#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	18:33:52 21 Feb 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	1_D22_AGTCAA_L002_R1_001.fastq
SNP	1	80	NC_007779	66457	A	frequency=1
SNP	2	85	NC_007779	97880	T	frequency=1
SNP	3	95	NC_007779	167632	A	frequency=1
SNP	4	103	NC_007779	274547	G	frequency=1
DEL	5	645,659	NC_007779	274733	97240	frequency=1
SNP	6	126	NC_007779	547694	G	frequency=1
INS	7	127	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	129	NC_007779	556858	T	frequency=1
SNP	9	132	NC_007779	569996	C	frequency=1
DEL	10	646,664	NC_007779	654214	1199	frequency=1
SNP	11	158	NC_007779	749354	A	frequency=1
SNP	12	160	NC_007779	758440	A	frequency=4.471397e-01
SNP	13	161	NC_007779	758562	A	frequency=5.196142e-02
SNP	14	171	NC_007779	887234	A	frequency=1
SNP	15	179	NC_007779	987574	T	frequency=1
SNP	16	194	NC_007779	1093686	C	frequency=1
SNP	17	195	NC_007779	1097580	T	frequency=1.838355e-01
SNP	18	204	NC_007779	1170573	T	frequency=1
SNP	19	207	NC_007779	1197797	T	frequency=3.173161e-02
SNP	20	208	NC_007779	1197809	T	frequency=2.665329e-02
SNP	21	209	NC_007779	1197822	C	frequency=2.594662e-02
SNP	22	210	NC_007779	1197824	G	frequency=2.560329e-02
SNP	23	212	NC_007779	1197857	C	frequency=1.411819e-02
DEL	24	648,671	NC_007779	1301041	1336	frequency=1
SNP	25	222	NC_007779	1306963	T	frequency=5.081511e-02
SNP	26	223	NC_007779	1318876	A	frequency=1
DEL	27	649,674	NC_007779	1413639	23060	frequency=1
SNP	28	247	NC_007779	1483588	A	frequency=1
DEL	29	248	NC_007779	1496775	1	frequency=1
SNP	30	255	NC_007779	1555625	A	frequency=4.593563e-02
SNP	31	264	NC_007779	1615814	A	frequency=1
DEL	32	275	NC_007779	1669599	1	frequency=1
SNP	33	290	NC_007779	1844073	A	frequency=1
SNP	34	297	NC_007779	1918872	A	frequency=1
SNP	35	301	NC_007779	1973476	A	frequency=1
SNP	36	304	NC_007779	2005401	T	frequency=1
SNP	37	319	NC_007779	2170094	A	frequency=1
DEL	38	651,683	NC_007779	2320795	1336	frequency=1
SNP	39	338	NC_007779	2406075	T	frequency=1
SNP	40	344	NC_007779	2416102	A	frequency=1
SNP	41	355	NC_007779	2538628	T	frequency=1
SNP	42	369	NC_007779	2733780	A	frequency=1.129346e-01
SNP	43	378	NC_007779	2865228	G	frequency=5.108261e-02
INS	44	690	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=2.146338e-01
INS	45	689	NC_007779	2865278	TTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACAGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGC	frequency=8.876907e-02
SNP	46	379	NC_007779	2866111	G	frequency=1
SNP	47	391	NC_007779	3003330	A	frequency=1
SNP	48	395	NC_007779	3049815	T	frequency=1
SNP	49	429	NC_007779	3397813	G	frequency=1
SNP	50	444	NC_007779	3449851	A	frequency=1.361036e-01
SNP	51	445	NC_007779	3450056	A	frequency=2.230201e-01
DEL	52	654,698	NC_007779	3742936	1336	frequency=1
DEL	53	655,700	NC_007779	3746911	1199	frequency=1
DEL	54	481	NC_007779	3750122	1	frequency=9.748602e-01
SNP	55	482	NC_007779	3750123	T	frequency=2.501774e-02
SNP	56	504	NC_007779	3898657	G	frequency=1
DEL	57	705	NC_007779	3958123	34	frequency=9.964681e-01
SNP	58	532	NC_007779	4090749	T	frequency=1
SNP	59	545	NC_007779	4165991	C	frequency=1
SNP	60	548	NC_007779	4200197	G	frequency=3.607302e-01
DEL	61	656,708	NC_007779	4310363	1199	frequency=1
SNP	62	567	NC_007779	4346527	G	frequency=3.876114e-02
SNP	63	568	NC_007779	4346883	A	frequency=3.321552e-02
SNP	64	569	NC_007779	4347339	T	frequency=2.840519e-02
DEL	65	573,574	NC_007779	4371271	2	frequency=1
SNP	66	575	NC_007779	4371461	C	frequency=2.350426e-02
SNP	67	622	NC_007779	4546535	A	frequency=1
RA	68	.	NC_007779	301	1	.	T	bias_e_value=2349510	bias_p_value=0.505671	fisher_strand_p_value=1	frequency=1.261806e-02	genotype_quality=1528.0	ks_quality_p_value=0.190079	log10_base_likelihood=-17.0552	log10_qual_likelihood_position_model=3.59895	log10_strand_likelihood_position_model=0.437963	new_cov=2/2	polymorphism_quality=11.7	quality=11.7	quality_position_model=4.22254e-15	ref_cov=136/177	reject=INDEL_HOMOPOLYMER	tot_cov=138/179
RA	69	.	NC_007779	5595	0	G	T	bias_e_value=0.0458099	bias_p_value=9.85936e-09	fisher_strand_p_value=4.3721e-10	frequency=5.549669e-02	genotype_quality=1011.3	ks_quality_p_value=1	log10_base_likelihood=-9.58428	log10_qual_likelihood_position_model=19.9068	log10_strand_likelihood_position_model=9.54646	new_cov=0/30	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=159/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/163
RA	70	.	NC_007779	11143	0	G	T	bias_e_value=0.126797	bias_p_value=2.72896e-08	fisher_strand_p_value=1.27023e-09	frequency=5.900574e-02	genotype_quality=1015.0	ks_quality_p_value=1	log10_base_likelihood=-11.0234	log10_qual_likelihood_position_model=25.2257	log10_strand_likelihood_position_model=8.95944	new_cov=0/29	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=151/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/160
RA	71	.	NC_007779	17050	0	A	C	bias_e_value=0.000153543	bias_p_value=3.30461e-11	fisher_strand_p_value=1.16023e-12	frequency=6.832647e-02	genotype_quality=712.8	ks_quality_p_value=1	log10_base_likelihood=-9.39433	log10_qual_likelihood_position_model=23.4892	log10_strand_likelihood_position_model=11.9355	new_cov=0/35	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=122/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/120
RA	72	.	NC_007779	22321	1	.	T	bias_e_value=3161810	bias_p_value=0.680495	fisher_strand_p_value=0.50249	frequency=6.192207e-03	genotype_quality=1620.4	ks_quality_p_value=0.629661	log10_base_likelihood=-8.13156	log10_qual_likelihood_position_model=0.978836	log10_strand_likelihood_position_model=0.528508	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.44575e-08	ref_cov=174/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=176/147
RA	73	.	NC_007779	29496	0	T	A	bias_e_value=9.48618	bias_p_value=2.04165e-06	fisher_strand_p_value=1.20587e-07	frequency=5.611753e-02	genotype_quality=829.0	ks_quality_p_value=1	log10_base_likelihood=-10.2295	log10_qual_likelihood_position_model=25.7567	log10_strand_likelihood_position_model=6.9187	new_cov=0/17	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=155/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=155/108
RA	74	.	NC_007779	34111	1	.	T	bias_e_value=2868610	bias_p_value=0.617391	fisher_strand_p_value=1	frequency=1.612854e-02	genotype_quality=1513.1	ks_quality_p_value=0.26535	log10_base_likelihood=-22.154	log10_qual_likelihood_position_model=2.94912	log10_strand_likelihood_position_model=0.458355	new_cov=3/2	polymorphism_quality=16.9	quality=16.9	quality_position_model=6.61028e-21	ref_cov=180/125	reject=INDEL_HOMOPOLYMER	tot_cov=183/127
RA	75	.	NC_007779	34112	0	T	.	bias_e_value=1568260	bias_p_value=0.337527	fisher_strand_p_value=0.268658	frequency=9.454727e-03	genotype_quality=1272.8	ks_quality_p_value=0.38405	log10_base_likelihood=-7.84547	log10_qual_likelihood_position_model=2.429	log10_strand_likelihood_position_model=0.704616	new_cov=3/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.38531e-06	ref_cov=182/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=185/132
RA	76	.	NC_007779	39910	0	G	T	bias_e_value=189705	bias_p_value=0.040829	fisher_strand_p_value=0.00681831	frequency=3.316498e-02	genotype_quality=769.9	ks_quality_p_value=1	log10_base_likelihood=-6.75812	log10_qual_likelihood_position_model=11.4653	log10_strand_likelihood_position_model=2.46735	new_cov=0/15	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=81/168	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=81/183
RA	77	.	NC_007779	47305	0	G	T	bias_e_value=3.66285e-06	bias_p_value=7.88332e-13	fisher_strand_p_value=2.43945e-14	frequency=8.318615e-02	genotype_quality=975.1	ks_quality_p_value=0.999091	log10_base_likelihood=-16.1024	log10_qual_likelihood_position_model=30.2388	log10_strand_likelihood_position_model=13.6127	new_cov=0/39	polymorphism_quality=10.8	quality=10.8	quality_position_model=Inf	ref_cov=162/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/151
RA	78	.	NC_007779	50358	0	G	T	bias_e_value=0.0180868	bias_p_value=3.8927e-09	fisher_strand_p_value=1.65634e-10	frequency=6.167650e-02	genotype_quality=844.6	ks_quality_p_value=0.999137	log10_base_likelihood=-9.76588	log10_qual_likelihood_position_model=22.4896	log10_strand_likelihood_position_model=9.91909	new_cov=0/31	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=140/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/144
RA	79	.	NC_007779	63418	1	.	T	bias_e_value=1486560	bias_p_value=0.319943	fisher_strand_p_value=0.236709	frequency=6.328583e-03	genotype_quality=1584.4	ks_quality_p_value=0.403718	log10_base_likelihood=-8.20103	log10_qual_likelihood_position_model=1.41503	log10_strand_likelihood_position_model=0.625785	new_cov=0/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.35447e-08	ref_cov=162/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/154
RA	80	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1276.3	new_cov=166/150	quality=1276.3	ref_cov=0/0	tot_cov=166/150
RA	81	.	NC_007779	69266	0	G	T	bias_e_value=208.306	bias_p_value=4.48323e-05	fisher_strand_p_value=3.29058e-06	frequency=4.891300e-02	genotype_quality=986.7	ks_quality_p_value=1	log10_base_likelihood=-9.463	log10_qual_likelihood_position_model=26.2589	log10_strand_likelihood_position_model=5.59859	new_cov=1/22	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=145/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/155
RA	82	.	NC_007779	70602	0	G	T	bias_e_value=0.00440107	bias_p_value=9.47214e-10	fisher_strand_p_value=3.78943e-11	frequency=4.856253e-02	genotype_quality=1006.3	ks_quality_p_value=1	log10_base_likelihood=-6.37536	log10_qual_likelihood_position_model=24.5594	log10_strand_likelihood_position_model=10.4214	new_cov=0/29	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=163/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/141
RA	83	.	NC_007779	75074	0	T	G	bias_e_value=4.25578e-32	bias_p_value=9.15944e-39	fisher_strand_p_value=9.83618e-41	frequency=1.999903e-01	genotype_quality=755.9	ks_quality_p_value=1	log10_base_likelihood=-44.9316	log10_qual_likelihood_position_model=50.8277	log10_strand_likelihood_position_model=40.0072	new_cov=66/0	polymorphism_quality=39.8	quality=39.8	quality_position_model=Inf	ref_cov=25/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/165
RA	84	.	NC_007779	75079	0	C	T	bias_e_value=0.00571065	bias_p_value=1.22907e-09	fisher_strand_p_value=4.97098e-11	frequency=5.606842e-02	genotype_quality=776.7	ks_quality_p_value=1	log10_base_likelihood=-9.32196	log10_qual_likelihood_position_model=19.1835	log10_strand_likelihood_position_model=10.3036	new_cov=14/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=31/170	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=45/170
RA	85	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=1147.4	new_cov=139/143	quality=1147.4	ref_cov=0/1	tot_cov=140/144
RA	86	.	NC_007779	101246	0	T	G	bias_e_value=109626	bias_p_value=0.023594	fisher_strand_p_value=0.00355339	frequency=1.569366e-02	genotype_quality=745.6	ks_quality_p_value=1	log10_base_likelihood=-6.78196	log10_qual_likelihood_position_model=4.73722	log10_strand_likelihood_position_model=2.44936	new_cov=4/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=45/147	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=49/147
RA	87	.	NC_007779	107544	1	.	T	bias_e_value=4645730	bias_p_value=0.999869	fisher_strand_p_value=1	frequency=9.708405e-03	genotype_quality=1536.6	ks_quality_p_value=0.983887	log10_base_likelihood=-12.5766	log10_qual_likelihood_position_model=2.57115	log10_strand_likelihood_position_model=0.417658	new_cov=2/1	polymorphism_quality=7.2	quality=7.2	quality_position_model=1.31863e-11	ref_cov=155/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/152
RA	88	.	NC_007779	115813	0	A	C	bias_e_value=0.000220064	bias_p_value=4.7363e-11	fisher_strand_p_value=1.68496e-12	frequency=3.622532e-02	genotype_quality=930.5	ks_quality_p_value=1	log10_base_likelihood=-6.62242	log10_qual_likelihood_position_model=23.7182	log10_strand_likelihood_position_model=11.7734	new_cov=0/30	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=166/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/128
RA	89	.	NC_007779	134366	0	G	T	bias_e_value=0.0576146	bias_p_value=1.24e-08	fisher_strand_p_value=5.56968e-10	frequency=5.614662e-02	genotype_quality=1137.7	ks_quality_p_value=0.997885	log10_base_likelihood=-13.2888	log10_qual_likelihood_position_model=21.9764	log10_strand_likelihood_position_model=9.37703	new_cov=0/30	polymorphism_quality=7.9	quality=7.9	quality_position_model=Inf	ref_cov=173/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/179
RA	90	.	NC_007779	136449	1	.	T	bias_e_value=3663670	bias_p_value=0.788509	fisher_strand_p_value=0.500218	frequency=6.944656e-03	genotype_quality=1445.0	ks_quality_p_value=0.849282	log10_base_likelihood=-8.36317	log10_qual_likelihood_position_model=1.34626	log10_strand_likelihood_position_model=0.550739	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.1042e-08	ref_cov=151/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/135
RA	91	.	NC_007779	150535	0	G	A	bias_e_value=212595	bias_p_value=0.0457554	fisher_strand_p_value=0.00782001	frequency=2.368546e-02	genotype_quality=1148.8	ks_quality_p_value=1	log10_base_likelihood=-9.61107	log10_qual_likelihood_position_model=9.83058	log10_strand_likelihood_position_model=2.24351	new_cov=8/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=141/132	reject=POLYMORPHISM_STRAND	tot_cov=149/132
RA	92	.	NC_007779	150537	0	A	C	bias_e_value=367479	bias_p_value=0.0790901	fisher_strand_p_value=0.0152612	frequency=1.607418e-02	genotype_quality=1106.9	ks_quality_p_value=1	log10_base_likelihood=-10.0777	log10_qual_likelihood_position_model=9.33683	log10_strand_likelihood_position_model=1.99068	new_cov=7/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=142/135	reject=POLYMORPHISM_STRAND	tot_cov=149/135
