fisher_strand_p_value=1.56904e-05	frequency=2.540684e-02	genotype_quality=1089.1	ks_quality_p_value=1	log10_base_likelihood=-6.44969	log10_qual_likelihood_position_model=11.8316	log10_strand_likelihood_position_model=4.80437	new_cov=0/13	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=173/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/136
RA	316	.	NC_007779	999606	0	A	T	bias_e_value=59583.5	bias_p_value=0.0128238	fisher_strand_p_value=0.00174441	frequency=4.500866e-02	genotype_quality=809.5	ks_quality_p_value=1	log10_base_likelihood=-10.5989	log10_qual_likelihood_position_model=13.5657	log10_strand_likelihood_position_model=2.8389	new_cov=12/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=122/93	reject=POLYMORPHISM_STRAND	tot_cov=135/93
RA	317	.	NC_007779	999607	0	A	C	bias_e_value=34930.1	bias_p_value=0.00751778	fisher_strand_p_value=0.000943778	frequency=3.494835e-02	genotype_quality=792.7	ks_quality_p_value=1	log10_base_likelihood=-6.7304	log10_qual_likelihood_position_model=13.9839	log10_strand_likelihood_position_model=3.08497	new_cov=13/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=121/93	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/93
RA	318	.	NC_007779	999613	0	A	T	bias_e_value=67967.4	bias_p_value=0.0146282	fisher_strand_p_value=0.00203206	frequency=7.600260e-02	genotype_quality=803.6	ks_quality_p_value=1	log10_base_likelihood=-28.6733	log10_qual_likelihood_position_model=20.2391	log10_strand_likelihood_position_model=2.82856	new_cov=17/1	polymorphism_quality=23.5	quality=23.5	quality_position_model=1.63176e-07	ref_cov=125/86	reject=POLYMORPHISM_STRAND	tot_cov=142/87
RA	319	.	NC_007779	1002109	0	T	G	bias_e_value=1.12057	bias_p_value=2.41174e-07	fisher_strand_p_value=1.25662e-08	frequency=3.148270e-02	genotype_quality=973.0	ks_quality_p_value=1	log10_base_likelihood=-6.24165	log10_qual_likelihood_position_model=19.2835	log10_strand_likelihood_position_model=7.9008	new_cov=20/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=107/174	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/174
RA	320	.	NC_007779	1002413	0	T	G	bias_e_value=8.22252e-05	bias_p_value=1.76968e-11	fisher_strand_p_value=6.07524e-13	frequency=3.921413e-02	genotype_quality=1050.1	ks_quality_p_value=1	log10_base_likelihood=-7.15283	log10_qual_likelihood_position_model=24.8601	log10_strand_likelihood_position_model=12.2164	new_cov=31/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=113/190	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/190
RA	321	.	NC_007779	1004576	0	G	.	bias_e_value=2708500	bias_p_value=0.582932	fisher_strand_p_value=0.293714	frequency=1.185131e-02	genotype_quality=1057.2	ks_quality_p_value=0.818136	log10_base_likelihood=-8.57901	log10_qual_likelihood_position_model=1.02501	log10_strand_likelihood_position_model=0.616513	new_cov=3/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=6.87612e-09	ref_cov=155/95	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=158/95
RA	322	.	NC_007779	1006080	0	C	A	bias_e_value=23.6607	bias_p_value=5.09234e-06	fisher_strand_p_value=3.19114e-07	frequency=4.149437e-02	genotype_quality=910.0	ks_quality_p_value=1	log10_base_likelihood=-6.41059	log10_qual_likelihood_position_model=17.3174	log10_strand_likelihood_position_model=6.54506	new_cov=22/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=130/139	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/139
RA	323	.	NC_007779	1020666	1	.	A	bias_e_value=3798890	bias_p_value=0.817611	fisher_strand_p_value=0.500504	frequency=6.533623e-03	genotype_quality=1513.3	ks_quality_p_value=0.920124	log10_base_likelihood=-6.83105	log10_qual_likelihood_position_model=3.16384	log10_strand_likelihood_position_model=0.548319	new_cov=0/2	polymorphism_quality=1.3	quality=1.3	quality_position_model=6.54678e-05	ref_cov=143/161	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/163
RA	324	.	NC_007779	1020800	0	A	.	bias_e_value=3811830	bias_p_value=0.820396	fisher_strand_p_value=1	frequency=1.012707e-02	genotype_quality=1159.0	ks_quality_p_value=0.464135	log10_base_likelihood=-7.95058	log10_qual_likelihood_position_model=1.26132	log10_strand_likelihood_position_model=0.359756	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.91151e-08	ref_cov=115/178	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/180
RA	325	.	NC_007779	1029749	0	T	G	bias_e_value=0.00528492	bias_p_value=1.13744e-09	fisher_strand_p_value=4.58542e-11	frequency=4.871750e-02	genotype_quality=750.0	ks_quality_p_value=1	log10_base_likelihood=-5.8324	log10_qual_likelihood_position_model=18.8498	log10_strand_likelihood_position_model=10.3386	new_cov=20/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=58/156	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=78/156
RA	326	.	NC_007779	1035834	0	C	A	bias_e_value=0.0978157	bias_p_value=2.10522e-08	fisher_strand_p_value=9.67645e-10	frequency=5.843353e-02	genotype_quality=1004.4	ks_quality_p_value=1	log10_base_likelihood=-13.0859	log10_qual_likelihood_position_model=22.4138	log10_strand_likelihood_position_model=9.20493	new_cov=29/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=133/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/159
RA	327	.	NC_007779	1049390	0	C	A	bias_e_value=0.0401124	bias_p_value=8.63313e-09	fisher_strand_p_value=3.80489e-10	frequency=4.289436e-02	genotype_quality=1112.7	ks_quality_p_value=1	log10_base_likelihood=-6.47803	log10_qual_likelihood_position_model=22.2909	log10_strand_likelihood_position_model=9.41966	new_cov=29/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=148/181	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=177/181
RA	328	.	NC_007779	1058914	0	A	C	bias_e_value=1.10187e-09	bias_p_value=2.37148e-16	fisher_strand_p_value=5.82907e-18	frequency=6.612682e-02	genotype_quality=820.7	ks_quality_p_value=1	log10_base_likelihood=-8.49278	log10_qual_likelihood_position_model=34.3505	log10_strand_likelihood_position_model=17.2344	new_cov=0/30	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=170/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/77
RA	329	.	NC_007779	1065606	0	C	A	bias_e_value=108087	bias_p_value=0.0232628	fisher_strand_p_value=0.00352379	frequency=1.556396e-02	genotype_quality=1206.0	ks_quality_p_value=0.991759	log10_base_likelihood=-6.15332	log10_qual_likelihood_position_model=10.1969	log10_strand_likelihood_position_model=2.6977	new_cov=9/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=159/163	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=168/163
RA	330	.	NC_007779	1068584	0	C	A	bias_e_value=1107.39	bias_p_value=0.000238336	fisher_strand_p_value=2.01868e-05	frequency=2.675533e-02	genotype_quality=1020.1	ks_quality_p_value=0.999637	log10_base_likelihood=-6.4563	log10_qual_likelihood_position_model=16.1619	log10_strand_likelihood_position_model=4.97264	new_cov=16/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=137/152	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/152
RA	331	.	NC_007779	1073325	0	C	A	bias_e_value=670.557	bias_p_value=0.00014432	fisher_strand_p_value=1.16785e-05	frequency=3.426933e-02	genotype_quality=1022.3	ks_quality_p_value=1	log10_base_likelihood=-7.23229	log10_qual_likelihood_position_model=17.4705	log10_strand_likelihood_position_model=5.08457	new_cov=18/1	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=129/163	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/164
RA	332	.	NC_007779	1086017	0	A	C	bias_e_value=0.0806366	bias_p_value=1.73549e-08	fisher_strand_p_value=7.90348e-10	frequency=3.945827e-02	genotype_quality=961.9	ks_quality_p_value=1	log10_base_likelihood=-5.6949	log10_qual_likelihood_position_model=24.8046	log10_strand_likelihood_position_model=9.10218	new_cov=0/28	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=155/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=155/155
RA	333	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1345.1	new_cov=133/178	quality=1345.1	ref_cov=0/0	tot_cov=133/178
RA	334	.	NC_007779	1093735	1	.	A	bias_e_value=4584830	bias_p_value=0.986763	fisher_strand_p_value=1	frequency=6.514549e-03	genotype_quality=1520.4	ks_quality_p_value=0.841765	log10_base_likelihood=-8.06745	log10_qual_likelihood_position_model=0.925196	log10_strand_likelihood_position_model=0.30128	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=8.64441e-09	ref_cov=162/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=163/144
RA	335	.	NC_007779	1097012	0	T	.	bias_e_value=2008410	bias_p_value=0.432258	fisher_strand_p_value=1	frequency=8.685112e-03	genotype_quality=1354.5	ks_quality_p_value=0.148785	log10_base_likelihood=-7.48822	log10_qual_likelihood_position_model=3.21707	log10_strand_likelihood_position_model=0.384279	new_cov=2/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.01129e-05	ref_cov=189/152	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=192/153
RA	336	.	NC_007779	1097580	0	C	T	bias_e_value=4924.06	bias_p_value=0.00105977	fisher_strand_p_value=0.603467	frequency=1.854119e-01	genotype_quality=961.4	ks_quality_p_value=0.000172695	log10_base_likelihood=-200.522	log10_qual_likelihood_position_model=25.1794	log10_strand_likelihood_position_model=1.04521	new_cov=36/36	polymorphism_quality=195.7	quality=195.7	quality_position_model=6.15891e-177	ref_cov=147/169	reject=KS_QUALITY_P_VALUE	tot_cov=185/205
RA	337	.	NC_007779	1097583	1	.	A	bias_e_value=3312530	bias_p_value=0.712934	fisher_strand_p_value=0.609676	frequency=8.426666e-03	genotype_quality=1267.4	ks_quality_p_value=0.567079	log10_base_likelihood=-12.3885	log10_qual_likelihood_position_model=1.75937	log10_strand_likelihood_position_model=0.442944	new_cov=2/1	polymorphism_quality=7.0	quality=7.0	quality_position_model=3.22923e-12	ref_cov=169/184	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=171/185
RA	338	.	NC_007779	1097742	0	C	.	bias_e_value=2933200	bias_p_value=0.631293	fisher_strand_p_value=0.558032	frequency=3.518105e-03	genotype_quality=3035.2	ks_quality_p_value=0.494572	log10_base_likelihood=-6.78958	log10_qual_likelihood_position_model=1.42433	log10_strand_likelihood_position_model=0.592631	new_cov=2/1	polymorphism_quality=1.3	quality=1.3	quality_position_model=1.1973e-06	ref_cov=310/538	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=312/539
RA	339	.	NC_007779	1105181	1	.	T	bias_e_value=2709320	bias_p_value=0.58311	fisher_strand_p_value=1	frequency=1.003361e-02	genotype_quality=1451.6	ks_quality_p_value=0.240422	log10_base_likelihood=-12.6364	log10_qual_likelihood_position_model=2.3558	log10_strand_likelihood_position_model=0.38609	new_cov=2/1	polymorphism_quality=7.3	quality=7.3	quality_position_model=6.40964e-12	ref_cov=163/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/134
RA	340	.	NC_007779	1115091	0	C	A	bias_e_value=81.9589	bias_p_value=1.76395e-05	fisher_strand_p_value=1.20584e-06	frequency=4.513741e-02	genotype_quality=916.7	ks_quality_p_value=1	log10_base_likelihood=-11.6355	log10_qual_likelihood_position_model=16.2803	log10_strand_likelihood_position_model=5.91871	new_cov=0/13	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=161/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/94
RA	341	.	NC_007779	1116582	0	G	C	bias_e_value=6.7151e-10	bias_p_value=1.44525e-16	fisher_strand_p_value=3.51199e-18	frequency=8.525467e-02	genotype_quality=712.8	ks_quality_p_value=0.999042	log10_base_likelihood=-27.0112	log10_qual_likelihood_position_model=17.386	log10_strand_likelihood_position_model=17.4544	new_cov=0/18	polymorphism_quality=21.8	quality=21.8	quality_position_model=Inf	ref_cov=173/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=173/30
RA	342	.	NC_007779	1120197	0	C	A	bias_e_value=0.0035256	bias_p_value=7.58792e-10	fisher_strand_p_value=3.00783e-11	frequency=5.195713e-02	genotype_quality=936.3	ks_quality_p_value=1	log10_base_likelihood=-7.70061	log10_qual_likelihood_position_model=21.9347	log10_strand_likelihood_position_model=10.5217	new_cov=31/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=122/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/164
RA	343	.	NC_007779	1122800	1	.	A	bias_e_value=4236640	bias_p_value=0.911824	fisher_strand_p_value=1	frequency=6.666183e-03	genotype_quality=1465.5	ks_quality_p_value=0.610615	log10_base_likelihood=-8.04486	log10_qual_likelihood_position_model=0.827637	log10_strand_likelihood_position_model=0.338655	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=7.9071e-09	ref_cov=193/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=194/106
RA	344	.	NC_007779	1148417	0	C	A	bias_e_value=0.00285174	bias_p_value=6.13762e-10	fisher_strand_p_value=2.7606e-11	frequency=5.289555e-02	genotype_quality=1111.1	ks_quality_p_value=0.87366	log10_base_likelihood=-7.20517	log10_qual_likelihood_position_model=32.9696	log10_strand_likelihood_position_model=10.6318	new_cov=34/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=147/173	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=181/173
RA	345	.	NC_007779	1151485	0	C	A	bias_e_value=0.000190745	bias_p_value=4.10528e-11	fisher_strand_p_value=1.45281e-12	frequency=7.124424e-02	genotype_quality=970.7	ks_quality_p_value=1	log10_base_likelihood=-15.2106	log10_qual_likelihood_position_model=21.5071	log10_strand_likelihood_position_model=11.8378	new_cov=34/0	polymorphism_quality=9.9	quality=9.9	quality_position_model=Inf	ref_cov=114/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/161
RA	346	.	NC_007779	1155150	0	T	G	bias_e_value=2591.74	bias_p_value=0.000557803	fisher_strand_p_value=5.12768e-05	frequency=2.251720e-02	genotype_quality=698.7	ks_quality_p_value=1	log10_base_likelihood=-8.0145	log10_qual_likelihood_position_model=5.93041	log10_strand_likelihood_position_model=4.29008	new_cov=5/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=22/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/155
RA	347	.	NC_007779	1158848	0	T	G	bias_e_value=6.33461e-12	bias_p_value=1.36336e-18	fisher_strand_p_value=2.96611e-20	frequency=8.429909e-02	genotype_quality=902.9	ks_quality_p_value=1	log10_base_likelihood=-9.13705	log10_qual_likelihood_position_model=35.1363	log10_strand_likelihood_position_model=19.5278	new_cov=49/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=88/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/168
RA	348	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1461.2	new_cov=245/126	quality=1461.2	ref_cov=0/0	tot_cov=245/127
RA	349	.	NC_007779	1176573	0	A	G	bias_e_value=2996.79	bias_p_value=0.00064498	fisher_strand_p_value=6.0176e-05	frequency=2.975368e-02	genotype_quality=971.4	ks_quality_p_value=1	log10_base_likelihood=-8.22148	log10_qual_likelihood_position_model=16.5723	log10_strand_likelihood_position_model=4.22058	new_cov=0/13	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=140/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/132
RA	350	.	NC_007779	1177683	0	A	G	bias_e_value=0.246309	bias_p_value=5.30116e-08	fisher_strand_p_value=2.55022e-09	frequency=6.776190e-02	genotype_quality=714.6	ks_quality_p_value=1	log10_base_likelihood=-10.4999	log10_qual_likelihood_position_model=19.5444	log10_strand_likelihood_position_model=8.59342	new_cov=20/0	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=75/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/144
RA	351	.	NC_007779	1197797	0	C	T	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=8.315706e-02	genotype_quality=1154.1	ks_quality_p_value=1	log10_base_likelihood=-62.9491	log10_qual_likelihood_position_model=8.12021	log10_strand_likelihood_position_model=0.789876	new_cov=14/12	polymorphism_quality=57.9	quality=57.9	quality_position_model=1.99989e-56	ref_cov=153/133	tot_cov=167/145
RA	352	.	NC_007779	1197809	0	C	T	bias_e_value=4462520	bias_p_value=0.960439	fisher_strand_p_value=0.835423	frequency=7.777882e-02	genotype_quality=1142.9	ks_quality_p_value=0.876484	log10_base_likelihood=-58.4044	log10_qual_likelihood_position_model=7.85845	log10_strand_likelihood_position_model=0.784851	new_cov=13/11	polymorphism_quality=53.4	quality=53.4	quality_position_model=3.95079e-52	ref_cov=147/137	tot_cov=160/148
RA	353	.	NC_007779	1197822	0	T	C	bias_e_value=2127090	bias_p_value=0.457801	fisher_strand_p_value=0.801379	frequency=5.293655e-02	genotype_quality=1089.4	ks_quality_p_value=0.202793	log10_base_likelihood=-42.1229	log10_qual_likelihood_position_model=6.45612	log10_strand_likelihood_position_model=0.714492	new_cov=8/8	polymorphism_quality=37.0	quality=37.0	quality_position_model=3.02985e-37	ref_cov=154/132	tot_cov=162/140
RA	354	.	NC_007779	1197824	0	A	G	bias_e_value=3454980	bias_p_value=0.743593	fisher_strand_p_value=0.803223	frequency=5.312443e-02	genotype_quality=1092.7	ks_quality_p_value=0.467863	log10_base_likelihood=-41.9139	log10_qual_likelihood_position_model=5.17433	log10_strand_likelihood_position_model=0.709613	new_cov=8/8	polymorphism_quality=36.8	quality=36.8	quality_position_model=2.49594e-38	ref_cov=152/133	tot_cov=161/141
RA	355	.	NC_007779	1197854	0	C	T	bias_e_value=3314980	bias_p_value=0.713461	fisher_strand_p_value=0.375185	frequency=2.002525e-02	genotype_quality=1015.8	ks_quality_p_value=0.922827	log10_base_likelihood=-9.07136	log10_qual_likelihood_position_model=2.96852	log10_strand_likelihood_position_model=0.728833	new_cov=4/1	polymorphism_quality=3.6	quality=3.6	quality_position_model=2.83722e-07	ref_cov=128/115	reject=POLYMORPHISM_STRAND	tot_cov=132/116
RA	356	.	NC_007779	1197857	0	G	C	bias_e_value=3706240	bias_p_value=0.79767	fisher_strand_p_value=0.624739	frequency=1.616955e-02	genotype_quality=1012.6	ks_quality_p_value=0.697392	log10_base_likelihood=-9.88494	log10_qual_likelihood_position_model=2.83864	log10_strand_likelihood_position_model=0.551866	new_cov=3/1	polymorphism_quality=4.4	quality=4.4	quality_position_model=1.96756e-08	ref_cov=128/115	reject=POLYMORPHISM_STRAND	tot_cov=131/116
RA	357	.	NC_007779	1197860	0	A	G	bias_e_value=4118370	bias_p_value=0.88637	fisher_strand_p_value=0.62437	frequency=1.600266e-02	genotype_quality=935.4	ks_quality_p_value=0.901542	log10_base_likelihood=-7.57786	log10_qual_likelihood_position_model=2.99853	log10_strand_likelihood_position_model=0.5552	new_cov=3/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=7.25684e-06	ref_cov=128/116	reject=POLYMORPHISM_STRAND	tot_cov=131/117
RA	358	.	NC_007779	1213001	0	T	C	bias_e_value=2392890	bias_p_value=0.515006	fisher_strand_p_value=0.473178	frequency=2.654648e-02	genotype_quality=1142.0	ks_quality_p_value=0.413697	log10_base_likelihood=-19.1623	log10_qual_likelihood_position_model=3.69366	log10_strand_likelihood_position_model=0.756636	new_cov=6/2	polymorphism_quality=13.9	quality=13.9	quality_position_model=8.05513e-17	ref_cov=165/128	tot_cov=171/130
RA	359	.	NC_007779	1213013	0	T	C	bias_e_value=2866130	bias_p_value=0.616859	fisher_strand_p_value=0.458879	frequency=2.292061e-02	genotype_quality=1157.5	ks_quality_p_value=0.577384	log10_base_likelihood=-16.4633	log10_qual_likelihood_position_model=3.54788	log10_strand_likelihood_position_model=0.687764	new_cov=5/2	polymorphism_quality=11.1	quality=11.1	quality_position_model=2.68768e-14	ref_cov=160/138	tot_cov=165/140
RA	360	.	NC_007779	1213026	0	C	T	bias_e_value=4210400	bias_p_value=0.906178	fisher_strand_p_value=0.690824	frequency=2.062607e-02	genotype_quality=1195.4	ks_quality_p_value=0.867628	log10_base_likelihood=-10.8665	log10_qual_likelihood_position_model=3.26624	log10_strand_likelihood_position_model=0.563985	new_cov=4/2	polymorphism_quality=5.4	quality=5.4	quality_position_model=5.44067e-09	ref_cov=152/130	tot_cov=157/132
RA	361	.	NC_007779	1213028	0	G	A	bias_e_value=4358220	bias_p_value=0.937991	fisher_strand_p_value=0.691582	frequency=2.103806e-02	genotype_quality=1172.1	ks_quality_p_value=0.967607	log10_base_likelihood=-10.8292	log10_qual_likelihood_position_model=3.89762	log10_strand_likelihood_position_model=0.560625	new_cov=4/2	polymorphism_quality=5.4	quality=5.4	quality_position_model=2.63831e-08	ref_cov=150/127	tot_cov=154/129
RA	362	.	NC_007779	1213058	0	T	C	bias_e_value=3084810	bias_p_value=0.663924	fisher_strand_p_value=0.346619	frequency=1.669025e-02	genotype_quality=915.1	ks_quality_p_value=0.872073	log10_base_likelihood=-8.33522	log10_qual_likelihood_position_model=2.32143	log10_strand_likelihood_position_model=0.652585	new_cov=3/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.92536e-07	ref_cov=110/125	reject=POLYMORPHISM_STRAND	tot_cov=114/126
RA	363	.	NC_007779	1213061	0	C	G	bias_e_value=1653360	bias_p_value=0.355841	fisher_strand_p_value=0.112221	frequency=1.162243e-02	genotype_quality=1075.6	ks_quality_p_value=0.992524	log10_base_likelihood=-5.95898	log10_qual_likelihood_position_model=2.5487	log10_strand_likelihood_position_model=0.949927	new_cov=3/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=0.00033128	ref_cov=121/132	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=124/132
RA	364	.	NC_007779	1213658	0	C	.	bias_e_value=4597860	bias_p_value=0.989567	fisher_strand_p_value=1	frequency=1.414394e-02	genotype_quality=889.6	ks_quality_p_value=0.859073	log10_base_likelihood=-8.65707	log10_qual_likelihood_position_model=0.92569	log10_strand_likelihood_position_model=0.370992	new_cov=1/2	polymorphism_quality=3.2	quality=3.2	quality_position_model=2.52511e-09	ref_cov=88/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=90/122
RA	365	.	NC_007779	1225577	1	.	G	bias_e_value=2267520	bias_p_value=0.488023	fisher_strand_p_value=0.202008	frequency=6.211281e-03	genotype_quality=1596.3	ks_quality_p_value=0.889203	log10_base_likelihood=-7.91985	log10_qual_likelihood_position_model=1.06351	log10_strand_likelihood_position_model=0.69463	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.33905e-08	ref_cov=143/177	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/177
RA	366	.	NC_007779	1262472	0	A	C	bias_e_value=1.32108e-06	bias_p_value=2.84328e-13	fisher_strand_p_value=8.51356e-15	frequency=6.676054e-02	genotype_quality=931.5	ks_quality_p_value=1	log10_base_likelihood=-12.7055	log10_qual_likelihood_position_model=27.4414	log10_strand_likelihood_position_model=14.0699	new_cov=0/36	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=172/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/137
RA	367	.	NC_007779	1273399	0	T	G	bias_e_value=2.55376e-31	bias_p_value=5.49629e-38	fisher_strand_p_value=6.01948e-40	frequency=1.319666e-01	genotype_quality=938.9	ks_quality_p_value=1	log10_base_likelihood=-28.8689	log10_qual_likelihood_position_model=50.5553	log10_strand_likelihood_position_model=39.2204	new_cov=55/0	polymorphism_quality=23.7	quality=23.7	quality_position_model=Inf	ref_cov=27/217	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/217
RA	368	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=118.3	new_cov=15/20	quality=118.3	ref_cov=0/0	tot_cov=15/20
RA	369	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=35.4	new_cov=6/7	quality=35.4	ref_cov=0/0	tot_cov=6/7
RA	370	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=54.8	new_cov=13/11	quality=54.8	ref_cov=0/0	tot_cov=13/11
RA	371	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1201.8	new_cov=135/171	quality=1201.8	ref_cov=0/0	tot_cov=135/171
RA	372	.	NC_007779	1325276	0	G	T	bias_e_value=6.32917	bias_p_value=1.36219e-06	fisher_strand_p_value=8.32715e-08	frequency=2.933502e-02	genotype_quality=1016.2	ks_quality_p_value=0.942269	log10_base_likelihood=-5.92853	log10_qual_likelihood_position_model=22.1518	log10_strand_likelihood_position_model=7.0795	new_cov=0/19	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=175/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/139
RA	373	.	NC_007779	1330179	0	T	G	bias_e_value=0.00880543	bias_p_value=1.89514e-09	fisher_strand_p_value=7.80748e-11	frequency=3.733444e-02	genotype_quality=897.6	ks_quality_p_value=1	log10_base_likelihood=-6.49043	log10_qual_likelihood_position_model=26.4191	log10_strand_likelihood_position_model=10.1075	new_cov=24/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=88/164	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/164
RA	374	.	NC_007779	1336531	0	G	T	bias_e_value=52.5801	bias_p_value=1.13165e-05	fisher_strand_p_value=7.80539e-07	frequency=4.370880e-02	genotype_quality=1039.0	ks_quality_p_value=0.959883	log10_base_likelihood=-11.014	log10_qual_likelihood_position_model=19.7764	log10_strand_likelihood_position_model=6.33854	new_cov=0/26	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=138/170	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/196
RA	375	.	NC_007779	1352913	1	.	T	bias_e_value=45359.3	bias_p_value=0.0097624	fisher_strand_p_value=0.00127786	frequency=2.293587e-02	genotype_quality=1013.4	ks_quality_p_value=0.99656	log10_base_likelihood=-21.0362	log10_qual_likelihood_position_model=4.03156	log10_strand_likelihood_position_model=2.89352	new_cov=5/0	polymorphism_quality=15.8	quality=15.8	quality_position_model=3.27908e-16	ref_cov=54/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=59/159
RA	376	.	NC_007779	1352922	0	T	C	bias_e_value=0.0278538	bias_p_value=5.99479e-09	fisher_strand_p_value=2.59842e-10	frequency=4.952955e-02	genotype_quality=645.9	ks_quality_p_value=1	log10_base_likelihood=-12.4165	log10_qual_likelihood_position_model=13.1966	log10_strand_likelihood_position_model=9.58529	new_cov=10/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=15/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=25/164
RA	377	.	NC_007779	1352924	0	A	C	bias_e_value=68.5446	bias_p_value=1.47524e-05	fisher_strand_p_value=9.95434e-07	frequency=4.057503e-02	genotype_quality=611.3	ks_quality_p_value=1	log10_base_likelihood=-7.78021	log10_qual_likelihood_position_model=14.2386	log10_strand_likelihood_position_model=6.01179	new_cov=8/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=17/166	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=25/168
RA	378	.	NC_007779	1371749	1	.	T	bias_e_value=4407200	bias_p_value=0.948533	fisher_strand_p_value=1	frequency=3.076935e-02	genotype_quality=1493.3	ks_quality_p_value=0.696825	log10_base_likelihood=-45.4484	log10_qual_likelihood_position_model=4.9006	log10_strand_likelihood_position_model=0.605689	new_cov=5/5	polymorphism_quality=40.3	quality=40.3	quality_position_model=2.90367e-42	ref_cov=151/164	reject=INDEL_HOMOPOLYMER	tot_cov=156/169
RA	379	.	NC_007779	1374596	0	C	A	bias_e_value=0.00228875	bias_p_value=4.92594e-10	fisher_strand_p_value=2.37209e-11	frequency=6.119204e-02	genotype_quality=1000.7	ks_quality_p_value=0.808751	log10_base_likelihood=-16.2691	log10_qual_likelihood_position_model=27.7447	log10_strand_likelihood_position_model=10.6249	new_cov=30/0	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=119/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/169
RA	380	.	NC_007779	1375289	0	G	T	bias_e_value=0.000120184	bias_p_value=2.58665e-11	fisher_strand_p_value=9.00134e-13	frequency=7.720470e-02	genotype_quality=964.4	ks_quality_p_value=1	log10_base_likelihood=-15.3565	log10_qual_likelihood_position_model=28.7489	log10_strand_likelihood_position_model=12.2222	new_cov=0/40	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=154/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/171
RA	381	.	NC_007779	1385794	1	.	T	bias_e_value=3233850	bias_p_value=0.696001	fisher_strand_p_value=0.50113	frequency=6.849289e-03	genotype_quality=1436.6	ks_quality_p_value=0.658769	log10_base_likelihood=-7.78846	log10_qual_likelihood_position_model=1.76611	log10_strand_likelihood_position_model=0.540252	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.19166e-07	ref_cov=155/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/135
RA	382	.	NC_007779	1405508	0	G	T	bias_e_value=1524.64	bias_p_value=0.000328139	fisher_strand_p_value=2.8945e-05	frequency=5.179310e-02	genotype_quality=626.0	ks_quality_p_value=0.989144	log10_base_likelihood=-12.1985	log10_qual_likelihood_position_model=13.3494	log10_strand_likelihood_position_model=4.54951	new_cov=8/1	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=30/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=38/129
RA	383	.	NC_007779	1409137	0	G	T	bias_e_value=9.29461e-17	bias_p_value=2.00042e-23	fisher_strand_p_value=3.51469e-25	frequency=1.759892e-01	genotype_quality=807.4	ks_quality_p_value=0.993044	log10_base_likelihood=-52.2617	log10_qual_likelihood_position_model=33.829	log10_strand_likelihood_position_model=24.4541	new_cov=0/66	polymorphism_quality=47.2	quality=47.2	quality_position_model=Inf	ref_cov=158/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/152
RA	384	.	NC_007779	1410956	1	.	T	bias_e_value=2283320	bias_p_value=0.491423	fisher_strand_p_value=0.424138	frequency=1.823711e-02	genotype_quality=1547.0	ks_quality_p_value=0.428194	log10_base_likelihood=-26.6409	log10_qual_likelihood_position_model=4.30635	log10_strand_likelihood_position_model=0.690552	new_cov=4/2	polymorphism_quality=21.4	quality=21.4	quality_position_model=7.80165e-24	ref_cov=150/173	reject=INDEL_HOMOPOLYMER	tot_cov=154/175
RA	385	.	NC_007779	1412694	0	C	A	bias_e_value=3.61247e-05	bias_p_value=7.7749e-12	fisher_strand_p_value=2.59581e-13	frequency=8.317804e-02	genotype_quality=921.0	ks_quality_p_value=0.999032	log10_base_likelihood=-19.3154	log10_qual_likelihood_position_model=24.4635	log10_strand_likelihood_position_model=12.7019	new_cov=39/0	polymorphism_quality=14.0	quality=14.0	quality_position_model=Inf	ref_cov=115/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/150
RA	386	.	NC_007779	1429593	0	T	A	deleted=1	frequency=1	genotype_quality=0.9	new_cov=0/1	quality=0.9	ref_cov=1/0	reject=EVALUE	tot_cov=1/1
RA	387	.	NC_007779	1429625	0	A	C	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	388	.	NC_007779	1429631	0	G	A	deleted=1	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	389	.	NC_007779	1429985	0	A	C	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	390	.	NC_007779	1430021	0	A	G	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	391	.	NC_007779	1430030	0	G	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	392	.	NC_007779	1430213	0	G	C	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	393	.	NC_007779	1430216	0	A	G	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	394	.	NC_007779	1430219	0	G	A	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	395	.	NC_007779	1430255	0	A	G	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	396	.	NC_007779	1430258	0	C	T	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	397	.	NC_007779	1437441	0	G	A	bias_e_value=0.0890817	bias_p_value=1.91725e-08	fisher_strand_p_value=8.77291e-10	frequency=6.097698e-02	genotype_quality=756.9	ks_quality_p_value=1	log10_base_likelihood=-13.2106	log10_qual_likelihood_position_model=19.8815	log10_strand_likelihood_position_model=9.05686	new_cov=0/14	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=159/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=159/53
RA	398	.	NC_007779	1437447	0	G	C	bias_e_value=9.52593e-05	bias_p_value=2.0502e-11	fisher_strand_p_value=7.07528e-13	frequency=7.428551e-02	genotype_quality=769.7	ks_quality_p_value=1	log10_base_likelihood=-8.57047	log10_qual_likelihood_position_model=23.151	log10_strand_likelihood_position_model=12.1503	new_cov=0/28	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=151/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/102
RA	399	.	NC_007779	1438937	0	T	.	bias_e_value=3110330	bias_p_value=0.669415	fisher_strand_p_value=1	frequency=2.315712e-02	genotype_quality=1002.2	ks_quality_p_value=0.306896	log10_base_likelihood=-17.8306	log10_qual_likelihood_position_model=2.59001	log10_strand_likelihood_position_model=0.503953	new_cov=3/3	polymorphism_quality=12.5	quality=12.5	quality_position_model=7.60486e-17	ref_cov=133/119	reject=INDEL_HOMOPOLYMER	tot_cov=137/122
RA	400	.	NC_007779	1439601	0	A	T	bias_e_value=1372970	bias_p_value=0.295496	fisher_strand_p_value=0.0853906	frequency=1.470566e-02	genotype_quality=1145.4	ks_quality_p_value=1	log10_base_likelihood=-6.06995	log10_qual_likelihood_position_model=7.97324	log10_strand_likelihood_position_model=1.12159	new_cov=5/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=173/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=178/119
RA	401	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=824.4	new_cov=174/39	quality=824.4	ref_cov=0/0	tot_cov=174/39
RA	402	.	NC_007779	1483616	0	C	G	bias_e_value=13.5391	bias_p_value=2.91393e-06	fisher_strand_p_value=1.76041e-07	frequency=3.475094e-02	genotype_quality=748.1	ks_quality_p_value=1	log10_base_likelihood=-11.8229	log10_qual_likelihood_position_model=6.94508	log10_strand_likelihood_position_model=6.75439	new_cov=0/8	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=170/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/33
RA	403	.	NC_007779	1493621	0	T	C	bias_e_value=0.363531	bias_p_value=7.82403e-08	fisher_strand_p_value=3.83946e-09	frequency=4.487514e-02	genotype_quality=935.2	ks_quality_p_value=1	log10_base_likelihood=-14.1931	log10_qual_likelihood_position_model=16.5302	log10_strand_likelihood_position_model=8.41573	new_cov=0/17	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=191/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=191/99
RA	404	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1544.0	new_cov=136/178	quality=1544.0	ref_cov=0/0	tot_cov=136/178
RA	405	.	NC_007779	1502096	0	T	.	bias_e_value=2515850	bias_p_value=0.54147	fisher_strand_p_value=0.348854	frequency=1.529408e-02	genotype_quality=1007.7	ks_quality_p_value=0.608854	log10_base_likelihood=-10.1797	log10_qual_likelihood_position_model=4.15165	log10_strand_likelihood_position_model=0.648066	new_cov=1/3	polymorphism_quality=4.7	quality=4.7	quality_position_model=2.79702e-07	ref_cov=136/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/124
RA	406	.	NC_007779	1515709	0	A	G	bias_e_value=2.45902e-06	bias_p_value=5.29239e-13	fisher_strand_p_value=1.61568e-14	frequency=8.945370e-02	genotype_quality=895.8	ks_quality_p_value=1	log10_base_likelihood=-17.4477	log10_qual_likelihood_position_model=41.4708	log10_strand_likelihood_position_model=13.7916	new_cov=36/0	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=105/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/174
RA	407	.	NC_007779	1515714	0	A	T	bias_e_value=336.533	bias_p_value=7.24298e-05	fisher_strand_p_value=5.52648e-06	frequency=3.875256e-02	genotype_quality=922.2	ks_quality_p_value=1	log10_base_likelihood=-7.4605	log10_qual_likelihood_position_model=17.9511	log10_strand_likelihood_position_model=5.25755	new_cov=15/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=121/160	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=136/160
RA	408	.	NC_007779	1527474	0	G	A	bias_e_value=2.27295	bias_p_value=4.89192e-07	fisher_strand_p_value=2.65212e-08	frequency=7.019758e-02	genotype_quality=917.9	ks_quality_p_value=1	log10_base_likelihood=-17.7777	log10_qual_likelihood_position_model=24.1856	log10_strand_likelihood_position_model=7.57641	new_cov=0/23	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=145/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/139
RA	409	.	NC_007779	1527479	0	C	A	bias_e_value=305.43	bias_p_value=6.57357e-05	fisher_strand_p_value=5.02913e-06	frequency=4.197025e-02	genotype_quality=981.0	ks_quality_p_value=0.989408	log10_base_likelihood=-8.3959	log10_qual_likelihood_position_model=20.3773	log10_strand_likelihood_position_model=5.29851	new_cov=0/15	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=148/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=148/125
RA	410	.	NC_007779	1533140	0	C	A	bias_e_value=462106	bias_p_value=0.0994562	fisher_strand_p_value=0.0209996	frequency=3.031445e-02	genotype_quality=932.2	ks_quality_p_value=0.967228	log10_base_likelihood=-11.3489	log10_qual_likelihood_position_model=9.97687	log10_strand_likelihood_position_model=1.72854	new_cov=0/7	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=98/124	reject=POLYMORPHISM_STRAND	tot_cov=98/131
RA	411	.	NC_007779	1533144	0	T	G	bias_e_value=1721860	bias_p_value=0.370586	fisher_strand_p_value=0.121867	frequency=2.039528e-02	genotype_quality=762.5	ks_quality_p_value=0.969852	log10_base_likelihood=-8.08831	log10_qual_likelihood_position_model=5.93034	log10_strand_likelihood_position_model=1.16447	new_cov=0/4	polymorphism_quality=2.6	quality=2.6	quality_position_model=0.0143208	ref_cov=95/97	reject=POLYMORPHISM_STRAND	tot_cov=95/102
RA	412	.	NC_007779	1537499	0	A	G	bias_e_value=9.91155e-05	bias_p_value=2.1332e-11	fisher_strand_p_value=7.37215e-13	frequency=9.108114e-02	genotype_quality=837.8	ks_quality_p_value=1	log10_base_likelihood=-18.1728	log10_qual_likelihood_position_model=25.5976	log10_strand_likelihood_position_model=12.1324	new_cov=35/0	polymorphism_quality=12.9	quality=12.9	quality_position_model=Inf	ref_cov=116/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/163
RA	413	.	NC_007779	1552377	0	A	C	bias_e_value=7.90564e-09	bias_p_value=1.70148e-15	fisher_strand_p_value=4.4009e-17	frequency=9.039402e-02	genotype_quality=762.0	ks_quality_p_value=1	log10_base_likelihood=-11.534	log10_qual_likelihood_position_model=33.1419	log10_strand_likelihood_position_model=16.3565	new_cov=0/41	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=143/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/117
RA	414	.	NC_007779	1562518	0	A	C	bias_e_value=0.000485369	bias_p_value=1.04463e-10	fisher_strand_p_value=3.82807e-12	frequency=7.780170e-02	genotype_quality=512.6	ks_quality_p_value=1	log10_base_likelihood=-6.54349	log10_qual_likelihood_position_model=22.1805	log10_strand_likelihood_position_model=11.417	new_cov=0/32	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=99/62	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=100/94
RA	415	.	NC_007779	1581577	1	.	T	bias_e_value=3438250	bias_p_value=0.739993	fisher_strand_p_value=0.591769	frequency=9.433746e-03	genotype_quality=1548.0	ks_quality_p_value=0.628857	log10_base_likelihood=-12.5092	log10_qual_likelihood_position_model=2.06835	log10_strand_likelihood_position_model=0.471804	new_cov=1/2	polymorphism_quality=7.1	quality=7.1	quality_position_model=5.37942e-12	ref_cov=173/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=174/144
RA	416	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=1123.3	new_cov=151/153	quality=1123.3	ref_cov=0/0	tot_cov=151/153
RA	417	.	NC_007779	1624530	1	.	A	bias_e_value=3455800	bias_p_value=0.743769	fisher_strand_p_value=0.499686	frequency=7.379532e-03	genotype_quality=1289.1	ks_quality_p_value=0.752429	log10_base_likelihood=-7.88775	log10_qual_likelihood_position_model=1.75173	log10_strand_likelihood_position_model=0.556709	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.73776e-07	ref_cov=128/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/143
RA	418	.	NC_007779	1628027	0	G	T	bias_e_value=0.0010498	bias_p_value=2.25941e-10	fisher_strand_p_value=1.00137e-11	frequency=1.908317e-01	genotype_quality=385.7	ks_quality_p_value=0.851845	log10_base_likelihood=-43.2518	log10_qual_likelihood_position_model=26.8159	log10_strand_likelihood_position_model=11.132	new_cov=32/0	polymorphism_quality=38.1	quality=38.1	quality_position_model=3.35489e-07	ref_cov=48/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=80/78
RA	419	.	NC_007779	1646737	0	T	A	bias_e_value=39551.6	bias_p_value=0.00851243	fisher_strand_p_value=0.00108808	frequency=2.467537e-02	genotype_quality=1279.6	ks_quality_p_value=1	log10_base_likelihood=-6.52574	log10_qual_likelihood_position_model=18.8764	log10_strand_likelihood_position_model=3.04313	new_cov=0/11	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=171/186	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=172/197
RA	420	.	NC_007779	1646748	0	A	C	bias_e_value=0.0594797	bias_p_value=1.28014e-08	fisher_strand_p_value=5.74641e-10	frequency=6.979656e-02	genotype_quality=995.9	ks_quality_p_value=1	log10_base_likelihood=-17.3085	log10_qual_likelihood_position_model=32.1454	log10_strand_likelihood_position_model=9.30393	new_cov=2/37	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=155/129	reject=FISHER_STRAND_P_VALUE	tot_cov=157/166
RA	421	.	NC_007779	1651009	0	T	G	bias_e_value=4.93109e-13	bias_p_value=1.06129e-19	fisher_strand_p_value=2.18494e-21	frequency=1.122541e-01	genotype_quality=707.2	ks_quality_p_value=1	log10_base_likelihood=-23.5389	log10_qual_likelihood_position_model=30.3873	log10_strand_likelihood_position_model=20.6606	new_cov=31/0	polymorphism_quality=18.3	quality=18.3	quality_position_model=Inf	ref_cov=28/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=59/156
RA	422	.	NC_007779	1658369	0	A	.	bias_e_value=2761670	bias_p_value=0.594375	fisher_strand_p_value=0.248489	frequency=1.027775e-02	genotype_quality=1133.2	ks_quality_p_value=0.999714	log10_base_likelihood=-6.24597	log10_qual_likelihood_position_model=5.83089	log10_strand_likelihood_position_model=0.858934	new_cov=3/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=148/140	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=151/140
RA	423	.	NC_007779	1658376	1	.	C	bias_e_value=3926440	bias_p_value=0.845062	fisher_strand_p_value=0.498612	frequency=6.599426e-03	genotype_quality=1497.5	ks_quality_p_value=0.998422	log10_base_likelihood=-7.11998	log10_qual_likelihood_position_model=3.75733	log10_strand_likelihood_position_model=0.583597	new_cov=2/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=0.000150721	ref_cov=153/148	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=155/148
RA	424	.	NC_007779	1660545	0	G	T	bias_e_value=0.171563	bias_p_value=3.69244e-08	fisher_strand_p_value=1.74445e-09	frequency=4.599190e-02	genotype_quality=975.6	ks_quality_p_value=1	log10_base_likelihood=-5.89699	log10_qual_likelihood_position_model=22.1706	log10_strand_likelihood_position_model=8.75834	new_cov=0/27	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=154/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/153
RA	425	.	NC_007779	1665005	0	G	T	bias_e_value=180925	bias_p_value=0.0389393	fisher_strand_p_value=0.00644572	frequency=1.945305e-02	genotype_quality=1153.3	ks_quality_p_value=0.999359	log10_base_likelihood=-7.13821	log10_qual_likelihood_position_model=8.61427	log10_strand_likelihood_position_model=2.19073	new_cov=7/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=140/152	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=147/153
RA	426	.	NC_007779	1669599	0	C	.	bias_e_value=1137960	bias_p_value=0.244915	fisher_strand_p_value=0.082	frequency=1	genotype_quality=1298.4	ks_quality_p_value=0.802727	log10_base_likelihood=-16.0868	log10_qual_likelihood_position_model=1.9965	log10_strand_likelihood_position_model=1.08619	new_cov=114/151	polymorphism_changed_to_consensus=1	polymorphism_quality=10.8	quality=10.8	quality_position_model=4.36489e-15	ref_cov=3/0	tot_cov=118/151
RA	427	.	NC_007779	1669767	0	T	G	bias_e_value=178708	bias_p_value=0.0384621	fisher_strand_p_value=0.00634715	frequency=2.807808e-02	genotype_quality=918.3	ks_quality_p_value=1	log10_base_likelihood=-5.72743	log10_qual_likelihood_position_model=15.0922	log10_strand_likelihood_position_model=2.32519	new_cov=0/10	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=103/140	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=103/150
RA	428	.	NC_007779	1669770	0	T	G	bias_e_value=512824	bias_p_value=0.110372	fisher_strand_p_value=0.0231618	frequency=2.337265e-02	genotype_quality=943.4	ks_quality_p_value=1	log10_base_likelihood=-5.78081	log10_qual_likelihood_position_model=12.2225	log10_strand_likelihood_position_model=1.81255	new_cov=0/8	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=101/143	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=101/151
RA	429	.	NC_007779	1669781	0	G	A	bias_e_value=517958	bias_p_value=0.111477	fisher_strand_p_value=0.0234558	frequency=2.881908e-02	genotype_quality=976.5	ks_quality_p_value=1	log10_base_likelihood=-8.96958	log10_qual_likelihood_position_model=9.35825	log10_strand_likelihood_position_model=1.7936	new_cov=0/8	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=101/145	reject=POLYMORPHISM_STRAND	tot_cov=101/153
RA	430	.	NC_007779	1677110	0	G	T	bias_e_value=0.0282214	bias_p_value=6.07391e-09	fisher_strand_p_value=4.38894e-10	frequency=8.793068e-02	genotype_quality=782.5	ks_quality_p_value=0.600207	log10_base_likelihood=-20.0744	log10_qual_likelihood_position_model=32.5371	log10_strand_likelihood_position_model=9.47885	new_cov=0/34	polymorphism_quality=14.8	quality=14.8	quality_position_model=Inf	ref_cov=126/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/159
RA	431	.	NC_007779	1681402	0	T	G	bias_e_value=0.0717731	bias_p_value=1.54473e-08	fisher_strand_p_value=6.99587e-10	frequency=4.395008e-02	genotype_quality=838.0	ks_quality_p_value=1	log10_base_likelihood=-7.85442	log10_qual_likelihood_position_model=21.9562	log10_strand_likelihood_position_model=9.15516	new_cov=22/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=84/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/153
RA	432	.	NC_007779	1705204	0	A	C	bias_e_value=7651.49	bias_p_value=0.00164678	fisher_strand_p_value=0.000170142	frequency=5.208111e-02	genotype_quality=693.2	ks_quality_p_value=1	log10_base_likelihood=-10.8626	log10_qual_likelihood_position_model=19.538	log10_strand_likelihood_position_model=3.90388	new_cov=15/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=103/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/91
RA	433	.	NC_007779	1705210	0	G	T	bias_e_value=47834.1	bias_p_value=0.010295	fisher_strand_p_value=0.00135486	frequency=6.862068e-02	genotype_quality=742.4	ks_quality_p_value=0.999174	log10_base_likelihood=-17.7881	log10_qual_likelihood_position_model=19.0052	log10_strand_likelihood_position_model=2.96272	new_cov=15/1	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=102/87	reject=POLYMORPHISM_STRAND	tot_cov=117/88
RA	434	.	NC_007779	1705211	0	C	G	bias_e_value=25971.5	bias_p_value=0.00558967	fisher_strand_p_value=0.000673169	frequency=5.280685e-02	genotype_quality=732.1	ks_quality_p_value=1	log10_base_likelihood=-7.54489	log10_qual_likelihood_position_model=16.5245	log10_strand_likelihood_position_model=3.36184	new_cov=13/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=100/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/87
RA	435	.	NC_007779	1705224	0	G	T	bias_e_value=7980.2	bias_p_value=0.00171753	fisher_strand_p_value=0.000178315	frequency=6.329393e-02	genotype_quality=753.4	ks_quality_p_value=1	log10_base_likelihood=-13.2129	log10_qual_likelihood_position_model=16.6513	log10_strand_likelihood_position_model=3.85278	new_cov=15/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=100/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/87
RA	436	.	NC_007779	1706129	0	A	.	bias_e_value=3462670	bias_p_value=0.745248	fisher_strand_p_value=1	frequency=1.035213e-02	genotype_quality=1527.9	ks_quality_p_value=0.377494	log10_base_likelihood=-10.3231	log10_qual_likelihood_position_model=2.1974	log10_strand_likelihood_position_model=0.424296	new_cov=2/2	polymorphism_quality=4.9	quality=4.9	quality_position_model=1.12701e-09	ref_cov=196/186	reject=INDEL_HOMOPOLYMER	tot_cov=198/188
RA	437	.	NC_007779	1707794	0	T	.	bias_e_value=3764270	bias_p_value=0.81016	fisher_strand_p_value=1	frequency=1.044369e-02	genotype_quality=1089.1	ks_quality_p_value=0.451043	log10_base_likelihood=-7.88866	log10_qual_likelihood_position_model=2.18556	log10_strand_likelihood_position_model=0.411378	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.45381e-07	ref_cov=146/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/139
RA	438	.	NC_007779	1711122	1	.	C	bias_e_value=3783950	bias_p_value=0.814396	fisher_strand_p_value=0.504728	frequency=6.873131e-03	genotype_quality=1406.5	ks_quality_p_value=0.904256	log10_base_likelihood=-8.28839	log10_qual_likelihood_position_model=2.3488	log10_strand_likelihood_position_model=0.50995	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.48412e-07	ref_cov=160/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/129
RA	439	.	NC_007779	1712902	0	A	.	bias_e_value=681316	bias_p_value=0.146635	fisher_strand_p_value=0.0736846	frequency=1.026440e-02	genotype_quality=1147.6	ks_quality_p_value=0.452094	log10_base_likelihood=-7.74546	log10_qual_likelihood_position_model=3.39446	log10_strand_likelihood_position_model=1.13262	new_cov=0/3	polymorphism_quality=2.3	quality=2.3	quality_position_model=5.13374e-05	ref_cov=169/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=169/123
RA	440	.	NC_007779	1713510	0	A	C	bias_e_value=0.00521633	bias_p_value=1.12268e-09	fisher_strand_p_value=4.52343e-11	frequency=4.880190e-02	genotype_quality=934.5	ks_quality_p_value=1	log10_base_likelihood=-7.24847	log10_qual_likelihood_position_model=36.4187	log10_strand_likelihood_position_model=10.4165	new_cov=0/33	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=148/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/155
RA	441	.	NC_007779	1716031	1	.	T	bias_e_value=5722.04	bias_p_value=0.00123152	fisher_strand_p_value=0.128188	frequency=2.447605e-02	genotype_quality=1324.6	ks_quality_p_value=0.000960491	log10_base_likelihood=-31.7846	log10_qual_likelihood_position_model=4.65233	log10_strand_likelihood_position_model=1.11445	new_cov=6/1	polymorphism_quality=26.6	quality=26.6	quality_position_model=3.01367e-28	ref_cov=148/131	reject=POLYMORPHISM_STRAND,KS_QUALITY_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=154/132
RA	442	.	NC_007779	1729203	0	G	.	bias_e_value=806446	bias_p_value=0.173566	fisher_strand_p_value=0.121567	frequency=9.195328e-03	genotype_quality=1370.2	ks_quality_p_value=0.341404	log10_base_likelihood=-8.08144	log10_qual_likelihood_position_model=1.26217	log10_strand_likelihood_position_model=0.915185	new_cov=0/3	polymorphism_quality=2.6	quality=2.6	quality_position_model=8.01171e-08	ref_cov=164/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=164/162
RA	443	.	NC_007779	1740536	0	G	T	bias_e_value=3997290	bias_p_value=0.860311	fisher_strand_p_value=1	frequency=4.040718e-02	genotype_quality=1173.0	ks_quality_p_value=0.520412	log10_base_likelihood=-20.6103	log10_qual_likelihood_position_model=7.6778	log10_strand_likelihood_position_model=0.632201	new_cov=7/5	polymorphism_quality=15.3	quality=15.3	quality_position_model=2.26718e-14	ref_cov=163/119	tot_cov=170/124
RA	444	.	NC_007779	1746048	0	C	A	bias_e_value=44.9794	bias_p_value=9.68063e-06	fisher_strand_p_value=6.34217e-07	frequency=3.353214e-02	genotype_quality=985.7	ks_quality_p_value=0.999512	log10_base_likelihood=-8.36862	log10_qual_likelihood_position_model=17.4226	log10_strand_likelihood_position_model=6.26551	new_cov=21/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=137/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/146
RA	445	.	NC_007779	1763744	0	C	A	bias_e_value=2.44631e-06	bias_p_value=5.26503e-13	fisher_strand_p_value=1.60824e-14	frequency=6.258440e-02	genotype_quality=968.9	ks_quality_p_value=0.999268	log10_base_likelihood=-13.7181	log10_qual_likelihood_position_model=21.7041	log10_strand_likelihood_position_model=13.7936	new_cov=36/0	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=112/184	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/184
RA	446	.	NC_007779	1784132	0	G	T	bias_e_value=9286.56	bias_p_value=0.00199869	fisher_strand_p_value=0.000211219	frequency=2.286148e-02	genotype_quality=1028.2	ks_quality_p_value=1	log10_base_likelihood=-5.72456	log10_qual_likelihood_position_model=13.3047	log10_strand_likelihood_position_model=3.78327	new_cov=0/15	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=133/161	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/176
RA	447	.	NC_007779	1820099	0	A	C	bias_e_value=0.087739	bias_p_value=1.88835e-08	fisher_strand_p_value=8.63439e-10	frequency=5.481100e-02	genotype_quality=945.4	ks_quality_p_value=1	log10_base_likelihood=-10.5049	log10_qual_likelihood_position_model=21.6583	log10_strand_likelihood_position_model=9.06377	new_cov=0/23	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=174/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=174/130
RA	448	.	NC_007779	1823574	0	A	.	bias_e_value=4104100	bias_p_value=0.883299	fisher_strand_p_value=1	frequency=1.487255e-02	genotype_quality=1319.6	ks_quality_p_value=0.557596	log10_base_likelihood=-13.9642	log10_qual_likelihood_position_model=2.32553	log10_strand_likelihood_position_model=0.461197	new_cov=3/2	polymorphism_quality=8.6	quality=8.6	quality_position_model=3.15063e-13	ref_cov=190/141	reject=INDEL_HOMOPOLYMER	tot_cov=193/143
RA	449	.	NC_007779	1837206	0	G	T	bias_e_value=25230.7	bias_p_value=0.00543024	fisher_strand_p_value=0.000659418	frequency=2.649879e-02	genotype_quality=894.5	ks_quality_p_value=0.987823	log10_base_likelihood=-7.22025	log10_qual_likelihood_position_model=12.7688	log10_strand_likelihood_position_model=3.18084	new_cov=8/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=97/152	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/153
RA	450	.	NC_007779	1840899	0	G	T	bias_e_value=0.0101188	bias_p_value=2.17781e-09	fisher_strand_p_value=9.02595e-11	frequency=5.504704e-02	genotype_quality=1022.0	ks_quality_p_value=1	log10_base_likelihood=-8.92378	log10_qual_likelihood_position_model=29.0122	log10_strand_likelihood_position_model=10.1932	new_cov=0/32	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=157/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/161
RA	451	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=1290.7	new_cov=177/151	quality=1290.7	ref_cov=0/1	tot_cov=177/152
RA	452	.	NC_007779	1844628	0	A	G	bias_e_value=0.00277346	bias_p_value=5.96915e-10	fisher_strand_p_value=2.34295e-11	frequency=5.230045e-02	genotype_quality=567.6	ks_quality_p_value=1	log10_base_likelihood=-8.89081	log10_qual_likelihood_position_model=13.3703	log10_strand_likelihood_position_model=10.6302	new_cov=11/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=12/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=23/146
RA	453	.	NC_007779	1855175	0	A	.	bias_e_value=4089730	bias_p_value=0.880206	fisher_strand_p_value=0.615756	frequency=9.336472e-03	genotype_quality=1272.3	ks_quality_p_value=0.897016	log10_base_likelihood=-7.68054	log10_qual_likelihood_position_model=2.76602	log10_strand_likelihood_position_model=0.434456	new_cov=1/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=2.41788e-06	ref_cov=163/155	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=164/157
RA	454	.	NC_007779	1861399	0	A	C	bias_e_value=1.59425e-13	bias_p_value=3.43119e-20	fisher_strand_p_value=6.9003e-22	frequency=1.197863e-01	genotype_quality=619.0	ks_quality_p_value=1	log10_base_likelihood=-14.4258	log10_qual_likelihood_position_model=32.3481	log10_strand_likelihood_position_model=21.1611	new_cov=0/41	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=131/38	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/80
RA	455	.	NC_007779	1864105	1	.	T	bias_e_value=1970850	bias_p_value=0.424174	fisher_strand_p_value=0.606096	frequency=9.835243e-03	genotype_quality=1488.8	ks_quality_p_value=0.238532	log10_base_likelihood=-11.4443	log10_qual_likelihood_position_model=3.49874	log10_strand_likelihood_position_model=0.447644	new_cov=2/1	polymorphism_quality=6.0	quality=6.0	quality_position_model=1.82364e-09	ref_cov=143/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/160
RA	456	.	NC_007779	1864988	1	.	G	bias_e_value=3839390	bias_p_value=0.826328	fisher_strand_p_value=0.503847	frequency=6.535530e-03	genotype_quality=1512.4	ks_quality_p_value=0.93669	log10_base_likelihood=-8.06803	log10_qual_likelihood_position_model=1.37145	log10_strand_likelihood_position_model=0.516825	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.15674e-08	ref_cov=167/137	reject=POLYMORPHISM_STRAND	tot_cov=169/137
RA	457	.	NC_007779	1879404	0	A	C	bias_e_value=5.88748e-14	bias_p_value=1.26712e-20	fisher_strand_p_value=2.49721e-22	frequency=8.962631e-02	genotype_quality=782.4	ks_quality_p_value=1	log10_base_likelihood=-19.4624	log10_qual_likelihood_position_model=31.4495	log10_strand_likelihood_position_model=21.6025	new_cov=0/30	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=176/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=176/57
RA	458	.	NC_007779	1889729	1	.	A	bias_e_value=1919900	bias_p_value=0.413207	fisher_strand_p_value=0.243884	frequency=7.017136e-03	genotype_quality=1391.8	ks_quality_p_value=0.569779	log10_base_likelihood=-8.10271	log10_qual_likelihood_position_model=1.1816	log10_strand_likelihood_position_model=0.612816	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.06204e-08	ref_cov=144/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/141
RA	459	.	NC_007779	1906475	1	.	C	bias_e_value=1135000	bias_p_value=0.244278	fisher_strand_p_value=0.0905887	frequency=1.048946e-02	genotype_quality=1364.7	ks_quality_p_value=0.724036	log10_base_likelihood=-13.449	log10_qual_likelihood_position_model=2.98388	log10_strand_likelihood_position_model=1.04293	new_cov=3/0	polymorphism_quality=8.1	quality=8.1	quality_position_model=1.94691e-11	ref_cov=126/157	reject=POLYMORPHISM_STRAND	tot_cov=129/157
RA	460	.	NC_007779	1906477	1	.	G	bias_e_value=41989.1	bias_p_value=0.00903705	fisher_strand_p_value=0.00129439	frequency=2.845478e-02	genotype_quality=1134.1	ks_quality_p_value=0.900315	log10_base_likelihood=-30.9864	log10_qual_likelihood_position_model=6.13256	log10_strand_likelihood_position_model=2.88793	new_cov=7/0	polymorphism_quality=25.8	quality=25.8	quality_position_model=3.69084e-24	ref_cov=90/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=97/149
RA	461	.	NC_007779	1906488	0	G	T	bias_e_value=37.4494	bias_p_value=8.05999e-06	fisher_strand_p_value=5.21336e-07	frequency=4.176617e-02	genotype_quality=921.3	ks_quality_p_value=0.999544	log10_base_likelihood=-8.37902	log10_qual_likelihood_position_model=14.1513	log10_strand_likelihood_position_model=6.28288	new_cov=14/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=81/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/160
RA	462	.	NC_007779	1909059	0	C	G	bias_e_value=2016490	bias_p_value=0.433996	fisher_strand_p_value=1	frequency=9.206772e-03	genotype_quality=1355.2	ks_quality_p_value=0.149699	log10_base_likelihood=-6.56435	log10_qual_likelihood_position_model=2.28513	log10_strand_likelihood_position_model=0.420652	new_cov=1/2	polymorphism_quality=1.0	quality=1.0	quality_position_model=1.08301e-05	ref_cov=160/162	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=161/164
RA	463	.	NC_007779	1909420	1	.	T	bias_e_value=2005100	bias_p_value=0.431545	fisher_strand_p_value=0.500784	frequency=6.211281e-03	genotype_quality=1589.7	ks_quality_p_value=0.296358	log10_base_likelihood=-7.89046	log10_qual_likelihood_position_model=1.22478	log10_strand_likelihood_position_model=0.545836	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.79349e-08	ref_cov=170/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=172/150
RA	464	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=1348.8	new_cov=178/175	quality=1348.8	ref_cov=0/0	tot_cov=179/175
RA	465	.	NC_007779	1920746	0	G	T	bias_e_value=0.014308	bias_p_value=3.07942e-09	fisher_strand_p_value=1.29568e-10	frequency=4.660273e-02	genotype_quality=1015.7	ks_quality_p_value=1	log10_base_likelihood=-10.8655	log10_qual_likelihood_position_model=21.3442	log10_strand_likelihood_position_model=9.8875	new_cov=0/27	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=169/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/142
RA	466	.	NC_007779	1938748	1	.	A	bias_e_value=4061630	bias_p_value=0.874158	fisher_strand_p_value=1	frequency=1.916885e-02	genotype_quality=1470.8	ks_quality_p_value=0.542309	log10_base_likelihood=-26.0457	log10_qual_likelihood_position_model=3.66563	log10_strand_likelihood_position_model=0.501614	new_cov=3/3	polymorphism_quality=20.8	quality=20.8	quality_position_model=4.52299e-24	ref_cov=157/150	reject=INDEL_HOMOPOLYMER	tot_cov=160/153
RA	467	.	NC_007779	1943906	1	.	T	bias_e_value=3849530	bias_p_value=0.828509	fisher_strand_p_value=0.498566	frequency=6.872177e-03	genotype_quality=1424.4	ks_quality_p_value=0.952463	log10_base_likelihood=-7.87799	log10_qual_likelihood_position_model=1.12944	log10_strand_likelihood_position_model=0.582843	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.29798e-08	ref_cov=142/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/149
RA	468	.	NC_007779	1971508	0	A	C	bias_e_value=1.59053e-16	bias_p_value=3.42319e-23	fisher_strand_p_value=6.03016e-25	frequency=1.197395e-01	genotype_quality=646.3	ks_quality_p_value=1	log10_base_likelihood=-42.3941	log10_qual_likelihood_position_model=22.2328	log10_strand_likelihood_position_model=24.2197	new_cov=0/25	polymorphism_quality=37.3	quality=37.3	quality_position_model=Inf	ref_cov=162/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=162/33
RA	469	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=1104.4	new_cov=143/146	quality=1104.4	ref_cov=0/0	tot_cov=143/146
RA	470	.	NC_007779	1993891	0	A	C	bias_e_value=0.983592	bias_p_value=2.11692e-07	fisher_strand_p_value=1.09516e-08	frequency=5.506229e-02	genotype_quality=904.8	ks_quality_p_value=1	log10_base_likelihood=-10.696	log10_qual_likelihood_position_model=25.03	log10_strand_likelihood_position_model=8.11033	new_cov=0/28	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=131/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/153
RA	471	.	NC_007779	1993894	0	A	C	bias_e_value=0.00321847	bias_p_value=6.9269e-10	fisher_strand_p_value=2.73551e-11	frequency=7.940245e-02	genotype_quality=946.3	ks_quality_p_value=1	log10_base_likelihood=-16.6776	log10_qual_likelihood_position_model=37.2153	log10_strand_likelihood_position_model=10.6232	new_cov=0/36	polymorphism_quality=11.4	quality=11.4	quality_position_model=Inf	ref_cov=141/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/165
RA	472	.	NC_007779	2004055	0	A	C	bias_e_value=1.00809e-27	bias_p_value=2.16965e-34	fisher_strand_p_value=2.61619e-36	frequency=2.195172e-01	genotype_quality=777.1	ks_quality_p_value=1	log10_base_likelihood=-64.0313	log10_qual_likelihood_position_model=56.917	log10_strand_likelihood_position_model=35.5823	new_cov=0/85	polymorphism_quality=59.0	quality=59.0	quality_position_model=Inf	ref_cov=167/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/150
RA	473	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=1223.2	new_cov=153/152	quality=1223.2	ref_cov=0/0	tot_cov=153/152
RA	474	.	NC_007779	2023811	0	C	A	bias_e_value=3.36236	bias_p_value=7.2366e-07	fisher_strand_p_value=4.01561e-08	frequency=4.328251e-02	genotype_quality=1007.9	ks_quality_p_value=0.999453	log10_base_likelihood=-7.18507	log10_qual_likelihood_position_model=20.8979	log10_strand_likelihood_position_model=7.42779	new_cov=25/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=140/150	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/151
RA	475	.	NC_007779	2024392	0	A	G	bias_e_value=4479600	bias_p_value=0.964114	fisher_strand_p_value=1	frequency=1.063347e-02	genotype_quality=1076.0	ks_quality_p_value=0.744349	log10_base_likelihood=-5.78416	log10_qual_likelihood_position_model=3.13099	log10_strand_likelihood_position_model=0.402917	new_cov=2/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.000558775	ref_cov=146/132	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=148/133
RA	476	.	NC_007779	2032185	0	G	C	bias_e_value=8.19218	bias_p_value=1.76315e-06	fisher_strand_p_value=1.03188e-07	frequency=4.225159e-02	genotype_quality=599.5	ks_quality_p_value=1	log10_base_likelihood=-7.89447	log10_qual_likelihood_position_model=9.33076	log10_strand_likelihood_position_model=6.98637	new_cov=7/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=11/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=18/133
RA	477	.	NC_007779	2095582	0	G	T	bias_e_value=0.0106042	bias_p_value=2.28228e-09	fisher_strand_p_value=9.47811e-11	frequency=6.146669e-02	genotype_quality=991.8	ks_quality_p_value=1	log10_base_likelihood=-12.0476	log10_qual_likelihood_position_model=26.022	log10_strand_likelihood_position_model=10.1066	new_cov=0/40	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=142/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/202
RA	478	.	NC_007779	2106206	1	.	T	bias_e_value=2267760	bias_p_value=0.488075	fisher_strand_p_value=0.499933	frequency=1.156044e-02	genotype_quality=841.3	ks_quality_p_value=0.359362	log10_base_likelihood=-8.40105	log10_qual_likelihood_position_model=1.08441	log10_strand_likelihood_position_model=0.541304	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.01007e-08	ref_cov=91/80	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=93/80
RA	479	.	NC_007779	2107010	1	.	A	bias_e_value=4607360	bias_p_value=0.991612	fisher_strand_p_value=1	frequency=6.919861e-03	genotype_quality=1404.0	ks_quality_p_value=0.873308	log10_base_likelihood=-7.82516	log10_qual_likelihood_position_model=1.85884	log10_strand_likelihood_position_model=0.312192	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.45368e-07	ref_cov=168/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=169/120
RA	480	.	NC_007779	2141731	0	A	C	bias_e_value=1.50369	bias_p_value=3.2363e-07	fisher_strand_p_value=1.71397e-08	frequency=3.262901e-02	genotype_quality=1044.6	ks_quality_p_value=1	log10_base_likelihood=-6.44956	log10_qual_likelihood_position_model=28.3665	log10_strand_likelihood_position_model=7.766	new_cov=0/21	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=173/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=173/140
RA	481	.	NC_007779	2156661	0	C	A	bias_e_value=0.128404	bias_p_value=2.76355e-08	fisher_strand_p_value=1.28712e-09	frequency=4.894733e-02	genotype_quality=1043.4	ks_quality_p_value=1	log10_base_likelihood=-9.55782	log10_qual_likelihood_position_model=23.1762	log10_strand_likelihood_position_model=9.09689	new_cov=31/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=147/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/157
RA	482	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1257.6	new_cov=124/193	quality=1257.6	ref_cov=0/0	tot_cov=124/193
RA	483	.	NC_007779	2174678	0	C	G	bias_e_value=1.94776	bias_p_value=4.19205e-07	fisher_strand_p_value=2.25873e-08	frequency=5.752420e-02	genotype_quality=812.2	ks_quality_p_value=0.997355	log10_base_likelihood=-12.5945	log10_qual_likelihood_position_model=18.113	log10_strand_likelihood_position_model=7.64614	new_cov=0/16	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=147/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/81
RA	484	.	NC_007779	2178210	0	A	C	bias_e_value=4525790	bias_p_value=0.974056	fisher_strand_p_value=1	frequency=1.203060e-02	genotype_quality=1315.0	ks_quality_p_value=0.781035	log10_base_likelihood=-9.53016	log10_qual_likelihood_position_model=2.53083	log10_strand_likelihood_position_model=0.424134	new_cov=2/2	polymorphism_quality=4.1	quality=4.1	quality_position_model=1.62418e-08	ref_cov=169/159	tot_cov=171/161
RA	485	.	NC_007779	2199432	0	G	C	bias_e_value=0.0548162	bias_p_value=1.17977e-08	fisher_strand_p_value=5.27562e-10	frequency=4.703522e-02	genotype_quality=860.2	ks_quality_p_value=1	log10_base_likelihood=-14.8495	log10_qual_likelihood_position_model=16.3351	log10_strand_likelihood_position_model=9.27773	new_cov=0/12	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=184/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=185/43
RA	486	.	NC_007779	2203780	1	.	A	bias_e_value=4417580	bias_p_value=0.950766	fisher_strand_p_value=1	frequency=7.167816e-03	genotype_quality=1373.0	ks_quality_p_value=0.703086	log10_base_likelihood=-7.76664	log10_qual_likelihood_position_model=2.13377	log10_strand_likelihood_position_model=0.305589	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=3.17241e-07	ref_cov=155/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/123
RA	487	.	NC_007779	2213136	0	G	T	bias_e_value=6.68341e-05	bias_p_value=1.43843e-11	fisher_strand_p_value=4.9068e-13	frequency=8.497572e-02	genotype_quality=753.6	ks_quality_p_value=0.999013	log10_base_likelihood=-23.5798	log10_qual_likelihood_position_model=24.5217	log10_strand_likelihood_position_model=12.3092	new_cov=21/0	polymorphism_quality=18.3	quality=18.3	quality_position_model=Inf	ref_cov=43/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=64/153