RA	93	.	NC_007779	164569	0	C	G	bias_e_value=1595.99	bias_p_value=0.000343495	fisher_strand_p_value=3.01023e-05	frequency=2.878380e-02	genotype_quality=560.6	ks_quality_p_value=1	log10_base_likelihood=-5.58928	log10_qual_likelihood_position_model=6.90566	log10_strand_likelihood_position_model=4.5214	new_cov=0/5	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=133/16	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/21
RA	94	.	NC_007779	164576	0	A	G	bias_e_value=0.00637739	bias_p_value=1.37256e-09	fisher_strand_p_value=5.57732e-11	frequency=6.212521e-02	genotype_quality=463.3	ks_quality_p_value=1	log10_base_likelihood=-7.31221	log10_qual_likelihood_position_model=14.4853	log10_strand_likelihood_position_model=10.2536	new_cov=0/13	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=127/18	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/31
RA	95	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=1140.3	new_cov=130/149	quality=1140.3	ref_cov=0/0	tot_cov=130/149
RA	96	.	NC_007779	193489	0	G	T	bias_e_value=154.485	bias_p_value=3.32488e-05	fisher_strand_p_value=2.38398e-06	frequency=4.694271e-02	genotype_quality=1047.8	ks_quality_p_value=1	log10_base_likelihood=-6.34277	log10_qual_likelihood_position_model=18.7175	log10_strand_likelihood_position_model=5.82675	new_cov=20/1	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=119/156	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/157
RA	97	.	NC_007779	193496	0	A	T	bias_e_value=982.199	bias_p_value=0.000211392	fisher_strand_p_value=1.77018e-05	frequency=4.022789e-02	genotype_quality=977.1	ks_quality_p_value=1	log10_base_likelihood=-9.89429	log10_qual_likelihood_position_model=19.9828	log10_strand_likelihood_position_model=4.75198	new_cov=13/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=112/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=125/157
RA	98	.	NC_007779	194247	0	G	T	bias_e_value=0.00235485	bias_p_value=5.0682e-10	fisher_strand_p_value=1.97611e-11	frequency=8.006668e-02	genotype_quality=825.5	ks_quality_p_value=1	log10_base_likelihood=-17.3897	log10_qual_likelihood_position_model=26.0439	log10_strand_likelihood_position_model=10.7042	new_cov=0/29	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=140/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/119
RA	99	.	NC_007779	207536	0	G	T	bias_e_value=0.0088212	bias_p_value=1.89853e-09	fisher_strand_p_value=7.82206e-11	frequency=6.691122e-02	genotype_quality=900.5	ks_quality_p_value=1	log10_base_likelihood=-14.4816	log10_qual_likelihood_position_model=20.4342	log10_strand_likelihood_position_model=10.1067	new_cov=0/30	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=156/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/148
RA	100	.	NC_007779	220369	0	A	G	bias_e_value=1123910	bias_p_value=0.241893	fisher_strand_p_value=0.618393	frequency=8.806229e-03	genotype_quality=1363.8	ks_quality_p_value=0.104652	log10_base_likelihood=-5.92517	log10_qual_likelihood_position_model=2.57766	log10_strand_likelihood_position_model=0.431272	new_cov=1/2	polymorphism_quality=0.4	quality=0.4	quality_position_model=0.000107572	ref_cov=171/165	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=172/167
RA	101	.	NC_007779	221543	1	.	A	bias_e_value=1974920	bias_p_value=0.425049	fisher_strand_p_value=0.501258	frequency=7.547379e-03	genotype_quality=1330.7	ks_quality_p_value=0.289325	log10_base_likelihood=-8.18884	log10_qual_likelihood_position_model=1.89061	log10_strand_likelihood_position_model=0.537225	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.12665e-07	ref_cov=141/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/122
RA	102	.	NC_007779	223974	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	103	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1379.7	new_cov=153/164	quality=1379.7	ref_cov=0/0	tot_cov=153/164
RA	104	.	NC_007779	289922	0	T	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	105	.	NC_007779	327547	0	A	G	deleted=1	frequency=1	genotype_quality=0.4	new_cov=0/1	quality=0.4	ref_cov=0/1	reject=EVALUE	tot_cov=0/2
RA	106	.	NC_007779	338285	0	A	C	deleted=1	frequency=1	genotype_quality=1.2	new_cov=1/0	quality=1.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	107	.	NC_007779	359514	0	T	G	deleted=1	frequency=1	genotype_quality=0.5	new_cov=1/0	quality=0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	108	.	NC_007779	365424	0	T	A	deleted=1	frequency=1	genotype_quality=3.6	new_cov=0/1	quality=3.6	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	109	.	NC_007779	374799	0	T	G	bias_e_value=3.73468e-09	bias_p_value=8.03792e-16	fisher_strand_p_value=2.03844e-17	frequency=5.640936e-02	genotype_quality=838.4	ks_quality_p_value=1	log10_base_likelihood=-6.11462	log10_qual_likelihood_position_model=25.7277	log10_strand_likelihood_position_model=16.6907	new_cov=31/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=54/170	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=85/170
RA	110	.	NC_007779	378715	0	T	.	bias_e_value=4608430	bias_p_value=0.991844	fisher_strand_p_value=1	frequency=9.041786e-03	genotype_quality=1328.7	ks_quality_p_value=0.875027	log10_base_likelihood=-6.63617	log10_qual_likelihood_position_model=4.16384	log10_strand_likelihood_position_model=0.394226	new_cov=2/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=0.000859794	ref_cov=176/151	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=178/152
RA	111	.	NC_007779	379236	1	.	G	bias_e_value=1930690	bias_p_value=0.41553	fisher_strand_p_value=0.661284	frequency=2.164555e-02	genotype_quality=1102.6	ks_quality_p_value=0.21192	log10_base_likelihood=-22.9817	log10_qual_likelihood_position_model=2.74232	log10_strand_likelihood_position_model=0.49856	new_cov=4/1	polymorphism_quality=17.7	quality=17.7	quality_position_model=6.5305e-22	ref_cov=147/79	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/80
RA	112	.	NC_007779	379237	0	G	.	bias_e_value=3853740	bias_p_value=0.829416	fisher_strand_p_value=1	frequency=4.279518e-02	genotype_quality=1049.6	ks_quality_p_value=0.476085	log10_base_likelihood=-37.6664	log10_qual_likelihood_position_model=4.1727	log10_strand_likelihood_position_model=0.610494	new_cov=7/4	polymorphism_quality=32.5	quality=32.5	quality_position_model=3.6609e-35	ref_cov=150/96	reject=INDEL_HOMOPOLYMER	tot_cov=157/100
RA	113	.	NC_007779	387919	0	A	G	bias_e_value=4.15478	bias_p_value=8.94206e-07	fisher_strand_p_value=5.0246e-08	frequency=4.238605e-02	genotype_quality=589.0	ks_quality_p_value=0.999419	log10_base_likelihood=-10.4205	log10_qual_likelihood_position_model=9.51225	log10_strand_likelihood_position_model=7.2989	new_cov=0/8	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=146/16	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/24
RA	114	.	NC_007779	407306	0	C	A	bias_e_value=0.00187759	bias_p_value=4.04101e-10	fisher_strand_p_value=1.56127e-11	frequency=6.894827e-02	genotype_quality=829.1	ks_quality_p_value=1	log10_base_likelihood=-10.5564	log10_qual_likelihood_position_model=22.2142	log10_strand_likelihood_position_model=10.8065	new_cov=31/0	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=99/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/141
RA	115	.	NC_007779	440767	0	G	T	bias_e_value=0.0128007	bias_p_value=2.75502e-09	fisher_strand_p_value=1.15355e-10	frequency=9.052420e-02	genotype_quality=936.7	ks_quality_p_value=1	log10_base_likelihood=-20.6401	log10_qual_likelihood_position_model=26.8267	log10_strand_likelihood_position_model=9.97771	new_cov=1/36	polymorphism_quality=15.4	quality=15.4	quality_position_model=Inf	ref_cov=146/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/157
RA	116	.	NC_007779	446019	0	T	.	bias_e_value=1773570	bias_p_value=0.381714	fisher_strand_p_value=0.250705	frequency=9.639740e-03	genotype_quality=1266.4	ks_quality_p_value=0.492444	log10_base_likelihood=-8.17609	log10_qual_likelihood_position_model=1.4909	log10_strand_likelihood_position_model=0.825355	new_cov=3/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=8.90237e-08	ref_cov=162/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/145
RA	117	.	NC_007779	467487	1	.	T	bias_e_value=1094070	bias_p_value=0.23547	fisher_strand_p_value=0.509969	frequency=6.944656e-03	genotype_quality=1422.8	ks_quality_p_value=0.122333	log10_base_likelihood=-8.13003	log10_qual_likelihood_position_model=2.15988	log10_strand_likelihood_position_model=0.479682	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.14827e-07	ref_cov=122/164	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/166
RA	118	.	NC_007779	474686	0	G	T	bias_e_value=0.00105362	bias_p_value=2.26764e-10	fisher_strand_p_value=8.58474e-12	frequency=6.610155e-02	genotype_quality=1011.5	ks_quality_p_value=0.997401	log10_base_likelihood=-16.472	log10_qual_likelihood_position_model=28.1981	log10_strand_likelihood_position_model=11.3673	new_cov=0/35	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=173/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/173
RA	119	.	NC_007779	493495	1	.	T	bias_e_value=3942340	bias_p_value=0.848484	fisher_strand_p_value=0.507276	frequency=5.235672e-03	genotype_quality=1930.1	ks_quality_p_value=0.991112	log10_base_likelihood=-7.40345	log10_qual_likelihood_position_model=3.1992	log10_strand_likelihood_position_model=0.496096	new_cov=0/2	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.55917e-05	ref_cov=166/214	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=166/216
RA	120	.	NC_007779	506363	1	.	A	bias_e_value=4090910	bias_p_value=0.88046	fisher_strand_p_value=1	frequency=6.115913e-03	genotype_quality=1638.0	ks_quality_p_value=0.552771	log10_base_likelihood=-8.25399	log10_qual_likelihood_position_model=1.8682	log10_strand_likelihood_position_model=0.303129	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.23691e-08	ref_cov=148/177	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/178
RA	121	.	NC_007779	506364	0	A	.	bias_e_value=3814600	bias_p_value=0.820991	fisher_strand_p_value=0.626997	frequency=1.200390e-02	genotype_quality=1342.0	ks_quality_p_value=0.741489	log10_base_likelihood=-10.9283	log10_qual_likelihood_position_model=2.62507	log10_strand_likelihood_position_model=0.541097	new_cov=1/3	polymorphism_quality=5.5	quality=5.5	quality_position_model=9.7629e-10	ref_cov=153/176	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/179
RA	122	.	NC_007779	513848	0	A	C	bias_e_value=9.89069e-24	bias_p_value=2.12871e-30	fisher_strand_p_value=2.89144e-32	frequency=1.614332e-01	genotype_quality=752.8	ks_quality_p_value=1	log10_base_likelihood=-22.4923	log10_qual_likelihood_position_model=44.0157	log10_strand_likelihood_position_model=31.5389	new_cov=0/62	polymorphism_quality=17.2	quality=17.2	quality_position_model=Inf	ref_cov=157/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/104
RA	123	.	NC_007779	522430	1	.	T	bias_e_value=4644650	bias_p_value=0.999639	fisher_strand_p_value=1	frequency=7.812500e-03	genotype_quality=1285.3	ks_quality_p_value=0.973236	log10_base_likelihood=-8.19371	log10_qual_likelihood_position_model=1.71648	log10_strand_likelihood_position_model=0.337225	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.56901e-08	ref_cov=164/90	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/91
RA	124	.	NC_007779	524490	0	T	G	bias_e_value=0.0136994	bias_p_value=2.94843e-09	fisher_strand_p_value=1.2382e-10	frequency=5.982351e-02	genotype_quality=903.2	ks_quality_p_value=1	log10_base_likelihood=-12.8425	log10_qual_likelihood_position_model=22.3425	log10_strand_likelihood_position_model=9.90721	new_cov=23/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=85/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/164
RA	125	.	NC_007779	528271	1	.	T	bias_e_value=4646290	bias_p_value=0.99999	fisher_strand_p_value=1	frequency=8.264542e-03	genotype_quality=1217.9	ks_quality_p_value=0.995602	log10_base_likelihood=-8.21192	log10_qual_likelihood_position_model=2.51056	log10_strand_likelihood_position_model=0.302836	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.6758e-07	ref_cov=131/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/110
RA	126	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=1136.4	new_cov=129/137	quality=1136.4	ref_cov=0/0	tot_cov=130/137
RA	127	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=1116.2	new_cov=123/138	quality=1116.2	ref_cov=1/0	tot_cov=124/138
RA	128	.	NC_007779	556653	0	A	C	bias_e_value=2.10657e-19	bias_p_value=4.53383e-26	fisher_strand_p_value=7.13913e-28	frequency=9.228134e-02	genotype_quality=878.3	ks_quality_p_value=1	log10_base_likelihood=-12.6581	log10_qual_likelihood_position_model=38.8241	log10_strand_likelihood_position_model=27.1464	new_cov=0/43	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=188/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=188/80
RA	129	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=1302.7	new_cov=167/151	quality=1302.7	ref_cov=1/0	tot_cov=168/151
RA	130	.	NC_007779	562819	0	T	C	bias_e_value=42852.8	bias_p_value=0.00922293	fisher_strand_p_value=0.00119293	frequency=3.515625e-02	genotype_quality=774.4	ks_quality_p_value=1	log10_base_likelihood=-6.14894	log10_qual_likelihood_position_model=16.1755	log10_strand_likelihood_position_model=2.96816	new_cov=0/11	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=99/109	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=99/120
RA	131	.	NC_007779	562836	0	C	A	bias_e_value=1127420	bias_p_value=0.242647	fisher_strand_p_value=0.0650177	frequency=3.656769e-02	genotype_quality=839.1	ks_quality_p_value=0.999604	log10_base_likelihood=-12.211	log10_qual_likelihood_position_model=9.89194	log10_strand_likelihood_position_model=1.52289	new_cov=1/7	polymorphism_quality=6.8	quality=6.8	quality_position_model=0.0248061	ref_cov=101/96	reject=POLYMORPHISM_STRAND	tot_cov=103/103
RA	132	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1166.4	new_cov=138/126	quality=1166.4	ref_cov=0/0	tot_cov=138/126
RA	133	.	NC_007779	582978	1	.	A	bias_e_value=3278300	bias_p_value=0.705568	fisher_strand_p_value=0.516129	frequency=1.075268e-02	genotype_quality=929.5	ks_quality_p_value=0.656549	log10_base_likelihood=-8.79877	log10_qual_likelihood_position_model=1.60931	log10_strand_likelihood_position_model=0.449969	new_cov=2/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=1.09974e-08	ref_cov=109/75	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/75