RA	488	.	NC_007779	2227306	0	A	C	bias_e_value=6456.96	bias_p_value=0.00138969	fisher_strand_p_value=0.000140828	frequency=2.446175e-02	genotype_quality=1091.5	ks_quality_p_value=1	log10_base_likelihood=-5.85581	log10_qual_likelihood_position_model=18.1014	log10_strand_likelihood_position_model=3.87197	new_cov=12/1	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=121/190	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/191
RA	489	.	NC_007779	2229341	0	G	T	bias_e_value=67.9852	bias_p_value=1.4632e-05	fisher_strand_p_value=9.86724e-07	frequency=3.095245e-02	genotype_quality=973.2	ks_quality_p_value=1	log10_base_likelihood=-6.12514	log10_qual_likelihood_position_model=20.3082	log10_strand_likelihood_position_model=6.30683	new_cov=0/20	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=154/134	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/154
RA	490	.	NC_007779	2249963	0	T	G	bias_e_value=2.49803e-07	bias_p_value=5.37635e-14	fisher_strand_p_value=1.53117e-15	frequency=1.476583e-01	genotype_quality=727.3	ks_quality_p_value=1	log10_base_likelihood=-19.5122	log10_qual_likelihood_position_model=50.1224	log10_strand_likelihood_position_model=15.0159	new_cov=55/1	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=96/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=152/122
RA	491	.	NC_007779	2254201	0	G	T	bias_e_value=9.30724e-10	bias_p_value=2.00314e-16	fisher_strand_p_value=4.90283e-18	frequency=9.447861e-02	genotype_quality=975.1	ks_quality_p_value=1	log10_base_likelihood=-17.476	log10_qual_likelihood_position_model=32.1102	log10_strand_likelihood_position_model=17.3096	new_cov=0/46	polymorphism_quality=12.2	quality=12.2	quality_position_model=Inf	ref_cov=173/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/149
RA	492	.	NC_007779	2262756	0	A	C	bias_e_value=3571520	bias_p_value=0.768675	fisher_strand_p_value=0.493234	frequency=2.408123e-02	genotype_quality=1256.1	ks_quality_p_value=0.815765	log10_base_likelihood=-21.7896	log10_qual_likelihood_position_model=4.06912	log10_strand_likelihood_position_model=0.67985	new_cov=3/5	polymorphism_quality=16.5	quality=16.5	quality_position_model=3.51856e-19	ref_cov=167/157	tot_cov=170/162
RA	493	.	NC_007779	2307309	0	T	C	bias_e_value=0.000547945	bias_p_value=1.17931e-10	fisher_strand_p_value=4.34163e-12	frequency=9.225368e-02	genotype_quality=681.2	ks_quality_p_value=1	log10_base_likelihood=-17.9682	log10_qual_likelihood_position_model=22.7765	log10_strand_likelihood_position_model=11.3623	new_cov=0/25	polymorphism_quality=12.7	quality=12.7	quality_position_model=Inf	ref_cov=147/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/92
RA	494	.	NC_007779	2316502	1	.	T	bias_e_value=4644870	bias_p_value=0.999686	fisher_strand_p_value=1	frequency=6.600380e-03	genotype_quality=1490.0	ks_quality_p_value=0.975054	log10_base_likelihood=-8.18813	log10_qual_likelihood_position_model=2.25218	log10_strand_likelihood_position_model=0.303057	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.52922e-07	ref_cov=164/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/138
RA	495	.	NC_007779	2331120	0	T	G	bias_e_value=4.45608e-18	bias_p_value=9.59053e-25	fisher_strand_p_value=1.58771e-26	frequency=1.356897e-01	genotype_quality=814.0	ks_quality_p_value=1	log10_base_likelihood=-23.0358	log10_qual_likelihood_position_model=43.8095	log10_strand_likelihood_position_model=25.7992	new_cov=60/0	polymorphism_quality=17.8	quality=17.8	quality_position_model=Inf	ref_cov=68/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/164
RA	496	.	NC_007779	2332580	0	A	C	bias_e_value=1.4301e-16	bias_p_value=3.07792e-23	fisher_strand_p_value=5.41162e-25	frequency=1.192427e-01	genotype_quality=815.5	ks_quality_p_value=1	log10_base_likelihood=-16.8325	log10_qual_likelihood_position_model=38.7572	log10_strand_likelihood_position_model=24.2667	new_cov=0/56	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=162/68	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/125
RA	497	.	NC_007779	2334630	0	C	A	bias_e_value=1067.51	bias_p_value=0.000229754	fisher_strand_p_value=2.19442e-05	frequency=2.888107e-02	genotype_quality=1053.6	ks_quality_p_value=0.883472	log10_base_likelihood=-8.54506	log10_qual_likelihood_position_model=14.583	log10_strand_likelihood_position_model=4.95128	new_cov=17/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=136/179	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/180
RA	498	.	NC_007779	2353815	0	A	C	bias_e_value=1.32333e-11	bias_p_value=2.84813e-18	fisher_strand_p_value=6.2996e-20	frequency=9.187841e-02	genotype_quality=707.1	ks_quality_p_value=1	log10_base_likelihood=-8.68273	log10_qual_likelihood_position_model=30.3139	log10_strand_likelihood_position_model=19.2007	new_cov=0/33	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=152/38	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/71
RA	499	.	NC_007779	2354291	0	A	C	bias_e_value=4.01459e-06	bias_p_value=8.64034e-13	fisher_strand_p_value=2.67912e-14	frequency=9.621906e-02	genotype_quality=950.3	ks_quality_p_value=1	log10_base_likelihood=-21.1773	log10_qual_likelihood_position_model=31.0281	log10_strand_likelihood_position_model=13.572	new_cov=0/39	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=165/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=165/154
RA	500	.	NC_007779	2395142	0	C	A	bias_e_value=1720.97	bias_p_value=0.000370394	fisher_strand_p_value=3.28958e-05	frequency=2.116776e-02	genotype_quality=1022.6	ks_quality_p_value=0.993942	log10_base_likelihood=-6.19545	log10_qual_likelihood_position_model=11.6808	log10_strand_likelihood_position_model=4.48286	new_cov=14/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=132/152	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/152
RA	501	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=1191.0	new_cov=164/141	quality=1191.0	ref_cov=0/0	tot_cov=164/141
RA	502	.	NC_007779	2410289	1	.	A	bias_e_value=1909550	bias_p_value=0.41098	fisher_strand_p_value=0.21497	frequency=6.451607e-03	genotype_quality=1500.3	ks_quality_p_value=0.641177	log10_base_likelihood=-7.98674	log10_qual_likelihood_position_model=1.76648	log10_strand_likelihood_position_model=0.667622	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.85196e-07	ref_cov=166/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/144
RA	503	.	NC_007779	2410316	0	A	C	bias_e_value=5.02006e-09	bias_p_value=1.08044e-15	fisher_strand_p_value=2.76127e-17	frequency=1.024585e-01	genotype_quality=847.0	ks_quality_p_value=1	log10_base_likelihood=-22.8367	log10_qual_likelihood_position_model=38.0013	log10_strand_likelihood_position_model=16.5589	new_cov=0/43	polymorphism_quality=17.6	quality=17.6	quality_position_model=Inf	ref_cov=157/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/135
RA	504	.	NC_007779	2414322	0	T	.	bias_e_value=948956	bias_p_value=0.204238	fisher_strand_p_value=0.0586859	frequency=1.128864e-02	genotype_quality=1381.9	ks_quality_p_value=0.877437	log10_base_likelihood=-10.4426	log10_qual_likelihood_position_model=2.71545	log10_strand_likelihood_position_model=1.23147	new_cov=0/4	polymorphism_quality=5.0	quality=5.0	quality_position_model=1.96174e-08	ref_cov=179/171	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=179/175
RA	505	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=1258.9	new_cov=145/182	quality=1258.9	ref_cov=0/0	tot_cov=145/183
RA	506	.	NC_007779	2417605	0	C	A	bias_e_value=2.0184e-06	bias_p_value=4.34408e-13	fisher_strand_p_value=5.07062e-14	frequency=1.134257e-01	genotype_quality=892.7	ks_quality_p_value=0.259925	log10_base_likelihood=-26.0695	log10_qual_likelihood_position_model=49.9644	log10_strand_likelihood_position_model=13.4371	new_cov=49/0	polymorphism_quality=20.8	quality=20.8	quality_position_model=Inf	ref_cov=135/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=184/140
RA	507	.	NC_007779	2418070	1	.	A	bias_e_value=3153400	bias_p_value=0.678687	fisher_strand_p_value=1	frequency=8.797646e-03	genotype_quality=1667.2	ks_quality_p_value=0.314831	log10_base_likelihood=-12.6706	log10_qual_likelihood_position_model=2.05586	log10_strand_likelihood_position_model=0.384848	new_cov=1/2	polymorphism_quality=7.3	quality=7.3	quality_position_model=2.91407e-12	ref_cov=151/187	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/189
RA	508	.	NC_007779	2418806	0	A	.	bias_e_value=3268490	bias_p_value=0.703455	fisher_strand_p_value=0.410681	frequency=1.817322e-02	genotype_quality=1309.6	ks_quality_p_value=0.820386	log10_base_likelihood=-17.2438	log10_qual_likelihood_position_model=2.731	log10_strand_likelihood_position_model=0.755797	new_cov=2/4	polymorphism_quality=11.9	quality=11.9	quality_position_model=7.50295e-16	ref_cov=183/141	reject=INDEL_HOMOPOLYMER	tot_cov=185/145
RA	509	.	NC_007779	2420902	0	G	C	bias_e_value=1342.73	bias_p_value=0.000288988	fisher_strand_p_value=2.58859e-05	frequency=3.018570e-02	genotype_quality=1075.4	ks_quality_p_value=0.962396	log10_base_likelihood=-10.4304	log10_qual_likelihood_position_model=12.5146	log10_strand_likelihood_position_model=4.58694	new_cov=10/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=98/194	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=108/195
RA	510	.	NC_007779	2422203	0	G	T	bias_e_value=102.471	bias_p_value=2.20542e-05	fisher_strand_p_value=1.53277e-06	frequency=3.330612e-02	genotype_quality=1201.6	ks_quality_p_value=1	log10_base_likelihood=-10.5483	log10_qual_likelihood_position_model=15.5891	log10_strand_likelihood_position_model=5.81452	new_cov=0/16	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=189/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=189/153
RA	511	.	NC_007779	2426889	0	A	C	bias_e_value=9.06548e-05	bias_p_value=1.9511e-11	fisher_strand_p_value=6.72138e-13	frequency=3.879070e-02	genotype_quality=699.7	ks_quality_p_value=1	log10_base_likelihood=-6.64593	log10_qual_likelihood_position_model=15.1218	log10_strand_likelihood_position_model=12.1725	new_cov=0/10	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=172/6	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/16
RA	512	.	NC_007779	2459734	0	T	.	bias_e_value=698947	bias_p_value=0.15043	fisher_strand_p_value=1	frequency=1.245213e-02	genotype_quality=1231.7	ks_quality_p_value=0.0344333	log10_base_likelihood=-10.8128	log10_qual_likelihood_position_model=3.33942	log10_strand_likelihood_position_model=0.436249	new_cov=2/2	polymorphism_quality=5.4	quality=5.4	quality_position_model=5.42969e-09	ref_cov=139/178	reject=INDEL_HOMOPOLYMER	tot_cov=141/180
RA	513	.	NC_007779	2468326	1	.	C	bias_e_value=4629300	bias_p_value=0.996335	fisher_strand_p_value=1	frequency=1.063728e-02	genotype_quality=1336.7	ks_quality_p_value=0.915617	log10_base_likelihood=-11.6589	log10_qual_likelihood_position_model=3.00686	log10_strand_likelihood_position_model=0.371743	new_cov=1/2	polymorphism_quality=6.3	quality=6.3	quality_position_model=2.87116e-10	ref_cov=118/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/163
RA	514	.	NC_007779	2468327	0	C	.	bias_e_value=1507950	bias_p_value=0.324546	fisher_strand_p_value=0.291309	frequency=2.786636e-02	genotype_quality=1155.9	ks_quality_p_value=0.334807	log10_base_likelihood=-24.8454	log10_qual_likelihood_position_model=3.52499	log10_strand_likelihood_position_model=0.831852	new_cov=5/3	polymorphism_quality=19.6	quality=19.6	quality_position_model=1.1463e-22	ref_cov=117/162	reject=INDEL_HOMOPOLYMER	tot_cov=122/165
RA	515	.	NC_007779	2472240	0	A	.	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=1.005554e-02	genotype_quality=1174.5	ks_quality_p_value=0.999727	log10_base_likelihood=-7.63085	log10_qual_likelihood_position_model=3.24584	log10_strand_likelihood_position_model=0.41324	new_cov=1/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=8.23567e-06	ref_cov=144/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/153
RA	516	.	NC_007779	2483692	0	A	.	bias_e_value=704571	bias_p_value=0.15164	fisher_strand_p_value=0.116364	frequency=1.005840e-02	genotype_quality=1183.9	ks_quality_p_value=0.299003	log10_base_likelihood=-7.86108	log10_qual_likelihood_position_model=1.94652	log10_strand_likelihood_position_model=0.934181	new_cov=3/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=7.2757e-07	ref_cov=143/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/152
RA	517	.	NC_007779	2497187	0	T	.	bias_e_value=2843840	bias_p_value=0.612061	fisher_strand_p_value=1	frequency=9.794235e-03	genotype_quality=1132.6	ks_quality_p_value=0.261355	log10_base_likelihood=-7.71826	log10_qual_likelihood_position_model=2.37415	log10_strand_likelihood_position_model=0.416226	new_cov=1/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=8.25093e-07	ref_cov=149/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/156
RA	518	.	NC_007779	2517218	0	A	C	bias_e_value=4.38755e-14	bias_p_value=9.44305e-21	fisher_strand_p_value=1.85007e-22	frequency=1.012034e-01	genotype_quality=728.9	ks_quality_p_value=1	log10_base_likelihood=-15.1308	log10_qual_likelihood_position_model=41.321	log10_strand_likelihood_position_model=21.7352	new_cov=1/38	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=163/35	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=164/73
RA	519	.	NC_007779	2519319	0	T	G	bias_e_value=34.5013	bias_p_value=7.42549e-06	fisher_strand_p_value=4.77371e-07	frequency=3.962517e-02	genotype_quality=1036.5	ks_quality_p_value=1	log10_base_likelihood=-6.02256	log10_qual_likelihood_position_model=22.0003	log10_strand_likelihood_position_model=6.53913	new_cov=21/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=138/156	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/156
RA	520	.	NC_007779	2536601	0	T	G	bias_e_value=7.55588	bias_p_value=1.6262e-06	fisher_strand_p_value=9.46976e-08	frequency=4.838991e-02	genotype_quality=930.6	ks_quality_p_value=1	log10_base_likelihood=-6.51509	log10_qual_likelihood_position_model=24.8563	log10_strand_likelihood_position_model=7.02366	new_cov=20/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=111/151	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/151
RA	521	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=1234.0	new_cov=151/162	quality=1234.0	ref_cov=0/0	tot_cov=151/162
RA	522	.	NC_007779	2556426	0	G	T	bias_e_value=0.00282363	bias_p_value=6.07711e-10	fisher_strand_p_value=3.81333e-11	frequency=6.478786e-02	genotype_quality=1020.3	ks_quality_p_value=0.625982	log10_base_likelihood=-14.1183	log10_qual_likelihood_position_model=32.5571	log10_strand_likelihood_position_model=10.4272	new_cov=1/31	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=183/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=184/148
RA	523	.	NC_007779	2581401	1	.	A	bias_e_value=4011220	bias_p_value=0.863308	fisher_strand_p_value=1	frequency=6.666183e-03	genotype_quality=1467.9	ks_quality_p_value=0.525032	log10_base_likelihood=-7.99649	log10_qual_likelihood_position_model=1.18787	log10_strand_likelihood_position_model=0.300527	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.90474e-08	ref_cov=156/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/143
RA	524	.	NC_007779	2581900	0	G	T	bias_e_value=0.0213326	bias_p_value=4.59127e-09	fisher_strand_p_value=1.96631e-10	frequency=5.966949e-02	genotype_quality=1026.1	ks_quality_p_value=1	log10_base_likelihood=-13.8784	log10_qual_likelihood_position_model=21.9804	log10_strand_likelihood_position_model=10.0074	new_cov=0/31	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=165/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/166
RA	525	.	NC_007779	2582251	0	G	C	bias_e_value=3599370	bias_p_value=0.774669	fisher_strand_p_value=0.409073	frequency=1.812744e-02	genotype_quality=1095.6	ks_quality_p_value=0.999839	log10_base_likelihood=-6.73778	log10_qual_likelihood_position_model=8.35073	log10_strand_likelihood_position_model=0.709657	new_cov=5/1	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=163/107	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=168/109
RA	526	.	NC_007779	2582259	0	A	C	bias_e_value=910645	bias_p_value=0.195992	fisher_strand_p_value=0.0487481	frequency=2.022743e-02	genotype_quality=1018.2	ks_quality_p_value=0.99981	log10_base_likelihood=-8.33508	log10_qual_likelihood_position_model=8.95926	log10_strand_likelihood_position_model=1.42897	new_cov=7/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=166/102	reject=POLYMORPHISM_STRAND	tot_cov=173/102
RA	527	.	NC_007779	2598509	1	.	T	bias_e_value=2547340	bias_p_value=0.548248	fisher_strand_p_value=0.248248	frequency=9.346008e-03	genotype_quality=1562.2	ks_quality_p_value=0.873344	log10_base_likelihood=-12.8236	log10_qual_likelihood_position_model=2.3933	log10_strand_likelihood_position_model=0.87093	new_cov=0/3	polymorphism_quality=7.4	quality=7.4	quality_position_model=1.40979e-11	ref_cov=156/162	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/165
RA	528	.	NC_007779	2601116	0	T	.	bias_e_value=4225940	bias_p_value=0.909523	fisher_strand_p_value=1	frequency=1.118469e-02	genotype_quality=1039.1	ks_quality_p_value=0.605984	log10_base_likelihood=-7.88382	log10_qual_likelihood_position_model=1.49133	log10_strand_likelihood_position_model=0.400528	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=6.49889e-08	ref_cov=140/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/126
RA	529	.	NC_007779	2601998	0	A	C	bias_e_value=1.83893e-14	bias_p_value=3.95782e-21	fisher_strand_p_value=7.62168e-23	frequency=1.003380e-01	genotype_quality=849.6	ks_quality_p_value=1	log10_base_likelihood=-37.6022	log10_qual_likelihood_position_model=28.8334	log10_strand_likelihood_position_model=22.1179	new_cov=0/26	polymorphism_quality=32.5	quality=32.5	quality_position_model=Inf	ref_cov=198/20	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=198/47
RA	530	.	NC_007779	2603072	0	T	.	bias_e_value=1925510	bias_p_value=0.414415	fisher_strand_p_value=0.256442	frequency=9.826660e-03	genotype_quality=1152.2	ks_quality_p_value=0.544266	log10_base_likelihood=-7.77527	log10_qual_likelihood_position_model=2.57048	log10_strand_likelihood_position_model=0.771882	new_cov=0/3	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.70836e-06	ref_cov=135/165	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/168
RA	531	.	NC_007779	2623159	0	T	G	bias_e_value=3.15623e-26	bias_p_value=6.79295e-33	fisher_strand_p_value=8.55056e-35	frequency=1.951861e-01	genotype_quality=783.7	ks_quality_p_value=1	log10_base_likelihood=-43.6369	log10_qual_likelihood_position_model=45.8422	log10_strand_likelihood_position_model=34.068	new_cov=74/0	polymorphism_quality=38.5	quality=38.5	quality_position_model=Inf	ref_cov=55/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/168
RA	532	.	NC_007779	2623173	0	G	T	bias_e_value=0.644007	bias_p_value=1.38606e-07	fisher_strand_p_value=7.00874e-09	frequency=4.759598e-02	genotype_quality=1075.0	ks_quality_p_value=1	log10_base_likelihood=-5.63248	log10_qual_likelihood_position_model=18.7251	log10_strand_likelihood_position_model=8.15436	new_cov=21/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=111/176	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/176
RA	533	.	NC_007779	2641345	0	T	G	bias_e_value=0.124525	bias_p_value=2.68006e-08	fisher_strand_p_value=1.24636e-09	frequency=5.165339e-02	genotype_quality=572.1	ks_quality_p_value=1	log10_base_likelihood=-6.3424	log10_qual_likelihood_position_model=16.2457	log10_strand_likelihood_position_model=8.90857	new_cov=12/1	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=17/133	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=29/134
RA	534	.	NC_007779	2648595	0	A	C	bias_e_value=3.91616e-05	bias_p_value=8.4285e-12	fisher_strand_p_value=2.81916e-13	frequency=5.542469e-02	genotype_quality=674.9	ks_quality_p_value=1	log10_base_likelihood=-7.60506	log10_qual_likelihood_position_model=18.7058	log10_strand_likelihood_position_model=12.5499	new_cov=0/15	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=156/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/34
RA	535	.	NC_007779	2653383	1	.	A	bias_e_value=4466910	bias_p_value=0.961384	fisher_strand_p_value=1	frequency=6.211281e-03	genotype_quality=1581.0	ks_quality_p_value=0.735289	log10_base_likelihood=-8.12062	log10_qual_likelihood_position_model=1.78905	log10_strand_likelihood_position_model=0.300753	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.92471e-08	ref_cov=168/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=169/153
RA	536	.	NC_007779	2672817	0	A	C	bias_e_value=2.06662e-09	bias_p_value=4.44786e-16	fisher_strand_p_value=1.11089e-17	frequency=9.148455e-02	genotype_quality=702.1	ks_quality_p_value=1	log10_base_likelihood=-10.9218	log10_qual_likelihood_position_model=32.3685	log10_strand_likelihood_position_model=16.9543	new_cov=0/42	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=137/69	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/111
RA	537	.	NC_007779	2680638	0	G	T	bias_e_value=35.8218	bias_p_value=7.7097e-06	fisher_strand_p_value=4.97939e-07	frequency=4.397583e-02	genotype_quality=995.9	ks_quality_p_value=0.997964	log10_base_likelihood=-10.232	log10_qual_likelihood_position_model=22.9399	log10_strand_likelihood_position_model=6.47867	new_cov=0/25	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=141/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/185
RA	538	.	NC_007779	2741186	1	.	A	bias_e_value=421072	bias_p_value=0.0906247	fisher_strand_p_value=0.237834	frequency=6.557465e-03	genotype_quality=1498.0	ks_quality_p_value=0.0760094	log10_base_likelihood=-8.0863	log10_qual_likelihood_position_model=1.40369	log10_strand_likelihood_position_model=0.623725	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.54184e-08	ref_cov=156/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/149
RA	539	.	NC_007779	2753432	1	.	A	bias_e_value=2371540	bias_p_value=0.510412	fisher_strand_p_value=0.500793	frequency=5.830765e-03	genotype_quality=1686.0	ks_quality_p_value=0.385285	log10_base_likelihood=-8.26913	log10_qual_likelihood_position_model=2.15763	log10_strand_likelihood_position_model=0.546798	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.79942e-07	ref_cov=181/160	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=183/160
RA	540	.	NC_007779	2756310	1	.	T	bias_e_value=3775380	bias_p_value=0.81255	fisher_strand_p_value=0.577657	frequency=9.346008e-03	genotype_quality=1567.8	ks_quality_p_value=0.786033	log10_base_likelihood=-12.2082	log10_qual_likelihood_position_model=1.98264	log10_strand_likelihood_position_model=0.503247	new_cov=2/1	polymorphism_quality=6.8	quality=6.8	quality_position_model=9.60935e-12	ref_cov=135/183	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/184
RA	541	.	NC_007779	2756639	0	T	.	bias_e_value=3841060	bias_p_value=0.826687	fisher_strand_p_value=1	frequency=9.700775e-03	genotype_quality=1212.4	ks_quality_p_value=0.472427	log10_base_likelihood=-7.87353	log10_qual_likelihood_position_model=2.12751	log10_strand_likelihood_position_model=0.423135	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.20588e-07	ref_cov=152/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/155
RA	542	.	NC_007779	2757983	1	.	A	bias_e_value=2164350	bias_p_value=0.465819	fisher_strand_p_value=0.498892	frequency=5.764008e-03	genotype_quality=1712.5	ks_quality_p_value=0.334662	log10_base_likelihood=-8.04253	log10_qual_likelihood_position_model=1.26985	log10_strand_likelihood_position_model=0.581012	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.04058e-08	ref_cov=176/169	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=178/169
RA	543	.	NC_007779	2759206	0	A	G	bias_e_value=4494240	bias_p_value=0.967265	fisher_strand_p_value=1	frequency=1.193047e-02	genotype_quality=1183.5	ks_quality_p_value=0.755292	log10_base_likelihood=-6.4238	log10_qual_likelihood_position_model=4.08689	log10_strand_likelihood_position_model=0.431988	new_cov=2/2	polymorphism_quality=0.9	quality=0.9	quality_position_model=0.00133013	ref_cov=168/137	reject=EVALUE	tot_cov=170/139
RA	544	.	NC_007779	2771144	0	G	T	bias_e_value=37.9707	bias_p_value=8.1722e-06	fisher_strand_p_value=5.72548e-07	frequency=4.168510e-02	genotype_quality=806.0	ks_quality_p_value=0.923691	log10_base_likelihood=-6.84629	log10_qual_likelihood_position_model=17.6685	log10_strand_likelihood_position_model=6.24219	new_cov=0/17	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=142/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/115
RA	545	.	NC_007779	2782992	1	.	T	bias_e_value=925001	bias_p_value=0.199082	fisher_strand_p_value=0.095082	frequency=1.239681e-02	genotype_quality=1176.5	ks_quality_p_value=0.52339	log10_base_likelihood=-13.0922	log10_qual_likelihood_position_model=1.79844	log10_strand_likelihood_position_model=1.0219	new_cov=3/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=2.64043e-12	ref_cov=108/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/131
RA	546	.	NC_007779	2791171	0	G	T	bias_e_value=0.10317	bias_p_value=2.22045e-08	fisher_strand_p_value=1.02324e-09	frequency=4.400158e-02	genotype_quality=960.0	ks_quality_p_value=1	log10_base_likelihood=-6.89663	log10_qual_likelihood_position_model=20.1035	log10_strand_likelihood_position_model=8.99002	new_cov=0/26	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=156/115	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/141
RA	547	.	NC_007779	2791635	0	C	T	bias_e_value=2.91438	bias_p_value=6.27243e-07	fisher_strand_p_value=3.44973e-08	frequency=4.522800e-02	genotype_quality=785.7	ks_quality_p_value=1	log10_base_likelihood=-7.9367	log10_qual_likelihood_position_model=13.3098	log10_strand_likelihood_position_model=7.46221	new_cov=0/15	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=154/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/79
RA	548	.	NC_007779	2797644	0	C	A	bias_e_value=188.514	bias_p_value=4.05726e-05	fisher_strand_p_value=2.95457e-06	frequency=4.135132e-02	genotype_quality=1153.6	ks_quality_p_value=1	log10_base_likelihood=-11.6516	log10_qual_likelihood_position_model=14.6072	log10_strand_likelihood_position_model=5.5432	new_cov=1/14	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=205/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=206/113
RA	549	.	NC_007779	2816615	0	G	C	bias_e_value=9.40086e-07	bias_p_value=2.02329e-13	fisher_strand_p_value=7.61326e-15	frequency=9.894276e-02	genotype_quality=850.4	ks_quality_p_value=0.787483	log10_base_likelihood=-34.1408	log10_qual_likelihood_position_model=30.0335	log10_strand_likelihood_position_model=14.1184	new_cov=30/0	polymorphism_quality=29.0	quality=29.0	quality_position_model=Inf	ref_cov=71/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=101/168
RA	550	.	NC_007779	2817028	1	.	C	bias_e_value=2651060	bias_p_value=0.57057	fisher_strand_p_value=0.231822	frequency=6.429672e-03	genotype_quality=1263.2	ks_quality_p_value=0.999625	log10_base_likelihood=-6.75793	log10_qual_likelihood_position_model=4.08103	log10_strand_likelihood_position_model=0.634845	new_cov=2/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=0.00094132	ref_cov=148/161	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=150/161
RA	551	.	NC_007779	2817030	0	G	C	bias_e_value=8.00504e-14	bias_p_value=1.72287e-20	fisher_strand_p_value=7.34122e-22	frequency=1.525230e-01	genotype_quality=781.8	ks_quality_p_value=0.465384	log10_base_likelihood=-58.4598	log10_qual_likelihood_position_model=41.836	log10_strand_likelihood_position_model=21.1342	new_cov=45/0	polymorphism_quality=53.4	quality=53.4	quality_position_model=Inf	ref_cov=63/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=108/165
RA	552	.	NC_007779	2825119	0	A	.	bias_e_value=2647660	bias_p_value=0.569839	fisher_strand_p_value=0.590302	frequency=9.305954e-03	genotype_quality=1241.7	ks_quality_p_value=0.391726	log10_base_likelihood=-7.53571	log10_qual_likelihood_position_model=2.79236	log10_strand_likelihood_position_model=0.474686	new_cov=1/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=4.02239e-06	ref_cov=176/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=177/145
RA	553	.	NC_007779	2833904	0	A	C	bias_e_value=7.53638e-09	bias_p_value=1.62201e-15	fisher_strand_p_value=4.19002e-17	frequency=7.008505e-02	genotype_quality=935.6	ks_quality_p_value=1	log10_base_likelihood=-10.5206	log10_qual_likelihood_position_model=33.0187	log10_strand_likelihood_position_model=16.3778	new_cov=0/42	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=174/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=174/141
RA	554	.	NC_007779	2833989	0	A	C	bias_e_value=3.40952e-14	bias_p_value=7.3381e-21	fisher_strand_p_value=1.43046e-22	frequency=1.029034e-01	genotype_quality=882.1	ks_quality_p_value=1	log10_base_likelihood=-28.58	log10_qual_likelihood_position_model=36.7938	log10_strand_likelihood_position_model=21.8468	new_cov=1/35	polymorphism_quality=23.4	quality=23.4	quality_position_model=Inf	ref_cov=195/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=196/72
RA	555	.	NC_007779	2847445	0	G	T	bias_e_value=0.000905071	bias_p_value=1.94793e-10	fisher_strand_p_value=7.31161e-12	frequency=6.590271e-02	genotype_quality=973.1	ks_quality_p_value=1	log10_base_likelihood=-11.2708	log10_qual_likelihood_position_model=22.9169	log10_strand_likelihood_position_model=11.136	new_cov=0/34	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=161/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/160
RA	556	.	NC_007779	2862772	0	A	.	bias_e_value=1859920	bias_p_value=0.400298	fisher_strand_p_value=0.132511	frequency=1.445961e-02	genotype_quality=1065.4	ks_quality_p_value=0.999892	log10_base_likelihood=-8.99494	log10_qual_likelihood_position_model=7.66227	log10_strand_likelihood_position_model=1.01985	new_cov=0/4	polymorphism_quality=3.5	quality=3.5	quality_position_model=0.113533	ref_cov=121/149	reject=POLYMORPHISM_STRAND	tot_cov=122/154
RA	557	.	NC_007779	2862781	0	C	G	bias_e_value=974020	bias_p_value=0.209632	fisher_strand_p_value=0.256595	frequency=1.078606e-02	genotype_quality=1127.4	ks_quality_p_value=0.207808	log10_base_likelihood=-6.90025	log10_qual_likelihood_position_model=2.45175	log10_strand_likelihood_position_model=0.769585	new_cov=0/3	polymorphism_quality=1.4	quality=1.4	quality_position_model=1.67375e-05	ref_cov=124/152	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=125/155
RA	558	.	NC_007779	2862783	1	.	T	bias_e_value=2825270	bias_p_value=0.608066	fisher_strand_p_value=0.25841	frequency=1.071072e-02	genotype_quality=1363.9	ks_quality_p_value=0.999923	log10_base_likelihood=-9.32886	log10_qual_likelihood_position_model=6.25763	log10_strand_likelihood_position_model=0.757451	new_cov=0/3	polymorphism_quality=3.9	quality=3.9	quality_position_model=0.000476909	ref_cov=123/154	reject=POLYMORPHISM_STRAND	tot_cov=123/157
RA	559	.	NC_007779	2865228	0	A	G	bias_e_value=2269360	bias_p_value=0.488419	fisher_strand_p_value=0.18145	frequency=2.429676e-02	genotype_quality=1372.7	ks_quality_p_value=0.991222	log10_base_likelihood=-16.481	log10_qual_likelihood_position_model=6.60408	log10_strand_likelihood_position_model=1.03638	new_cov=7/2	polymorphism_quality=11.2	quality=11.2	quality_position_model=7.66034e-11	ref_cov=187/170	tot_cov=194/172
RA	560	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1378.1	new_cov=143/181	quality=1378.1	ref_cov=0/0	tot_cov=143/181
RA	561	.	NC_007779	2868094	0	C	A	bias_e_value=6.62953e-05	bias_p_value=1.42683e-11	fisher_strand_p_value=4.86105e-13	frequency=7.760429e-02	genotype_quality=1078.4	ks_quality_p_value=1	log10_base_likelihood=-14.7735	log10_qual_likelihood_position_model=29.598	log10_strand_likelihood_position_model=12.3211	new_cov=40/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=138/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=178/163
RA	562	.	NC_007779	2872916	0	T	G	bias_e_value=0.227305	bias_p_value=4.89214e-08	fisher_strand_p_value=2.34394e-09	frequency=3.637409e-02	genotype_quality=1003.9	ks_quality_p_value=1	log10_base_likelihood=-5.9184	log10_qual_likelihood_position_model=33.3618	log10_strand_likelihood_position_model=8.63005	new_cov=25/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=124/166	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/166
RA	563	.	NC_007779	2875204	1	.	A	bias_e_value=4380970	bias_p_value=0.942889	fisher_strand_p_value=1	frequency=6.779671e-03	genotype_quality=1441.0	ks_quality_p_value=0.68166	log10_base_likelihood=-7.96353	log10_qual_likelihood_position_model=1.57569	log10_strand_likelihood_position_model=0.301	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.18507e-08	ref_cov=155/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/139
RA	564	.	NC_007779	2880754	0	A	T	bias_e_value=4630650	bias_p_value=0.996626	fisher_strand_p_value=1	frequency=7.355690e-03	genotype_quality=1597.0	ks_quality_p_value=0.918981	log10_base_likelihood=-5.85719	log10_qual_likelihood_position_model=2.61401	log10_strand_likelihood_position_model=0.403147	new_cov=1/2	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.000129721	ref_cov=191/212	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=192/214
RA	565	.	NC_007779	2895131	0	A	C	bias_e_value=1.53835e-15	bias_p_value=3.31089e-22	fisher_strand_p_value=6.07981e-24	frequency=1.349134e-01	genotype_quality=753.0	ks_quality_p_value=1	log10_base_likelihood=-29.1163	log10_qual_likelihood_position_model=49.0272	log10_strand_likelihood_position_model=23.2161	new_cov=0/48	polymorphism_quality=23.9	quality=23.9	quality_position_model=Inf	ref_cov=153/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/100
RA	566	.	NC_007779	2895144	0	G	C	bias_e_value=600.42	bias_p_value=0.000129224	fisher_strand_p_value=1.03562e-05	frequency=6.138182e-02	genotype_quality=740.7	ks_quality_p_value=1	log10_base_likelihood=-8.92226	log10_qual_likelihood_position_model=17.9285	log10_strand_likelihood_position_model=5.0133	new_cov=2/17	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=129/77	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/95
RA	567	.	NC_007779	2898837	0	G	T	bias_e_value=1.13241e-05	bias_p_value=2.43721e-12	fisher_strand_p_value=7.81661e-14	frequency=6.147337e-02	genotype_quality=1130.1	ks_quality_p_value=1	log10_base_likelihood=-11.0495	log10_qual_likelihood_position_model=31.1558	log10_strand_likelihood_position_model=13.107	new_cov=0/36	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=185/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=185/159