RA	134	.	NC_007779	583702	1	.	T	bias_e_value=3827840	bias_p_value=0.823842	fisher_strand_p_value=1	frequency=3.030300e-02	genotype_quality=945.0	ks_quality_p_value=0.468654	log10_base_likelihood=-27.8641	log10_qual_likelihood_position_model=4.21274	log10_strand_likelihood_position_model=0.512125	new_cov=3/3	polymorphism_quality=22.7	quality=22.7	quality_position_model=2.41382e-25	ref_cov=106/86	reject=INDEL_HOMOPOLYMER	tot_cov=109/89
RA	135	.	NC_007779	583703	0	T	.	bias_e_value=291655	bias_p_value=0.062771	fisher_strand_p_value=0.198248	frequency=9.703636e-03	genotype_quality=825.2	ks_quality_p_value=0.0579165	log10_base_likelihood=-5.6467	log10_qual_likelihood_position_model=1.60196	log10_strand_likelihood_position_model=0.702792	new_cov=0/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=3.79756e-05	ref_cov=114/90	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/92
RA	136	.	NC_007779	589157	0	T	G	bias_e_value=4.34812e-10	bias_p_value=9.35819e-17	fisher_strand_p_value=2.24758e-18	frequency=7.808781e-02	genotype_quality=804.9	ks_quality_p_value=1	log10_base_likelihood=-8.16839	log10_qual_likelihood_position_model=42.1552	log10_strand_likelihood_position_model=17.6483	new_cov=37/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=61/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/158
RA	137	.	NC_007779	598799	0	T	G	bias_e_value=1.28841e-21	bias_p_value=2.77295e-28	fisher_strand_p_value=4.03738e-30	frequency=1.812596e-01	genotype_quality=623.8	ks_quality_p_value=1	log10_base_likelihood=-30.8836	log10_qual_likelihood_position_model=38.5676	log10_strand_likelihood_position_model=29.3939	new_cov=46/0	polymorphism_quality=25.7	quality=25.7	quality_position_model=Inf	ref_cov=20/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=66/137
RA	138	.	NC_007779	606911	1	.	G	bias_e_value=561565	bias_p_value=0.120862	fisher_strand_p_value=0.0286644	frequency=1.826477e-02	genotype_quality=1091.8	ks_quality_p_value=0.906771	log10_base_likelihood=-18.0059	log10_qual_likelihood_position_model=2.19837	log10_strand_likelihood_position_model=1.54266	new_cov=4/0	polymorphism_quality=12.7	quality=12.7	quality_position_model=2.28937e-16	ref_cov=87/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=91/128
RA	139	.	NC_007779	606915	0	T	G	bias_e_value=1890.99	bias_p_value=0.000406987	fisher_strand_p_value=3.62576e-05	frequency=2.642822e-02	genotype_quality=589.7	ks_quality_p_value=1	log10_base_likelihood=-5.74169	log10_qual_likelihood_position_model=6.44981	log10_strand_likelihood_position_model=4.4406	new_cov=4/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=9/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=13/136
RA	140	.	NC_007779	623811	1	.	G	bias_e_value=3621510	bias_p_value=0.779434	fisher_strand_p_value=1	frequency=8.733749e-03	genotype_quality=1157.1	ks_quality_p_value=0.414376	log10_base_likelihood=-8.3961	log10_qual_likelihood_position_model=1.78126	log10_strand_likelihood_position_model=0.185781	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.29809e-08	ref_cov=183/44	reject=POLYMORPHISM_STRAND	tot_cov=185/44
RA	141	.	NC_007779	623841	1	.	G	bias_e_value=2148030	bias_p_value=0.462306	fisher_strand_p_value=1	frequency=1.764679e-02	genotype_quality=847.8	ks_quality_p_value=0.165004	log10_base_likelihood=-13.3379	log10_qual_likelihood_position_model=3.10615	log10_strand_likelihood_position_model=0.031209	new_cov=3/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=3.12215e-12	ref_cov=163/4	reject=POLYMORPHISM_STRAND	tot_cov=166/4
RA	142	.	NC_007779	623849	0	C	T	bias_e_value=3800050	bias_p_value=0.817861	fisher_strand_p_value=1	frequency=1.320934e-02	genotype_quality=955.7	ks_quality_p_value=0.460848	log10_base_likelihood=-5.65221	log10_qual_likelihood_position_model=1.63494	log10_strand_likelihood_position_model=0.276338	new_cov=3/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=1.44004e-05	ref_cov=180/43	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=183/43
RA	143	.	NC_007779	623850	0	T	C	bias_e_value=3833620	bias_p_value=0.825085	fisher_strand_p_value=1	frequency=1.307106e-02	genotype_quality=877.7	ks_quality_p_value=0.470298	log10_base_likelihood=-6.55055	log10_qual_likelihood_position_model=1.54622	log10_strand_likelihood_position_model=0.293595	new_cov=3/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=1.38902e-06	ref_cov=180/46	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=183/46
RA	144	.	NC_007779	623856	1	.	A	bias_e_value=4622550	bias_p_value=0.994882	fisher_strand_p_value=1	frequency=8.264542e-03	genotype_quality=1201.4	ks_quality_p_value=0.900548	log10_base_likelihood=-7.96792	log10_qual_likelihood_position_model=1.76932	log10_strand_likelihood_position_model=0.257707	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=7.33922e-08	ref_cov=178/62	reject=POLYMORPHISM_STRAND	tot_cov=180/62
RA	145	.	NC_007779	623859	0	C	A	bias_e_value=4031110	bias_p_value=0.86759	fisher_strand_p_value=0.573139	frequency=1.187325e-02	genotype_quality=1066.1	ks_quality_p_value=0.927775	log10_base_likelihood=-6.40181	log10_qual_likelihood_position_model=2.74417	log10_strand_likelihood_position_model=0.383502	new_cov=3/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=4.48043e-05	ref_cov=185/64	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=188/64
RA	146	.	NC_007779	645964	1	.	G	bias_e_value=2047580	bias_p_value=0.440687	fisher_strand_p_value=0.153254	frequency=8.092880e-03	genotype_quality=1245.1	ks_quality_p_value=0.999934	log10_base_likelihood=-6.43175	log10_qual_likelihood_position_model=3.4826	log10_strand_likelihood_position_model=0.814589	new_cov=2/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=0.000746271	ref_cov=95/150	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=97/150
RA	147	.	NC_007779	645970	0	T	G	bias_e_value=9.11051e-24	bias_p_value=1.9608e-30	fisher_strand_p_value=2.66036e-32	frequency=1.808100e-01	genotype_quality=737.3	ks_quality_p_value=1	log10_base_likelihood=-45.6168	log10_qual_likelihood_position_model=45.2623	log10_strand_likelihood_position_model=31.5751	new_cov=49/0	polymorphism_quality=40.5	quality=40.5	quality_position_model=Inf	ref_cov=24/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/158
RA	148	.	NC_007779	645983	0	T	C	bias_e_value=0.302127	bias_p_value=6.50247e-08	fisher_strand_p_value=3.16077e-09	frequency=5.636883e-02	genotype_quality=716.2	ks_quality_p_value=1	log10_base_likelihood=-6.26595	log10_qual_likelihood_position_model=17.2518	log10_strand_likelihood_position_model=8.50021	new_cov=19/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=63/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/132
RA	149	.	NC_007779	646433	0	A	C	bias_e_value=0.000425736	bias_p_value=9.16283e-11	fisher_strand_p_value=3.34109e-12	frequency=3.867626e-02	genotype_quality=869.7	ks_quality_p_value=1	log10_base_likelihood=-10.1341	log10_qual_likelihood_position_model=17.6715	log10_strand_likelihood_position_model=11.4761	new_cov=0/12	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=203/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=203/31
RA	150	.	NC_007779	646440	0	C	A	bias_e_value=0.00014552	bias_p_value=3.13194e-11	fisher_strand_p_value=1.09746e-12	frequency=5.351257e-02	genotype_quality=958.4	ks_quality_p_value=1	log10_base_likelihood=-19.1924	log10_qual_likelihood_position_model=20.4284	log10_strand_likelihood_position_model=11.962	new_cov=1/13	polymorphism_quality=13.9	quality=13.9	quality_position_model=Inf	ref_cov=206/16	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=207/29
RA	151	.	NC_007779	657963	1	.	T	bias_e_value=2707770	bias_p_value=0.582775	fisher_strand_p_value=1	frequency=9.900093e-03	genotype_quality=1465.1	ks_quality_p_value=0.240187	log10_base_likelihood=-11.9925	log10_qual_likelihood_position_model=3.54129	log10_strand_likelihood_position_model=0.402042	new_cov=1/2	polymorphism_quality=6.6	quality=6.6	quality_position_model=4.955e-10	ref_cov=142/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/160
RA	152	.	NC_007779	657964	0	T	.	bias_e_value=4343820	bias_p_value=0.934893	fisher_strand_p_value=1	frequency=9.484291e-03	genotype_quality=1168.1	ks_quality_p_value=0.661575	log10_base_likelihood=-7.71471	log10_qual_likelihood_position_model=2.05805	log10_strand_likelihood_position_model=0.403993	new_cov=1/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=3.79187e-07	ref_cov=148/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/165
RA	153	.	NC_007779	660356	0	T	G	bias_e_value=1.88843e-16	bias_p_value=4.06435e-23	fisher_strand_p_value=7.18171e-25	frequency=9.930849e-02	genotype_quality=828.7	ks_quality_p_value=1	log10_base_likelihood=-12.6562	log10_qual_likelihood_position_model=35.1694	log10_strand_likelihood_position_model=24.1438	new_cov=47/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=54/173	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/173
RA	154	.	NC_007779	667452	0	G	T	bias_e_value=81247.5	bias_p_value=0.0174864	fisher_strand_p_value=0.00250129	frequency=3.207970e-02	genotype_quality=1081.8	ks_quality_p_value=1	log10_base_likelihood=-10.1385	log10_qual_likelihood_position_model=15.0875	log10_strand_likelihood_position_model=2.65114	new_cov=10/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=136/119	reject=POLYMORPHISM_STRAND	tot_cov=146/119
RA	155	.	NC_007779	667899	1	.	G	bias_e_value=1834680	bias_p_value=0.394866	fisher_strand_p_value=0.242591	frequency=6.622314e-03	genotype_quality=1523.9	ks_quality_p_value=0.535149	log10_base_likelihood=-8.04663	log10_qual_likelihood_position_model=2.49918	log10_strand_likelihood_position_model=0.615125	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=8.16364e-07	ref_cov=147/153	reject=POLYMORPHISM_STRAND	tot_cov=149/153
RA	156	.	NC_007779	686495	0	A	C	bias_e_value=3.68575e-24	bias_p_value=7.9326e-31	fisher_strand_p_value=1.06304e-32	frequency=1.122346e-01	genotype_quality=911.8	ks_quality_p_value=1	log10_base_likelihood=-17.2001	log10_qual_likelihood_position_model=45.7005	log10_strand_likelihood_position_model=31.9734	new_cov=0/45	polymorphism_quality=11.9	quality=11.9	quality_position_model=Inf	ref_cov=198/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=198/72
RA	157	.	NC_007779	706385	1	.	T	bias_e_value=4639160	bias_p_value=0.998456	fisher_strand_p_value=1	frequency=1.000023e-02	genotype_quality=1482.9	ks_quality_p_value=0.944941	log10_base_likelihood=-12.4111	log10_qual_likelihood_position_model=3.00798	log10_strand_likelihood_position_model=0.408069	new_cov=1/2	polymorphism_quality=7.0	quality=7.0	quality_position_model=5.32269e-11	ref_cov=143/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/156
RA	158	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=1156.4	new_cov=128/153	quality=1156.4	ref_cov=0/0	tot_cov=128/153
RA	159	.	NC_007779	752693	0	A	C	bias_e_value=2.15268e-05	bias_p_value=4.63307e-12	fisher_strand_p_value=1.51824e-13	frequency=7.427835e-02	genotype_quality=909.0	ks_quality_p_value=1	log10_base_likelihood=-11.765	log10_qual_likelihood_position_model=31.2703	log10_strand_likelihood_position_model=12.8187	new_cov=0/32	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=159/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=159/122
RA	160	.	NC_007779	758440	0	T	A	bias_e_value=1044800	bias_p_value=0.224865	error=polymorphic_without_reference_base	fisher_strand_p_value=0.163879	frequency=4.471397e-01	genotype_quality=146.5	ks_quality_p_value=0.357614	log10_base_likelihood=-564.217	log10_qual_likelihood_position_model=9.14762	log10_strand_likelihood_position_model=1.46911	new_cov=66/69	polymorphism_quality=inf	quality=inf	quality_position_model=0	ref_cov=68/99	tot_cov=134/168
RA	161	.	NC_007779	758562	0	T	A	bias_e_value=3596340	bias_p_value=0.774017	fisher_strand_p_value=0.625251	frequency=5.196142e-02	genotype_quality=1236.8	ks_quality_p_value=0.652984	log10_base_likelihood=-50.7363	log10_qual_likelihood_position_model=6.74355	log10_strand_likelihood_position_model=0.754377	new_cov=9/8	polymorphism_quality=45.7	quality=45.7	quality_position_model=1.41138e-45	ref_cov=182/128	tot_cov=191/136
RA	162	.	NC_007779	759019	0	C	G	bias_e_value=2.89057e-21	bias_p_value=6.22119e-28	fisher_strand_p_value=9.16743e-30	frequency=8.758545e-02	genotype_quality=1017.5	ks_quality_p_value=1	log10_base_likelihood=-37.8413	log10_qual_likelihood_position_model=28.8964	log10_strand_likelihood_position_model=29.0378	new_cov=0/23	polymorphism_quality=32.7	quality=32.7	quality_position_model=Inf	ref_cov=228/3	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=228/26
RA	163	.	NC_007779	796581	0	G	T	bias_e_value=0.0385518	bias_p_value=8.29726e-09	fisher_strand_p_value=3.65018e-10	frequency=5.657434e-02	genotype_quality=921.6	ks_quality_p_value=1	log10_base_likelihood=-8.15387	log10_qual_likelihood_position_model=19.9927	log10_strand_likelihood_position_model=9.43769	new_cov=0/28	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=155/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/147
RA	164	.	NC_007779	817515	0	G	T	bias_e_value=2.60463e-05	bias_p_value=5.60578e-12	fisher_strand_p_value=1.84893e-13	frequency=9.968042e-02	genotype_quality=907.9	ks_quality_p_value=1	log10_base_likelihood=-31.4902	log10_qual_likelihood_position_model=23.1515	log10_strand_likelihood_position_model=12.7331	new_cov=0/38	polymorphism_quality=26.3	quality=26.3	quality_position_model=Inf	ref_cov=151/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/150
RA	165	.	NC_007779	847635	0	A	C	bias_e_value=0.000979944	bias_p_value=2.10907e-10	fisher_strand_p_value=7.94109e-12	frequency=3.643322e-02	genotype_quality=802.6	ks_quality_p_value=1	log10_base_likelihood=-6.19173	log10_qual_likelihood_position_model=27.694	log10_strand_likelihood_position_model=11.1001	new_cov=19/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=53/178	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=72/179