RA	568	.	NC_007779	2898953	1	.	A	bias_e_value=4498610	bias_p_value=0.968206	fisher_strand_p_value=1	frequency=1.840496e-02	genotype_quality=1546.1	ks_quality_p_value=0.75867	log10_base_likelihood=-26.0501	log10_qual_likelihood_position_model=3.02104	log10_strand_likelihood_position_model=0.502911	new_cov=3/3	polymorphism_quality=20.8	quality=20.8	quality_position_model=1.0035e-24	ref_cov=154/166	reject=INDEL_HOMOPOLYMER	tot_cov=157/169
RA	569	.	NC_007779	2898954	0	A	.	bias_e_value=42485.8	bias_p_value=0.00914394	fisher_strand_p_value=0.0325715	frequency=2.416134e-02	genotype_quality=1303.7	ks_quality_p_value=0.0362649	log10_base_likelihood=-24.5273	log10_qual_likelihood_position_model=4.41828	log10_strand_likelihood_position_model=1.59771	new_cov=7/1	polymorphism_quality=19.3	quality=19.3	quality_position_model=1.14321e-20	ref_cov=154/169	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=161/170
RA	570	.	NC_007779	2899175	1	.	G	bias_e_value=2588710	bias_p_value=0.557151	fisher_strand_p_value=0.222713	frequency=6.057739e-03	genotype_quality=1621.0	ks_quality_p_value=0.999852	log10_base_likelihood=-5.96438	log10_qual_likelihood_position_model=4.13262	log10_strand_likelihood_position_model=0.652254	new_cov=2/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=0.00867332	ref_cov=154/174	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=156/174
RA	571	.	NC_007779	2911644	0	G	T	bias_e_value=1.38835e-06	bias_p_value=2.98806e-13	fisher_strand_p_value=1.0901e-14	frequency=8.728313e-02	genotype_quality=1000.5	ks_quality_p_value=0.822018	log10_base_likelihood=-21.1761	log10_qual_likelihood_position_model=35.1263	log10_strand_likelihood_position_model=13.9625	new_cov=0/41	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=167/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/161
RA	572	.	NC_007779	2926157	0	T	G	bias_e_value=1.46379e-20	bias_p_value=3.15043e-27	fisher_strand_p_value=4.75787e-29	frequency=1.293588e-01	genotype_quality=752.2	ks_quality_p_value=1	log10_base_likelihood=-30.7285	log10_qual_likelihood_position_model=37.2075	log10_strand_likelihood_position_model=28.3226	new_cov=40/0	polymorphism_quality=25.5	quality=25.5	quality_position_model=Inf	ref_cov=24/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=64/176
RA	573	.	NC_007779	2941550	0	T	.	bias_e_value=3100740	bias_p_value=0.667353	fisher_strand_p_value=1	frequency=8.712769e-03	genotype_quality=1360.0	ks_quality_p_value=0.305154	log10_base_likelihood=-7.77548	log10_qual_likelihood_position_model=2.21533	log10_strand_likelihood_position_model=0.393416	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=4.65703e-07	ref_cov=184/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=186/158
RA	574	.	NC_007779	2953753	0	C	.	bias_e_value=3842250	bias_p_value=0.826942	fisher_strand_p_value=0.615198	frequency=7.947922e-03	genotype_quality=1528.8	ks_quality_p_value=0.768479	log10_base_likelihood=-7.52905	log10_qual_likelihood_position_model=2.31858	log10_strand_likelihood_position_model=0.435613	new_cov=1/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.1909e-06	ref_cov=192/182	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=193/184
RA	575	.	NC_007779	2974959	1	.	A	bias_e_value=4177740	bias_p_value=0.899147	fisher_strand_p_value=1	frequency=6.024361e-03	genotype_quality=1622.5	ks_quality_p_value=0.58594	log10_base_likelihood=-7.90818	log10_qual_likelihood_position_model=1.24163	log10_strand_likelihood_position_model=0.300288	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.6679e-08	ref_cov=171/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=172/160
RA	576	.	NC_007779	2974960	0	A	.	bias_e_value=4610560	bias_p_value=0.992302	fisher_strand_p_value=1	frequency=8.947372e-03	genotype_quality=1329.4	ks_quality_p_value=0.878511	log10_base_likelihood=-7.83107	log10_qual_likelihood_position_model=1.61561	log10_strand_likelihood_position_model=0.411025	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.01585e-07	ref_cov=171/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=173/162
RA	577	.	NC_007779	2981813	0	G	T	bias_e_value=13237.9	bias_p_value=0.0028491	fisher_strand_p_value=0.000314291	frequency=2.435398e-02	genotype_quality=1047.4	ks_quality_p_value=1	log10_base_likelihood=-5.57636	log10_qual_likelihood_position_model=11.9164	log10_strand_likelihood_position_model=3.54321	new_cov=0/13	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=144/158	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/172
RA	578	.	NC_007779	2983097	0	A	C	bias_e_value=0.000349586	bias_p_value=7.52391e-11	fisher_strand_p_value=2.72317e-12	frequency=4.852724e-02	genotype_quality=727.8	ks_quality_p_value=1	log10_base_likelihood=-5.59491	log10_qual_likelihood_position_model=30.9333	log10_strand_likelihood_position_model=11.5649	new_cov=0/27	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=137/68	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/95
RA	579	.	NC_007779	2987535	0	A	C	bias_e_value=1.36435e-12	bias_p_value=2.93641e-19	fisher_strand_p_value=6.17757e-21	frequency=9.957647e-02	genotype_quality=1017.3	ks_quality_p_value=1	log10_base_likelihood=-17.3741	log10_qual_likelihood_position_model=46.9326	log10_strand_likelihood_position_model=20.2092	new_cov=0/50	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=191/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=191/151
RA	580	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=1221.3	new_cov=153/152	quality=1221.3	ref_cov=0/0	tot_cov=153/152
RA	581	.	NC_007779	3029385	0	C	A	bias_e_value=1.69386	bias_p_value=3.64559e-07	fisher_strand_p_value=2.00826e-08	frequency=3.436470e-02	genotype_quality=1004.8	ks_quality_p_value=0.967844	log10_base_likelihood=-10.0187	log10_qual_likelihood_position_model=15.4069	log10_strand_likelihood_position_model=7.69718	new_cov=0/11	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=208/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=208/58
RA	582	.	NC_007779	3034413	0	A	C	bias_e_value=8.02877e-18	bias_p_value=1.72798e-24	fisher_strand_p_value=2.8893e-26	frequency=1.656451e-01	genotype_quality=662.2	ks_quality_p_value=1	log10_base_likelihood=-30.8498	log10_qual_likelihood_position_model=41.047	log10_strand_likelihood_position_model=25.5392	new_cov=0/55	polymorphism_quality=25.7	quality=25.7	quality_position_model=Inf	ref_cov=141/48	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/105
RA	583	.	NC_007779	3035390	0	T	C	bias_e_value=2.86596e-09	bias_p_value=6.16822e-16	fisher_strand_p_value=1.55358e-17	frequency=1.237569e-01	genotype_quality=628.1	ks_quality_p_value=1	log10_base_likelihood=-31.8339	log10_qual_likelihood_position_model=24.4817	log10_strand_likelihood_position_model=16.8087	new_cov=0/35	polymorphism_quality=26.6	quality=26.6	quality_position_model=Inf	ref_cov=160/62	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/97
RA	584	.	NC_007779	3044705	1	.	T	bias_e_value=26630.6	bias_p_value=0.00573153	fisher_strand_p_value=0.000728366	frequency=2.336407e-02	genotype_quality=967.8	ks_quality_p_value=0.950938	log10_base_likelihood=-22.5415	log10_qual_likelihood_position_model=5.89348	log10_strand_likelihood_position_model=3.13765	new_cov=5/0	polymorphism_quality=17.3	quality=17.3	quality_position_model=1.33562e-15	ref_cov=47/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=52/162
RA	585	.	NC_007779	3044712	0	T	C	bias_e_value=6.19785e-05	bias_p_value=1.33392e-11	fisher_strand_p_value=4.53375e-13	frequency=5.644608e-02	genotype_quality=637.4	ks_quality_p_value=1	log10_base_likelihood=-13.4524	log10_qual_likelihood_position_model=16.8263	log10_strand_likelihood_position_model=12.3435	new_cov=13/0	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=15/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=28/171
RA	586	.	NC_007779	3044714	0	A	C	bias_e_value=0.0287246	bias_p_value=6.1822e-09	fisher_strand_p_value=2.68339e-10	frequency=4.786587e-02	genotype_quality=593.0	ks_quality_p_value=1	log10_base_likelihood=-11.5931	log10_qual_likelihood_position_model=13.4511	log10_strand_likelihood_position_model=9.5751	new_cov=12/1	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=20/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=32/176
RA	587	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=1319.1	new_cov=165/171	quality=1319.1	ref_cov=0/0	tot_cov=165/171
RA	588	.	NC_007779	3084663	0	C	A	bias_e_value=5.97073	bias_p_value=1.28504e-06	fisher_strand_p_value=7.37577e-08	frequency=4.504585e-02	genotype_quality=1066.4	ks_quality_p_value=1	log10_base_likelihood=-11.2235	log10_qual_likelihood_position_model=18.4881	log10_strand_likelihood_position_model=7.19992	new_cov=28/0	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=169/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=197/148
RA	589	.	NC_007779	3088549	0	G	T	bias_e_value=0.000556448	bias_p_value=1.19761e-10	fisher_strand_p_value=4.4116e-12	frequency=8.349657e-02	genotype_quality=958.9	ks_quality_p_value=1	log10_base_likelihood=-19.1802	log10_qual_likelihood_position_model=24.2071	log10_strand_likelihood_position_model=11.5456	new_cov=0/42	polymorphism_quality=13.9	quality=13.9	quality_position_model=Inf	ref_cov=150/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/191
RA	590	.	NC_007779	3090796	0	A	C	bias_e_value=0.0234253	bias_p_value=5.04167e-09	fisher_strand_p_value=2.16828e-10	frequency=5.066538e-02	genotype_quality=894.4	ks_quality_p_value=1	log10_base_likelihood=-7.73239	log10_qual_likelihood_position_model=27.1243	log10_strand_likelihood_position_model=9.9077	new_cov=0/33	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=143/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/161
RA	591	.	NC_007779	3124046	0	C	A	bias_e_value=3.891	bias_p_value=8.37435e-07	fisher_strand_p_value=4.68666e-08	frequency=3.230476e-02	genotype_quality=993.9	ks_quality_p_value=0.999555	log10_base_likelihood=-6.54931	log10_qual_likelihood_position_model=15.6466	log10_strand_likelihood_position_model=7.32914	new_cov=21/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=127/170	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/170
RA	592	.	NC_007779	3124070	0	G	.	bias_e_value=4645840	bias_p_value=0.999894	fisher_strand_p_value=1	frequency=1.722813e-02	genotype_quality=1179.0	ks_quality_p_value=0.985467	log10_base_likelihood=-13.8104	log10_qual_likelihood_position_model=3.98276	log10_strand_likelihood_position_model=0.475003	new_cov=2/3	polymorphism_quality=8.4	quality=8.4	quality_position_model=2.29322e-11	ref_cov=132/153	tot_cov=134/156
RA	593	.	NC_007779	3124071	0	C	.	bias_e_value=4645980	bias_p_value=0.999924	fisher_strand_p_value=1	frequency=1.740932e-02	genotype_quality=1169.1	ks_quality_p_value=0.98772	log10_base_likelihood=-13.9099	log10_qual_likelihood_position_model=3.97083	log10_strand_likelihood_position_model=0.475716	new_cov=2/3	polymorphism_quality=8.5	quality=8.5	quality_position_model=1.76715e-11	ref_cov=131/151	tot_cov=133/154
RA	594	.	NC_007779	3152854	1	.	A	bias_e_value=4400580	bias_p_value=0.947109	fisher_strand_p_value=1	frequency=6.288528e-03	genotype_quality=1555.3	ks_quality_p_value=0.692914	log10_base_likelihood=-7.51457	log10_qual_likelihood_position_model=2.48497	log10_strand_likelihood_position_model=0.301746	new_cov=1/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.33311e-06	ref_cov=147/169	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/170
RA	595	.	NC_007779	3160153	0	G	C	bias_e_value=0.0962354	bias_p_value=2.07121e-08	fisher_strand_p_value=9.53577e-10	frequency=5.121279e-02	genotype_quality=752.9	ks_quality_p_value=0.997577	log10_base_likelihood=-11.7241	log10_qual_likelihood_position_model=15.0561	log10_strand_likelihood_position_model=9.02064	new_cov=12/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=29/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=41/164
RA	596	.	NC_007779	3190386	0	C	A	bias_e_value=8498.81	bias_p_value=0.00182914	fisher_strand_p_value=0.000192931	frequency=2.459145e-02	genotype_quality=1101.9	ks_quality_p_value=0.991542	log10_base_likelihood=-6.67051	log10_qual_likelihood_position_model=15.4044	log10_strand_likelihood_position_model=3.7633	new_cov=15/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=142/157	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/158
RA	597	.	NC_007779	3195467	0	A	C	bias_e_value=4.11016	bias_p_value=8.84603e-07	fisher_strand_p_value=4.96456e-08	frequency=3.464127e-02	genotype_quality=1035.3	ks_quality_p_value=1	log10_base_likelihood=-5.57694	log10_qual_likelihood_position_model=20.6412	log10_strand_likelihood_position_model=7.30412	new_cov=0/18	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=186/111	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=186/129
RA	598	.	NC_007779	3212355	0	G	C	bias_e_value=2.34727	bias_p_value=5.05187e-07	fisher_strand_p_value=2.85504e-08	frequency=4.776096e-02	genotype_quality=906.9	ks_quality_p_value=0.961072	log10_base_likelihood=-13.0245	log10_qual_likelihood_position_model=18.4023	log10_strand_likelihood_position_model=7.54439	new_cov=15/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=70/170	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=85/170
RA	599	.	NC_007779	3231302	0	C	G	bias_e_value=35.3168	bias_p_value=7.601e-06	fisher_strand_p_value=4.9164e-07	frequency=4.212856e-02	genotype_quality=830.7	ks_quality_p_value=0.995525	log10_base_likelihood=-7.40584	log10_qual_likelihood_position_model=17.0835	log10_strand_likelihood_position_model=6.30835	new_cov=0/13	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=154/68	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/81
RA	600	.	NC_007779	3231832	1	.	G	bias_e_value=474710	bias_p_value=0.102169	fisher_strand_p_value=0.0347835	frequency=1.234531e-02	genotype_quality=1179.0	ks_quality_p_value=0.60404	log10_base_likelihood=-12.8659	log10_qual_likelihood_position_model=1.9091	log10_strand_likelihood_position_model=1.45863	new_cov=3/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=1.62813e-11	ref_cov=77/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=80/163
RA	601	.	NC_007779	3238279	0	C	G	bias_e_value=11894.3	bias_p_value=0.00255993	fisher_strand_p_value=0.000279787	frequency=2.165318e-02	genotype_quality=706.6	ks_quality_p_value=0.9961	log10_base_likelihood=-6.923	log10_qual_likelihood_position_model=4.87711	log10_strand_likelihood_position_model=3.55317	new_cov=0/4	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=158/21	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/25
RA	602	.	NC_007779	3258468	0	G	T	bias_e_value=167.861	bias_p_value=3.61276e-05	fisher_strand_p_value=2.63685e-06	frequency=5.264139e-02	genotype_quality=1009.3	ks_quality_p_value=0.988726	log10_base_likelihood=-21.7739	log10_qual_likelihood_position_model=14.8696	log10_strand_likelihood_position_model=5.74212	new_cov=1/20	polymorphism_quality=16.5	quality=16.5	quality_position_model=0.00908234	ref_cov=165/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/149
RA	603	.	NC_007779	3259711	0	A	C	bias_e_value=9.68662e-07	bias_p_value=2.08479e-13	fisher_strand_p_value=6.18321e-15	frequency=1.082044e-01	genotype_quality=771.8	ks_quality_p_value=1	log10_base_likelihood=-19.6218	log10_qual_likelihood_position_model=26.8142	log10_strand_likelihood_position_model=14.2148	new_cov=1/42	polymorphism_quality=14.3	quality=14.3	quality_position_model=Inf	ref_cov=145/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/129
RA	604	.	NC_007779	3266843	0	C	G	bias_e_value=289.13	bias_p_value=6.22275e-05	fisher_strand_p_value=4.71874e-06	frequency=3.130054e-02	genotype_quality=854.5	ks_quality_p_value=0.993751	log10_base_likelihood=-8.35899	log10_qual_likelihood_position_model=12.6191	log10_strand_likelihood_position_model=5.32617	new_cov=0/10	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=160/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/71
RA	605	.	NC_007779	3270337	0	C	.	bias_e_value=1618460	bias_p_value=0.348331	fisher_strand_p_value=0.2499	frequency=9.926796e-03	genotype_quality=1207.5	ks_quality_p_value=0.432107	log10_base_likelihood=-8.15392	log10_qual_likelihood_position_model=1.08955	log10_strand_likelihood_position_model=0.835405	new_cov=0/3	polymorphism_quality=2.7	quality=2.7	quality_position_model=3.69768e-08	ref_cov=142/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/159
RA	606	.	NC_007779	3274975	0	G	T	bias_e_value=0.00522092	bias_p_value=1.12366e-09	fisher_strand_p_value=4.52757e-11	frequency=3.305817e-02	genotype_quality=1159.1	ks_quality_p_value=1	log10_base_likelihood=-5.77383	log10_qual_likelihood_position_model=18.4039	log10_strand_likelihood_position_model=10.3441	new_cov=0/18	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=224/72	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=224/90
RA	607	.	NC_007779	3280326	0	A	C	bias_e_value=1.57174e-27	bias_p_value=3.38275e-34	fisher_strand_p_value=4.10121e-36	frequency=1.687813e-01	genotype_quality=816.1	ks_quality_p_value=1	log10_base_likelihood=-32.7502	log10_qual_likelihood_position_model=51.3715	log10_strand_likelihood_position_model=35.3871	new_cov=0/71	polymorphism_quality=27.6	quality=27.6	quality_position_model=Inf	ref_cov=180/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=180/122
RA	608	.	NC_007779	3285688	1	.	G	bias_e_value=600779	bias_p_value=0.129302	fisher_strand_p_value=0.0797854	frequency=1.013470e-02	genotype_quality=1449.2	ks_quality_p_value=0.355107	log10_base_likelihood=-12.6308	log10_qual_likelihood_position_model=1.6749	log10_strand_likelihood_position_model=1.09808	new_cov=3/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=6.98714e-12	ref_cov=125/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/168
RA	609	.	NC_007779	3300073	0	T	G	bias_e_value=2.70793e-05	bias_p_value=5.8281e-12	fisher_strand_p_value=1.92481e-13	frequency=1.204762e-01	genotype_quality=641.3	ks_quality_p_value=1	log10_base_likelihood=-18.3202	log10_qual_likelihood_position_model=38.2818	log10_strand_likelihood_position_model=12.7314	new_cov=39/0	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=80/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/111
RA	610	.	NC_007779	3325139	0	G	T	bias_e_value=5.35287	bias_p_value=1.15206e-06	fisher_strand_p_value=6.56882e-08	frequency=3.159428e-02	genotype_quality=1190.7	ks_quality_p_value=1	log10_base_likelihood=-6.55406	log10_qual_likelihood_position_model=18.6335	log10_strand_likelihood_position_model=7.27593	new_cov=0/24	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=175/161	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/185
RA	611	.	NC_007779	3326059	0	T	.	bias_e_value=1030440	bias_p_value=0.221774	fisher_strand_p_value=0.120662	frequency=8.734703e-03	genotype_quality=1251.3	ks_quality_p_value=0.4767	log10_base_likelihood=-7.35832	log10_qual_likelihood_position_model=1.95418	log10_strand_likelihood_position_model=0.91843	new_cov=0/3	polymorphism_quality=1.9	quality=1.9	quality_position_model=2.38525e-06	ref_cov=173/167	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=173/170
RA	612	.	NC_007779	3326067	1	.	C	bias_e_value=1650080	bias_p_value=0.355137	fisher_strand_p_value=0.120367	frequency=9.345055e-03	genotype_quality=1569.5	ks_quality_p_value=0.922685	log10_base_likelihood=-11.8678	log10_qual_likelihood_position_model=2.45585	log10_strand_likelihood_position_model=0.919492	new_cov=0/3	polymorphism_quality=6.5	quality=6.5	quality_position_model=1.74043e-10	ref_cov=162/156	reject=POLYMORPHISM_STRAND	tot_cov=162/159
RA	613	.	NC_007779	3326071	0	C	G	bias_e_value=1697980	bias_p_value=0.365444	fisher_strand_p_value=0.12271	frequency=9.181976e-03	genotype_quality=1346.4	ks_quality_p_value=0.943659	log10_base_likelihood=-6.17753	log10_qual_likelihood_position_model=2.11943	log10_strand_likelihood_position_model=0.91112	new_cov=0/3	polymorphism_quality=0.6	quality=0.6	quality_position_model=6.11215e-05	ref_cov=164/160	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=164/164
RA	614	.	NC_007779	3326077	0	T	A	bias_e_value=1036000	bias_p_value=0.222972	fisher_strand_p_value=0.0579999	frequency=9.880066e-03	genotype_quality=1352.6	ks_quality_p_value=0.998962	log10_base_likelihood=-6.7405	log10_qual_likelihood_position_model=3.88624	log10_strand_likelihood_position_model=1.23657	new_cov=0/4	polymorphism_quality=1.2	quality=1.2	quality_position_model=0.0027642	ref_cov=179/170	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=179/174
RA	615	.	NC_007779	3326085	0	T	A	bias_e_value=1445170	bias_p_value=0.311034	fisher_strand_p_value=0.106486	frequency=8.613586e-03	genotype_quality=1339.5	ks_quality_p_value=0.862097	log10_base_likelihood=-5.90556	log10_qual_likelihood_position_model=3.06201	log10_strand_likelihood_position_model=0.972709	new_cov=0/3	polymorphism_quality=0.4	quality=0.4	quality_position_model=0.00144995	ref_cov=182/162	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=182/165
RA	616	.	NC_007779	3326101	0	T	G	bias_e_value=826598	bias_p_value=0.177903	fisher_strand_p_value=0.248012	frequency=8.857727e-03	genotype_quality=1295.2	ks_quality_p_value=0.172869	log10_base_likelihood=-6.58462	log10_qual_likelihood_position_model=2.63389	log10_strand_likelihood_position_model=0.883912	new_cov=0/3	polymorphism_quality=1.1	quality=1.1	quality_position_model=7.43645e-05	ref_cov=166/169	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=166/172
RA	617	.	NC_007779	3326107	0	C	G	bias_e_value=967724	bias_p_value=0.208277	fisher_strand_p_value=0.249069	frequency=8.964539e-03	genotype_quality=1353.1	ks_quality_p_value=0.212234	log10_base_likelihood=-6.71957	log10_qual_likelihood_position_model=2.14543	log10_strand_likelihood_position_model=0.853205	new_cov=0/3	polymorphism_quality=1.2	quality=1.2	quality_position_model=1.51158e-05	ref_cov=160/171	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=160/174
RA	618	.	NC_007779	3326125	0	T	G	bias_e_value=233634	bias_p_value=0.0502836	fisher_strand_p_value=0.251908	frequency=8.886337e-03	genotype_quality=1294.2	ks_quality_p_value=0.0347936	log10_base_likelihood=-6.90818	log10_qual_likelihood_position_model=2.46368	log10_strand_likelihood_position_model=0.81321	new_cov=0/3	polymorphism_quality=1.4	quality=1.4	quality_position_model=1.87882e-05	ref_cov=156/178	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=156/181
RA	619	.	NC_007779	3333429	1	.	A	bias_e_value=1019900	bias_p_value=0.219506	fisher_strand_p_value=1	frequency=7.092476e-03	genotype_quality=1380.3	ks_quality_p_value=0.0567271	log10_base_likelihood=-8.09312	log10_qual_likelihood_position_model=1.62203	log10_strand_likelihood_position_model=0.299684	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.24016e-08	ref_cov=137/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/144
RA	620	.	NC_007779	3333612	0	T	G	bias_e_value=1.85424e-05	bias_p_value=3.99075e-12	fisher_strand_p_value=1.30118e-13	frequency=4.627037e-02	genotype_quality=708.3	ks_quality_p_value=1	log10_base_likelihood=-9.3757	log10_qual_likelihood_position_model=16.0662	log10_strand_likelihood_position_model=12.8857	new_cov=11/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=7/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=18/174
RA	621	.	NC_007779	3350033	0	C	.	bias_e_value=4022980	bias_p_value=0.86584	fisher_strand_p_value=0.580332	frequency=9.668350e-03	genotype_quality=1287.0	ks_quality_p_value=0.91152	log10_base_likelihood=-7.81034	log10_qual_likelihood_position_model=2.01397	log10_strand_likelihood_position_model=0.496281	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=3.38538e-07	ref_cov=175/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=176/134
RA	622	.	NC_007779	3350708	0	A	C	bias_e_value=0.000393522	bias_p_value=8.46951e-11	fisher_strand_p_value=3.07911e-12	frequency=7.900667e-02	genotype_quality=907.9	ks_quality_p_value=1	log10_base_likelihood=-16.6582	log10_qual_likelihood_position_model=30.0341	log10_strand_likelihood_position_model=11.5474	new_cov=0/39	polymorphism_quality=11.3	quality=11.3	quality_position_model=Inf	ref_cov=145/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/168
RA	623	.	NC_007779	3357279	0	C	A	bias_e_value=0.703146	bias_p_value=1.51334e-07	fisher_strand_p_value=9.37746e-09	frequency=4.338837e-02	genotype_quality=888.0	ks_quality_p_value=0.819873	log10_base_likelihood=-6.15443	log10_qual_likelihood_position_model=22.7213	log10_strand_likelihood_position_model=8.02791	new_cov=21/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=104/162	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/163
RA	624	.	NC_007779	3382034	0	T	.	bias_e_value=1529480	bias_p_value=0.329181	fisher_strand_p_value=0.248203	frequency=9.698868e-03	genotype_quality=1214.3	ks_quality_p_value=0.401012	log10_base_likelihood=-7.66988	log10_qual_likelihood_position_model=2.10753	log10_strand_likelihood_position_model=0.869694	new_cov=3/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.45064e-06	ref_cov=156/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/150
RA	625	.	NC_007779	3385701	0	T	.	bias_e_value=3183100	bias_p_value=0.685078	fisher_strand_p_value=0.59368	frequency=9.081841e-03	genotype_quality=1262.0	ks_quality_p_value=0.53969	log10_base_likelihood=-7.72339	log10_qual_likelihood_position_model=1.54286	log10_strand_likelihood_position_model=0.468366	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.26578e-07	ref_cov=148/178	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/179
RA	626	.	NC_007779	3389914	0	A	C	bias_e_value=6.82782e-10	bias_p_value=1.46951e-16	fisher_strand_p_value=3.56899e-18	frequency=7.931995e-02	genotype_quality=892.0	ks_quality_p_value=1	log10_base_likelihood=-10.8434	log10_qual_likelihood_position_model=34.2739	log10_strand_likelihood_position_model=17.4475	new_cov=0/46	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=161/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/140
RA	627	.	NC_007779	3392267	0	C	A	bias_e_value=5.17183e-05	bias_p_value=1.1131e-11	fisher_strand_p_value=3.75928e-13	frequency=4.197788e-02	genotype_quality=1263.8	ks_quality_p_value=1	log10_base_likelihood=-9.34183	log10_qual_likelihood_position_model=19.781	log10_strand_likelihood_position_model=12.4249	new_cov=28/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=118/235	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/235
RA	628	.	NC_007779	3397405	0	A	C	bias_e_value=3.92135e-22	bias_p_value=8.43967e-29	fisher_strand_p_value=1.20758e-30	frequency=1.715174e-01	genotype_quality=744.4	ks_quality_p_value=1	log10_base_likelihood=-28.5232	log10_qual_likelihood_position_model=45.1354	log10_strand_likelihood_position_model=29.9181	new_cov=0/69	polymorphism_quality=23.3	quality=23.3	quality_position_model=Inf	ref_cov=156/59	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/129
RA	629	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1396.0	new_cov=172/156	quality=1396.0	ref_cov=0/1	tot_cov=172/157
RA	630	.	NC_007779	3400106	1	.	G	bias_e_value=2676300	bias_p_value=0.576003	fisher_strand_p_value=0.247475	frequency=6.733894e-03	genotype_quality=1452.5	ks_quality_p_value=0.951498	log10_base_likelihood=-7.64484	log10_qual_likelihood_position_model=1.75092	log10_strand_likelihood_position_model=0.606469	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=3.48928e-07	ref_cov=146/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/149
RA	631	.	NC_007779	3404070	0	T	G	bias_e_value=0.0389656	bias_p_value=8.38632e-09	fisher_strand_p_value=3.69118e-10	frequency=7.499123e-02	genotype_quality=701.9	ks_quality_p_value=1	log10_base_likelihood=-11.3957	log10_qual_likelihood_position_model=21.9167	log10_strand_likelihood_position_model=9.43284	new_cov=27/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=86/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/123
RA	632	.	NC_007779	3407746	0	C	A	bias_e_value=8.17335	bias_p_value=1.7591e-06	fisher_strand_p_value=1.02937e-07	frequency=4.187870e-02	genotype_quality=1067.8	ks_quality_p_value=1	log10_base_likelihood=-11.7082	log10_qual_likelihood_position_model=23.6623	log10_strand_likelihood_position_model=6.98743	new_cov=22/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=139/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/163
RA	633	.	NC_007779	3412753	0	C	T	bias_e_value=3.30158e-05	bias_p_value=7.10578e-12	fisher_strand_p_value=2.36751e-13	frequency=4.760551e-02	genotype_quality=1050.2	ks_quality_p_value=0.998002	log10_base_likelihood=-9.26737	log10_qual_likelihood_position_model=23.759	log10_strand_likelihood_position_model=12.6257	new_cov=0/20	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=217/56	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=217/76
RA	634	.	NC_007779	3412772	0	A	C	bias_e_value=1.47256e-08	bias_p_value=3.1693e-15	fisher_strand_p_value=8.33511e-17	frequency=4.345703e-02	genotype_quality=942.7	ks_quality_p_value=1	log10_base_likelihood=-8.34769	log10_qual_likelihood_position_model=27.8403	log10_strand_likelihood_position_model=16.0791	new_cov=0/25	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=202/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=202/72
RA	635	.	NC_007779	3421203	0	T	C	bias_e_value=7.34335e-06	bias_p_value=1.58046e-12	fisher_strand_p_value=4.99714e-14	frequency=4.968357e-02	genotype_quality=919.8	ks_quality_p_value=1	log10_base_likelihood=-6.36201	log10_qual_likelihood_position_model=20.8811	log10_strand_likelihood_position_model=13.3013	new_cov=0/23	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=208/63	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=208/86
RA	636	.	NC_007779	3431060	0	C	A	bias_e_value=417.699	bias_p_value=8.98987e-05	fisher_strand_p_value=6.98412e-06	frequency=4.874134e-02	genotype_quality=855.9	ks_quality_p_value=1	log10_base_likelihood=-7.08511	log10_qual_likelihood_position_model=17.7687	log10_strand_likelihood_position_model=5.15589	new_cov=0/16	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=117/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/114
RA	637	.	NC_007779	3439598	1	.	T	bias_e_value=1773520	bias_p_value=0.381703	fisher_strand_p_value=0.123453	frequency=1.777744e-02	genotype_quality=1062.9	ks_quality_p_value=1	log10_base_likelihood=-16.0444	log10_qual_likelihood_position_model=5.0117	log10_strand_likelihood_position_model=1.13186	new_cov=4/0	polymorphism_quality=10.7	quality=10.7	quality_position_model=6.31502e-12	ref_cov=114/107	reject=POLYMORPHISM_STRAND	tot_cov=118/107
RA	638	.	NC_007779	3439601	0	G	T	bias_e_value=18056.1	bias_p_value=0.00388611	fisher_strand_p_value=0.000446719	frequency=4.695749e-02	genotype_quality=845.4	ks_quality_p_value=0.998137	log10_base_likelihood=-11.5345	log10_qual_likelihood_position_model=15.1011	log10_strand_likelihood_position_model=3.44497	new_cov=12/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=111/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/110
RA	639	.	NC_007779	3439607	0	G	T	bias_e_value=5226.9	bias_p_value=0.00112495	fisher_strand_p_value=0.00011135	frequency=4.501724e-02	genotype_quality=903.4	ks_quality_p_value=1	log10_base_likelihood=-8.6701	log10_qual_likelihood_position_model=14.7539	log10_strand_likelihood_position_model=4.0231	new_cov=14/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=112/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/112
RA	640	.	NC_007779	3440270	0	C	A	bias_e_value=2.7155e-05	bias_p_value=5.8444e-12	fisher_strand_p_value=1.93038e-13	frequency=6.711578e-02	genotype_quality=1066.4	ks_quality_p_value=1	log10_base_likelihood=-10.857	log10_qual_likelihood_position_model=27.5059	log10_strand_likelihood_position_model=12.7144	new_cov=38/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=131/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/174
RA	641	.	NC_007779	3441352	0	A	G	bias_e_value=3440510	bias_p_value=0.740479	fisher_strand_p_value=1	frequency=9.278297e-03	genotype_quality=1208.5	ks_quality_p_value=0.37263	log10_base_likelihood=-5.6994	log10_qual_likelihood_position_model=2.17363	log10_strand_likelihood_position_model=0.404502	new_cov=1/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=6.50878e-05	ref_cov=152/167	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=153/169
RA	642	.	NC_007779	3441356	0	T	G	bias_e_value=3551460	bias_p_value=0.764359	fisher_strand_p_value=1	frequency=9.140015e-03	genotype_quality=1238.4	ks_quality_p_value=0.397653	log10_base_likelihood=-7.34641	log10_qual_likelihood_position_model=2.19973	log10_strand_likelihood_position_model=0.402612	new_cov=1/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=1.28223e-06	ref_cov=154/171	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=155/173
RA	643	.	NC_007779	3441358	0	C	G	bias_e_value=4645960	bias_p_value=0.99992	fisher_strand_p_value=1	frequency=1.344967e-02	genotype_quality=1291.6	ks_quality_p_value=0.987349	log10_base_likelihood=-9.41334	log10_qual_likelihood_position_model=4.34882	log10_strand_likelihood_position_model=0.483281	new_cov=2/3	polymorphism_quality=4.0	quality=4.0	quality_position_model=1.89581e-06	ref_cov=151/166	tot_cov=153/169
RA	644	.	NC_007779	3441361	0	G	C	bias_e_value=4616660	bias_p_value=0.993613	fisher_strand_p_value=1	frequency=9.761810e-03	genotype_quality=1252.0	ks_quality_p_value=0.889131	log10_base_likelihood=-5.90745	log10_qual_likelihood_position_model=2.50438	log10_strand_likelihood_position_model=0.403322	new_cov=1/2	polymorphism_quality=0.4	quality=0.4	quality_position_model=8.76458e-05	ref_cov=143/158	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=145/160
RA	645	.	NC_007779	3441370	0	A	C	bias_e_value=4636460	bias_p_value=0.997876	fisher_strand_p_value=1	frequency=9.675980e-03	genotype_quality=1193.7	ks_quality_p_value=0.935528	log10_base_likelihood=-6.75671	log10_qual_likelihood_position_model=3.86524	log10_strand_likelihood_position_model=0.427829	new_cov=2/2	polymorphism_quality=1.2	quality=1.2	quality_position_model=0.000328585	ref_cov=145/168	reject=EVALUE	tot_cov=147/170
RA	646	.	NC_007779	3441379	0	G	C	bias_e_value=4185400	bias_p_value=0.900796	fisher_strand_p_value=1	frequency=9.419441e-03	genotype_quality=1312.7	ks_quality_p_value=0.589041	log10_base_likelihood=-6.85485	log10_qual_likelihood_position_model=1.61186	log10_strand_likelihood_position_model=0.409033	new_cov=1/2	polymorphism_quality=1.3	quality=1.3	quality_position_model=1.03348e-06	ref_cov=152/163	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=153/165
RA	647	.	NC_007779	3441382	0	G	C	bias_e_value=2904300	bias_p_value=0.625073	fisher_strand_p_value=1	frequency=9.316444e-03	genotype_quality=1276.3	ks_quality_p_value=0.271188	log10_base_likelihood=-6.3553	log10_qual_likelihood_position_model=2.25264	log10_strand_likelihood_position_model=0.410401	new_cov=1/2	polymorphism_quality=0.8	quality=0.8	quality_position_model=1.62044e-05	ref_cov=154/164	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=155/166
RA	648	.	NC_007779	3441388	0	T	C	bias_e_value=3580060	bias_p_value=0.770513	fisher_strand_p_value=0.447728	frequency=1.943588e-02	genotype_quality=1122.5	ks_quality_p_value=0.903201	log10_base_likelihood=-11.4156	log10_qual_likelihood_position_model=4.10829	log10_strand_likelihood_position_model=0.631576	new_cov=2/4	polymorphism_quality=6.0	quality=6.0	quality_position_model=1.27935e-08	ref_cov=152/149	tot_cov=154/153
RA	649	.	NC_007779	3441391	0	C	G	bias_e_value=3605810	bias_p_value=0.776054	fisher_strand_p_value=0.447728	frequency=1.906204e-02	genotype_quality=1232.7	ks_quality_p_value=0.916985	log10_base_likelihood=-13.0863	log10_qual_likelihood_position_model=4.06786	log10_strand_likelihood_position_model=0.631576	new_cov=2/4	polymorphism_quality=7.7	quality=7.7	quality_position_model=2.23275e-10	ref_cov=152/149	tot_cov=154/153
RA	650	.	NC_007779	3441401	0	C	A	bias_e_value=4622550	bias_p_value=0.994882	fisher_strand_p_value=1	frequency=1.937389e-02	genotype_quality=1217.2	ks_quality_p_value=0.900544	log10_base_likelihood=-8.62143	log10_qual_likelihood_position_model=6.52137	log10_strand_likelihood_position_model=0.558959	new_cov=3/4	polymorphism_quality=3.2	quality=3.2	quality_position_model=0.00336626	ref_cov=154/153	tot_cov=158/157
RA	651	.	NC_007779	3441402	0	G	A	bias_e_value=3789950	bias_p_value=0.815687	fisher_strand_p_value=0.684533	frequency=1.859951e-02	genotype_quality=1255.3	ks_quality_p_value=0.669147	log10_base_likelihood=-10.1941	log10_qual_likelihood_position_model=5.00041	log10_strand_likelihood_position_model=0.628742	new_cov=2/4	polymorphism_quality=4.8	quality=4.8	quality_position_model=1.97152e-06	ref_cov=158/156	tot_cov=160/160
RA	652	.	NC_007779	3441403	0	C	G	bias_e_value=3477380	bias_p_value=0.748413	fisher_strand_p_value=0.446574	frequency=1.848888e-02	genotype_quality=1310.5	ks_quality_p_value=0.852616	log10_base_likelihood=-14.229	log10_qual_likelihood_position_model=3.3675	log10_strand_likelihood_position_model=0.634255	new_cov=2/4	polymorphism_quality=8.9	quality=8.9	quality_position_model=2.93226e-12	ref_cov=161/157	tot_cov=163/161
RA	653	.	NC_007779	3441404	0	T	G	bias_e_value=1738820	bias_p_value=0.374235	fisher_strand_p_value=0.443588	frequency=1.890182e-02	genotype_quality=1202.1	ks_quality_p_value=0.270313	log10_base_likelihood=-14.8224	log10_qual_likelihood_position_model=3.26511	log10_strand_likelihood_position_model=0.640044	new_cov=2/4	polymorphism_quality=9.5	quality=9.5	quality_position_model=5.80166e-13	ref_cov=159/153	tot_cov=162/157
RA	654	.	NC_007779	3441406	0	T	C	bias_e_value=4146270	bias_p_value=0.892376	fisher_strand_p_value=0.684495	frequency=1.894951e-02	genotype_quality=1168.2	ks_quality_p_value=0.837873	log10_base_likelihood=-12.1878	log10_qual_likelihood_position_model=3.53951	log10_strand_likelihood_position_model=0.628726	new_cov=2/4	polymorphism_quality=6.8	quality=6.8	quality_position_model=5.31387e-10	ref_cov=156/154	tot_cov=159/158
RA	655	.	NC_007779	3441431	0	T	C	bias_e_value=3295920	bias_p_value=0.709359	fisher_strand_p_value=0.371361	frequency=1.378155e-02	genotype_quality=1299.7	ks_quality_p_value=0.921969	log10_base_likelihood=-8.50457	log10_qual_likelihood_position_model=3.35454	log10_strand_likelihood_position_model=0.801097	new_cov=1/4	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.31516e-06	ref_cov=169/168	reject=POLYMORPHISM_STRAND	tot_cov=170/172
RA	656	.	NC_007779	3441440	0	A	T	bias_e_value=534594	bias_p_value=0.115057	fisher_strand_p_value=0.247852	frequency=8.764267e-03	genotype_quality=1310.8	ks_quality_p_value=0.0985063	log10_base_likelihood=-5.89001	log10_qual_likelihood_position_model=4.19303	log10_strand_likelihood_position_model=0.89546	new_cov=0/3	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.0244316	ref_cov=169/169	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=169/172
RA	657	.	NC_007779	3441441	0	G	C	bias_e_value=602111	bias_p_value=0.129589	fisher_strand_p_value=0.247956	frequency=8.768082e-03	genotype_quality=1388.7	ks_quality_p_value=0.114588	log10_base_likelihood=-6.23337	log10_qual_likelihood_position_model=3.20181	log10_strand_likelihood_position_model=0.887862	new_cov=0/3	polymorphism_quality=0.7	quality=0.7	quality_position_model=0.000729371	ref_cov=168/170	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=168/173
RA	658	.	NC_007779	3447060	0	T	A	bias_e_value=101826	bias_p_value=0.0219153	fisher_strand_p_value=0.00325799	frequency=2.535820e-02	genotype_quality=1157.2	ks_quality_p_value=1	log10_base_likelihood=-6.60832	log10_qual_likelihood_position_model=19.3977	log10_strand_likelihood_position_model=2.69326	new_cov=1/10	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=189/149	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=190/159
RA	659	.	NC_007779	3450031	0	A	T	bias_e_value=4617780	bias_p_value=0.993856	fisher_strand_p_value=1	frequency=2.476501e-02	genotype_quality=1516.5	ks_quality_p_value=0.891213	log10_base_likelihood=-24.6829	log10_qual_likelihood_position_model=5.51615	log10_strand_likelihood_position_model=0.604555	new_cov=5/5	polymorphism_quality=19.4	quality=19.4	quality_position_model=1.01542e-20	ref_cov=201/192	tot_cov=206/197
RA	660	.	NC_007779	3451585	0	T	G	bias_e_value=4645590	bias_p_value=0.999841	fisher_strand_p_value=1	frequency=1.170254e-02	genotype_quality=1302.3	ks_quality_p_value=0.982233	log10_base_likelihood=-8.00755	log10_qual_likelihood_position_model=2.70833	log10_strand_likelihood_position_model=0.431177	new_cov=2/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=9.52361e-07	ref_cov=152/184	tot_cov=154/186
RA	661	.	NC_007779	3451588	0	T	A	bias_e_value=4643660	bias_p_value=0.999425	fisher_strand_p_value=1	frequency=1.173306e-02	genotype_quality=1311.0	ks_quality_p_value=0.966283	log10_base_likelihood=-7.32037	log10_qual_likelihood_position_model=4.05431	log10_strand_likelihood_position_model=0.432274	new_cov=2/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=0.000131731	ref_cov=150/184	reject=EVALUE	tot_cov=152/186
RA	662	.	NC_007779	3451600	0	T	C	bias_e_value=4635610	bias_p_value=0.997692	fisher_strand_p_value=1	frequency=1.116562e-02	genotype_quality=1359.1	ks_quality_p_value=0.932839	log10_base_likelihood=-7.14043	log10_qual_likelihood_position_model=3.39101	log10_strand_likelihood_position_model=0.426861	new_cov=2/2	polymorphism_quality=1.6	quality=1.6	quality_position_model=3.9814e-05	ref_cov=165/187	reject=EVALUE	tot_cov=167/189
RA	663	.	NC_007779	3451602	0	C	G	bias_e_value=4642690	bias_p_value=0.999216	fisher_strand_p_value=1	frequency=1.119041e-02	genotype_quality=1472.3	ks_quality_p_value=0.960668	log10_base_likelihood=-7.73943	log10_qual_likelihood_position_model=3.37495	log10_strand_likelihood_position_model=0.428579	new_cov=2/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=8.98199e-06	ref_cov=162/189	tot_cov=165/191
RA	664	.	NC_007779	3451605	0	G	T	bias_e_value=4624470	bias_p_value=0.995294	fisher_strand_p_value=1	frequency=1.175499e-02	genotype_quality=1424.6	ks_quality_p_value=0.904569	log10_base_likelihood=-6.38833	log10_qual_likelihood_position_model=6.14149	log10_strand_likelihood_position_model=0.475754	new_cov=2/3	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=158/183	reject=EVALUE	tot_cov=160/186
RA	665	.	NC_007779	3451615	0	T	C	bias_e_value=3416520	bias_p_value=0.735316	fisher_strand_p_value=1	frequency=1.104164e-02	genotype_quality=1364.4	ks_quality_p_value=0.367437	log10_base_likelihood=-7.91738	log10_qual_likelihood_position_model=2.5494	log10_strand_likelihood_position_model=0.429208	new_cov=2/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=8.03843e-07	ref_cov=164/193	tot_cov=166/195
RA	666	.	NC_007779	3451630	0	A	G	bias_e_value=2608830	bias_p_value=0.561482	fisher_strand_p_value=1	frequency=1.107979e-02	genotype_quality=1320.5	ks_quality_p_value=0.225577	log10_base_likelihood=-6.79781	log10_qual_likelihood_position_model=3.77388	log10_strand_likelihood_position_model=0.42827	new_cov=2/2	polymorphism_quality=1.3	quality=1.3	quality_position_model=0.000236956	ref_cov=161/187	reject=EVALUE	tot_cov=163/189
RA	667	.	NC_007779	3451648	0	T	A	bias_e_value=4641930	bias_p_value=0.999052	fisher_strand_p_value=1	frequency=1.131630e-02	genotype_quality=1256.6	ks_quality_p_value=0.956768	log10_base_likelihood=-6.71793	log10_qual_likelihood_position_model=3.96782	log10_strand_likelihood_position_model=0.428244	new_cov=2/2	polymorphism_quality=1.2	quality=1.2	quality_position_model=0.000467406	ref_cov=153/178	reject=EVALUE	tot_cov=156/180
RA	668	.	NC_007779	3451672	0	A	G	bias_e_value=4250290	bias_p_value=0.914763	fisher_strand_p_value=0.682905	frequency=1.394176e-02	genotype_quality=1285.7	ks_quality_p_value=0.902954	log10_base_likelihood=-7.43034	log10_qual_likelihood_position_model=4.1988	log10_strand_likelihood_position_model=0.506543	new_cov=3/2	polymorphism_quality=1.9	quality=1.9	quality_position_model=0.000172188	ref_cov=166/170	reject=EVALUE,SURROUNDING_HOMOPOLYMER	tot_cov=169/172
RA	669	.	NC_007779	3451702	0	C	A	bias_e_value=2681620	bias_p_value=0.577148	fisher_strand_p_value=1	frequency=1.038265e-02	genotype_quality=1163.4	ks_quality_p_value=0.236265	log10_base_likelihood=-5.58102	log10_qual_likelihood_position_model=2.49212	log10_strand_likelihood_position_model=0.400817	new_cov=2/1	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.000188601	ref_cov=150/134	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=152/135
RA	670	.	NC_007779	3451714	0	G	C	bias_e_value=4389240	bias_p_value=0.944668	fisher_strand_p_value=1	frequency=1.080418e-02	genotype_quality=1150.8	ks_quality_p_value=0.686346	log10_base_likelihood=-6.61176	log10_qual_likelihood_position_model=2.04717	log10_strand_likelihood_position_model=0.413759	new_cov=2/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=5.34428e-06	ref_cov=140/134	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=142/135
RA	671	.	NC_007779	3451731	0	T	G	bias_e_value=2526190	bias_p_value=0.543696	fisher_strand_p_value=0.618366	frequency=1.061630e-02	genotype_quality=1072.4	ks_quality_p_value=0.345816	log10_base_likelihood=-6.86084	log10_qual_likelihood_position_model=2.39257	log10_strand_likelihood_position_model=0.430762	new_cov=2/1	polymorphism_quality=1.3	quality=1.3	quality_position_model=7.02596e-06	ref_cov=137/142	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=139/143
RA	672	.	NC_007779	3451735	0	T	C	bias_e_value=4128770	bias_p_value=0.888608	fisher_strand_p_value=1	frequency=1.067257e-02	genotype_quality=1057.8	ks_quality_p_value=0.566814	log10_base_likelihood=-5.75287	log10_qual_likelihood_position_model=2.55006	log10_strand_likelihood_position_model=0.424415	new_cov=2/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.000150964	ref_cov=138/139	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=140/140
RA	673	.	NC_007779	3451753	0	A	G	bias_e_value=4515720	bias_p_value=0.97189	fisher_strand_p_value=1	frequency=9.884834e-03	genotype_quality=1154.8	ks_quality_p_value=0.77246	log10_base_likelihood=-5.59429	log10_qual_likelihood_position_model=2.65031	log10_strand_likelihood_position_model=0.398408	new_cov=2/1	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.000268212	ref_cov=159/140	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=161/141
RA	674	.	NC_007779	3452916	0	G	T	bias_e_value=1058790	bias_p_value=0.227876	fisher_strand_p_value=0.146414	frequency=2.062893e-02	genotype_quality=1603.1	ks_quality_p_value=0.407544	log10_base_likelihood=-13.9799	log10_qual_likelihood_position_model=5.75988	log10_strand_likelihood_position_model=1.18144	new_cov=6/2	polymorphism_quality=8.6	quality=8.6	quality_position_model=5.41096e-09	ref_cov=165/211	tot_cov=171/214
RA	675	.	NC_007779	3460325	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	676	.	NC_007779	3460327	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	677	.	NC_007779	3460328	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	678	.	NC_007779	3460329	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	679	.	NC_007779	3460330	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	680	.	NC_007779	3460331	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	681	.	NC_007779	3460332	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	682	.	NC_007779	3460333	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	683	.	NC_007779	3460335	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	684	.	NC_007779	3460336	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	685	.	NC_007779	3460339	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=1/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	686	.	NC_007779	3460341	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	687	.	NC_007779	3460342	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	688	.	NC_007779	3460344	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	689	.	NC_007779	3460345	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	690	.	NC_007779	3460347	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	691	.	NC_007779	3460348	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	3475527	0	T	G	bias_e_value=6.80719e-11	bias_p_value=1.46507e-17	fisher_strand_p_value=3.36522e-19	frequency=1.225424e-01	genotype_quality=917.3	ks_quality_p_value=1	log10_base_likelihood=-25.2344	log10_qual_likelihood_position_model=37.5712	log10_strand_likelihood_position_model=18.4903	new_cov=58/0	polymorphism_quality=20.0	quality=20.0	quality_position_model=Inf	ref_cov=115/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/155
RA	693	.	NC_007779	3475533	0	C	T	bias_e_value=1.37775e-06	bias_p_value=2.96525e-13	fisher_strand_p_value=8.89027e-15	frequency=1.217356e-01	genotype_quality=977.3	ks_quality_p_value=1	log10_base_likelihood=-41.6332	log10_qual_likelihood_position_model=50.8541	log10_strand_likelihood_position_model=14.1706	new_cov=46/0	polymorphism_quality=36.5	quality=36.5	quality_position_model=Inf	ref_cov=140/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=186/169
RA	694	.	NC_007779	3475539	0	G	T	bias_e_value=6559.23	bias_p_value=0.0014117	fisher_strand_p_value=0.000143313	frequency=3.032207e-02	genotype_quality=1067.7	ks_quality_p_value=1	log10_base_likelihood=-6.96132	log10_qual_likelihood_position_model=9.50765	log10_strand_likelihood_position_model=3.84371	new_cov=11/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=130/168	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/168
RA	695	.	NC_007779	3478396	0	T	.	bias_e_value=2328900	bias_p_value=0.501234	fisher_strand_p_value=0.255464	frequency=8.920670e-03	genotype_quality=1319.6	ks_quality_p_value=0.733639	log10_base_likelihood=-7.81971	log10_qual_likelihood_position_model=1.35022	log10_strand_likelihood_position_model=0.78069	new_cov=0/3	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.33831e-07	ref_cov=151/182	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/185
RA	696	.	NC_007779	3484372	0	A	C	bias_e_value=2.65127e-05	bias_p_value=5.70616e-12	fisher_strand_p_value=1.88318e-13	frequency=6.448078e-02	genotype_quality=777.3	ks_quality_p_value=1	log10_base_likelihood=-7.70612	log10_qual_likelihood_position_model=30.4521	log10_strand_likelihood_position_model=12.7251	new_cov=0/37	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=138/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=138/135
RA	697	.	NC_007779	3499066	0	A	C	bias_e_value=0.00959876	bias_p_value=2.06588e-09	fisher_strand_p_value=8.54256e-11	frequency=6.071568e-02	genotype_quality=827.5	ks_quality_p_value=1	log10_base_likelihood=-13.3348	log10_qual_likelihood_position_model=22.3721	log10_strand_likelihood_position_model=10.0684	new_cov=0/18	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=166/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/72
RA	698	.	NC_007779	3502834	0	C	A	bias_e_value=2395990	bias_p_value=0.515673	fisher_strand_p_value=0.19649	frequency=1.555061e-02	genotype_quality=1260.7	ks_quality_p_value=0.998331	log10_base_likelihood=-7.1238	log10_qual_likelihood_position_model=4.55707	log10_strand_likelihood_position_model=0.87051	new_cov=4/1	polymorphism_quality=1.6	quality=1.6	quality_position_model=0.00226068	ref_cov=145/162	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=149/163
RA	699	.	NC_007779	3523734	0	G	T	bias_e_value=0.0070906	bias_p_value=1.52606e-09	fisher_strand_p_value=6.22903e-11	frequency=6.020117e-02	genotype_quality=1104.7	ks_quality_p_value=1	log10_base_likelihood=-13.3316	log10_qual_likelihood_position_model=28.6239	log10_strand_likelihood_position_model=10.3754	new_cov=0/35	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=165/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/191
RA	700	.	NC_007779	3523811	1	.	T	bias_e_value=414442	bias_p_value=0.0891976	fisher_strand_p_value=0.217776	frequency=6.192207e-03	genotype_quality=1596.4	ks_quality_p_value=0.0813814	log10_base_likelihood=-8.03634	log10_qual_likelihood_position_model=1.35847	log10_strand_likelihood_position_model=0.66199	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=6.13922e-08	ref_cov=149/172	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/172
RA	701	.	NC_007779	3543542	0	G	T	bias_e_value=0.243221	bias_p_value=5.23468e-08	fisher_strand_p_value=2.51663e-09	frequency=4.247665e-02	genotype_quality=939.8	ks_quality_p_value=1	log10_base_likelihood=-6.73045	log10_qual_likelihood_position_model=23.8765	log10_strand_likelihood_position_model=8.59918	new_cov=0/23	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=158/104	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/127
RA	702	.	NC_007779	3543547	0	A	C	bias_e_value=1.89268e-18	bias_p_value=4.07349e-25	fisher_strand_p_value=6.64783e-27	frequency=1.691279e-01	genotype_quality=866.2	ks_quality_p_value=1	log10_base_likelihood=-42.1374	log10_qual_likelihood_position_model=60.9051	log10_strand_likelihood_position_model=26.1773	new_cov=0/70	polymorphism_quality=37.0	quality=37.0	quality_position_model=Inf	ref_cov=164/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/160
RA	703	.	NC_007779	3560478	0	G	T	bias_e_value=87.7565	bias_p_value=1.88873e-05	fisher_strand_p_value=1.29765e-06	frequency=3.361893e-02	genotype_quality=1142.1	ks_quality_p_value=1	log10_base_likelihood=-7.45929	log10_qual_likelihood_position_model=18.8412	log10_strand_likelihood_position_model=5.98529	new_cov=0/20	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=165/156	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/177
RA	704	.	NC_007779	3566189	1	.	T	bias_e_value=357889	bias_p_value=0.0770262	fisher_strand_p_value=0.0153189	frequency=1.265812e-02	genotype_quality=760.0	ks_quality_p_value=0.964144	log10_base_likelihood=-8.00009	log10_qual_likelihood_position_model=3.49147	log10_strand_likelihood_position_model=1.81477	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=0.000185935	ref_cov=18/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=20/138
RA	705	.	NC_007779	3576400	1	.	A	bias_e_value=1577630	bias_p_value=0.339544	fisher_strand_p_value=1	frequency=5.618095e-03	genotype_quality=1729.7	ks_quality_p_value=0.104068	log10_base_likelihood=-7.58262	log10_qual_likelihood_position_model=1.89431	log10_strand_likelihood_position_model=0.300686	new_cov=1/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=2.74642e-07	ref_cov=169/185	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=170/186
RA	706	.	NC_007779	3576401	0	A	.	bias_e_value=4155170	bias_p_value=0.894291	fisher_strand_p_value=0.603308	frequency=8.296013e-03	genotype_quality=1425.0	ks_quality_p_value=0.956365	log10_base_likelihood=-7.01739	log10_qual_likelihood_position_model=3.53511	log10_strand_likelihood_position_model=0.452414	new_cov=2/1	polymorphism_quality=1.5	quality=1.5	quality_position_model=8.14089e-05	ref_cov=168/190	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=170/191
RA	707	.	NC_007779	3580297	0	G	T	bias_e_value=0.00355397	bias_p_value=7.64897e-10	fisher_strand_p_value=3.03489e-11	frequency=7.441473e-02	genotype_quality=1152.4	ks_quality_p_value=0.999389	log10_base_likelihood=-23.7071	log10_qual_likelihood_position_model=23.3595	log10_strand_likelihood_position_model=10.7522	new_cov=0/38	polymorphism_quality=18.5	quality=18.5	quality_position_model=Inf	ref_cov=169/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/203
RA	708	.	NC_007779	3586832	0	T	.	bias_e_value=3346020	bias_p_value=0.720142	fisher_strand_p_value=0.600443	frequency=7.471085e-03	genotype_quality=1587.4	ks_quality_p_value=0.587209	log10_base_likelihood=-7.3523	log10_qual_likelihood_position_model=2.66554	log10_strand_likelihood_position_model=0.457288	new_cov=1/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=4.42096e-06	ref_cov=213/185	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=214/187
RA	709	.	NC_007779	3595895	1	.	G	bias_e_value=3909860	bias_p_value=0.841495	fisher_strand_p_value=0.496914	frequency=1.818180e-02	genotype_quality=434.9	ks_quality_p_value=0.991618	log10_base_likelihood=-8.26199	log10_qual_likelihood_position_model=2.27264	log10_strand_likelihood_position_model=0.559516	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.48297e-07	ref_cov=56/52	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=58/52
RA	710	.	NC_007779	3605534	1	.	T	bias_e_value=3906800	bias_p_value=0.840836	fisher_strand_p_value=0.498797	frequency=5.916595e-03	genotype_quality=1661.8	ks_quality_p_value=0.98601	log10_base_likelihood=-7.48368	log10_qual_likelihood_position_model=2.72209	log10_strand_likelihood_position_model=0.582972	new_cov=0/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=4.99778e-06	ref_cov=165/171	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/173
RA	711	.	NC_007779	3609441	0	T	G	bias_e_value=1.48296e-09	bias_p_value=3.19169e-16	fisher_strand_p_value=7.9043e-18	frequency=4.027081e-02	genotype_quality=1136.1	ks_quality_p_value=1	log10_base_likelihood=-6.66931	log10_qual_likelihood_position_model=30.4208	log10_strand_likelihood_position_model=17.1021	new_cov=37/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=97/219	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/220
RA	712	.	NC_007779	3627545	0	T	.	bias_e_value=4569830	bias_p_value=0.983536	fisher_strand_p_value=1	frequency=1.380062e-02	genotype_quality=1390.5	ks_quality_p_value=0.824113	log10_base_likelihood=-13.2662	log10_qual_likelihood_position_model=3.46781	log10_strand_likelihood_position_model=0.472411	new_cov=3/2	polymorphism_quality=7.9	quality=7.9	quality_position_model=2.44173e-11	ref_cov=194/163	reject=INDEL_HOMOPOLYMER	tot_cov=197/165
RA	713	.	NC_007779	3651632	0	C	T	bias_e_value=56787.2	bias_p_value=0.0122219	fisher_strand_p_value=0.00165273	frequency=2.288246e-02	genotype_quality=1186.3	ks_quality_p_value=0.99839	log10_base_likelihood=-6.02349	log10_qual_likelihood_position_model=11.8711	log10_strand_likelihood_position_model=2.7818	new_cov=8/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=130/165	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=138/165
RA	714	.	NC_007779	3651641	0	G	C	bias_e_value=141.644	bias_p_value=3.04851e-05	fisher_strand_p_value=2.17127e-06	frequency=4.509926e-02	genotype_quality=1242.9	ks_quality_p_value=1	log10_base_likelihood=-24.7609	log10_qual_likelihood_position_model=15.1377	log10_strand_likelihood_position_model=5.66329	new_cov=16/0	polymorphism_quality=19.5	quality=19.5	quality_position_model=8.47602e-06	ref_cov=129/173	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/173
RA	715	.	NC_007779	3651644	0	A	T	bias_e_value=546.9	bias_p_value=0.000117706	fisher_strand_p_value=9.35704e-06	frequency=4.128551e-02	genotype_quality=1186.0	ks_quality_p_value=1	log10_base_likelihood=-14.7624	log10_qual_likelihood_position_model=18.9387	log10_strand_likelihood_position_model=5.02886	new_cov=15/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=139/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/171
RA	716	.	NC_007779	3651649	0	A	T	bias_e_value=18958.2	bias_p_value=0.00408026	fisher_strand_p_value=0.000471142	frequency=2.358913e-02	genotype_quality=1166.7	ks_quality_p_value=1	log10_base_likelihood=-6.96149	log10_qual_likelihood_position_model=13.1714	log10_strand_likelihood_position_model=3.32685	new_cov=10/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=137/164	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/164
RA	717	.	NC_007779	3653997	0	G	.	bias_e_value=4631170	bias_p_value=0.996737	fisher_strand_p_value=1	frequency=8.999825e-03	genotype_quality=1350.8	ks_quality_p_value=0.920308	log10_base_likelihood=-7.76266	log10_qual_likelihood_position_model=1.74876	log10_strand_likelihood_position_model=0.362554	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.46336e-07	ref_cov=198/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=200/133
RA	718	.	NC_007779	3673380	0	G	T	bias_e_value=4.74182	bias_p_value=1.02055e-06	fisher_strand_p_value=7.66509e-08	frequency=3.785801e-02	genotype_quality=1025.4	ks_quality_p_value=0.753629	log10_base_likelihood=-9.13	log10_qual_likelihood_position_model=24.9842	log10_strand_likelihood_position_model=7.11548	new_cov=0/22	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=164/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/159
RA	719	.	NC_007779	3677212	0	C	G	bias_e_value=0.365931	bias_p_value=7.87569e-08	fisher_strand_p_value=3.86811e-09	frequency=4.199314e-02	genotype_quality=741.4	ks_quality_p_value=0.999488	log10_base_likelihood=-10.2933	log10_qual_likelihood_position_model=12.284	log10_strand_likelihood_position_model=8.4125	new_cov=0/9	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=166/17	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/26
RA	720	.	NC_007779	3677217	0	T	G	bias_e_value=19213.6	bias_p_value=0.00413522	fisher_strand_p_value=0.000478324	frequency=4.632378e-02	genotype_quality=537.9	ks_quality_p_value=1	log10_base_likelihood=-5.83655	log10_qual_likelihood_position_model=16.1716	log10_strand_likelihood_position_model=3.37997	new_cov=9/9	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=155/23	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=165/32
RA	721	.	NC_007779	3686205	0	A	.	bias_e_value=4223900	bias_p_value=0.909082	fisher_strand_p_value=0.625068	frequency=1.264858e-02	genotype_quality=1244.5	ks_quality_p_value=0.968064	log10_base_likelihood=-10.6773	log10_qual_likelihood_position_model=4.06763	log10_strand_likelihood_position_model=0.554917	new_cov=3/1	polymorphism_quality=5.3	quality=5.3	quality_position_model=5.59663e-08	ref_cov=164/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=167/149
RA	722	.	NC_007779	3688852	0	C	T	bias_e_value=2.80355	bias_p_value=6.0339e-07	fisher_strand_p_value=3.31107e-08	frequency=4.578209e-02	genotype_quality=812.3	ks_quality_p_value=1	log10_base_likelihood=-6.55622	log10_qual_likelihood_position_model=16.2807	log10_strand_likelihood_position_model=7.48003	new_cov=0/18	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=148/83	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/101
RA	723	.	NC_007779	3688858	0	A	C	bias_e_value=2.65396e-24	bias_p_value=5.71194e-31	fisher_strand_p_value=7.62055e-33	frequency=1.774197e-01	genotype_quality=734.1	ks_quality_p_value=1	log10_base_likelihood=-29.3384	log10_qual_likelihood_position_model=46.9735	log10_strand_likelihood_position_model=32.118	new_cov=0/69	polymorphism_quality=24.1	quality=24.1	quality_position_model=Inf	ref_cov=157/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/119
RA	724	.	NC_007779	3696097	1	.	G	bias_e_value=2108940	bias_p_value=0.453893	fisher_strand_p_value=0.211337	frequency=6.308556e-03	genotype_quality=1560.1	ks_quality_p_value=0.758843	log10_base_likelihood=-7.93348	log10_qual_likelihood_position_model=1.13683	log10_strand_likelihood_position_model=0.675025	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.77321e-08	ref_cov=144/171	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/171
RA	725	.	NC_007779	3701118	0	G	T	bias_e_value=8.09948e-05	bias_p_value=1.7432e-11	fisher_strand_p_value=5.98112e-13	frequency=6.631470e-02	genotype_quality=980.4	ks_quality_p_value=1	log10_base_likelihood=-12.5233	log10_qual_likelihood_position_model=24.4038	log10_strand_likelihood_position_model=12.2232	new_cov=0/32	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=172/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/139
RA	726	.	NC_007779	3728146	1	.	T	bias_e_value=1148100	bias_p_value=0.247098	fisher_strand_p_value=0.0895343	frequency=1.020432e-02	genotype_quality=947.7	ks_quality_p_value=0.744161	log10_base_likelihood=-8.08283	log10_qual_likelihood_position_model=2.48192	log10_strand_likelihood_position_model=1.04801	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.02943e-06	ref_cov=57/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=59/137
RA	727	.	NC_007779	3728155	0	T	C	bias_e_value=0.000116002	bias_p_value=2.49663e-11	fisher_strand_p_value=8.67702e-13	frequency=5.987930e-02	genotype_quality=577.9	ks_quality_p_value=1	log10_base_likelihood=-14.5982	log10_qual_likelihood_position_model=13.4751	log10_strand_likelihood_position_model=12.0616	new_cov=13/0	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=14/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=27/154
RA	728	.	NC_007779	3728157	0	A	C	bias_e_value=7.27058	bias_p_value=1.5648e-06	fisher_strand_p_value=9.09056e-08	frequency=3.387356e-02	genotype_quality=540.2	ks_quality_p_value=1	log10_base_likelihood=-6.19803	log10_qual_likelihood_position_model=9.98984	log10_strand_likelihood_position_model=7.04141	new_cov=8/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=19/154	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=27/154
RA	729	.	NC_007779	3731041	1	.	T	bias_e_value=4357800	bias_p_value=0.937901	fisher_strand_p_value=0.708173	frequency=2.147198e-02	genotype_quality=1540.3	ks_quality_p_value=0.944622	log10_base_likelihood=-31.058	log10_qual_likelihood_position_model=5.2097	log10_strand_likelihood_position_model=0.600142	new_cov=4/3	polymorphism_quality=25.9	quality=25.9	quality_position_model=1.79957e-27	ref_cov=147/172	reject=INDEL_HOMOPOLYMER	tot_cov=151/175
RA	730	.	NC_007779	3732310	0	G	T	bias_e_value=0.00028493	bias_p_value=6.13236e-11	fisher_strand_p_value=2.20261e-12	frequency=5.143642e-02	genotype_quality=978.3	ks_quality_p_value=1	log10_base_likelihood=-8.02215	log10_qual_likelihood_position_model=24.2692	log10_strand_likelihood_position_model=11.6571	new_cov=0/29	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=173/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/128
RA	731	.	NC_007779	3734126	0	G	T	bias_e_value=154.762	bias_p_value=3.33083e-05	fisher_strand_p_value=2.41441e-06	frequency=3.363037e-02	genotype_quality=1171.1	ks_quality_p_value=0.989305	log10_base_likelihood=-8.29443	log10_qual_likelihood_position_model=17.4957	log10_strand_likelihood_position_model=5.61719	new_cov=0/17	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=180/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=180/166
RA	732	.	NC_007779	3741461	0	A	T	bias_e_value=5752.91	bias_p_value=0.00123816	fisher_strand_p_value=0.000123861	frequency=2.645493e-02	genotype_quality=1032.6	ks_quality_p_value=1	log10_base_likelihood=-5.94274	log10_qual_likelihood_position_model=16.9524	log10_strand_likelihood_position_model=3.90706	new_cov=10/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=120/183	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=130/183
RA	733	.	NC_007779	3745476	0	A	.	bias_e_value=387046	bias_p_value=0.0833013	fisher_strand_p_value=0.260015	frequency=8.893013e-03	genotype_quality=1303.8	ks_quality_p_value=0.0625962	log10_base_likelihood=-7.64058	log10_qual_likelihood_position_model=2.9124	log10_strand_likelihood_position_model=0.749641	new_cov=0/3	polymorphism_quality=2.1	quality=2.1	quality_position_model=8.10211e-06	ref_cov=147/187	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/190
RA	734	.	NC_007779	3746950	0	T	G	frequency=1	genotype_quality=0.8	new_cov=1/0	quality=0.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	735	.	NC_007779	3746968	0	C	A	frequency=1	genotype_quality=1.2	new_cov=1/0	quality=1.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	736	.	NC_007779	3750122	0	C	.	bias_e_value=467412	bias_p_value=0.100598	fisher_strand_p_value=1	frequency=9.698629e-01	genotype_quality=1713.9	ks_quality_p_value=0.020605	log10_base_likelihood=-51.5161	log10_qual_likelihood_position_model=7.14593	log10_strand_likelihood_position_model=0.631141	new_cov=181/173	polymorphism_quality=46.4	quality=46.4	quality_position_model=4.43105e-46	ref_cov=6/5	tot_cov=187/178
RA	737	.	NC_007779	3750123	0	C	T	bias_e_value=4567310	bias_p_value=0.982993	fisher_strand_p_value=1	frequency=2.999878e-02	genotype_quality=1428.9	ks_quality_p_value=0.821333	log10_base_likelihood=-21.1636	log10_qual_likelihood_position_model=7.08994	log10_strand_likelihood_position_model=0.631141	new_cov=6/5	polymorphism_quality=15.9	quality=15.9	quality_position_model=1.56526e-15	ref_cov=181/173	tot_cov=187/178
RA	738	.	NC_007779	3758414	0	G	T	bias_e_value=90.6334	bias_p_value=1.95064e-05	fisher_strand_p_value=1.34339e-06	frequency=2.828884e-02	genotype_quality=1102.2	ks_quality_p_value=1	log10_base_likelihood=-6.16969	log10_qual_likelihood_position_model=19.8336	log10_strand_likelihood_position_model=5.95869	new_cov=0/20	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=163/155	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/176