RA	166	.	NC_007779	868836	1	.	C	bias_e_value=4189460	bias_p_value=0.901671	fisher_strand_p_value=1	frequency=7.490158e-03	genotype_quality=1327.0	ks_quality_p_value=0.590698	log10_base_likelihood=-8.31211	log10_qual_likelihood_position_model=1.55914	log10_strand_likelihood_position_model=0.300138	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.1719e-08	ref_cov=138/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/128
RA	167	.	NC_007779	881118	0	T	.	bias_e_value=4646250	bias_p_value=0.999982	fisher_strand_p_value=1	frequency=8.536339e-03	genotype_quality=1411.2	ks_quality_p_value=0.994074	log10_base_likelihood=-7.5975	log10_qual_likelihood_position_model=2.88426	log10_strand_likelihood_position_model=0.421044	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=3.80064e-06	ref_cov=175/173	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=177/174
RA	168	.	NC_007779	884184	0	T	A	bias_e_value=2702910	bias_p_value=0.581729	fisher_strand_p_value=0.247665	frequency=1.009846e-02	genotype_quality=1171.0	ks_quality_p_value=0.966849	log10_base_likelihood=-5.70299	log10_qual_likelihood_position_model=3.48076	log10_strand_likelihood_position_model=0.885498	new_cov=0/3	polymorphism_quality=0.1	quality=0.1	quality_position_model=0.00572576	ref_cov=145/147	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=145/152
RA	169	.	NC_007779	884191	1	.	T	bias_e_value=3930670	bias_p_value=0.845973	fisher_strand_p_value=0.499134	frequency=6.405830e-03	genotype_quality=1562.8	ks_quality_p_value=1	log10_base_likelihood=-6.26471	log10_qual_likelihood_position_model=3.48177	log10_strand_likelihood_position_model=0.570574	new_cov=0/2	polymorphism_quality=0.7	quality=0.7	quality_position_model=0.000614228	ref_cov=150/160	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=150/162
RA	170	.	NC_007779	884196	0	T	G	bias_e_value=1771200	bias_p_value=0.381203	fisher_strand_p_value=0.123374	frequency=1.229858e-02	genotype_quality=1257.7	ks_quality_p_value=0.998703	log10_base_likelihood=-7.44133	log10_qual_likelihood_position_model=6.05759	log10_strand_likelihood_position_model=1.15782	new_cov=0/4	polymorphism_quality=1.9	quality=1.9	quality_position_model=0.159727	ref_cov=153/159	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=153/163
RA	171	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=1047.2	new_cov=146/122	quality=1047.2	ref_cov=0/0	tot_cov=146/122
RA	172	.	NC_007779	904838	0	C	A	bias_e_value=5.61184e-07	bias_p_value=1.2078e-13	fisher_strand_p_value=5.41857e-15	frequency=1.225657e-01	genotype_quality=935.7	ks_quality_p_value=0.650247	log10_base_likelihood=-38.2997	log10_qual_likelihood_position_model=35.9151	log10_strand_likelihood_position_model=14.2823	new_cov=47/0	polymorphism_quality=33.2	quality=33.2	quality_position_model=Inf	ref_cov=124/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/149
RA	173	.	NC_007779	932754	1	.	A	bias_e_value=4636440	bias_p_value=0.997872	fisher_strand_p_value=1	frequency=9.836197e-03	genotype_quality=1526.1	ks_quality_p_value=0.935473	log10_base_likelihood=-12.6759	log10_qual_likelihood_position_model=1.82562	log10_strand_likelihood_position_model=0.399818	new_cov=2/1	polymorphism_quality=7.3	quality=7.3	quality_position_model=1.73568e-12	ref_cov=160/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/143
RA	174	.	NC_007779	944733	1	.	T	bias_e_value=2337080	bias_p_value=0.502995	fisher_strand_p_value=0.222839	frequency=7.692337e-03	genotype_quality=1295.3	ks_quality_p_value=0.845775	log10_base_likelihood=-8.25767	log10_qual_likelihood_position_model=1.38517	log10_strand_likelihood_position_model=0.652008	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=3.77287e-08	ref_cov=121/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/137
RA	175	.	NC_007779	953568	0	T	.	bias_e_value=3838490	bias_p_value=0.826133	fisher_strand_p_value=0.622427	frequency=1.023102e-02	genotype_quality=1168.2	ks_quality_p_value=0.757823	log10_base_likelihood=-8.08485	log10_qual_likelihood_position_model=1.99619	log10_strand_likelihood_position_model=0.425984	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.42436e-07	ref_cov=146/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/146
RA	176	.	NC_007779	954820	0	A	C	bias_e_value=0.000250207	bias_p_value=5.38504e-11	fisher_strand_p_value=1.92487e-12	frequency=6.922436e-02	genotype_quality=673.1	ks_quality_p_value=1	log10_base_likelihood=-8.31911	log10_qual_likelihood_position_model=24.5191	log10_strand_likelihood_position_model=11.7156	new_cov=0/33	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=118/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/110
RA	177	.	NC_007779	969494	0	C	A	bias_e_value=0.194471	bias_p_value=4.18548e-08	fisher_strand_p_value=1.98974e-09	frequency=7.689571e-02	genotype_quality=854.6	ks_quality_p_value=1	log10_base_likelihood=-21.89	log10_qual_likelihood_position_model=14.8926	log10_strand_likelihood_position_model=8.7012	new_cov=26/0	polymorphism_quality=16.6	quality=16.6	quality_position_model=Inf	ref_cov=110/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/143
RA	178	.	NC_007779	986260	1	.	A	bias_e_value=2966870	bias_p_value=0.63854	fisher_strand_p_value=0.348272	frequency=1.384068e-02	genotype_quality=1428.1	ks_quality_p_value=0.808738	log10_base_likelihood=-17.5954	log10_qual_likelihood_position_model=2.09455	log10_strand_likelihood_position_model=0.650041	new_cov=3/1	polymorphism_quality=12.3	quality=12.3	quality_position_model=5.82484e-17	ref_cov=134/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/152
RA	179	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=986.3	new_cov=84/155	quality=986.3	ref_cov=0/0	tot_cov=84/155
RA	180	.	NC_007779	987916	0	T	G	bias_e_value=6.93565e-05	bias_p_value=1.49271e-11	fisher_strand_p_value=5.09361e-13	frequency=6.669903e-02	genotype_quality=620.1	ks_quality_p_value=1	log10_base_likelihood=-12.4043	log10_qual_likelihood_position_model=18.1181	log10_strand_likelihood_position_model=12.293	new_cov=14/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=14/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=28/138
RA	181	.	NC_007779	991407	0	G	T	bias_e_value=0.71583	bias_p_value=1.54063e-07	fisher_strand_p_value=1.01932e-08	frequency=3.916931e-02	genotype_quality=1077.1	ks_quality_p_value=0.768599	log10_base_likelihood=-9.27643	log10_qual_likelihood_position_model=26.2212	log10_strand_likelihood_position_model=7.99169	new_cov=0/23	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=175/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=176/155
RA	182	.	NC_007779	999606	0	A	T	bias_e_value=154819	bias_p_value=0.0333208	fisher_strand_p_value=0.00534747	frequency=3.534222e-02	genotype_quality=813.9	ks_quality_p_value=1	log10_base_likelihood=-7.91763	log10_qual_likelihood_position_model=10.4864	log10_strand_likelihood_position_model=2.31266	new_cov=9/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=114/96	reject=POLYMORPHISM_STRAND	tot_cov=123/96
RA	183	.	NC_007779	999607	0	A	C	bias_e_value=89395.1	bias_p_value=0.0192399	fisher_strand_p_value=0.00279679	frequency=2.892208e-02	genotype_quality=791.9	ks_quality_p_value=1	log10_base_likelihood=-6.86759	log10_qual_likelihood_position_model=11.7859	log10_strand_likelihood_position_model=2.84504	new_cov=11/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=112/96	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=123/96
RA	184	.	NC_007779	999613	0	A	T	bias_e_value=2572.26	bias_p_value=0.000553611	fisher_strand_p_value=5.08526e-05	frequency=7.394361e-02	genotype_quality=792.5	ks_quality_p_value=1	log10_base_likelihood=-25.5209	log10_qual_likelihood_position_model=19.6385	log10_strand_likelihood_position_model=4.35127	new_cov=17/0	polymorphism_quality=20.3	quality=20.3	quality_position_model=0.00345381	ref_cov=107/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/93
RA	185	.	NC_007779	999623	0	A	T	bias_e_value=163094	bias_p_value=0.0351018	fisher_strand_p_value=0.00568998	frequency=4.450893e-02	genotype_quality=770.6	ks_quality_p_value=1	log10_base_likelihood=-11.6905	log10_qual_likelihood_position_model=12.1996	log10_strand_likelihood_position_model=2.43934	new_cov=10/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=110/87	reject=POLYMORPHISM_STRAND	tot_cov=120/87
RA	186	.	NC_007779	999625	0	T	C	bias_e_value=161049	bias_p_value=0.0346614	fisher_strand_p_value=0.00560492	frequency=3.469753e-02	genotype_quality=735.8	ks_quality_p_value=1	log10_base_likelihood=-6.3489	log10_qual_likelihood_position_model=14.0671	log10_strand_likelihood_position_model=2.46704	new_cov=10/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=107/86	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=117/86
RA	187	.	NC_007779	1006080	0	C	A	bias_e_value=0.143712	bias_p_value=3.09301e-08	fisher_strand_p_value=1.44853e-09	frequency=6.348324e-02	genotype_quality=903.6	ks_quality_p_value=1	log10_base_likelihood=-12.3152	log10_qual_likelihood_position_model=19.725	log10_strand_likelihood_position_model=8.83907	new_cov=27/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=117/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/147
RA	188	.	NC_007779	1019390	1	.	A	bias_e_value=4246900	bias_p_value=0.914033	fisher_strand_p_value=1	frequency=7.272720e-03	genotype_quality=1372.7	ks_quality_p_value=0.615126	log10_base_likelihood=-8.31128	log10_qual_likelihood_position_model=1.28071	log10_strand_likelihood_position_model=0.311235	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.15359e-08	ref_cov=159/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/115
RA	189	.	NC_007779	1020800	0	A	.	bias_e_value=3953430	bias_p_value=0.850871	fisher_strand_p_value=0.571167	frequency=1.023102e-02	genotype_quality=1187.1	ks_quality_p_value=0.886354	log10_base_likelihood=-8.07504	log10_qual_likelihood_position_model=1.93572	log10_strand_likelihood_position_model=0.521527	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.58532e-07	ref_cov=119/171	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=121/172
RA	190	.	NC_007779	1035834	0	C	A	bias_e_value=0.0791708	bias_p_value=1.70394e-08	fisher_strand_p_value=7.75302e-10	frequency=4.842949e-02	genotype_quality=1030.0	ks_quality_p_value=1	log10_base_likelihood=-9.85572	log10_qual_likelihood_position_model=23.5677	log10_strand_likelihood_position_model=9.11053	new_cov=26/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=123/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/169
RA	191	.	NC_007779	1037529	0	T	G	bias_e_value=991.913	bias_p_value=0.000213483	fisher_strand_p_value=1.83576e-05	frequency=2.469635e-02	genotype_quality=632.0	ks_quality_p_value=0.97469	log10_base_likelihood=-7.71747	log10_qual_likelihood_position_model=4.5175	log10_strand_likelihood_position_model=4.73618	new_cov=4/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=8/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=12/149
RA	192	.	NC_007779	1058914	0	A	C	bias_e_value=0.00036177	bias_p_value=7.78615e-11	fisher_strand_p_value=2.82171e-12	frequency=4.805422e-02	genotype_quality=804.2	ks_quality_p_value=1	log10_base_likelihood=-5.82158	log10_qual_likelihood_position_model=27.1822	log10_strand_likelihood_position_model=11.5495	new_cov=0/21	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=157/51	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/73
RA	193	.	NC_007779	1079013	0	C	A	bias_e_value=0.311201	bias_p_value=6.69777e-08	fisher_strand_p_value=3.26063e-09	frequency=6.948996e-02	genotype_quality=807.8	ks_quality_p_value=1	log10_base_likelihood=-12.9549	log10_qual_likelihood_position_model=18.2986	log10_strand_likelihood_position_model=8.73972	new_cov=27/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=102/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/128
RA	194	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1118.8	new_cov=103/150	quality=1118.8	ref_cov=0/0	tot_cov=103/151
RA	195	.	NC_007779	1097580	0	C	T	bias_e_value=1251640	bias_p_value=0.269383	fisher_strand_p_value=0.898335	frequency=1.838355e-01	genotype_quality=1062.0	ks_quality_p_value=0.0835362	log10_base_likelihood=-216.028	log10_qual_likelihood_position_model=18.3181	log10_strand_likelihood_position_model=0.995333	new_cov=33/42	polymorphism_quality=211.3	quality=211.3	quality_position_model=2.21903e-199	ref_cov=149/182	tot_cov=182/224
RA	196	.	NC_007779	1097764	1	.	A	bias_e_value=3544650	bias_p_value=0.762891	fisher_strand_p_value=0.515429	frequency=3.305435e-03	genotype_quality=2513.5	ks_quality_p_value=0.768418	log10_base_likelihood=-7.53468	log10_qual_likelihood_position_model=1.25517	log10_strand_likelihood_position_model=0.458674	new_cov=0/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=9.76918e-08	ref_cov=248/355	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=248/357
RA	197	.	NC_007779	1098027	1	.	T	bias_e_value=2598020	bias_p_value=0.559155	fisher_strand_p_value=0.247801	frequency=5.865097e-03	genotype_quality=1723.1	ks_quality_p_value=0.904023	log10_base_likelihood=-8.03377	log10_qual_likelihood_position_model=1.13196	log10_strand_likelihood_position_model=0.605898	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=3.15353e-08	ref_cov=168/171	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=170/171
RA	198	.	NC_007779	1105181	1	.	T	bias_e_value=4239060	bias_p_value=0.912345	fisher_strand_p_value=1	frequency=7.352829e-03	genotype_quality=1361.3	ks_quality_p_value=0.611673	log10_base_likelihood=-8.14927	log10_qual_likelihood_position_model=2.25475	log10_strand_likelihood_position_model=0.301336	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.6812e-07	ref_cov=126/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/145
RA	199	.	NC_007779	1116582	0	G	C	bias_e_value=2.62593e-21	bias_p_value=5.65163e-28	fisher_strand_p_value=8.31619e-30	frequency=1.695704e-01	genotype_quality=602.3	ks_quality_p_value=1	log10_base_likelihood=-56.0467	log10_qual_likelihood_position_model=27.0214	log10_strand_likelihood_position_model=29.0801	new_cov=0/33	polymorphism_quality=51.0	quality=51.0	quality_position_model=Inf	ref_cov=150/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=150/42
RA	200	.	NC_007779	1148417	0	C	A	bias_e_value=2.0791	bias_p_value=4.47471e-07	fisher_strand_p_value=2.80255e-08	frequency=6.106234e-02	genotype_quality=1116.4	ks_quality_p_value=0.861215	log10_base_likelihood=-21.7054	log10_qual_likelihood_position_model=24.4933	log10_strand_likelihood_position_model=7.61715	new_cov=29/1	polymorphism_quality=16.4	quality=16.4	quality_position_model=Inf	ref_cov=155/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=184/172
RA	201	.	NC_007779	1153441	1	.	G	bias_e_value=2035340	bias_p_value=0.438054	fisher_strand_p_value=0.152191	frequency=6.801605e-03	genotype_quality=1466.1	ks_quality_p_value=0.997719	log10_base_likelihood=-6.88096	log10_qual_likelihood_position_model=2.90179	log10_strand_likelihood_position_model=0.817612	new_cov=2/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=5.8982e-05	ref_cov=113/179	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=115/179
RA	202	.	NC_007779	1158848	0	T	G	bias_e_value=1.50427e-10	bias_p_value=3.23755e-17	fisher_strand_p_value=7.57783e-19	frequency=9.164095e-02	genotype_quality=866.0	ks_quality_p_value=1	log10_base_likelihood=-13.7269	log10_qual_likelihood_position_model=35.4298	log10_strand_likelihood_position_model=18.1205	new_cov=47/0	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=87/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/157
RA	203	.	NC_007779	1158958	1	.	G	bias_e_value=3917290	bias_p_value=0.843093	fisher_strand_p_value=0.499017	frequency=6.389618e-03	genotype_quality=1577.7	ks_quality_p_value=0.991978	log10_base_likelihood=-7.41647	log10_qual_likelihood_position_model=3.25731	log10_strand_likelihood_position_model=0.573358	new_cov=2/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=2.09818e-05	ref_cov=160/151	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=162/151
RA	204	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1185.2	new_cov=190/102	quality=1185.2	ref_cov=0/0	tot_cov=190/102
RA	205	.	NC_007779	1177683	0	A	G	bias_e_value=0.000581063	bias_p_value=1.25058e-10	fisher_strand_p_value=4.61438e-12	frequency=8.264160e-02	genotype_quality=728.8	ks_quality_p_value=1	log10_base_likelihood=-10.4136	log10_qual_likelihood_position_model=21.6308	log10_strand_likelihood_position_model=11.3359	new_cov=25/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=70/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/152
RA	206	.	NC_007779	1186236	0	C	A	bias_e_value=6.66157	bias_p_value=1.43373e-06	fisher_strand_p_value=8.28442e-08	frequency=2.879047e-02	genotype_quality=1023.3	ks_quality_p_value=1	log10_base_likelihood=-6.06509	log10_qual_likelihood_position_model=15.7583	log10_strand_likelihood_position_model=7.08174	new_cov=19/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=116/171	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/171
RA	207	.	NC_007779	1197797	0	C	T	bias_e_value=1740560	bias_p_value=0.374609	fisher_strand_p_value=1	frequency=3.173161e-02	genotype_quality=1178.6	ks_quality_p_value=0.120083	log10_base_likelihood=-20.0728	log10_qual_likelihood_position_model=4.58279	log10_strand_likelihood_position_model=0.581688	new_cov=5/4	polymorphism_quality=14.8	quality=14.8	quality_position_model=5.09283e-17	ref_cov=146/128	tot_cov=151/132
RA	208	.	NC_007779	1197809	0	C	T	bias_e_value=480945	bias_p_value=0.103511	fisher_strand_p_value=1	frequency=2.665329e-02	genotype_quality=1246.5	ks_quality_p_value=0.0213587	log10_base_likelihood=-17.8647	log10_qual_likelihood_position_model=3.58666	log10_strand_likelihood_position_model=0.563003	new_cov=4/4	polymorphism_quality=12.6	quality=12.6	quality_position_model=8.27645e-16	ref_cov=154/137	tot_cov=159/141
RA	209	.	NC_007779	1197822	0	T	C	bias_e_value=3210330	bias_p_value=0.690938	fisher_strand_p_value=1	frequency=2.594662e-02	genotype_quality=1207.0	ks_quality_p_value=0.325588	log10_base_likelihood=-19.758	log10_qual_likelihood_position_model=3.7119	log10_strand_likelihood_position_model=0.574328	new_cov=4/4	polymorphism_quality=14.5	quality=14.5	quality_position_model=1.36666e-17	ref_cov=165/135	tot_cov=169/139
RA	210	.	NC_007779	1197824	0	A	G	bias_e_value=3505910	bias_p_value=0.754554	fisher_strand_p_value=1	frequency=2.560329e-02	genotype_quality=1222.6	ks_quality_p_value=0.387172	log10_base_likelihood=-19.1298	log10_qual_likelihood_position_model=3.65966	log10_strand_likelihood_position_model=0.576245	new_cov=4/4	polymorphism_quality=13.8	quality=13.8	quality_position_model=5.26726e-17	ref_cov=168/136	tot_cov=172/140
RA	211	.	NC_007779	1197854	0	C	T	bias_e_value=4601200	bias_p_value=0.990286	fisher_strand_p_value=1	frequency=1.405430e-02	genotype_quality=1198.0	ks_quality_p_value=0.863892	log10_base_likelihood=-7.27827	log10_qual_likelihood_position_model=2.3135	log10_strand_likelihood_position_model=0.445288	new_cov=2/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=2.19921e-06	ref_cov=162/117	reject=EVALUE	tot_cov=164/119
RA	212	.	NC_007779	1197857	0	G	C	bias_e_value=4270870	bias_p_value=0.919191	fisher_strand_p_value=1	frequency=1.411819e-02	genotype_quality=1188.0	ks_quality_p_value=0.625935	log10_base_likelihood=-9.98111	log10_qual_likelihood_position_model=2.6965	log10_strand_likelihood_position_model=0.445288	new_cov=2/2	polymorphism_quality=4.5	quality=4.5	quality_position_model=8.67846e-09	ref_cov=162/117	tot_cov=164/119
RA	213	.	NC_007779	1207211	1	.	G	bias_e_value=1016800	bias_p_value=0.218839	fisher_strand_p_value=0.0910156	frequency=1.034451e-02	genotype_quality=1452.5	ks_quality_p_value=0.620717	log10_base_likelihood=-12.99	log10_qual_likelihood_position_model=3.86734	log10_strand_likelihood_position_model=1.04088	new_cov=3/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=4.58779e-10	ref_cov=128/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/159
RA	214	.	NC_007779	1213001	0	T	C	bias_e_value=4056350	bias_p_value=0.873022	fisher_strand_p_value=0.651658	frequency=1.965809e-02	genotype_quality=1008.5	ks_quality_p_value=0.829357	log10_base_likelihood=-12.0474	log10_qual_likelihood_position_model=1.83787	log10_strand_likelihood_position_model=0.561104	new_cov=4/1	polymorphism_quality=6.7	quality=6.7	quality_position_model=1.14333e-11	ref_cov=152/97	reject=POLYMORPHISM_STRAND	tot_cov=156/98
RA	215	.	NC_007779	1213013	0	T	C	bias_e_value=3773090	bias_p_value=0.812057	fisher_strand_p_value=1	frequency=1.129723e-02	genotype_quality=1061.5	ks_quality_p_value=0.453433	log10_base_likelihood=-6.63464	log10_qual_likelihood_position_model=1.54475	log10_strand_likelihood_position_model=0.366802	new_cov=2/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=1.34842e-06	ref_cov=154/108	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=156/109
RA	216	.	NC_007779	1224173	0	G	A	bias_e_value=6.34215	bias_p_value=1.36498e-06	fisher_strand_p_value=7.86781e-08	frequency=5.272484e-02	genotype_quality=938.6	ks_quality_p_value=0.999451	log10_base_likelihood=-6.90244	log10_qual_likelihood_position_model=21.3421	log10_strand_likelihood_position_model=7.10415	new_cov=0/20	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=151/109	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/130
RA	217	.	NC_007779	1262472	0	A	C	bias_e_value=0.00136554	bias_p_value=2.93897e-10	fisher_strand_p_value=1.12114e-11	frequency=5.618000e-02	genotype_quality=812.5	ks_quality_p_value=1	log10_base_likelihood=-6.43436	log10_qual_likelihood_position_model=24.6496	log10_strand_likelihood_position_model=11.2514	new_cov=0/34	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=137/103	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/137
RA	218	.	NC_007779	1273399	0	T	G	bias_e_value=4.06591e-29	bias_p_value=8.75079e-36	fisher_strand_p_value=1.0154e-37	frequency=1.805577e-01	genotype_quality=819.1	ks_quality_p_value=1	log10_base_likelihood=-46.8328	log10_qual_likelihood_position_model=48.5739	log10_strand_likelihood_position_model=36.9934	new_cov=57/0	polymorphism_quality=41.7	quality=41.7	quality_position_model=Inf	ref_cov=26/179	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=83/180
RA	219	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=96.0	new_cov=13/13	quality=96.0	ref_cov=0/0	tot_cov=13/13
RA	220	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=16.4	new_cov=2/3	quality=16.4	ref_cov=0/0	tot_cov=2/3
RA	221	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=33.8	new_cov=10/5	quality=33.8	ref_cov=0/0	tot_cov=10/5
RA	222	.	NC_007779	1306963	0	C	T	bias_e_value=2123570	bias_p_value=0.457041	fisher_strand_p_value=0.184632	frequency=5.081511e-02	genotype_quality=1153.0	ks_quality_p_value=0.877943	log10_base_likelihood=-34.2261	log10_qual_likelihood_position_model=5.72538	log10_strand_likelihood_position_model=1.15399	new_cov=5/10	polymorphism_quality=29.1	quality=29.1	quality_position_model=1.3789e-29	ref_cov=148/130	tot_cov=153/140
RA	223	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1297.1	new_cov=148/172	quality=1297.1	ref_cov=0/0	tot_cov=148/172
RA	224	.	NC_007779	1333546	0	A	.	bias_e_value=2759000	bias_p_value=0.593802	fisher_strand_p_value=0.248929	frequency=1.059151e-02	genotype_quality=1147.3	ks_quality_p_value=0.996297	log10_base_likelihood=-7.99468	log10_qual_likelihood_position_model=2.6254	log10_strand_likelihood_position_model=0.84881	new_cov=0/3	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.194e-06	ref_cov=135/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/148
RA	225	.	NC_007779	1350819	0	C	A	bias_e_value=2251.18	bias_p_value=0.000484508	fisher_strand_p_value=4.39132e-05	frequency=5.161047e-02	genotype_quality=808.1	ks_quality_p_value=1	log10_base_likelihood=-11.0705	log10_qual_likelihood_position_model=14.7257	log10_strand_likelihood_position_model=4.59478	new_cov=18/1	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=112/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/127
RA	226	.	NC_007779	1352917	1	.	T	bias_e_value=919300	bias_p_value=0.197855	fisher_strand_p_value=0.0495144	frequency=1.669121e-02	genotype_quality=857.3	ks_quality_p_value=0.996813	log10_base_likelihood=-7.74814	log10_qual_likelihood_position_model=3.41921	log10_strand_likelihood_position_model=1.30527	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=8.26564e-05	ref_cov=38/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=41/138
RA	227	.	NC_007779	1352917	2	.	C	bias_e_value=946427	bias_p_value=0.203693	fisher_strand_p_value=0.051472	frequency=1.117134e-02	genotype_quality=865.0	ks_quality_p_value=0.996849	log10_base_likelihood=-6.86267	log10_qual_likelihood_position_model=3.02615	log10_strand_likelihood_position_model=1.28843	new_cov=2/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=0.000266547	ref_cov=39/138	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=41/138
RA	228	.	NC_007779	1360909	0	G	T	bias_e_value=2.81191	bias_p_value=6.05189e-07	fisher_strand_p_value=3.32152e-08	frequency=3.589153e-02	genotype_quality=1074.7	ks_quality_p_value=1	log10_base_likelihood=-6.00502	log10_qual_likelihood_position_model=17.9167	log10_strand_likelihood_position_model=7.47866	new_cov=0/21	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=170/123	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/144
RA	229	.	NC_007779	1362103	0	A	C	bias_e_value=21.2033	bias_p_value=4.56345e-06	fisher_strand_p_value=2.83891e-07	frequency=3.093529e-02	genotype_quality=1143.2	ks_quality_p_value=1	log10_base_likelihood=-6.17562	log10_qual_likelihood_position_model=30.8964	log10_strand_likelihood_position_model=6.54685	new_cov=0/20	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=177/147	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=177/168
RA	230	.	NC_007779	1371749	1	.	T	bias_e_value=1742440	bias_p_value=0.375014	fisher_strand_p_value=0.170788	frequency=3.703690e-02	genotype_quality=1616.9	ks_quality_p_value=0.704233	log10_base_likelihood=-61.4204	log10_qual_likelihood_position_model=6.21754	log10_strand_likelihood_position_model=1.07334	new_cov=9/4	polymorphism_quality=56.4	quality=56.4	quality_position_model=1.62236e-56	ref_cov=166/172	reject=INDEL_HOMOPOLYMER	tot_cov=175/176
RA	231	.	NC_007779	1371749	2	.	T	bias_e_value=2051280	bias_p_value=0.441484	fisher_strand_p_value=0.247863	frequency=5.698204e-03	genotype_quality=1744.7	ks_quality_p_value=0.619974	log10_base_likelihood=-7.9331	log10_qual_likelihood_position_model=1.82267	log10_strand_likelihood_position_model=0.605788	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.07681e-07	ref_cov=173/176	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=175/176
RA	232	.	NC_007779	1375289	0	G	T	bias_e_value=0.0134927	bias_p_value=2.90395e-09	fisher_strand_p_value=1.21871e-10	frequency=4.996347e-02	genotype_quality=1107.7	ks_quality_p_value=1	log10_base_likelihood=-9.70436	log10_qual_likelihood_position_model=24.6922	log10_strand_likelihood_position_model=10.0329	new_cov=0/32	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=179/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/185
RA	233	.	NC_007779	1378219	0	A	C	bias_e_value=1.38077e-11	bias_p_value=2.97174e-18	fisher_strand_p_value=6.57935e-20	frequency=7.952213e-02	genotype_quality=896.5	ks_quality_p_value=1	log10_base_likelihood=-11.8577	log10_qual_likelihood_position_model=55.8591	log10_strand_likelihood_position_model=19.1818	new_cov=0/49	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=162/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=162/139
RA	234	.	NC_007779	1405508	0	G	T	bias_e_value=4.32135e-05	bias_p_value=9.30056e-12	fisher_strand_p_value=3.12148e-13	frequency=8.492470e-02	genotype_quality=649.9	ks_quality_p_value=1	log10_base_likelihood=-22.832	log10_qual_likelihood_position_model=17.7794	log10_strand_likelihood_position_model=12.5056	new_cov=15/0	polymorphism_quality=17.6	quality=17.6	quality_position_model=Inf	ref_cov=16/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=31/137