RA	739	.	NC_007779	3761469	0	A	C	bias_e_value=1.96118e-06	bias_p_value=4.22093e-13	fisher_strand_p_value=1.27947e-14	frequency=4.643583e-02	genotype_quality=743.7	ks_quality_p_value=1	log10_base_likelihood=-6.82252	log10_qual_likelihood_position_model=25.7792	log10_strand_likelihood_position_model=13.893	new_cov=0/19	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=169/29	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/48
RA	740	.	NC_007779	3772840	0	A	.	bias_e_value=1461140	bias_p_value=0.314471	fisher_strand_p_value=0.254047	frequency=9.959221e-03	genotype_quality=1184.3	ks_quality_p_value=0.367038	log10_base_likelihood=-8.05419	log10_qual_likelihood_position_model=1.42311	log10_strand_likelihood_position_model=0.790462	new_cov=3/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.31951e-08	ref_cov=161/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/136
RA	741	.	NC_007779	3773982	1	.	T	bias_e_value=1775670	bias_p_value=0.382166	fisher_strand_p_value=0.212065	frequency=5.951881e-03	genotype_quality=1633.8	ks_quality_p_value=0.58319	log10_base_likelihood=-7.95926	log10_qual_likelihood_position_model=1.4159	log10_strand_likelihood_position_model=0.673532	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=8.69288e-08	ref_cov=153/181	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=155/181
RA	742	.	NC_007779	3788380	0	G	T	bias_e_value=0.00264269	bias_p_value=5.68769e-10	fisher_strand_p_value=2.22808e-11	frequency=6.937790e-02	genotype_quality=942.4	ks_quality_p_value=1	log10_base_likelihood=-10.7885	log10_qual_likelihood_position_model=21.6425	log10_strand_likelihood_position_model=10.7062	new_cov=0/34	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=148/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/158
RA	743	.	NC_007779	3789662	1	.	T	bias_e_value=875904	bias_p_value=0.188515	fisher_strand_p_value=0.256051	frequency=9.009361e-03	genotype_quality=1581.2	ks_quality_p_value=0.180764	log10_base_likelihood=-12.4559	log10_qual_likelihood_position_model=2.52158	log10_strand_likelihood_position_model=0.77607	new_cov=3/0	polymorphism_quality=7.1	quality=7.1	quality_position_model=3.62404e-11	ref_cov=181/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=184/149
RA	744	.	NC_007779	3789663	0	T	.	bias_e_value=4639730	bias_p_value=0.99858	fisher_strand_p_value=1	frequency=8.835793e-03	genotype_quality=1285.9	ks_quality_p_value=0.947185	log10_base_likelihood=-7.22809	log10_qual_likelihood_position_model=3.34054	log10_strand_likelihood_position_model=0.387236	new_cov=2/1	polymorphism_quality=1.7	quality=1.7	quality_position_model=2.58273e-05	ref_cov=184/151	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=186/153
RA	745	.	NC_007779	3812429	0	G	T	bias_e_value=0.00696391	bias_p_value=1.4988e-09	fisher_strand_p_value=6.11304e-11	frequency=6.312799e-02	genotype_quality=1083.4	ks_quality_p_value=1	log10_base_likelihood=-20.1508	log10_qual_likelihood_position_model=20.817	log10_strand_likelihood_position_model=10.2137	new_cov=0/31	polymorphism_quality=14.9	quality=14.9	quality_position_model=Inf	ref_cov=171/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/167
RA	746	.	NC_007779	3813810	0	T	G	bias_e_value=1.39315e-09	bias_p_value=2.99838e-16	fisher_strand_p_value=7.4138e-18	frequency=5.680656e-02	genotype_quality=861.9	ks_quality_p_value=1	log10_base_likelihood=-6.51462	log10_qual_likelihood_position_model=26.942	log10_strand_likelihood_position_model=17.13	new_cov=34/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=65/179	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/179
RA	747	.	NC_007779	3818667	0	G	T	bias_e_value=2.77811	bias_p_value=5.97914e-07	fisher_strand_p_value=3.28072e-08	frequency=2.564907e-02	genotype_quality=1027.5	ks_quality_p_value=0.999564	log10_base_likelihood=-5.74358	log10_qual_likelihood_position_model=16.5452	log10_strand_likelihood_position_model=7.48403	new_cov=0/21	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=174/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/148
RA	748	.	NC_007779	3820993	0	A	.	bias_e_value=2019140	bias_p_value=0.434566	fisher_strand_p_value=0.312709	frequency=1.203442e-02	genotype_quality=1297.1	ks_quality_p_value=0.479675	log10_base_likelihood=-10.3245	log10_qual_likelihood_position_model=3.97805	log10_strand_likelihood_position_model=0.769444	new_cov=3/1	polymorphism_quality=4.9	quality=4.9	quality_position_model=1.74734e-07	ref_cov=136/192	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/193
RA	749	.	NC_007779	3824606	1	.	T	bias_e_value=1641870	bias_p_value=0.353368	fisher_strand_p_value=0.244499	frequency=6.308556e-03	genotype_quality=1523.6	ks_quality_p_value=0.450952	log10_base_likelihood=-8.02638	log10_qual_likelihood_position_model=1.42302	log10_strand_likelihood_position_model=0.611722	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=6.50396e-08	ref_cov=160/155	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/157
RA	750	.	NC_007779	3824607	0	T	.	bias_e_value=3514270	bias_p_value=0.756354	fisher_strand_p_value=0.620437	frequency=9.109497e-03	genotype_quality=1289.3	ks_quality_p_value=0.627096	log10_base_likelihood=-7.70404	log10_qual_likelihood_position_model=1.66235	log10_strand_likelihood_position_model=0.428686	new_cov=1/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.60353e-07	ref_cov=165/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/163
RA	751	.	NC_007779	3828029	0	G	T	bias_e_value=2.293	bias_p_value=4.93507e-07	fisher_strand_p_value=2.78467e-08	frequency=4.971409e-02	genotype_quality=1205.1	ks_quality_p_value=0.961284	log10_base_likelihood=-11.2823	log10_qual_likelihood_position_model=27.2443	log10_strand_likelihood_position_model=7.56639	new_cov=21/1	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=118/205	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/206
RA	752	.	NC_007779	3840146	1	.	A	bias_e_value=4615350	bias_p_value=0.993332	fisher_strand_p_value=1	frequency=6.644249e-03	genotype_quality=1480.0	ks_quality_p_value=0.886762	log10_base_likelihood=-8.04196	log10_qual_likelihood_position_model=0.925817	log10_strand_likelihood_position_model=0.300165	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.17241e-09	ref_cov=144/155	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/156
RA	753	.	NC_007779	3845596	0	G	T	bias_e_value=0.0485089	bias_p_value=1.04403e-08	fisher_strand_p_value=4.64203e-10	frequency=4.525089e-02	genotype_quality=978.6	ks_quality_p_value=1	log10_base_likelihood=-7.83271	log10_qual_likelihood_position_model=22.2616	log10_strand_likelihood_position_model=9.34971	new_cov=0/31	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=151/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/167
RA	754	.	NC_007779	3859254	1	.	T	bias_e_value=345469	bias_p_value=0.074353	fisher_strand_p_value=0.0164981	frequency=1.574802e-02	genotype_quality=1212.1	ks_quality_p_value=0.856989	log10_base_likelihood=-17.4363	log10_qual_likelihood_position_model=2.1407	log10_strand_likelihood_position_model=1.78257	new_cov=4/0	polymorphism_quality=12.1	quality=12.1	quality_position_model=1.32733e-15	ref_cov=88/162	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=92/162
RA	755	.	NC_007779	3859263	0	T	C	bias_e_value=3.57794e-07	bias_p_value=7.70058e-14	fisher_strand_p_value=2.21645e-15	frequency=8.429241e-02	genotype_quality=661.3	ks_quality_p_value=1	log10_base_likelihood=-19.1265	log10_qual_likelihood_position_model=23.2007	log10_strand_likelihood_position_model=14.6543	new_cov=23/0	polymorphism_quality=13.8	quality=13.8	quality_position_model=Inf	ref_cov=38/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/165
RA	756	.	NC_007779	3859265	0	A	C	bias_e_value=0.000459322	bias_p_value=9.88569e-11	fisher_strand_p_value=3.61505e-12	frequency=7.712555e-02	genotype_quality=572.0	ks_quality_p_value=1	log10_base_likelihood=-16.4552	log10_qual_likelihood_position_model=12.2592	log10_strand_likelihood_position_model=11.4512	new_cov=22/2	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=40/161	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=63/166
RA	757	.	NC_007779	3859270	0	G	C	bias_e_value=0.162026	bias_p_value=3.48718e-08	fisher_strand_p_value=1.64282e-09	frequency=5.281878e-02	genotype_quality=773.8	ks_quality_p_value=1	log10_base_likelihood=-15.1259	log10_qual_likelihood_position_model=13.4774	log10_strand_likelihood_position_model=8.78441	new_cov=12/0	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=31/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=43/164
RA	758	.	NC_007779	3859381	0	T	G	bias_e_value=6.45397	bias_p_value=1.38905e-06	fisher_strand_p_value=8.0107e-08	frequency=3.898716e-02	genotype_quality=562.6	ks_quality_p_value=1	log10_base_likelihood=-6.59536	log10_qual_likelihood_position_model=11.5936	log10_strand_likelihood_position_model=7.10031	new_cov=1/8	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=156/13	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/22
RA	759	.	NC_007779	3873374	1	.	T	bias_e_value=4268920	bias_p_value=0.918771	fisher_strand_p_value=1	frequency=8.955002e-03	genotype_quality=1634.1	ks_quality_p_value=0.62504	log10_base_likelihood=-12.0908	log10_qual_likelihood_position_model=1.9979	log10_strand_likelihood_position_model=0.366262	new_cov=1/2	polymorphism_quality=6.7	quality=6.7	quality_position_model=9.51209e-12	ref_cov=136/196	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/198
RA	760	.	NC_007779	3873375	0	T	.	bias_e_value=4243720	bias_p_value=0.913348	fisher_strand_p_value=1	frequency=1.178932e-02	genotype_quality=1314.9	ks_quality_p_value=0.613719	log10_base_likelihood=-10.4802	log10_qual_likelihood_position_model=2.20781	log10_strand_likelihood_position_model=0.454109	new_cov=2/2	polymorphism_quality=5.1	quality=5.1	quality_position_model=8.54953e-10	ref_cov=136/199	reject=INDEL_HOMOPOLYMER	tot_cov=138/201
RA	761	.	NC_007779	3891906	1	.	T	bias_e_value=4151610	bias_p_value=0.893524	fisher_strand_p_value=1	frequency=6.024361e-03	genotype_quality=1626.2	ks_quality_p_value=0.575593	log10_base_likelihood=-7.99924	log10_qual_likelihood_position_model=1.3661	log10_strand_likelihood_position_model=0.299783	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.88498e-08	ref_cov=167/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=168/164
RA	762	.	NC_007779	3891907	0	T	.	bias_e_value=1816690	bias_p_value=0.390994	fisher_strand_p_value=0.214695	frequency=1.806164e-02	genotype_quality=1283.1	ks_quality_p_value=0.595881	log10_base_likelihood=-16.826	log10_qual_likelihood_position_model=3.88342	log10_strand_likelihood_position_model=1.01364	new_cov=5/1	polymorphism_quality=11.5	quality=11.5	quality_position_model=5.41112e-14	ref_cov=163/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=168/164
RA	763	.	NC_007779	3893880	0	G	T	bias_e_value=0.0197808	bias_p_value=4.25729e-09	fisher_strand_p_value=1.8183e-10	frequency=5.423784e-02	genotype_quality=947.8	ks_quality_p_value=0.999359	log10_base_likelihood=-11.2788	log10_qual_likelihood_position_model=23.3881	log10_strand_likelihood_position_model=9.74033	new_cov=0/27	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=164/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/145
RA	764	.	NC_007779	3895373	0	T	G	bias_e_value=0.00390464	bias_p_value=8.40371e-10	fisher_strand_p_value=3.34531e-11	frequency=4.183102e-02	genotype_quality=908.3	ks_quality_p_value=1	log10_base_likelihood=-7.28668	log10_qual_likelihood_position_model=30.1323	log10_strand_likelihood_position_model=10.4756	new_cov=25/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=92/170	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/171
RA	765	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1227.3	new_cov=131/161	quality=1227.3	ref_cov=0/0	tot_cov=131/161
RA	766	.	NC_007779	3900676	1	.	G	bias_e_value=5995.51	bias_p_value=0.00129037	fisher_strand_p_value=0.00803796	frequency=1.736069e-02	genotype_quality=1395.7	ks_quality_p_value=0.0161335	log10_base_likelihood=-21.9545	log10_qual_likelihood_position_model=3.44616	log10_strand_likelihood_position_model=2.09485	new_cov=5/0	polymorphism_quality=16.7	quality=16.7	quality_position_model=1.51863e-18	ref_cov=106/177	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/177
RA	767	.	NC_007779	3900680	0	T	G	bias_e_value=9.31229e-05	bias_p_value=2.00422e-11	fisher_strand_p_value=6.911e-13	frequency=4.141140e-02	genotype_quality=793.5	ks_quality_p_value=1	log10_base_likelihood=-6.51882	log10_qual_likelihood_position_model=20.4468	log10_strand_likelihood_position_model=12.1605	new_cov=14/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=21/180	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=36/180
RA	768	.	NC_007779	3910746	0	C	A	bias_e_value=0.014661	bias_p_value=3.15539e-09	fisher_strand_p_value=1.32985e-10	frequency=5.616808e-02	genotype_quality=1129.9	ks_quality_p_value=0.999412	log10_base_likelihood=-11.8132	log10_qual_likelihood_position_model=29.1235	log10_strand_likelihood_position_model=10.0328	new_cov=38/0	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=177/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=216/164
RA	769	.	NC_007779	3912296	1	.	G	bias_e_value=48749.6	bias_p_value=0.0104921	fisher_strand_p_value=0.113638	frequency=1.167297e-02	genotype_quality=1211.6	ks_quality_p_value=0.0121757	log10_base_likelihood=-13.0833	log10_qual_likelihood_position_model=3.38398	log10_strand_likelihood_position_model=0.944476	new_cov=3/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=9.37476e-11	ref_cov=122/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/132
RA	770	.	NC_007779	3930443	0	T	G	bias_e_value=3.70762e-10	bias_p_value=7.97968e-17	fisher_strand_p_value=1.90902e-18	frequency=7.059574e-02	genotype_quality=777.3	ks_quality_p_value=1	log10_base_likelihood=-9.90801	log10_qual_likelihood_position_model=27.722	log10_strand_likelihood_position_model=17.7192	new_cov=38/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=63/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/157
RA	771	.	NC_007779	3932327	0	T	.	bias_e_value=1728250	bias_p_value=0.37196	fisher_strand_p_value=0.123094	frequency=1.014137e-02	genotype_quality=1550.2	ks_quality_p_value=0.965418	log10_base_likelihood=-10.2258	log10_qual_likelihood_position_model=2.77279	log10_strand_likelihood_position_model=1.21079	new_cov=4/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=3.58292e-08	ref_cov=193/197	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=197/197
RA	772	.	NC_007779	3933153	0	G	T	bias_e_value=1.20972	bias_p_value=2.6036e-07	fisher_strand_p_value=1.36232e-08	frequency=4.200459e-02	genotype_quality=1121.4	ks_quality_p_value=1	log10_base_likelihood=-10.8614	log10_qual_likelihood_position_model=18.4234	log10_strand_likelihood_position_model=7.86572	new_cov=0/22	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=178/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=178/150
RA	773	.	NC_007779	3952095	1	.	G	bias_e_value=897790	bias_p_value=0.193226	fisher_strand_p_value=0.049816	frequency=1.293087e-02	genotype_quality=1129.2	ks_quality_p_value=0.96005	log10_base_likelihood=-12.2932	log10_qual_likelihood_position_model=1.85473	log10_strand_likelihood_position_model=1.30263	new_cov=3/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=3.82051e-11	ref_cov=83/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=86/146
RA	774	.	NC_007779	3975445	1	.	A	bias_e_value=2607260	bias_p_value=0.561144	fisher_strand_p_value=1	frequency=6.873131e-03	genotype_quality=1426.0	ks_quality_p_value=0.22535	log10_base_likelihood=-7.92706	log10_qual_likelihood_position_model=1.7416	log10_strand_likelihood_position_model=0.29954	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=8.36593e-08	ref_cov=144/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/146
RA	775	.	NC_007779	3981332	1	.	A	bias_e_value=3930920	bias_p_value=0.846027	fisher_strand_p_value=0.500954	frequency=6.535530e-03	genotype_quality=1494.2	ks_quality_p_value=0.996523	log10_base_likelihood=-7.3843	log10_qual_likelihood_position_model=3.7659	log10_strand_likelihood_position_model=0.54299	new_cov=2/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=7.28174e-05	ref_cov=162/142	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=164/142
RA	776	.	NC_007779	3982690	0	A	.	bias_e_value=2678290	bias_p_value=0.576431	fisher_strand_p_value=1	frequency=8.514404e-03	genotype_quality=1396.4	ks_quality_p_value=0.235768	log10_base_likelihood=-7.718	log10_qual_likelihood_position_model=1.85441	log10_strand_likelihood_position_model=0.390342	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=2.23844e-07	ref_cov=190/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=192/160
RA	777	.	NC_007779	3986830	0	T	.	bias_e_value=1121310	bias_p_value=0.241333	fisher_strand_p_value=0.577039	frequency=1.161861e-02	genotype_quality=1016.7	ks_quality_p_value=0.111798	log10_base_likelihood=-7.97484	log10_qual_likelihood_position_model=1.74544	log10_strand_likelihood_position_model=0.503591	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.22526e-07	ref_cov=147/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/110
RA	778	.	NC_007779	3989387	1	.	T	bias_e_value=2369840	bias_p_value=0.510046	fisher_strand_p_value=0.498208	frequency=7.246017e-03	genotype_quality=1363.2	ks_quality_p_value=0.386837	log10_base_likelihood=-8.11068	log10_qual_likelihood_position_model=1.30252	log10_strand_likelihood_position_model=0.597348	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.86077e-08	ref_cov=137/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/137
RA	779	.	NC_007779	4023064	1	.	G	bias_e_value=505834	bias_p_value=0.108867	fisher_strand_p_value=0.0592743	frequency=1.492500e-02	genotype_quality=1295.3	ks_quality_p_value=0.384031	log10_base_likelihood=-17.4518	log10_qual_likelihood_position_model=2.48284	log10_strand_likelihood_position_model=1.22713	new_cov=4/0	polymorphism_quality=12.1	quality=12.1	quality_position_model=7.77394e-16	ref_cov=129/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/135
RA	780	.	NC_007779	4023068	0	T	G	bias_e_value=4.90995e-06	bias_p_value=1.05674e-12	fisher_strand_p_value=3.29788e-14	frequency=7.247782e-02	genotype_quality=672.5	ks_quality_p_value=1	log10_base_likelihood=-11.9385	log10_qual_likelihood_position_model=23.6328	log10_strand_likelihood_position_model=13.4818	new_cov=24/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=41/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=65/140
RA	781	.	NC_007779	4029633	0	T	G	bias_e_value=1.26567e-16	bias_p_value=2.72402e-23	fisher_strand_p_value=4.77895e-25	frequency=1.478753e-01	genotype_quality=643.2	ks_quality_p_value=1	log10_base_likelihood=-32.4308	log10_qual_likelihood_position_model=31.83	log10_strand_likelihood_position_model=24.3207	new_cov=39/0	polymorphism_quality=27.2	quality=27.2	quality_position_model=Inf	ref_cov=27/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=66/145
RA	782	.	NC_007779	4031691	1	.	T	bias_e_value=114258	bias_p_value=0.0245911	fisher_strand_p_value=0.0042428	frequency=1.860428e-02	genotype_quality=1022.2	ks_quality_p_value=0.879363	log10_base_likelihood=-17.5784	log10_qual_likelihood_position_model=3.57851	log10_strand_likelihood_position_model=2.37235	new_cov=4/0	polymorphism_quality=12.3	quality=12.3	quality_position_model=1.09661e-13	ref_cov=52/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=56/159
RA	783	.	NC_007779	4031696	0	C	T	bias_e_value=15.5576	bias_p_value=3.34837e-06	fisher_strand_p_value=2.04112e-07	frequency=2.992058e-02	genotype_quality=806.2	ks_quality_p_value=1	log10_base_likelihood=-6.15765	log10_qual_likelihood_position_model=10.7786	log10_strand_likelihood_position_model=6.69013	new_cov=8/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=27/184	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/184
RA	784	.	NC_007779	4035478	0	A	C	bias_e_value=2.68605e-05	bias_p_value=5.78102e-12	fisher_strand_p_value=1.90874e-13	frequency=4.902601e-02	genotype_quality=835.3	ks_quality_p_value=1	log10_base_likelihood=-8.13177	log10_qual_likelihood_position_model=21.7047	log10_strand_likelihood_position_model=12.7193	new_cov=0/17	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=187/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=187/49
RA	785	.	NC_007779	4036507	0	G	T	bias_e_value=0.00287612	bias_p_value=6.19009e-10	fisher_strand_p_value=2.95679e-11	frequency=4.419899e-02	genotype_quality=1223.4	ks_quality_p_value=0.822949	log10_base_likelihood=-8.46487	log10_qual_likelihood_position_model=33.5229	log10_strand_likelihood_position_model=10.6307	new_cov=0/34	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=192/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=192/199
RA	786	.	NC_007779	4043703	0	C	A	bias_e_value=8.12466e-06	bias_p_value=1.74862e-12	fisher_strand_p_value=5.54713e-14	frequency=8.940935e-02	genotype_quality=955.1	ks_quality_p_value=1	log10_base_likelihood=-18.7842	log10_qual_likelihood_position_model=23.7608	log10_strand_likelihood_position_model=13.3041	new_cov=46/0	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=139/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=186/153
RA	787	.	NC_007779	4052978	0	G	T	bias_e_value=0.000181499	bias_p_value=3.90629e-11	fisher_strand_p_value=1.37987e-12	frequency=8.131361e-02	genotype_quality=964.5	ks_quality_p_value=1	log10_base_likelihood=-16.9984	log10_qual_likelihood_position_model=22.2918	log10_strand_likelihood_position_model=12.1612	new_cov=0/37	polymorphism_quality=11.7	quality=11.7	quality_position_model=Inf	ref_cov=160/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/160
RA	788	.	NC_007779	4055100	0	G	T	bias_e_value=0.031408	bias_p_value=6.75973e-09	fisher_strand_p_value=2.97423e-10	frequency=4.418278e-02	genotype_quality=1181.8	ks_quality_p_value=0.99051	log10_base_likelihood=-12.1509	log10_qual_likelihood_position_model=24.8657	log10_strand_likelihood_position_model=9.52663	new_cov=20/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=98/216	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/216
RA	789	.	NC_007779	4055329	0	T	G	bias_e_value=5.8387e-14	bias_p_value=1.25663e-20	fisher_strand_p_value=2.4761e-22	frequency=1.029220e-01	genotype_quality=808.6	ks_quality_p_value=1	log10_base_likelihood=-19.1133	log10_qual_likelihood_position_model=33.0346	log10_strand_likelihood_position_model=21.6062	new_cov=35/0	polymorphism_quality=13.8	quality=13.8	quality_position_model=Inf	ref_cov=41/182	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=76/182
RA	790	.	NC_007779	4059485	0	T	.	bias_e_value=1134010	bias_p_value=0.244065	fisher_strand_p_value=1	frequency=1.747227e-02	genotype_quality=1117.6	ks_quality_p_value=0.0655114	log10_base_likelihood=-13.9841	log10_qual_likelihood_position_model=3.23535	log10_strand_likelihood_position_model=0.502097	new_cov=3/2	polymorphism_quality=8.6	quality=8.6	quality_position_model=2.80152e-12	ref_cov=140/141	reject=INDEL_HOMOPOLYMER	tot_cov=143/143
RA	791	.	NC_007779	4062114	0	T	G	bias_e_value=8.56192e-17	bias_p_value=1.84273e-23	fisher_strand_p_value=3.21042e-25	frequency=1.044183e-01	genotype_quality=783.0	ks_quality_p_value=1	log10_base_likelihood=-19.2767	log10_qual_likelihood_position_model=36.6701	log10_strand_likelihood_position_model=24.4934	new_cov=41/0	polymorphism_quality=14.0	quality=14.0	quality_position_model=Inf	ref_cov=39/173	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=80/173
RA	792	.	NC_007779	4063618	0	G	T	bias_e_value=89.1598	bias_p_value=1.91893e-05	fisher_strand_p_value=1.31995e-06	frequency=3.026199e-02	genotype_quality=1141.5	ks_quality_p_value=1	log10_base_likelihood=-8.4869	log10_qual_likelihood_position_model=16.7204	log10_strand_likelihood_position_model=5.87944	new_cov=0/18	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=172/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/163
RA	793	.	NC_007779	4064463	0	G	T	bias_e_value=2.1511e-05	bias_p_value=4.62968e-12	fisher_strand_p_value=1.51709e-13	frequency=8.666849e-02	genotype_quality=905.7	ks_quality_p_value=1	log10_base_likelihood=-13.8127	log10_qual_likelihood_position_model=25.8405	log10_strand_likelihood_position_model=12.9767	new_cov=0/42	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=148/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/165
RA	794	.	NC_007779	4076934	0	A	C	bias_e_value=0.0350102	bias_p_value=7.53503e-09	fisher_strand_p_value=3.30023e-10	frequency=5.556631e-02	genotype_quality=918.1	ks_quality_p_value=1	log10_base_likelihood=-7.73752	log10_qual_likelihood_position_model=23.9612	log10_strand_likelihood_position_model=9.48146	new_cov=0/23	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=169/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=169/118
RA	795	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1288.6	new_cov=141/188	quality=1288.6	ref_cov=0/0	tot_cov=141/189
RA	796	.	NC_007779	4098730	0	G	T	bias_e_value=0.000576715	bias_p_value=1.24123e-10	fisher_strand_p_value=4.57854e-12	frequency=8.037853e-02	genotype_quality=924.3	ks_quality_p_value=1	log10_base_likelihood=-21.2688	log10_qual_likelihood_position_model=19.6034	log10_strand_likelihood_position_model=11.3472	new_cov=1/35	polymorphism_quality=16.0	quality=16.0	quality_position_model=Inf	ref_cov=169/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/149
RA	797	.	NC_007779	4115396	0	G	T	bias_e_value=27.4295	bias_p_value=5.90347e-06	fisher_strand_p_value=3.73638e-07	frequency=3.587914e-02	genotype_quality=791.2	ks_quality_p_value=1	log10_base_likelihood=-8.53342	log10_qual_likelihood_position_model=13.7879	log10_strand_likelihood_position_model=6.42755	new_cov=0/10	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=154/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/50
RA	798	.	NC_007779	4115400	0	T	C	bias_e_value=0.00697797	bias_p_value=1.50182e-09	fisher_strand_p_value=6.12591e-11	frequency=6.670952e-02	genotype_quality=715.7	ks_quality_p_value=1	log10_base_likelihood=-9.02	log10_qual_likelihood_position_model=19.7773	log10_strand_likelihood_position_model=10.2128	new_cov=0/21	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=150/62	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/83
RA	799	.	NC_007779	4115400	1	.	C	bias_e_value=754498	bias_p_value=0.162386	fisher_strand_p_value=0.0380365	frequency=1.338196e-02	genotype_quality=1048.2	ks_quality_p_value=1	log10_base_likelihood=-8.07015	log10_qual_likelihood_position_model=3.38139	log10_strand_likelihood_position_model=1.4198	new_cov=0/3	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.53743e-05	ref_cov=148/73	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/76
RA	800	.	NC_007779	4124346	0	A	.	bias_e_value=2179380	bias_p_value=0.469054	fisher_strand_p_value=0.251205	frequency=9.365082e-03	genotype_quality=1254.7	ks_quality_p_value=0.671855	log10_base_likelihood=-7.62611	log10_qual_likelihood_position_model=2.13916	log10_strand_likelihood_position_model=0.820036	new_cov=0/3	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.54312e-06	ref_cov=149/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/171
RA	801	.	NC_007779	4124974	0	G	T	bias_e_value=1.17524e-05	bias_p_value=2.52939e-12	fisher_strand_p_value=8.12222e-14	frequency=6.881857e-02	genotype_quality=1048.4	ks_quality_p_value=1	log10_base_likelihood=-13.8508	log10_qual_likelihood_position_model=21.5708	log10_strand_likelihood_position_model=13.0903	new_cov=0/39	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=173/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/168
RA	802	.	NC_007779	4128670	0	T	.	bias_e_value=1687740	bias_p_value=0.363242	fisher_strand_p_value=0.352693	frequency=1.293564e-02	genotype_quality=1170.9	ks_quality_p_value=0.325431	log10_base_likelihood=-10.7656	log10_qual_likelihood_position_model=3.59523	log10_strand_likelihood_position_model=0.640551	new_cov=3/1	polymorphism_quality=5.3	quality=5.3	quality_position_model=1.80896e-08	ref_cov=145/160	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/161
RA	803	.	NC_007779	4148399	0	A	C	bias_e_value=1.78947e-16	bias_p_value=3.85136e-23	fisher_strand_p_value=6.79877e-25	frequency=9.508228e-02	genotype_quality=905.4	ks_quality_p_value=1	log10_base_likelihood=-12.5202	log10_qual_likelihood_position_model=37.9841	log10_strand_likelihood_position_model=24.1676	new_cov=0/48	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=186/62	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=186/110
RA	804	.	NC_007779	4153710	0	A	C	bias_e_value=4587010	bias_p_value=0.987232	fisher_strand_p_value=1	frequency=5.443907e-02	genotype_quality=1231.3	ks_quality_p_value=0.844513	log10_base_likelihood=-56.1292	log10_qual_likelihood_position_model=8.25008	log10_strand_likelihood_position_model=0.736849	new_cov=9/10	polymorphism_quality=51.1	quality=51.1	quality_position_model=1.68714e-49	ref_cov=163/167	tot_cov=172/177
RA	805	.	NC_007779	4157323	0	C	A	bias_e_value=0.0521441	bias_p_value=1.12226e-08	fisher_strand_p_value=6.22486e-10	frequency=5.217028e-02	genotype_quality=980.6	ks_quality_p_value=0.804313	log10_base_likelihood=-9.42119	log10_qual_likelihood_position_model=26.904	log10_strand_likelihood_position_model=9.20587	new_cov=27/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=123/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/163
RA	806	.	NC_007779	4158580	1	.	A	bias_e_value=2849310	bias_p_value=0.613239	fisher_strand_p_value=0.265863	frequency=1.020336e-02	genotype_quality=1435.0	ks_quality_p_value=0.986348	log10_base_likelihood=-11.282	log10_qual_likelihood_position_model=5.54327	log10_strand_likelihood_position_model=0.716953	new_cov=0/3	polymorphism_quality=5.9	quality=5.9	quality_position_model=6.5888e-07	ref_cov=124/167	reject=POLYMORPHISM_STRAND	tot_cov=124/170
RA	807	.	NC_007779	4163966	1	.	T	bias_e_value=1934820	bias_p_value=0.416418	fisher_strand_p_value=0.602455	frequency=1.000023e-02	genotype_quality=1433.5	ks_quality_p_value=0.233365	log10_base_likelihood=-12.7499	log10_qual_likelihood_position_model=2.17736	log10_strand_likelihood_position_model=0.453143	new_cov=1/2	polymorphism_quality=7.4	quality=7.4	quality_position_model=3.778e-12	ref_cov=158/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/141
RA	808	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1487.1	new_cov=179/177	quality=1487.1	ref_cov=0/0	tot_cov=179/178
RA	809	.	NC_007779	4166106	0	G	C	bias_e_value=980758	bias_p_value=0.211082	fisher_strand_p_value=0.112985	frequency=9.935379e-03	genotype_quality=1250.2	ks_quality_p_value=0.476327	log10_base_likelihood=-7.015	log10_qual_likelihood_position_model=1.87974	log10_strand_likelihood_position_model=0.946978	new_cov=3/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=4.88255e-06	ref_cov=144/156	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=148/156
RA	810	.	NC_007779	4166127	0	A	G	bias_e_value=726904	bias_p_value=0.156447	fisher_strand_p_value=0.0367251	frequency=1.149845e-02	genotype_quality=1281.0	ks_quality_p_value=0.986605	log10_base_likelihood=-6.23811	log10_qual_likelihood_position_model=3.05207	log10_strand_likelihood_position_model=1.43504	new_cov=4/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=0.0019658	ref_cov=147/192	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=151/192
RA	811	.	NC_007779	4169401	0	A	T	bias_e_value=4353170	bias_p_value=0.936904	fisher_strand_p_value=1	frequency=1.136589e-02	genotype_quality=871.7	ks_quality_p_value=0.666488	log10_base_likelihood=-6.24403	log10_qual_likelihood_position_model=2.88269	log10_strand_likelihood_position_model=0.386164	new_cov=2/1	polymorphism_quality=0.7	quality=0.7	quality_position_model=9.30862e-05	ref_cov=143/117	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=145/118
RA	812	.	NC_007779	4169404	0	T	C	bias_e_value=3906490	bias_p_value=0.840769	fisher_strand_p_value=1	frequency=1.260471e-02	genotype_quality=790.5	ks_quality_p_value=0.491726	log10_base_likelihood=-5.71514	log10_qual_likelihood_position_model=2.89033	log10_strand_likelihood_position_model=0.390384	new_cov=2/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.000353293	ref_cov=127/107	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=129/108
RA	813	.	NC_007779	4169413	0	T	C	bias_e_value=3902670	bias_p_value=0.839946	fisher_strand_p_value=1	frequency=1.329899e-02	genotype_quality=753.8	ks_quality_p_value=0.490568	log10_base_likelihood=-6.31002	log10_qual_likelihood_position_model=2.27237	log10_strand_likelihood_position_model=0.400879	new_cov=2/1	polymorphism_quality=0.8	quality=0.8	quality_position_model=1.85396e-05	ref_cov=117/105	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=119/106