RA	235	.	NC_007779	1409137	0	G	T	bias_e_value=1.11675e-15	bias_p_value=2.40352e-22	fisher_strand_p_value=4.38732e-24	frequency=1.903691e-01	genotype_quality=784.8	ks_quality_p_value=1	log10_base_likelihood=-56.0325	log10_qual_likelihood_position_model=31.0807	log10_strand_likelihood_position_model=23.3615	new_cov=0/67	polymorphism_quality=51.0	quality=51.0	quality_position_model=0.00296605	ref_cov=145/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/154
RA	236	.	NC_007779	1410956	1	.	T	bias_e_value=2663520	bias_p_value=0.573253	fisher_strand_p_value=0.619224	frequency=9.259224e-03	genotype_quality=1585.0	ks_quality_p_value=0.377206	log10_base_likelihood=-12.0946	log10_qual_likelihood_position_model=3.23411	log10_strand_likelihood_position_model=0.430121	new_cov=2/1	polymorphism_quality=6.7	quality=6.7	quality_position_model=2.01495e-10	ref_cov=158/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/164
RA	237	.	NC_007779	1412694	0	C	A	bias_e_value=0.00728911	bias_p_value=1.56879e-09	fisher_strand_p_value=6.41095e-11	frequency=8.202410e-02	genotype_quality=936.6	ks_quality_p_value=1	log10_base_likelihood=-19.9341	log10_qual_likelihood_position_model=21.1608	log10_strand_likelihood_position_model=10.2675	new_cov=34/1	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=115/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/157
RA	238	.	NC_007779	1420555	0	T	C	deleted=1	frequency=1	genotype_quality=2.7	new_cov=0/1	quality=2.7	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	239	.	NC_007779	1420558	0	C	A	deleted=1	frequency=1	genotype_quality=1.2	new_cov=0/1	quality=1.2	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	240	.	NC_007779	1429811	0	A	C	deleted=1	frequency=1	genotype_quality=0.2	new_cov=1/0	quality=0.2	ref_cov=0/1	reject=EVALUE	tot_cov=1/1
RA	241	.	NC_007779	1433657	0	G	A	deleted=1	frequency=1	genotype_quality=1.1	new_cov=1/0	quality=1.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	242	.	NC_007779	1433678	0	T	A	deleted=1	frequency=1	genotype_quality=0.6	new_cov=1/0	quality=0.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	243	.	NC_007779	1437441	0	G	A	bias_e_value=3.68258	bias_p_value=7.92578e-07	fisher_strand_p_value=4.41924e-08	frequency=3.763771e-02	genotype_quality=923.0	ks_quality_p_value=1	log10_base_likelihood=-5.84543	log10_qual_likelihood_position_model=17.4326	log10_strand_likelihood_position_model=7.35465	new_cov=0/11	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=179/43	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=179/54
RA	244	.	NC_007779	1437447	0	G	C	bias_e_value=5.70513	bias_p_value=1.22788e-06	fisher_strand_p_value=7.0282e-08	frequency=3.357697e-02	genotype_quality=973.0	ks_quality_p_value=1	log10_base_likelihood=-5.96215	log10_qual_likelihood_position_model=12.8869	log10_strand_likelihood_position_model=7.15316	new_cov=0/14	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=187/76	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=187/90
RA	245	.	NC_007779	1438937	0	T	.	bias_e_value=2248130	bias_p_value=0.48385	fisher_strand_p_value=0.585262	frequency=1.194572e-02	genotype_quality=1006.2	ks_quality_p_value=0.30278	log10_base_likelihood=-8.59248	log10_qual_likelihood_position_model=1.34733	log10_strand_likelihood_position_model=0.483848	new_cov=1/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=1.04426e-08	ref_cov=139/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/111
RA	246	.	NC_007779	1476021	0	T	G	bias_e_value=3432270	bias_p_value=0.738705	fisher_strand_p_value=0.504438	frequency=7.779121e-03	genotype_quality=1030.7	ks_quality_p_value=0.735148	log10_base_likelihood=-5.75728	log10_qual_likelihood_position_model=0.641908	log10_strand_likelihood_position_model=0.510549	new_cov=0/2	polymorphism_quality=0.2	quality=0.2	quality_position_model=1.79135e-06	ref_cov=114/141	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=114/143
RA	247	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=841.9	new_cov=164/50	quality=841.9	ref_cov=1/0	tot_cov=165/50
RA	248	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1473.8	new_cov=120/183	quality=1473.8	ref_cov=0/0	tot_cov=120/183
RA	249	.	NC_007779	1504851	0	C	A	bias_e_value=25401	bias_p_value=0.00546689	fisher_strand_p_value=0.000685212	frequency=3.484821e-02	genotype_quality=864.9	ks_quality_p_value=0.957932	log10_base_likelihood=-5.69306	log10_qual_likelihood_position_model=13.1459	log10_strand_likelihood_position_model=3.25106	new_cov=19/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=191/97	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=211/97
RA	250	.	NC_007779	1515709	0	A	G	bias_e_value=8.81418e-13	bias_p_value=1.89702e-19	fisher_strand_p_value=3.9538e-21	frequency=1.366348e-01	genotype_quality=800.4	ks_quality_p_value=1	log10_base_likelihood=-33.4392	log10_qual_likelihood_position_model=48.1662	log10_strand_likelihood_position_model=20.403	new_cov=47/0	polymorphism_quality=28.3	quality=28.3	quality_position_model=Inf	ref_cov=78/173	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/173
RA	251	.	NC_007779	1527474	0	G	A	bias_e_value=0.213414	bias_p_value=4.59317e-08	fisher_strand_p_value=2.19374e-09	frequency=9.636116e-02	genotype_quality=861.6	ks_quality_p_value=1	log10_base_likelihood=-21.892	log10_qual_likelihood_position_model=30.5521	log10_strand_likelihood_position_model=8.79117	new_cov=0/32	polymorphism_quality=16.6	quality=16.6	quality_position_model=Inf	ref_cov=128/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/161
RA	252	.	NC_007779	1527479	0	C	A	bias_e_value=4041.55	bias_p_value=0.000869837	fisher_strand_p_value=8.8297e-05	frequency=3.689384e-02	genotype_quality=1024.5	ks_quality_p_value=0.948346	log10_base_likelihood=-7.04452	log10_qual_likelihood_position_model=22.0258	log10_strand_likelihood_position_model=4.07697	new_cov=0/15	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=133/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/160
RA	253	.	NC_007779	1537499	0	A	G	bias_e_value=2.35279e-05	bias_p_value=5.06376e-12	fisher_strand_p_value=1.66439e-13	frequency=1.237535e-01	genotype_quality=821.8	ks_quality_p_value=1	log10_base_likelihood=-24.1982	log10_qual_likelihood_position_model=29.1914	log10_strand_likelihood_position_model=13.0172	new_cov=49/0	polymorphism_quality=19.0	quality=19.0	quality_position_model=Inf	ref_cov=136/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=185/135
RA	254	.	NC_007779	1552377	0	A	C	bias_e_value=7.29858e-15	bias_p_value=1.57083e-21	fisher_strand_p_value=2.97108e-23	frequency=1.150184e-01	genotype_quality=826.4	ks_quality_p_value=1	log10_base_likelihood=-15.1129	log10_qual_likelihood_position_model=39.6798	log10_strand_likelihood_position_model=22.5271	new_cov=0/55	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=154/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/127
RA	255	.	NC_007779	1555625	0	G	A	bias_e_value=2261430	bias_p_value=0.486713	fisher_strand_p_value=1	frequency=4.593563e-02	genotype_quality=1300.4	ks_quality_p_value=0.178865	log10_base_likelihood=-35.1677	log10_qual_likelihood_position_model=4.74692	log10_strand_likelihood_position_model=0.684149	new_cov=8/7	polymorphism_quality=30.0	quality=30.0	quality_position_model=5.39151e-32	ref_cov=162/149	tot_cov=170/156
RA	256	.	NC_007779	1561902	0	A	C	bias_e_value=32.351	bias_p_value=6.96269e-06	fisher_strand_p_value=4.45648e-07	frequency=4.401779e-02	genotype_quality=797.9	ks_quality_p_value=1	log10_base_likelihood=-6.06227	log10_qual_likelihood_position_model=18.3292	log10_strand_likelihood_position_model=6.35101	new_cov=0/18	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=132/96	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/114
RA	257	.	NC_007779	1567404	0	A	.	bias_e_value=3179030	bias_p_value=0.684202	fisher_strand_p_value=0.592933	frequency=9.638786e-03	genotype_quality=1211.7	ks_quality_p_value=0.539073	log10_base_likelihood=-8.09482	log10_qual_likelihood_position_model=1.20018	log10_strand_likelihood_position_model=0.469516	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.31972e-08	ref_cov=168/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=170/141
RA	258	.	NC_007779	1581577	1	.	T	bias_e_value=4636020	bias_p_value=0.997781	fisher_strand_p_value=1	frequency=7.326126e-03	genotype_quality=1361.9	ks_quality_p_value=0.934132	log10_base_likelihood=-8.08308	log10_qual_likelihood_position_model=2.04336	log10_strand_likelihood_position_model=0.305073	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.19973e-07	ref_cov=151/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/121
RA	259	.	NC_007779	1586641	1	.	T	bias_e_value=2132140	bias_p_value=0.458886	fisher_strand_p_value=0.237913	frequency=6.514549e-03	genotype_quality=1530.6	ks_quality_p_value=0.685597	log10_base_likelihood=-8.11283	log10_qual_likelihood_position_model=1.22904	log10_strand_likelihood_position_model=0.623582	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.43287e-08	ref_cov=148/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/157
RA	260	.	NC_007779	1595838	1	.	C	bias_e_value=3843890	bias_p_value=0.827295	fisher_strand_p_value=0.500842	frequency=6.778717e-03	genotype_quality=1456.1	ks_quality_p_value=0.944887	log10_base_likelihood=-7.34085	log10_qual_likelihood_position_model=2.06195	log10_strand_likelihood_position_model=0.543613	new_cov=0/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=1.30953e-06	ref_cov=137/156	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/158
RA	261	.	NC_007779	1595962	1	.	C	bias_e_value=3486530	bias_p_value=0.750383	fisher_strand_p_value=0.503966	frequency=8.096695e-03	genotype_quality=1207.3	ks_quality_p_value=0.75958	log10_base_likelihood=-8.07152	log10_qual_likelihood_position_model=2.46557	log10_strand_likelihood_position_model=0.513373	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.56144e-07	ref_cov=135/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/110
RA	262	.	NC_007779	1598481	1	.	C	bias_e_value=3765980	bias_p_value=0.810527	fisher_strand_p_value=1	frequency=6.349564e-03	genotype_quality=1543.5	ks_quality_p_value=0.451503	log10_base_likelihood=-8.34677	log10_qual_likelihood_position_model=1.60963	log10_strand_likelihood_position_model=0.305683	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.28507e-08	ref_cov=175/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=176/139
RA	263	.	NC_007779	1602599	0	C	A	bias_e_value=0.845806	bias_p_value=1.82037e-07	fisher_strand_p_value=9.34056e-09	frequency=5.207872e-02	genotype_quality=920.4	ks_quality_p_value=1	log10_base_likelihood=-10.227	log10_qual_likelihood_position_model=21.5821	log10_strand_likelihood_position_model=8.02963	new_cov=24/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=111/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/143
RA	264	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=1126.5	new_cov=130/159	quality=1126.5	ref_cov=0/0	tot_cov=130/159
RA	265	.	NC_007779	1626064	0	T	.	bias_e_value=1432500	bias_p_value=0.308308	fisher_strand_p_value=0.622238	frequency=1.480770e-02	genotype_quality=1089.4	ks_quality_p_value=0.145704	log10_base_likelihood=-11.5118	log10_qual_likelihood_position_model=2.72533	log10_strand_likelihood_position_model=0.59562	new_cov=3/1	polymorphism_quality=6.1	quality=6.1	quality_position_model=3.54607e-10	ref_cov=133/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/134
RA	266	.	NC_007779	1628027	0	G	T	bias_e_value=1.07916e-06	bias_p_value=2.32262e-13	fisher_strand_p_value=7.5651e-15	frequency=2.329183e-01	genotype_quality=450.7	ks_quality_p_value=0.913589	log10_base_likelihood=-60.3408	log10_qual_likelihood_position_model=33.1118	log10_strand_likelihood_position_model=14.1717	new_cov=42/0	polymorphism_quality=55.3	quality=55.3	quality_position_model=3.85425e-15	ref_cov=49/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/81
RA	267	.	NC_007779	1628037	0	T	C	bias_e_value=666162	bias_p_value=0.143374	fisher_strand_p_value=0.0451072	frequency=3.013325e-02	genotype_quality=429.7	ks_quality_p_value=0.717351	log10_base_likelihood=-7.2579	log10_qual_likelihood_position_model=5.65156	log10_strand_likelihood_position_model=1.479	new_cov=7/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=0.254773	ref_cov=87/57	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=94/57
RA	268	.	NC_007779	1637694	0	C	T	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	269	.	NC_007779	1640334	0	T	.	bias_e_value=961795	bias_p_value=0.207001	fisher_strand_p_value=0.567231	frequency=1.127243e-02	genotype_quality=1068.3	ks_quality_p_value=0.0924272	log10_base_likelihood=-8.43386	log10_qual_likelihood_position_model=1.29117	log10_strand_likelihood_position_model=0.534338	new_cov=2/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.50124e-08	ref_cov=105/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/159
RA	270	.	NC_007779	1641155	0	T	.	bias_e_value=1301940	bias_p_value=0.280209	fisher_strand_p_value=0.123468	frequency=1.453781e-02	genotype_quality=1103.4	ks_quality_p_value=0.642022	log10_base_likelihood=-11.3005	log10_qual_likelihood_position_model=2.84154	log10_strand_likelihood_position_model=1.14484	new_cov=4/0	polymorphism_quality=5.9	quality=5.9	quality_position_model=2.81739e-09	ref_cov=139/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/132
RA	271	.	NC_007779	1651009	0	T	G	bias_e_value=2.0169e-11	bias_p_value=4.34084e-18	fisher_strand_p_value=9.69365e-20	frequency=1.108599e-01	genotype_quality=694.2	ks_quality_p_value=1	log10_base_likelihood=-20.5208	log10_qual_likelihood_position_model=33.9174	log10_strand_likelihood_position_model=19.0135	new_cov=34/0	polymorphism_quality=15.2	quality=15.2	quality_position_model=Inf	ref_cov=37/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=71/140
RA	272	.	NC_007779	1659871	1	.	T	bias_e_value=3943540	bias_p_value=0.848742	fisher_strand_p_value=0.503468	frequency=8.437157e-03	genotype_quality=1139.6	ks_quality_p_value=0.999354	log10_base_likelihood=-7.09478	log10_qual_likelihood_position_model=2.71424	log10_strand_likelihood_position_model=0.516446	new_cov=2/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=1.0686e-05	ref_cov=129/106	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/106
RA	273	.	NC_007779	1660545	0	G	T	bias_e_value=0.0172453	bias_p_value=3.7116e-09	fisher_strand_p_value=1.57459e-10	frequency=5.972672e-02	genotype_quality=951.9	ks_quality_p_value=1	log10_base_likelihood=-11.0478	log10_qual_likelihood_position_model=20.1738	log10_strand_likelihood_position_model=9.80283	new_cov=0/27	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=159/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/135
RA	274	.	NC_007779	1660637	0	G	T	bias_e_value=10.8972	bias_p_value=2.34533e-06	fisher_strand_p_value=1.39741e-07	frequency=4.884291e-02	genotype_quality=931.2	ks_quality_p_value=1	log10_base_likelihood=-11.3224	log10_qual_likelihood_position_model=18.1549	log10_strand_likelihood_position_model=6.93576	new_cov=0/25	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=133/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/161
RA	275	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=1390.0	new_cov=133/141	quality=1390.0	ref_cov=1/0	tot_cov=134/141
RA	276	.	NC_007779	1669765	0	C	A	bias_e_value=138719	bias_p_value=0.0298557	fisher_strand_p_value=0.00469436	frequency=2.973080e-02	genotype_quality=1189.6	ks_quality_p_value=0.999722	log10_base_likelihood=-5.66293	log10_qual_likelihood_position_model=17.375	log10_strand_likelihood_position_model=2.43762	new_cov=0/12	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=110/178	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=111/190
RA	277	.	NC_007779	1677110	0	G	T	bias_e_value=0.00986813	bias_p_value=2.12385e-09	fisher_strand_p_value=1.29365e-10	frequency=4.133987e-02	genotype_quality=991.6	ks_quality_p_value=0.679686	log10_base_likelihood=-7.26776	log10_qual_likelihood_position_model=33.2868	log10_strand_likelihood_position_model=9.88818	new_cov=0/30	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=166/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/161
RA	278	.	NC_007779	1681402	0	T	G	bias_e_value=3.25011e-09	bias_p_value=6.99501e-16	fisher_strand_p_value=1.76756e-17	frequency=7.303333e-02	genotype_quality=953.0	ks_quality_p_value=1	log10_base_likelihood=-14.7961	log10_qual_likelihood_position_model=37.3248	log10_strand_likelihood_position_model=16.7526	new_cov=36/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=75/178	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/178
RA	279	.	NC_007779	1703335	0	G	C	bias_e_value=141.621	bias_p_value=3.04802e-05	fisher_strand_p_value=2.17168e-06	frequency=3.139782e-02	genotype_quality=845.0	ks_quality_p_value=0.999641	log10_base_likelihood=-9.2634	log10_qual_likelihood_position_model=9.1226	log10_strand_likelihood_position_model=5.6632	new_cov=8/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=37/170	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=45/170
RA	280	.	NC_007779	1705204	0	A	C	bias_e_value=13504.9	bias_p_value=0.00290658	fisher_strand_p_value=0.000321427	frequency=3.362465e-02	genotype_quality=878.9	ks_quality_p_value=1	log10_base_likelihood=-9.40474	log10_qual_likelihood_position_model=20.1225	log10_strand_likelihood_position_model=3.52403	new_cov=13/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=120/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/110
RA	281	.	NC_007779	1705210	0	G	T	bias_e_value=118667	bias_p_value=0.0255398	fisher_strand_p_value=0.00390133	frequency=5.372953e-02	genotype_quality=895.1	ks_quality_p_value=1	log10_base_likelihood=-16.1039	log10_qual_likelihood_position_model=17.438	log10_strand_likelihood_position_model=2.68587	new_cov=13/1	polymorphism_quality=10.8	quality=10.8	quality_position_model=Inf	ref_cov=116/105	reject=POLYMORPHISM_STRAND	tot_cov=129/106
RA	282	.	NC_007779	1716031	1	.	T	bias_e_value=2351890	bias_p_value=0.506182	fisher_strand_p_value=0.224944	frequency=7.604599e-03	genotype_quality=1292.5	ks_quality_p_value=0.846377	log10_base_likelihood=-7.73797	log10_qual_likelihood_position_model=2.78904	log10_strand_likelihood_position_model=0.647925	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=3.72081e-06	ref_cov=123/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/138
RA	283	.	NC_007779	1734359	1	.	A	bias_e_value=3108850	bias_p_value=0.669098	fisher_strand_p_value=1	frequency=6.689072e-03	genotype_quality=1487.7	ks_quality_p_value=0.306627	log10_base_likelihood=-8.22345	log10_qual_likelihood_position_model=1.74685	log10_strand_likelihood_position_model=0.299619	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.18431e-08	ref_cov=150/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/148
RA	284	.	NC_007779	1759411	1	.	T	bias_e_value=4470950	bias_p_value=0.962254	fisher_strand_p_value=1	frequency=6.779671e-03	genotype_quality=1470.6	ks_quality_p_value=0.738136	log10_base_likelihood=-8.18416	log10_qual_likelihood_position_model=1.11587	log10_strand_likelihood_position_model=0.30016	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.02749e-08	ref_cov=141/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/153
RA	285	.	NC_007779	1763744	0	C	A	bias_e_value=0.022775	bias_p_value=4.90171e-09	fisher_strand_p_value=2.11065e-10	frequency=6.175756e-02	genotype_quality=927.6	ks_quality_p_value=0.997525	log10_base_likelihood=-15.4916	log10_qual_likelihood_position_model=15.8684	log10_strand_likelihood_position_model=9.67558	new_cov=26/0	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=110/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/167
RA	286	.	NC_007779	1781197	1	.	T	bias_e_value=480325	bias_p_value=0.103377	fisher_strand_p_value=0.24087	frequency=6.689072e-03	genotype_quality=1505.8	ks_quality_p_value=0.0885292	log10_base_likelihood=-8.24938	log10_qual_likelihood_position_model=1.30427	log10_strand_likelihood_position_model=0.618217	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.92961e-08	ref_cov=145/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/152
RA	287	.	NC_007779	1824805	0	G	T	bias_e_value=9.36162	bias_p_value=2.01484e-06	fisher_strand_p_value=1.22078e-07	frequency=4.492760e-02	genotype_quality=914.6	ks_quality_p_value=0.97401	log10_base_likelihood=-9.67246	log10_qual_likelihood_position_model=23.0229	log10_strand_likelihood_position_model=6.91336	new_cov=0/20	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=150/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/133
RA	288	.	NC_007779	1832491	0	G	T	bias_e_value=0.00552288	bias_p_value=1.18865e-09	fisher_strand_p_value=4.80077e-11	frequency=7.263756e-02	genotype_quality=882.9	ks_quality_p_value=1	log10_base_likelihood=-12.7145	log10_qual_likelihood_position_model=23.7117	log10_strand_likelihood_position_model=10.3187	new_cov=0/31	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=140/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/137
RA	289	.	NC_007779	1837206	0	G	T	bias_e_value=207.145	bias_p_value=4.45825e-05	fisher_strand_p_value=3.33774e-06	frequency=3.983784e-02	genotype_quality=893.0	ks_quality_p_value=0.979944	log10_base_likelihood=-9.6923	log10_qual_likelihood_position_model=15.5005	log10_strand_likelihood_position_model=5.47655	new_cov=12/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=78/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/157
RA	290	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=1225.6	new_cov=153/148	quality=1225.6	ref_cov=0/0	tot_cov=153/148
RA	291	.	NC_007779	1844628	0	A	G	bias_e_value=4.85353e-08	bias_p_value=1.04459e-14	fisher_strand_p_value=2.83872e-16	frequency=8.605242e-02	genotype_quality=613.5	ks_quality_p_value=1	log10_base_likelihood=-12.1833	log10_qual_likelihood_position_model=23.7823	log10_strand_likelihood_position_model=15.5469	new_cov=19/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=17/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=36/147
RA	292	.	NC_007779	1861399	0	A	C	bias_e_value=3.7797e-13	bias_p_value=8.1348e-20	fisher_strand_p_value=1.66546e-21	frequency=9.814405e-02	genotype_quality=736.9	ks_quality_p_value=1	log10_base_likelihood=-11.6517	log10_qual_likelihood_position_model=34.1463	log10_strand_likelihood_position_model=20.7785	new_cov=0/40	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=148/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/85
RA	293	.	NC_007779	1879404	0	A	C	bias_e_value=3.61893e-14	bias_p_value=7.78879e-21	fisher_strand_p_value=1.52012e-22	frequency=6.954098e-02	genotype_quality=851.3	ks_quality_p_value=1	log10_base_likelihood=-12.4031	log10_qual_likelihood_position_model=31.0396	log10_strand_likelihood_position_model=21.8181	new_cov=0/29	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=186/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=186/56
RA	294	.	NC_007779	1906475	1	.	C	bias_e_value=1750460	bias_p_value=0.376741	fisher_strand_p_value=0.193336	frequency=7.407188e-03	genotype_quality=1327.7	ks_quality_p_value=0.626327	log10_base_likelihood=-9.35538	log10_qual_likelihood_position_model=2.37539	log10_strand_likelihood_position_model=0.713687	new_cov=2/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=3.38354e-08	ref_cov=117/151	reject=POLYMORPHISM_STRAND	tot_cov=119/151
RA	295	.	NC_007779	1906477	1	.	G	bias_e_value=128429	bias_p_value=0.027641	fisher_strand_p_value=0.00432703	frequency=2.458954e-02	genotype_quality=1161.1	ks_quality_p_value=0.989926	log10_base_likelihood=-24.0829	log10_qual_likelihood_position_model=7.40668	log10_strand_likelihood_position_model=2.36381	new_cov=6/0	polymorphism_quality=18.8	quality=18.8	quality_position_model=2.04871e-16	ref_cov=94/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=100/144
RA	296	.	NC_007779	1906488	0	G	T	bias_e_value=150.431	bias_p_value=3.23762e-05	fisher_strand_p_value=2.31666e-06	frequency=3.943443e-02	genotype_quality=926.9	ks_quality_p_value=1	log10_base_likelihood=-8.63638	log10_qual_likelihood_position_model=13.8271	log10_strand_likelihood_position_model=5.63514	new_cov=13/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=83/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=96/154
RA	297	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=1097.6	new_cov=136/142	quality=1097.6	ref_cov=0/0	tot_cov=136/142
RA	298	.	NC_007779	1920746	0	G	T	bias_e_value=5.48608e-08	bias_p_value=1.18073e-14	fisher_strand_p_value=3.21971e-16	frequency=1.290607e-01	genotype_quality=826.1	ks_quality_p_value=1	log10_base_likelihood=-30.125	log10_qual_likelihood_position_model=26.8442	log10_strand_likelihood_position_model=15.7932	new_cov=0/46	polymorphism_quality=24.9	quality=24.9	quality_position_model=Inf	ref_cov=139/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/139
RA	299	.	NC_007779	1945417	0	G	T	bias_e_value=12571.2	bias_p_value=0.00270561	fisher_strand_p_value=0.000296562	frequency=2.571201e-02	genotype_quality=1012.8	ks_quality_p_value=1	log10_base_likelihood=-6.24548	log10_qual_likelihood_position_model=12.9149	log10_strand_likelihood_position_model=3.68984	new_cov=0/16	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=125/170	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/186
RA	300	.	NC_007779	1971508	0	A	C	bias_e_value=4.27259e-07	bias_p_value=9.19562e-14	fisher_strand_p_value=2.66076e-15	frequency=8.368254e-02	genotype_quality=733.3	ks_quality_p_value=1	log10_base_likelihood=-26.4618	log10_qual_likelihood_position_model=21.2648	log10_strand_likelihood_position_model=14.5773	new_cov=1/18	polymorphism_quality=21.2	quality=21.2	quality_position_model=Inf	ref_cov=169/17	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=170/35
RA	301	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=1059.2	new_cov=139/127	quality=1059.2	ref_cov=0/0	tot_cov=139/127
RA	302	.	NC_007779	1993894	0	A	C	bias_e_value=0.189108	bias_p_value=4.07005e-08	fisher_strand_p_value=1.93217e-09	frequency=6.028891e-02	genotype_quality=1008.1	ks_quality_p_value=1	log10_base_likelihood=-15.9482	log10_qual_likelihood_position_model=29.4402	log10_strand_likelihood_position_model=8.93576	new_cov=0/28	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=151/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=151/153
RA	303	.	NC_007779	2004055	0	A	C	bias_e_value=1.19721e-23	bias_p_value=2.57667e-30	fisher_strand_p_value=3.50915e-32	frequency=1.888552e-01	genotype_quality=895.5	ks_quality_p_value=1	log10_base_likelihood=-49.7836	log10_qual_likelihood_position_model=51.5786	log10_strand_likelihood_position_model=31.4548	new_cov=0/78	polymorphism_quality=44.7	quality=44.7	quality_position_model=Inf	ref_cov=172/76	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/155
RA	304	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=1237.9	new_cov=144/158	quality=1237.9	ref_cov=0/0	tot_cov=144/158
RA	305	.	NC_007779	2005921	0	A	.	bias_e_value=2164650	bias_p_value=0.465884	fisher_strand_p_value=0.581062	frequency=7.867813e-03	genotype_quality=1537.5	ks_quality_p_value=0.287398	log10_base_likelihood=-7.93024	log10_qual_likelihood_position_model=1.48217	log10_strand_likelihood_position_model=0.495445	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=7.13698e-08	ref_cov=215/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=216/165
RA	306	.	NC_007779	2011708	0	A	.	bias_e_value=4607190	bias_p_value=0.991576	fisher_strand_p_value=1	frequency=1.019382e-02	genotype_quality=1193.0	ks_quality_p_value=0.87304	log10_base_likelihood=-7.80565	log10_qual_likelihood_position_model=2.4398	log10_strand_likelihood_position_model=0.400141	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=7.53607e-07	ref_cov=137/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/156
RA	307	.	NC_007779	2014008	0	T	.	bias_e_value=480125	bias_p_value=0.103334	fisher_strand_p_value=0.0939092	frequency=1.122856e-02	genotype_quality=1076.1	ks_quality_p_value=0.226952	log10_base_likelihood=-8.20826	log10_qual_likelihood_position_model=1.63666	log10_strand_likelihood_position_model=1.02729	new_cov=3/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.88916e-07	ref_cov=118/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/145