RA	814	.	NC_007779	4169476	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	815	.	NC_007779	4169478	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	816	.	NC_007779	4169479	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	817	.	NC_007779	4169481	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	818	.	NC_007779	4169482	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	819	.	NC_007779	4169483	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	820	.	NC_007779	4169484	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	821	.	NC_007779	4169485	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	822	.	NC_007779	4169486	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	823	.	NC_007779	4169487	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	824	.	NC_007779	4169488	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=1/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	825	.	NC_007779	4169489	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	826	.	NC_007779	4170016	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	827	.	NC_007779	4170018	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	828	.	NC_007779	4170019	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	829	.	NC_007779	4170020	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	830	.	NC_007779	4170021	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	831	.	NC_007779	4170022	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	832	.	NC_007779	4170023	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	833	.	NC_007779	4170024	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	834	.	NC_007779	4170025	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	835	.	NC_007779	4170029	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	836	.	NC_007779	4170031	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	837	.	NC_007779	4170032	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	838	.	NC_007779	4170035	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	839	.	NC_007779	4170036	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	840	.	NC_007779	4170037	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	841	.	NC_007779	4170038	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	842	.	NC_007779	4170039	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	843	.	NC_007779	4170040	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	844	.	NC_007779	4170041	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	845	.	NC_007779	4170042	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	846	.	NC_007779	4170043	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	847	.	NC_007779	4170044	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	848	.	NC_007779	4170046	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	849	.	NC_007779	4170048	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	850	.	NC_007779	4170049	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	851	.	NC_007779	4170050	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	852	.	NC_007779	4170051	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	853	.	NC_007779	4170052	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	854	.	NC_007779	4170053	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	855	.	NC_007779	4170054	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	856	.	NC_007779	4170055	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	857	.	NC_007779	4170056	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	858	.	NC_007779	4170057	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	859	.	NC_007779	4170058	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	860	.	NC_007779	4170062	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/2	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/2
RA	861	.	NC_007779	4170063	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/2	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/2
RA	862	.	NC_007779	4170064	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	863	.	NC_007779	4170065	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	864	.	NC_007779	4170067	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	865	.	NC_007779	4170068	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	866	.	NC_007779	4170069	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	867	.	NC_007779	4170070	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	868	.	NC_007779	4170071	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	869	.	NC_007779	4170072	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	870	.	NC_007779	4170073	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	871	.	NC_007779	4170074	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	872	.	NC_007779	4170076	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	873	.	NC_007779	4170077	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	874	.	NC_007779	4170078	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	875	.	NC_007779	4170079	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	876	.	NC_007779	4170080	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	877	.	NC_007779	4170082	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	878	.	NC_007779	4170083	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	879	.	NC_007779	4170084	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	880	.	NC_007779	4170085	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	881	.	NC_007779	4170086	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	882	.	NC_007779	4170087	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	883	.	NC_007779	4170088	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/2
RA	884	.	NC_007779	4170090	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	885	.	NC_007779	4170091	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/2
RA	886	.	NC_007779	4170093	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	887	.	NC_007779	4170094	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/2
RA	888	.	NC_007779	4170095	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	889	.	NC_007779	4170097	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	890	.	NC_007779	4170098	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	891	.	NC_007779	4170099	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	892	.	NC_007779	4170100	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/2
RA	893	.	NC_007779	4170102	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/2	reject=EVALUE	tot_cov=0/2
RA	894	.	NC_007779	4170103	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/2
RA	895	.	NC_007779	4170104	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	896	.	NC_007779	4170105	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	897	.	NC_007779	4170106	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	898	.	NC_007779	4170108	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	899	.	NC_007779	4170109	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	900	.	NC_007779	4170111	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	901	.	NC_007779	4170112	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	902	.	NC_007779	4170113	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	903	.	NC_007779	4170116	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	904	.	NC_007779	4170117	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	905	.	NC_007779	4170118	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	906	.	NC_007779	4170119	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	907	.	NC_007779	4170120	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	908	.	NC_007779	4170121	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	909	.	NC_007779	4170122	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	910	.	NC_007779	4170125	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	911	.	NC_007779	4170126	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	912	.	NC_007779	4170127	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	913	.	NC_007779	4170128	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	914	.	NC_007779	4170129	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	915	.	NC_007779	4170131	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	916	.	NC_007779	4170133	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	917	.	NC_007779	4170135	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	918	.	NC_007779	4170136	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	919	.	NC_007779	4170137	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	920	.	NC_007779	4170138	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	921	.	NC_007779	4170141	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	922	.	NC_007779	4170142	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/1	reject=EVALUE	tot_cov=0/1
RA	923	.	NC_007779	4174729	1	.	T	bias_e_value=3827650	bias_p_value=0.823801	fisher_strand_p_value=0.501829	frequency=6.689072e-03	genotype_quality=1463.9	ks_quality_p_value=0.933783	log10_base_likelihood=-8.04936	log10_qual_likelihood_position_model=2.21269	log10_strand_likelihood_position_model=0.533547	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.36098e-07	ref_cov=137/160	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/162
RA	924	.	NC_007779	4174730	0	T	.	bias_e_value=1817430	bias_p_value=0.391154	fisher_strand_p_value=0.130501	frequency=2.332020e-02	genotype_quality=1153.8	ks_quality_p_value=0.980913	log10_base_likelihood=-20.0829	log10_qual_likelihood_position_model=5.13554	log10_strand_likelihood_position_model=1.0947	new_cov=1/6	polymorphism_quality=14.8	quality=14.8	quality_position_model=5.99957e-16	ref_cov=136/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/163
RA	925	.	NC_007779	4197139	0	T	G	bias_e_value=2.66394e-20	bias_p_value=5.73342e-27	fisher_strand_p_value=8.73902e-29	frequency=1.561503e-01	genotype_quality=687.0	ks_quality_p_value=1	log10_base_likelihood=-41.685	log10_qual_likelihood_position_model=37.4382	log10_strand_likelihood_position_model=28.0585	new_cov=40/0	polymorphism_quality=36.6	quality=36.6	quality_position_model=Inf	ref_cov=21/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/159
RA	926	.	NC_007779	4207565	0	C	A	bias_e_value=0.000608159	bias_p_value=1.3089e-10	fisher_strand_p_value=4.84242e-12	frequency=8.501053e-02	genotype_quality=918.9	ks_quality_p_value=0.999089	log10_base_likelihood=-18.5986	log10_qual_likelihood_position_model=28.2201	log10_strand_likelihood_position_model=11.418	new_cov=40/0	polymorphism_quality=13.3	quality=13.3	quality_position_model=Inf	ref_cov=134/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/143
RA	927	.	NC_007779	4214454	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	928	.	NC_007779	4214455	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	929	.	NC_007779	4214456	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	930	.	NC_007779	4214458	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	931	.	NC_007779	4214459	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	932	.	NC_007779	4214460	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	933	.	NC_007779	4214462	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	934	.	NC_007779	4214463	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	935	.	NC_007779	4214464	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	936	.	NC_007779	4214466	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	937	.	NC_007779	4214467	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	938	.	NC_007779	4214468	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	939	.	NC_007779	4214469	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	940	.	NC_007779	4214470	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	941	.	NC_007779	4214471	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	942	.	NC_007779	4214472	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	943	.	NC_007779	4214473	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	944	.	NC_007779	4214474	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	945	.	NC_007779	4214475	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	946	.	NC_007779	4214478	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	947	.	NC_007779	4215291	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	948	.	NC_007779	4215292	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	949	.	NC_007779	4215293	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	950	.	NC_007779	4215294	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	951	.	NC_007779	4215295	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	952	.	NC_007779	4215298	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	953	.	NC_007779	4215299	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	954	.	NC_007779	4215302	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	955	.	NC_007779	4215303	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	956	.	NC_007779	4215305	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	957	.	NC_007779	4215306	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	958	.	NC_007779	4215307	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	959	.	NC_007779	4215312	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	960	.	NC_007779	4215313	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	961	.	NC_007779	4215314	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	962	.	NC_007779	4215315	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	963	.	NC_007779	4215316	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	964	.	NC_007779	4215317	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	965	.	NC_007779	4215318	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	966	.	NC_007779	4215319	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	967	.	NC_007779	4215320	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	968	.	NC_007779	4218761	0	C	G	bias_e_value=124088	bias_p_value=0.0267067	fisher_strand_p_value=0.00411273	frequency=2.778244e-02	genotype_quality=1103.2	ks_quality_p_value=1	log10_base_likelihood=-11.5766	log10_qual_likelihood_position_model=11.9498	log10_strand_likelihood_position_model=2.48631	new_cov=0/9	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=128/139	reject=POLYMORPHISM_STRAND	tot_cov=128/148
RA	969	.	NC_007779	4227183	0	T	G	bias_e_value=3.11908e-09	bias_p_value=6.713e-16	fisher_strand_p_value=1.69449e-17	frequency=4.478359e-02	genotype_quality=1056.4	ks_quality_p_value=1	log10_base_likelihood=-6.79883	log10_qual_likelihood_position_model=30.2478	log10_strand_likelihood_position_model=16.771	new_cov=32/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=78/220	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/221
RA	970	.	NC_007779	4244592	0	G	C	bias_e_value=18.1403	bias_p_value=3.90421e-06	fisher_strand_p_value=2.41086e-07	frequency=4.464340e-02	genotype_quality=529.3	ks_quality_p_value=0.997125	log10_base_likelihood=-11.0211	log10_qual_likelihood_position_model=6.49486	log10_strand_likelihood_position_model=6.61783	new_cov=0/7	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=124/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/19
RA	971	.	NC_007779	4259646	0	T	.	bias_e_value=3284980	bias_p_value=0.707005	fisher_strand_p_value=0.629065	frequency=1.382732e-02	genotype_quality=1023.2	ks_quality_p_value=0.540793	log10_base_likelihood=-10.3365	log10_qual_likelihood_position_model=3.69908	log10_strand_likelihood_position_model=0.527052	new_cov=1/3	polymorphism_quality=4.9	quality=4.9	quality_position_model=4.90282e-08	ref_cov=129/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/157
RA	972	.	NC_007779	4289840	0	G	T	bias_e_value=0.00583201	bias_p_value=1.25519e-09	fisher_strand_p_value=5.08113e-11	frequency=5.539083e-02	genotype_quality=921.0	ks_quality_p_value=1	log10_base_likelihood=-7.03084	log10_qual_likelihood_position_model=23.3483	log10_strand_likelihood_position_model=10.5573	new_cov=0/37	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=150/143	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/180
RA	973	.	NC_007779	4311992	0	G	C	bias_e_value=3.01859	bias_p_value=6.49672e-07	fisher_strand_p_value=3.5831e-08	frequency=4.668713e-02	genotype_quality=529.7	ks_quality_p_value=0.999248	log10_base_likelihood=-10.7132	log10_qual_likelihood_position_model=8.2331	log10_strand_likelihood_position_model=7.44574	new_cov=0/7	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=125/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=125/15
RA	974	.	NC_007779	4318994	0	A	G	bias_e_value=0.0149693	bias_p_value=3.22174e-09	fisher_strand_p_value=1.36772e-10	frequency=2.957153e-02	genotype_quality=811.3	ks_quality_p_value=0.993078	log10_base_likelihood=-10.8955	log10_qual_likelihood_position_model=6.68339	log10_strand_likelihood_position_model=9.864	new_cov=0/7	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=216/5	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=216/12
RA	975	.	NC_007779	4321435	0	G	C	bias_e_value=0.143127	bias_p_value=3.08043e-08	fisher_strand_p_value=1.4433e-09	frequency=4.941607e-02	genotype_quality=629.4	ks_quality_p_value=0.999342	log10_base_likelihood=-15.7002	log10_qual_likelihood_position_model=9.19435	log10_strand_likelihood_position_model=8.84064	new_cov=8/0	polymorphism_quality=10.4	quality=10.4	quality_position_model=Inf	ref_cov=8/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/144
RA	976	.	NC_007779	4328528	0	T	.	bias_e_value=1338550	bias_p_value=0.288088	fisher_strand_p_value=0.0890018	frequency=9.135246e-03	genotype_quality=1251.7	ks_quality_p_value=0.925839	log10_base_likelihood=-7.423	log10_qual_likelihood_position_model=3.05792	log10_strand_likelihood_position_model=1.0506	new_cov=3/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=4.06057e-05	ref_cov=144/181	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/181
RA	977	.	NC_007779	4337469	0	A	C	bias_e_value=2.34099e-18	bias_p_value=5.03836e-25	fisher_strand_p_value=8.25158e-27	frequency=1.206293e-01	genotype_quality=717.2	ks_quality_p_value=1	log10_base_likelihood=-16.0154	log10_qual_likelihood_position_model=37.7262	log10_strand_likelihood_position_model=26.0835	new_cov=0/45	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=157/35	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/80
RA	978	.	NC_007779	4342787	1	.	A	bias_e_value=1820720	bias_p_value=0.391862	fisher_strand_p_value=0.52752	frequency=6.173134e-03	genotype_quality=1580.7	ks_quality_p_value=0.243317	log10_base_likelihood=-8.10228	log10_qual_likelihood_position_model=1.46032	log10_strand_likelihood_position_model=0.415521	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.71992e-08	ref_cov=199/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=201/123
RA	979	.	NC_007779	4348529	0	T	G	bias_e_value=8.18432e-06	bias_p_value=1.76146e-12	fisher_strand_p_value=5.58921e-14	frequency=6.447840e-02	genotype_quality=874.4	ks_quality_p_value=1	log10_base_likelihood=-10.2227	log10_qual_likelihood_position_model=34.5248	log10_strand_likelihood_position_model=13.2526	new_cov=31/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=83/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/165
RA	980	.	NC_007779	4348862	0	G	C	bias_e_value=355075	bias_p_value=0.0764205	fisher_strand_p_value=0.0146452	frequency=1.949596e-02	genotype_quality=1273.0	ks_quality_p_value=0.998694	log10_base_likelihood=-9.33931	log10_qual_likelihood_position_model=10.07	log10_strand_likelihood_position_model=2.09764	new_cov=7/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=152/155	reject=POLYMORPHISM_STRAND	tot_cov=159/155
RA	981	.	NC_007779	4351353	0	T	G	bias_e_value=3.61095e-12	bias_p_value=7.77161e-19	fisher_strand_p_value=1.66992e-20	frequency=6.393290e-02	genotype_quality=952.1	ks_quality_p_value=1	log10_base_likelihood=-9.96531	log10_qual_likelihood_position_model=44.5572	log10_strand_likelihood_position_model=19.7773	new_cov=39/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=69/195	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/195
RA	982	.	NC_007779	4357170	1	.	A	bias_e_value=3945570	bias_p_value=0.849179	fisher_strand_p_value=0.508403	frequency=7.325172e-03	genotype_quality=1332.0	ks_quality_p_value=0.990904	log10_base_likelihood=-7.72987	log10_qual_likelihood_position_model=3.22728	log10_strand_likelihood_position_model=0.487275	new_cov=0/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=7.41301e-06	ref_cov=117/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/156
RA	983	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=1198.0	new_cov=121/118	quality=1198.0	ref_cov=0/0	tot_cov=121/118
RA	984	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=1198.0	new_cov=121/118	quality=1198.0	ref_cov=0/0	tot_cov=121/118
RA	985	.	NC_007779	4413560	0	A	.	bias_e_value=562470	bias_p_value=0.121057	fisher_strand_p_value=0.248001	frequency=8.892059e-03	genotype_quality=1320.8	ks_quality_p_value=0.105021	log10_base_likelihood=-7.53496	log10_qual_likelihood_position_model=3.33668	log10_strand_likelihood_position_model=0.883799	new_cov=0/3	polymorphism_quality=2.0	quality=2.0	quality_position_model=4.0606e-05	ref_cov=165/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/172
RA	986	.	NC_007779	4414724	1	.	T	bias_e_value=2289870	bias_p_value=0.492834	fisher_strand_p_value=0.601193	frequency=1.257896e-02	genotype_quality=1540.1	ks_quality_p_value=0.303466	log10_base_likelihood=-17.0602	log10_qual_likelihood_position_model=2.79434	log10_strand_likelihood_position_model=0.530395	new_cov=2/2	polymorphism_quality=11.7	quality=11.7	quality_position_model=7.8904e-16	ref_cov=103/211	reject=INDEL_HOMOPOLYMER	tot_cov=105/213
RA	987	.	NC_007779	4416420	1	.	T	bias_e_value=2740520	bias_p_value=0.589825	fisher_strand_p_value=0.247938	frequency=8.620262e-03	genotype_quality=1695.7	ks_quality_p_value=0.988819	log10_base_likelihood=-11.4075	log10_qual_likelihood_position_model=4.96777	log10_strand_likelihood_position_model=0.891885	new_cov=3/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=1.8733e-07	ref_cov=173/172	reject=POLYMORPHISM_STRAND	tot_cov=176/172
RA	988	.	NC_007779	4416432	0	A	.	bias_e_value=2663350	bias_p_value=0.573215	fisher_strand_p_value=0.248371	frequency=8.345604e-03	genotype_quality=1378.1	ks_quality_p_value=0.940325	log10_base_likelihood=-7.37086	log10_qual_likelihood_position_model=2.85891	log10_strand_likelihood_position_model=0.874146	new_cov=3/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.84933e-05	ref_cov=180/174	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=185/174
RA	989	.	NC_007779	4419586	0	T	G	bias_e_value=0.0271133	bias_p_value=5.83542e-09	fisher_strand_p_value=2.52625e-10	frequency=5.799103e-02	genotype_quality=955.2	ks_quality_p_value=1	log10_base_likelihood=-7.87576	log10_qual_likelihood_position_model=29.2064	log10_strand_likelihood_position_model=9.59752	new_cov=26/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=110/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=138/165
RA	990	.	NC_007779	4429120	0	G	T	bias_e_value=0.700168	bias_p_value=1.50693e-07	fisher_strand_p_value=9.60326e-09	frequency=4.625797e-02	genotype_quality=1026.1	ks_quality_p_value=0.797023	log10_base_likelihood=-14.2032	log10_qual_likelihood_position_model=27.4672	log10_strand_likelihood_position_model=8.01758	new_cov=0/25	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=168/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/166
RA	991	.	NC_007779	4455463	0	T	G	bias_e_value=6.05833e-08	bias_p_value=1.3039e-14	fisher_strand_p_value=3.56547e-16	frequency=6.225109e-02	genotype_quality=910.9	ks_quality_p_value=1	log10_base_likelihood=-8.12189	log10_qual_likelihood_position_model=35.4953	log10_strand_likelihood_position_model=15.4479	new_cov=33/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=76/179	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/179
RA	992	.	NC_007779	4479134	0	G	T	bias_e_value=3.89651	bias_p_value=8.3862e-07	fisher_strand_p_value=4.71702e-08	frequency=3.858376e-02	genotype_quality=831.9	ks_quality_p_value=0.994611	log10_base_likelihood=-7.52436	log10_qual_likelihood_position_model=18.0445	log10_strand_likelihood_position_model=7.47642	new_cov=0/24	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=145/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/150
RA	993	.	NC_007779	4522244	0	G	T	bias_e_value=701.606	bias_p_value=0.000151002	fisher_strand_p_value=1.22681e-05	frequency=3.969955e-02	genotype_quality=856.7	ks_quality_p_value=1	log10_base_likelihood=-6.86547	log10_qual_likelihood_position_model=12.1567	log10_strand_likelihood_position_model=4.97803	new_cov=0/17	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=125/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/138
RA	994	.	NC_007779	4540870	0	T	G	bias_e_value=8.48278e-24	bias_p_value=1.82569e-30	fisher_strand_p_value=2.47462e-32	frequency=1.107349e-01	genotype_quality=915.8	ks_quality_p_value=1	log10_base_likelihood=-15.8023	log10_qual_likelihood_position_model=48.3934	log10_strand_likelihood_position_model=31.6065	new_cov=61/0	polymorphism_quality=10.5	quality=10.5	quality_position_model=Inf	ref_cov=55/192	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=117/192
RA	995	.	NC_007779	4540877	0	A	T	bias_e_value=3.33982e-07	bias_p_value=7.18808e-14	fisher_strand_p_value=2.06472e-15	frequency=8.953762e-02	genotype_quality=886.8	ks_quality_p_value=1	log10_base_likelihood=-22.8883	log10_qual_likelihood_position_model=23.5012	log10_strand_likelihood_position_model=14.6851	new_cov=30/0	polymorphism_quality=17.6	quality=17.6	quality_position_model=Inf	ref_cov=78/194	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/194
RA	996	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=1084.1	new_cov=155/115	quality=1084.1	ref_cov=0/0	tot_cov=155/115
RA	997	.	NC_007779	4547676	0	A	T	bias_e_value=3676130	bias_p_value=0.791189	fisher_strand_p_value=0.574001	frequency=9.145737e-03	genotype_quality=1286.6	ks_quality_p_value=0.745591	log10_base_likelihood=-6.70187	log10_qual_likelihood_position_model=2.96216	log10_strand_likelihood_position_model=0.513514	new_cov=1/2	polymorphism_quality=1.2	quality=1.2	quality_position_model=5.03658e-05	ref_cov=189/135	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=191/137
RA	998	.	NC_007779	4554525	1	.	T	bias_e_value=616748	bias_p_value=0.132739	fisher_strand_p_value=0.0593738	frequency=1.339245e-02	genotype_quality=1058.4	ks_quality_p_value=0.493507	log10_base_likelihood=-12.4237	log10_qual_likelihood_position_model=3.68926	log10_strand_likelihood_position_model=1.22641	new_cov=3/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=1.78052e-09	ref_cov=85/136	reject=POLYMORPHISM_STRAND	tot_cov=88/136
RA	999	.	NC_007779	4561440	1	.	T	bias_e_value=3963770	bias_p_value=0.853097	fisher_strand_p_value=1	frequency=1.123619e-02	genotype_quality=1297.7	ks_quality_p_value=0.509542	log10_base_likelihood=-12.5238	log10_qual_likelihood_position_model=1.81376	log10_strand_likelihood_position_model=0.374078	new_cov=2/1	polymorphism_quality=7.1	quality=7.1	quality_position_model=2.27128e-12	ref_cov=151/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/114
RA	1000	.	NC_007779	4561441	0	T	.	bias_e_value=2460060	bias_p_value=0.529463	fisher_strand_p_value=0.408374	frequency=2.188873e-02	genotype_quality=1049.4	ks_quality_p_value=0.501358	log10_base_likelihood=-17.6643	log10_qual_likelihood_position_model=3.12266	log10_strand_likelihood_position_model=0.768551	new_cov=2/4	polymorphism_quality=12.4	quality=12.4	quality_position_model=7.22605e-16	ref_cov=153/115	reject=INDEL_HOMOPOLYMER	tot_cov=155/119
RA	1001	.	NC_007779	4577568	0	A	T	bias_e_value=3255290	bias_p_value=0.700616	fisher_strand_p_value=1	frequency=8.102417e-03	genotype_quality=1445.7	ks_quality_p_value=0.334316	log10_base_likelihood=-6.03828	log10_qual_likelihood_position_model=3.32218	log10_strand_likelihood_position_model=0.392332	new_cov=2/1	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.000465191	ref_cov=196/166	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=198/167
RA	1002	.	NC_007779	4584556	0	C	A	bias_e_value=0.00647948	bias_p_value=1.39454e-09	fisher_strand_p_value=5.67415e-11	frequency=5.675697e-02	genotype_quality=1068.2	ks_quality_p_value=0.999342	log10_base_likelihood=-12.7687	log10_qual_likelihood_position_model=29.2527	log10_strand_likelihood_position_model=10.5113	new_cov=35/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=146/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=182/163
RA	1003	.	NC_007779	4584731	0	G	T	bias_e_value=5.12565	bias_p_value=1.10316e-06	fisher_strand_p_value=6.27354e-08	frequency=2.548027e-02	genotype_quality=1078.7	ks_quality_p_value=1	log10_base_likelihood=-5.95074	log10_qual_likelihood_position_model=12.2053	log10_strand_likelihood_position_model=7.20249	new_cov=0/15	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=214/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=214/115
RA	1004	.	NC_007779	4594551	0	G	T	bias_e_value=118.59	bias_p_value=2.55233e-05	fisher_strand_p_value=1.79409e-06	frequency=3.240967e-02	genotype_quality=1044.7	ks_quality_p_value=0.999644	log10_base_likelihood=-8.24718	log10_qual_likelihood_position_model=15.2462	log10_strand_likelihood_position_model=5.74616	new_cov=0/16	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=169/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/140
RA	1005	.	NC_007779	4599760	0	C	A	bias_e_value=0.000120633	bias_p_value=2.5963e-11	fisher_strand_p_value=9.03615e-13	frequency=5.573940e-02	genotype_quality=1091.8	ks_quality_p_value=1	log10_base_likelihood=-11.4589	log10_qual_likelihood_position_model=20.1712	log10_strand_likelihood_position_model=12.044	new_cov=26/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=96/208	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/209
RA	1006	.	NC_007779	4601746	1	.	T	bias_e_value=4186160	bias_p_value=0.90096	fisher_strand_p_value=1	frequency=8.955002e-03	genotype_quality=1620.9	ks_quality_p_value=0.58935	log10_base_likelihood=-12.5759	log10_qual_likelihood_position_model=2.38222	log10_strand_likelihood_position_model=0.387868	new_cov=2/1	polymorphism_quality=7.2	quality=7.2	quality_position_model=7.89615e-12	ref_cov=182/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=184/151
RA	1007	.	NC_007779	4610781	0	A	C	bias_e_value=0.00152163	bias_p_value=3.27491e-10	fisher_strand_p_value=1.25468e-11	frequency=5.975771e-02	genotype_quality=1025.8	ks_quality_p_value=1	log10_base_likelihood=-14.8542	log10_qual_likelihood_position_model=33.0616	log10_strand_likelihood_position_model=10.909	new_cov=1/28	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=189/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=190/124
RA	1008	.	NC_007779	4610887	1	.	G	bias_e_value=473977	bias_p_value=0.102011	fisher_strand_p_value=0.251049	frequency=1.048946e-02	genotype_quality=1390.3	ks_quality_p_value=0.0835285	log10_base_likelihood=-12.8029	log10_qual_likelihood_position_model=2.47384	log10_strand_likelihood_position_model=0.819017	new_cov=3/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=1.5833e-11	ref_cov=150/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/133
RA	1009	.	NC_007779	4611002	1	.	G	bias_e_value=4123870	bias_p_value=0.887553	fisher_strand_p_value=1	frequency=7.490158e-03	genotype_quality=1297.0	ks_quality_p_value=0.564961	log10_base_likelihood=-7.86804	log10_qual_likelihood_position_model=3.03185	log10_strand_likelihood_position_model=0.302635	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.12603e-06	ref_cov=144/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/122
RA	1010	.	NC_007779	4613456	0	C	A	bias_e_value=751.78	bias_p_value=0.000161801	fisher_strand_p_value=1.32263e-05	frequency=3.700829e-02	genotype_quality=1040.8	ks_quality_p_value=1	log10_base_likelihood=-9.24527	log10_qual_likelihood_position_model=18.384	log10_strand_likelihood_position_model=5.12192	new_cov=22/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=179/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=203/135
RA	1011	.	NC_007779	4622612	0	G	T	bias_e_value=4635550	bias_p_value=0.997679	fisher_strand_p_value=1	frequency=1.211929e-02	genotype_quality=1307.6	ks_quality_p_value=0.932652	log10_base_likelihood=-5.75545	log10_qual_likelihood_position_model=4.32024	log10_strand_likelihood_position_model=0.423536	new_cov=2/2	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.0136281	ref_cov=160/154	reject=EVALUE	tot_cov=162/156
RA	1012	.	NC_007779	4636470	0	C	G	bias_e_value=2.38434e-05	bias_p_value=5.13166e-12	fisher_strand_p_value=1.68747e-13	frequency=6.924629e-02	genotype_quality=914.2	ks_quality_p_value=1	log10_base_likelihood=-14.1199	log10_qual_likelihood_position_model=19.4773	log10_strand_likelihood_position_model=12.7728	new_cov=23/0	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=59/183	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=82/183
RA	1013	.	NC_007779	4636473	0	A	G	bias_e_value=1.26672e-12	bias_p_value=2.72628e-19	fisher_strand_p_value=5.72637e-21	frequency=8.543825e-02	genotype_quality=745.2	ks_quality_p_value=1	log10_base_likelihood=-13.3185	log10_qual_likelihood_position_model=30.1758	log10_strand_likelihood_position_model=20.2421	new_cov=25/0	polymorphism_quality=7.9	quality=7.9	quality_position_model=Inf	ref_cov=22/186	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=47/186
RA	1014	.	NC_007779	4639643	1	.	G	bias_e_value=879035	bias_p_value=0.189189	fisher_strand_p_value=0.0515105	frequency=1.388836e-02	genotype_quality=1051.6	ks_quality_p_value=0.90281	log10_base_likelihood=-12.4266	log10_qual_likelihood_position_model=1.99292	log10_strand_likelihood_position_model=1.2881	new_cov=3/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=3.73383e-11	ref_cov=78/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=81/135
RA	1015	.	NC_007779	4640524	0	C	A	bias_e_value=2898.93	bias_p_value=0.000623919	fisher_strand_p_value=5.80128e-05	frequency=2.681255e-02	genotype_quality=1020.1	ks_quality_p_value=1	log10_base_likelihood=-6.9119	log10_qual_likelihood_position_model=12.3266	log10_strand_likelihood_position_model=4.23648	new_cov=13/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=138/162	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/163
RA	1016	.	NC_007779	4644244	1	.	T	bias_e_value=3877960	bias_p_value=0.834629	fisher_strand_p_value=1	frequency=5.988121e-03	genotype_quality=1614.0	ks_quality_p_value=0.483181	log10_base_likelihood=-8.1546	log10_qual_likelihood_position_model=1.74953	log10_strand_likelihood_position_model=0.321587	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.22665e-08	ref_cov=203/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=204/130
MC	1017	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=318	right_inside_cov=0	right_outside_cov=319
MC	1018	.	NC_007779	654214	655412	1196	0	left_inside_cov=0	left_outside_cov=328	right_inside_cov=0	right_outside_cov=323
MC	1019	.	NC_007779	1288305	1288510	100	51	left_inside_cov=237	left_outside_cov=239	right_inside_cov=237	right_outside_cov=241
MC	1020	.	NC_007779	1301041	1302376	1327	0	left_inside_cov=0	left_outside_cov=316	right_inside_cov=0	right_outside_cov=313
MC	1021	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=360	right_inside_cov=0	right_outside_cov=353
MC	1022	.	NC_007779	2176983	2178208	0	0	left_inside_cov=0	left_outside_cov=367	right_inside_cov=0	right_outside_cov=413
MC	1023	.	NC_007779	2320795	2322130	1330	0	left_inside_cov=0	left_outside_cov=354	right_inside_cov=0	right_outside_cov=355
MC	1024	.	NC_007779	3128829	3147473	1173	0	left_inside_cov=237	left_outside_cov=240	right_inside_cov=0	right_outside_cov=340
MC	1025	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=354	right_inside_cov=0	right_outside_cov=283
MC	1026	.	NC_007779	3742936	3744271	1328	0	left_inside_cov=0	left_outside_cov=377	right_inside_cov=2	right_outside_cov=377
MC	1027	.	NC_007779	3750591	3751789	1198	0	left_inside_cov=0	left_outside_cov=392	right_inside_cov=0	right_outside_cov=390
MC	1028	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=332	right_inside_cov=0	right_outside_cov=334
MC	1029	.	NC_007779	4310363	4311561	0	1197	left_inside_cov=0	left_outside_cov=333	right_inside_cov=0	right_outside_cov=330
JC	1030	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=156	coverage_plus=195	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1__1__NC_007779__4646332__-1__0____101__101__0__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=48	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=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=354	pos_hash_score=140	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=351
JC	1031	.	NC_007779	273179	1	NC_007779	657877	1	0	alignment_overlap=0	coverage_minus=101	coverage_plus=105	flanking_left=101	flanking_right=101	frequency=7.013423e-01	junction_possible_overlap_registers=90	key=NC_007779__273179__1__NC_007779__657877__1__0____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.69	new_junction_frequency=7.013423e-01	new_junction_read_count=209	pos_hash_score=121	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=0.29	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=89	side_2_redundant=0	total_non_overlap_reads=206
JC	1032	.	NC_007779	274373	-1	NC_007779	657880	-1	0	alignment_overlap=0	coverage_minus=75	coverage_plus=108	flanking_left=101	flanking_right=101	frequency=6.606498e-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=82	max_left_plus=83	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=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.60	new_junction_frequency=6.606498e-01	new_junction_read_count=183	pos_hash_score=107	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.31	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=94	side_2_redundant=0	total_non_overlap_reads=183
JC	1033	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=10	coverage_minus=105	coverage_plus=123	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371963__1__10____101__101__0__0	max_left=85	max_left_minus=85	max_left_plus=85	max_min_left=45	max_min_left_minus=45	max_min_left_plus=45	max_min_right=45	max_min_right_minus=45	max_min_right_plus=45	max_pos_hash_score=160	max_right=85	max_right_minus=84	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.85	new_junction_frequency=1.000000e+00	new_junction_read_count=229	pos_hash_score=126	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=10	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=80	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=228
JC	1034	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=136	coverage_plus=92	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=57	key=NC_007779__289856__1__NC_007779__2176982__-1__-33__CTATTGCAATACCGCATTGTGAGGCGATTCATG__101__101__1__0	max_left=62	max_left_minus=62	max_left_plus=62	max_min_left=33	max_min_left_minus=33	max_min_left_plus=33	max_min_right=34	max_min_right_minus=34	max_min_right_plus=34	max_pos_hash_score=114	max_right=62	max_right_minus=62	max_right_plus=60	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.19	new_junction_frequency=1.000000e+00	new_junction_read_count=229	pos_hash_score=99	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	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	1035	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=164	coverage_plus=95	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=91	max_left_minus=91	max_left_plus=89	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=48	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=0.85	new_junction_frequency=NA	new_junction_read_count=259	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=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=259
JC	1036	.	NC_007779	380484	1	NC_007779	431208	1	0	alignment_overlap=0	coverage_minus=5	coverage_plus=0	flanking_left=101	flanking_right=101	frequency=1.779359e-02	junction_possible_overlap_registers=90	key=NC_007779__380484__1__NC_007779__431208__1__0____101__101__1__0	max_left=87	max_left_minus=87	max_left_plus=0	max_min_left=45	max_min_left_minus=45	max_min_left_plus=0	max_min_right=27	max_min_right_minus=27	max_min_right_plus=0	max_pos_hash_score=180	max_right=60	max_right_minus=60	max_right_plus=0	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=1.779359e-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=0.91	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=276	side_2_redundant=0	total_non_overlap_reads=5
JC	1037	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=115	coverage_plus=153	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=88	key=NC_007779__381401__1__NC_007779__381814__-1__2____101__101__1__1	max_left=93	max_left_minus=93	max_left_plus=92	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=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=NA	new_junction_read_count=268	pos_hash_score=138	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=268
JC	1038	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=79	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=7.571897e-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=90	max_left_plus=92	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=49	max_min_right_minus=48	max_min_right_plus=49	max_pos_hash_score=174	max_right=93	max_right_minus=92	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.71	new_junction_frequency=7.571897e-01	new_junction_read_count=208	pos_hash_score=117	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=0.23	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=69	side_2_redundant=0	total_non_overlap_reads=208
JC	1039	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=152	coverage_plus=116	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=85	key=NC_007779__654213__-1__NC_007779__655408__1__5____101__101__0__0	max_left=90	max_left_minus=90	max_left_plus=90	max_min_left=47	max_min_left_minus=47	max_min_left_plus=46	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=170	max_right=90	max_right_minus=90	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=272	pos_hash_score=133	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=268
JC	1040	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=19	coverage_plus=28	flanking_left=101	flanking_right=101	frequency=2.225964e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=77	max_left_minus=74	max_left_plus=77	max_min_left=42	max_min_left_minus=34	max_min_left_plus=42	max_min_right=42	max_min_right_minus=41	max_min_right_plus=42	max_pos_hash_score=148	max_right=78	max_right_minus=78	max_right_plus=77	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.19	new_junction_frequency=2.225964e-01	new_junction_read_count=47	pos_hash_score=38	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.61	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=184	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.71	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=177	side_2_redundant=0	total_non_overlap_reads=47
JC	1041	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=27	coverage_plus=17	flanking_left=101	flanking_right=101	frequency=2.126517e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=79	max_left_minus=79	max_left_plus=79	max_min_left=41	max_min_left_minus=41	max_min_left_plus=37	max_min_right=42	max_min_right_minus=42	max_min_right_plus=40	max_pos_hash_score=148	max_right=77	max_right_minus=77	max_right_plus=68	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.18	new_junction_frequency=2.126517e-01	new_junction_read_count=44	pos_hash_score=35	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.60	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=181	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.71	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=177	side_2_redundant=0	total_non_overlap_reads=44
JC	1042	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=112	coverage_plus=150	flanking_left=101	flanking_right=101	frequency=9.816819e-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=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=91	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.88	new_junction_frequency=9.816819e-01	new_junction_read_count=262	pos_hash_score=131	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=5	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=262
JC	1043	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=143	coverage_plus=89	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1221495__-1__NC_007779__1302369__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=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=88	max_right_minus=88	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.77	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=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=232
JC	1044	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=117	coverage_plus=140	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=83	key=NC_007779__1301040__-1__NC_007779__1302370__1__7____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=86	max_min_left=46	max_min_left_minus=42	max_min_left_plus=46	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=166	max_right=88	max_right_minus=87	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=258	pos_hash_score=128	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=7	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=83	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=257
JC	1045	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=124	coverage_plus=116	flanking_left=101	flanking_right=101	frequency=7.630352e-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=89	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.83	new_junction_frequency=7.630352e-01	new_junction_read_count=240	pos_hash_score=132	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.26	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=78	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=240
JC	1046	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=136	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=88	max_left_minus=88	max_left_plus=88	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=1.000000e+00	new_junction_read_count=261	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=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=258
JC	1047	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=101	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=64	key=NC_007779__1413638__-1__NC_007779__1436673__1__26____101__101__0__0	max_left=69	max_left_minus=69	max_left_plus=69	max_min_left=37	max_min_left_minus=37	max_min_left_plus=37	max_min_right=37	max_min_right_minus=37	max_min_right_plus=37	max_pos_hash_score=128	max_right=69	max_right_minus=69	max_right_plus=69	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=218	pos_hash_score=102	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=26	side_1_possible_overlap_registers=90	side_1_read_count=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=64	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=216
JC	1048	.	NC_007779	1624374	-1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=2	coverage_plus=1	flanking_left=101	flanking_right=101	frequency=1.016949e-02	junction_possible_overlap_registers=90	key=NC_007779__1624374__-1__NC_007779__2412225__-1__0____101__101__0__1	max_left=73	max_left_minus=73	max_left_plus=56	max_min_left=19	max_min_left_minus=19	max_min_left_plus=0	max_min_right=45	max_min_right_minus=28	max_min_right_plus=45	max_pos_hash_score=180	max_right=82	max_right_minus=82	max_right_plus=45	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.01	new_junction_frequency=1.016949e-02	new_junction_read_count=3	pos_hash_score=3	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.96	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=292	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	1049	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=146	coverage_plus=144	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1672780__-1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=85	max_right_minus=85	max_right_plus=83	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=291	pos_hash_score=128	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=290
JC	1050	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=151	coverage_plus=120	flanking_left=101	flanking_right=101	frequency=9.575972e-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=94	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=88	max_right_minus=88	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.89	new_junction_frequency=9.575972e-01	new_junction_read_count=271	pos_hash_score=129	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=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=271
JC	1051	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=118	coverage_plus=155	flanking_left=101	flanking_right=101	frequency=9.484536e-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=94	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=49	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=0.91	new_junction_frequency=9.484536e-01	new_junction_read_count=276	pos_hash_score=135	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=15	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=273
JC	1052	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=168	coverage_plus=47	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=94	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=48	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=0.71	new_junction_frequency=1.000000e+00	new_junction_read_count=215	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=215
JC	1053	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=162	coverage_plus=136	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__1980095__-1__NC_007779__2176983__1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=300	pos_hash_score=140	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=298
JC	1054	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=154	coverage_plus=150	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=304	pos_hash_score=141	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=304
JC	1055	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=132	coverage_plus=162	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=88	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=296	pos_hash_score=137	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=294
JC	1056	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=76	coverage_plus=185	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=83	max_left_plus=85	max_min_left=50	max_min_left_minus=48	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=1.000000e+00	new_junction_read_count=262	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=261
JC	1057	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=150	coverage_plus=149	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=90	max_left_minus=82	max_left_plus=90	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=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=300	pos_hash_score=130	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=299
JC	1058	.	NC_007779	2411458	1	NC_007779	2941519	1	0	alignment_overlap=0	coverage_minus=8	coverage_plus=5	flanking_left=101	flanking_right=101	frequency=3.823529e-02	junction_possible_overlap_registers=90	key=NC_007779__2411458__1__NC_007779__2941519__1__0____101__101__1__0	max_left=84	max_left_minus=84	max_left_plus=76	max_min_left=38	max_min_left_minus=38	max_min_left_plus=32	max_min_right=46	max_min_right_minus=46	max_min_right_plus=27	max_pos_hash_score=180	max_right=93	max_right_minus=85	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.04	new_junction_frequency=3.823529e-02	new_junction_read_count=13	pos_hash_score=11	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.08	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=327	side_2_redundant=0	total_non_overlap_reads=13
JC	1059	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=153	coverage_plus=158	flanking_left=101	flanking_right=101	frequency=9.454545e-01	junction_possible_overlap_registers=90	key=NC_007779__2411458__1__NC_007779__2985055__-1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.03	new_junction_frequency=9.454545e-01	new_junction_read_count=312	pos_hash_score=148	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=0.06	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=18	side_2_redundant=0	total_non_overlap_reads=311
JC	1060	.	NC_007779	2411459	1	NC_007779	2941449	1	0	alignment_overlap=1	coverage_minus=3	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.630730e-02	junction_possible_overlap_registers=89	key=NC_007779__2411458__1__NC_007779__2941449__1__1____101__101__1__0	max_left=80	max_left_minus=55	max_left_plus=80	max_min_left=48	max_min_left_minus=48	max_min_left_plus=24	max_min_right=45	max_min_right_minus=45	max_min_right_plus=19	max_pos_hash_score=178	max_right=90	max_right_minus=90	max_right_plus=76	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=1.630730e-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=1.01	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=305	side_2_redundant=0	total_non_overlap_reads=5
JC	1061	.	NC_007779	2412224	-1	NC_007779	2941459	-1	0	alignment_overlap=1	coverage_minus=3	coverage_plus=1	flanking_left=101	flanking_right=101	frequency=1.361728e-02	junction_possible_overlap_registers=89	key=NC_007779__2412225__-1__NC_007779__2941459__-1__1____101__101__1__0	max_left=93	max_left_minus=60	max_left_plus=93	max_min_left=46	max_min_left_minus=46	max_min_left_plus=0	max_min_right=40	max_min_right_minus=40	max_min_right_plus=7	max_pos_hash_score=178	max_right=74	max_right_minus=74	max_right_plus=7	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.01	new_junction_frequency=1.361728e-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=0.97	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=293	side_2_redundant=0	total_non_overlap_reads=4
JC	1062	.	NC_007779	2412225	-1	NC_007779	2941527	-1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=6	flanking_left=101	flanking_right=101	frequency=2.623907e-02	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2941527__-1__0____101__101__1__0	max_left=78	max_left_minus=74	max_left_plus=78	max_min_left=48	max_min_left_minus=17	max_min_left_plus=48	max_min_right=31	max_min_right_minus=27	max_min_right_plus=31	max_pos_hash_score=180	max_right=84	max_right_minus=84	max_right_plus=70	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.03	new_junction_frequency=2.623907e-02	new_junction_read_count=9	pos_hash_score=7	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=1.10	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=334	side_2_redundant=0	total_non_overlap_reads=9
JC	1063	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=114	coverage_plus=135	flanking_left=101	flanking_right=101	frequency=9.233577e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=88	max_left_minus=87	max_left_plus=88	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.83	new_junction_frequency=9.233577e-01	new_junction_read_count=253	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=0.07	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=21	side_2_redundant=0	total_non_overlap_reads=249
JC	1064	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=122	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=6.641583e-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=90	max_left_plus=91	max_min_left=45	max_min_left_minus=45	max_min_left_plus=45	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=1.05	new_junction_frequency=6.641583e-01	new_junction_read_count=304	pos_hash_score=123	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.56	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=170	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.50	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=145	side_2_redundant=0	total_non_overlap_reads=254
JC	1065	.	NC_007779	2865229	1	NC_007779	2865278	-1	-42	alignment_overlap=-42	coverage_minus=41	coverage_plus=37	flanking_left=101	flanking_right=101	frequency=4.777070e-01	junction_possible_overlap_registers=48	key=NC_007779__2865229__1__NC_007779__2865278__-1__-42__CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA__101__101__0__0	max_left=45	max_left_minus=45	max_left_plus=42	max_min_left=29	max_min_left_minus=27	max_min_left_plus=29	max_min_right=29	max_min_right_minus=29	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=0.49	new_junction_frequency=4.777070e-01	new_junction_read_count=80	pos_hash_score=40	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.56	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=170	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.52	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=158	side_2_redundant=0	total_non_overlap_reads=78	unique_read_sequence=CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA
JC	1066	.	NC_007779	2941414	-1	NC_007779	2941423	1	0	alignment_overlap=0	coverage_minus=7	coverage_plus=11	flanking_left=101	flanking_right=101	frequency=1.136388e-01	junction_possible_overlap_registers=90	key=NC_007779__2941414__-1__NC_007779__2941423__1__0____101__101__0__0	max_left=93	max_left_minus=90	max_left_plus=93	max_min_left=44	max_min_left_minus=44	max_min_left_plus=39	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	max_pos_hash_score=168	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.13	new_junction_frequency=1.136388e-01	new_junction_read_count=38	pos_hash_score=17	side_1_annotate_key=gene	side_1_continuation=6	side_1_coverage=0.98	side_1_overlap=0	side_1_possible_overlap_registers=84	side_1_read_count=277	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.98	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=296	side_2_redundant=0	total_non_overlap_reads=18
JC	1067	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=146	coverage_plus=159	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=94	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=88	max_right_minus=88	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=306	pos_hash_score=138	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=305
JC	1068	.	NC_007779	3174999	-1	NC_007779	3175003	1	0	alignment_overlap=0	coverage_minus=4	coverage_plus=4	flanking_left=101	flanking_right=101	frequency=1.175830e-01	junction_possible_overlap_registers=90	key=NC_007779__3174999__-1__NC_007779__3175003__1__0____101__101__0__0	max_left=89	max_left_minus=89	max_left_plus=59	max_min_left=48	max_min_left_minus=48	max_min_left_plus=45	max_min_right=44	max_min_right_minus=12	max_min_right_plus=44	max_pos_hash_score=162	max_right=89	max_right_minus=89	max_right_plus=80	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.12	new_junction_frequency=1.175830e-01	new_junction_read_count=36	pos_hash_score=8	side_1_annotate_key=gene	side_1_continuation=9	side_1_coverage=0.87	side_1_overlap=0	side_1_possible_overlap_registers=81	side_1_read_count=237	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=277	side_2_redundant=0	total_non_overlap_reads=8
JC	1069	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=167	coverage_plus=144	flanking_left=101	flanking_right=101	frequency=9.753480e-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=47	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=1.04	new_junction_frequency=9.753480e-01	new_junction_read_count=313	pos_hash_score=144	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=1	side_2_possible_overlap_registers=90	side_2_read_count=8	side_2_redundant=0	total_non_overlap_reads=311
JC	1070	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=187	coverage_plus=130	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=47	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.13	new_junction_frequency=1.000000e+00	new_junction_read_count=319	pos_hash_score=139	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=317	unique_read_sequence=CTTTGC
JC	1071	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=131	coverage_plus=150	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=94	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=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=1.000000e+00	new_junction_read_count=281	pos_hash_score=139	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=281
JC	1072	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=119	coverage_plus=148	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=86	max_left_minus=86	max_left_plus=83	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=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=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=268	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=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=267
JC	1073	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=184	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=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=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=299	pos_hash_score=143	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=299
JC	1074	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=127	coverage_plus=176	flanking_left=101	flanking_right=101	frequency=9.594277e-01	junction_possible_overlap_registers=89	key=NC_007779__3512759__-1__NC_007779__3744263__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=9.594277e-01	new_junction_read_count=304	pos_hash_score=145	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=13	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=303
JC	1075	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=155	coverage_plus=159	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=82	key=NC_007779__3742935__-1__NC_007779__3744264__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=87	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=46	max_min_right_minus=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=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=315	pos_hash_score=138	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=314
JC	1076	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=205	coverage_plus=145	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3744263__-1__NC_007779__3903274__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=47	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=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=353	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=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=350
JC	1077	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=131	coverage_plus=163	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=89	max_left_plus=91	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=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=294	pos_hash_score=141	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=294
JC	1078	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=150	coverage_plus=133	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3746911__1__NC_007779__3748646__-1__0____101__101__1__0	max_left=92	max_left_minus=92	max_left_plus=92	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=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=336	pos_hash_score=129	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=283
JC	1079	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=157	coverage_plus=194	flanking_left=101	flanking_right=101	frequency=9.971910e-01	junction_possible_overlap_registers=90	key=NC_007779__3748105__-1__NC_007779__3748643__1__0____101__101__1__0	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=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=1.17	new_junction_frequency=9.971910e-01	new_junction_read_count=355	pos_hash_score=153	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=1	side_2_redundant=0	total_non_overlap_reads=351
JC	1080	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=159	coverage_plus=181	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=90	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.18	new_junction_frequency=1.000000e+00	new_junction_read_count=342	pos_hash_score=140	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=340
JC	1081	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=171	coverage_plus=151	flanking_left=101	flanking_right=101	frequency=9.819619e-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=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=9.819619e-01	new_junction_read_count=323	pos_hash_score=134	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=6	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=322
JC	1082	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=136	coverage_plus=150	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=92	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=1.000000e+00	new_junction_read_count=288	pos_hash_score=139	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=286
JC	1083	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=124	coverage_plus=154	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=178	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=1.000000e+00	new_junction_read_count=279	pos_hash_score=138	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=278
JC	1084	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=167	coverage_plus=173	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=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.12	new_junction_frequency=1.000000e+00	new_junction_read_count=340	pos_hash_score=147	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=340
JC	1085	.	NC_007779	4080560	-1	NC_007779	4080625	1	0	alignment_overlap=1	coverage_minus=2	coverage_plus=4	flanking_left=101	flanking_right=101	frequency=1.873699e-02	junction_possible_overlap_registers=89	key=NC_007779__4080560__-1__NC_007779__4080624__1__1____101__101__0__0	max_left=92	max_left_minus=50	max_left_plus=92	max_min_left=44	max_min_left_minus=32	max_min_left_plus=44	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=178	max_right=68	max_right_minus=68	max_right_plus=56	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=1.873699e-02	new_junction_read_count=6	pos_hash_score=6	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.06	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=320	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.04	side_2_overlap=0	side_2_possible_overlap_registers=89	side_2_read_count=312	side_2_redundant=0	total_non_overlap_reads=6
JC	1086	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=151	coverage_plus=143	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=47	max_min_right_plus=48	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=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=295	pos_hash_score=125	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=294
JC	1087	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=154	coverage_plus=143	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4310363__1__NC_007779__4353540__1__0____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=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=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=303	pos_hash_score=149	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=297
JC	1088	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=130	coverage_plus=183	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4311557__-1__NC_007779__4353543__-1__0____101__101__1__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=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=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=328	pos_hash_score=138	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=313
JC	1089	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=130	coverage_plus=180	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4355060__1__NC_007779__4502861__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=310	pos_hash_score=142	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=310
JC	1090	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=146	coverage_plus=151	flanking_left=101	flanking_right=101	frequency=9.870455e-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=49	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=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=9.870455e-01	new_junction_read_count=298	pos_hash_score=144	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=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=297
JC	1091	.	NC_007779	4547362	1	NC_007779	4547676	1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.564027e-02	junction_possible_overlap_registers=81	key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0	max_left=72	max_left_minus=31	max_left_plus=72	max_min_left=31	max_min_left_minus=31	max_min_left_plus=26	max_min_right=20	max_min_right_minus=0	max_min_right_plus=20	max_pos_hash_score=162	max_right=74	max_right_minus=74	max_right_plus=66	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.01	new_junction_frequency=1.564027e-02	new_junction_read_count=4	pos_hash_score=4	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.87	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=265	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.97	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=265	side_2_redundant=0	total_non_overlap_reads=4
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