RA	308	.	NC_007779	2023811	0	C	A	bias_e_value=4.80038	bias_p_value=1.03316e-06	fisher_strand_p_value=5.85229e-08	frequency=4.900837e-02	genotype_quality=928.2	ks_quality_p_value=1	log10_base_likelihood=-9.63265	log10_qual_likelihood_position_model=21.7959	log10_strand_likelihood_position_model=7.34854	new_cov=26/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=134/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/135
RA	309	.	NC_007779	2060392	0	T	G	bias_e_value=3.08294e-05	bias_p_value=6.6352e-12	fisher_strand_p_value=2.20112e-13	frequency=6.919098e-02	genotype_quality=920.2	ks_quality_p_value=1	log10_base_likelihood=-9.96419	log10_qual_likelihood_position_model=53.0245	log10_strand_likelihood_position_model=12.6968	new_cov=46/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=135/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=181/140
RA	310	.	NC_007779	2065611	0	C	A	bias_e_value=15025	bias_p_value=0.00323374	fisher_strand_p_value=0.000362416	frequency=2.591133e-02	genotype_quality=931.2	ks_quality_p_value=1	log10_base_likelihood=-5.84272	log10_qual_likelihood_position_model=14.5724	log10_strand_likelihood_position_model=3.68142	new_cov=14/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=144/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/126
RA	311	.	NC_007779	2079936	0	G	T	bias_e_value=0.496176	bias_p_value=1.06789e-07	fisher_strand_p_value=5.32594e-09	frequency=4.009342e-02	genotype_quality=1211.3	ks_quality_p_value=1	log10_base_likelihood=-6.54708	log10_qual_likelihood_position_model=22.8044	log10_strand_likelihood_position_model=8.2736	new_cov=0/26	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=184/157	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=184/183
RA	312	.	NC_007779	2081843	0	C	A	bias_e_value=724.259	bias_p_value=0.000155878	fisher_strand_p_value=1.26999e-05	frequency=3.014088e-02	genotype_quality=1037.4	ks_quality_p_value=1	log10_base_likelihood=-6.8524	log10_qual_likelihood_position_model=15.7212	log10_strand_likelihood_position_model=4.97127	new_cov=17/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=141/144	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/144
RA	313	.	NC_007779	2082880	1	.	A	bias_e_value=2640490	bias_p_value=0.568296	fisher_strand_p_value=0.230195	frequency=7.016182e-03	genotype_quality=1427.5	ks_quality_p_value=0.99995	log10_base_likelihood=-7.24162	log10_qual_likelihood_position_model=2.66761	log10_strand_likelihood_position_model=0.637904	new_cov=0/2	polymorphism_quality=1.7	quality=1.7	quality_position_model=8.97753e-06	ref_cov=148/135	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/137
RA	314	.	NC_007779	2089417	1	.	G	bias_e_value=2529090	bias_p_value=0.54432	fisher_strand_p_value=0.234033	frequency=6.173134e-03	genotype_quality=1636.4	ks_quality_p_value=0.915453	log10_base_likelihood=-8.03245	log10_qual_likelihood_position_model=1.38729	log10_strand_likelihood_position_model=0.630723	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=6.16028e-08	ref_cov=155/167	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/167
RA	315	.	NC_007779	2098223	0	T	G	bias_e_value=0.00242276	bias_p_value=5.21436e-10	fisher_strand_p_value=2.03545e-11	frequency=3.979111e-02	genotype_quality=924.8	ks_quality_p_value=1	log10_base_likelihood=-5.96408	log10_qual_likelihood_position_model=22.5369	log10_strand_likelihood_position_model=10.6913	new_cov=28/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=103/165	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/165
RA	316	.	NC_007779	2099403	1	.	A	bias_e_value=1637330	bias_p_value=0.352391	fisher_strand_p_value=0.221169	frequency=6.779671e-03	genotype_quality=1451.2	ks_quality_p_value=0.496519	log10_base_likelihood=-8.2083	log10_qual_likelihood_position_model=1.10528	log10_strand_likelihood_position_model=0.655275	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.19831e-08	ref_cov=137/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/156
RA	317	.	NC_007779	2141731	0	A	C	bias_e_value=70.8392	bias_p_value=1.52463e-05	fisher_strand_p_value=1.03121e-06	frequency=3.660393e-02	genotype_quality=984.0	ks_quality_p_value=1	log10_base_likelihood=-6.85564	log10_qual_likelihood_position_model=23.6574	log10_strand_likelihood_position_model=5.98665	new_cov=0/18	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=150/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=150/139
RA	318	.	NC_007779	2156661	0	C	A	bias_e_value=0.00635446	bias_p_value=1.36763e-09	fisher_strand_p_value=5.55642e-11	frequency=5.651331e-02	genotype_quality=991.8	ks_quality_p_value=1	log10_base_likelihood=-8.73082	log10_qual_likelihood_position_model=24.977	log10_strand_likelihood_position_model=10.4143	new_cov=35/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=140/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/155
RA	319	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1139.6	new_cov=103/172	quality=1139.6	ref_cov=0/0	tot_cov=103/172
RA	320	.	NC_007779	2174678	0	C	G	bias_e_value=3196.28	bias_p_value=0.000687915	fisher_strand_p_value=6.47827e-05	frequency=2.598190e-02	genotype_quality=856.3	ks_quality_p_value=0.997339	log10_base_likelihood=-6.32895	log10_qual_likelihood_position_model=8.68873	log10_strand_likelihood_position_model=4.18854	new_cov=0/7	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=163/51	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/58
RA	321	.	NC_007779	2183367	1	.	T	bias_e_value=3934810	bias_p_value=0.846863	fisher_strand_p_value=0.500418	frequency=5.825996e-03	genotype_quality=1726.2	ks_quality_p_value=1	log10_base_likelihood=-5.58356	log10_qual_likelihood_position_model=4.29117	log10_strand_likelihood_position_model=0.55157	new_cov=0/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.0290674	ref_cov=161/180	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=161/182
RA	322	.	NC_007779	2189203	0	G	.	bias_e_value=1178520	bias_p_value=0.253644	fisher_strand_p_value=0.0832314	frequency=1.051903e-02	genotype_quality=1182.5	ks_quality_p_value=0.829745	log10_base_likelihood=-8.20668	log10_qual_likelihood_position_model=3.49722	log10_strand_likelihood_position_model=1.07971	new_cov=0/3	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.88586e-05	ref_cov=160/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/125
RA	323	.	NC_007779	2200801	1	.	A	bias_e_value=2333530	bias_p_value=0.50223	fisher_strand_p_value=0.212664	frequency=6.600380e-03	genotype_quality=1521.7	ks_quality_p_value=0.884089	log10_base_likelihood=-8.02265	log10_qual_likelihood_position_model=1.49547	log10_strand_likelihood_position_model=0.672307	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=9.00823e-08	ref_cov=163/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=163/140
RA	324	.	NC_007779	2213136	0	G	T	bias_e_value=7.09662e-09	bias_p_value=1.52736e-15	fisher_strand_p_value=4.40431e-17	frequency=1.560225e-01	genotype_quality=726.4	ks_quality_p_value=0.894406	log10_base_likelihood=-58.2931	log10_qual_likelihood_position_model=35.7043	log10_strand_likelihood_position_model=16.3561	new_cov=36/0	polymorphism_quality=53.2	quality=53.2	quality_position_model=3.66473e-08	ref_cov=54/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/132
RA	325	.	NC_007779	2216556	0	C	A	bias_e_value=14.8096	bias_p_value=3.18738e-06	fisher_strand_p_value=1.93678e-07	frequency=2.978230e-02	genotype_quality=1200.6	ks_quality_p_value=1	log10_base_likelihood=-6.3258	log10_qual_likelihood_position_model=18.0439	log10_strand_likelihood_position_model=6.71292	new_cov=18/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=134/195	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/195
RA	326	.	NC_007779	2226024	0	C	A	bias_e_value=0.0106103	bias_p_value=2.28358e-09	fisher_strand_p_value=9.48376e-11	frequency=4.599571e-02	genotype_quality=1065.8	ks_quality_p_value=1	log10_base_likelihood=-6.61027	log10_qual_likelihood_position_model=20.8003	log10_strand_likelihood_position_model=10.023	new_cov=28/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=128/182	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/182
RA	327	.	NC_007779	2254201	0	G	T	bias_e_value=0.0952687	bias_p_value=2.05041e-08	fisher_strand_p_value=9.41252e-10	frequency=4.629803e-02	genotype_quality=1186.0	ks_quality_p_value=1	log10_base_likelihood=-10.0974	log10_qual_likelihood_position_model=23.6674	log10_strand_likelihood_position_model=9.02629	new_cov=0/27	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=184/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=184/172
RA	328	.	NC_007779	2266892	0	G	T	bias_e_value=38.9325	bias_p_value=8.37919e-06	fisher_strand_p_value=5.43193e-07	frequency=3.995895e-02	genotype_quality=1055.2	ks_quality_p_value=1	log10_base_likelihood=-6.75553	log10_qual_likelihood_position_model=17.0476	log10_strand_likelihood_position_model=6.51703	new_cov=1/22	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=167/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/149
RA	329	.	NC_007779	2267489	0	T	.	bias_e_value=4371400	bias_p_value=0.940829	fisher_strand_p_value=1	frequency=1.350307e-02	genotype_quality=1196.8	ks_quality_p_value=0.67634	log10_base_likelihood=-10.9488	log10_qual_likelihood_position_model=2.72371	log10_strand_likelihood_position_model=0.423179	new_cov=2/2	polymorphism_quality=5.5	quality=5.5	quality_position_model=8.88674e-10	ref_cov=144/148	reject=INDEL_HOMOPOLYMER	tot_cov=146/150
RA	330	.	NC_007779	2271208	1	.	C	bias_e_value=3870270	bias_p_value=0.832974	fisher_strand_p_value=0.502561	frequency=6.534576e-03	genotype_quality=1472.8	ks_quality_p_value=0.956924	log10_base_likelihood=-6.64605	log10_qual_likelihood_position_model=3.89084	log10_strand_likelihood_position_model=0.527197	new_cov=0/2	polymorphism_quality=1.1	quality=1.1	quality_position_model=0.000590684	ref_cov=139/165	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=139/167
RA	331	.	NC_007779	2271592	0	G	T	bias_e_value=0.0760545	bias_p_value=1.63687e-08	fisher_strand_p_value=7.43362e-10	frequency=4.338646e-02	genotype_quality=1118.9	ks_quality_p_value=1	log10_base_likelihood=-6.83637	log10_qual_likelihood_position_model=22.6954	log10_strand_likelihood_position_model=9.1288	new_cov=0/26	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=167/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/148
RA	332	.	NC_007779	2278635	0	C	A	bias_e_value=0.00101792	bias_p_value=2.1908e-10	fisher_strand_p_value=8.2667e-12	frequency=7.212687e-02	genotype_quality=1034.7	ks_quality_p_value=0.999321	log10_base_likelihood=-16.843	log10_qual_likelihood_position_model=26.4838	log10_strand_likelihood_position_model=11.3365	new_cov=35/0	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=135/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/169
RA	333	.	NC_007779	2331114	0	G	.	bias_e_value=4589600	bias_p_value=0.987789	fisher_strand_p_value=1	frequency=9.703636e-03	genotype_quality=1327.7	ks_quality_p_value=0.847853	log10_base_likelihood=-8.66793	log10_qual_likelihood_position_model=1.16261	log10_strand_likelihood_position_model=0.383281	new_cov=1/2	polymorphism_quality=3.2	quality=3.2	quality_position_model=4.44017e-09	ref_cov=136/170	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/172
RA	334	.	NC_007779	2331120	0	T	G	bias_e_value=9.50336e-16	bias_p_value=2.04535e-22	fisher_strand_p_value=3.72235e-24	frequency=9.414864e-02	genotype_quality=919.4	ks_quality_p_value=1	log10_base_likelihood=-14.729	log10_qual_likelihood_position_model=37.4759	log10_strand_likelihood_position_model=23.4292	new_cov=54/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=79/180	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/180
RA	335	.	NC_007779	2332580	0	A	C	bias_e_value=1.36141e-13	bias_p_value=2.93007e-20	fisher_strand_p_value=5.87348e-22	frequency=9.456301e-02	genotype_quality=887.5	ks_quality_p_value=1	log10_base_likelihood=-12.8699	log10_qual_likelihood_position_model=34.8819	log10_strand_likelihood_position_model=21.2311	new_cov=0/50	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=171/79	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/130
RA	336	.	NC_007779	2353815	0	A	C	bias_e_value=9.63596e-09	bias_p_value=2.07389e-15	fisher_strand_p_value=5.39247e-17	frequency=7.381058e-02	genotype_quality=743.6	ks_quality_p_value=1	log10_base_likelihood=-8.00759	log10_qual_likelihood_position_model=26.2077	log10_strand_likelihood_position_model=16.2682	new_cov=0/27	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=154/38	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/65
RA	337	.	NC_007779	2361733	1	.	A	bias_e_value=1120040	bias_p_value=0.241059	fisher_strand_p_value=0.503669	frequency=6.409645e-03	genotype_quality=1573.1	ks_quality_p_value=0.127886	log10_base_likelihood=-8.12571	log10_qual_likelihood_position_model=1.39186	log10_strand_likelihood_position_model=0.51839	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.81833e-08	ref_cov=170/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=172/140
RA	338	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=1190.5	new_cov=151/146	quality=1190.5	ref_cov=0/0	tot_cov=151/146
RA	339	.	NC_007779	2409404	0	A	C	bias_e_value=7.56928	bias_p_value=1.62909e-06	fisher_strand_p_value=9.4876e-08	frequency=5.894089e-02	genotype_quality=874.5	ks_quality_p_value=1	log10_base_likelihood=-14.812	log10_qual_likelihood_position_model=18.4583	log10_strand_likelihood_position_model=7.02284	new_cov=0/20	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=141/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/123
RA	340	.	NC_007779	2409821	0	A	.	bias_e_value=3768920	bias_p_value=0.811161	fisher_strand_p_value=1	frequency=8.894920e-03	genotype_quality=1391.2	ks_quality_p_value=0.452302	log10_base_likelihood=-7.92276	log10_qual_likelihood_position_model=2.28457	log10_strand_likelihood_position_model=0.386231	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.79823e-07	ref_cov=150/184	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/186
RA	341	.	NC_007779	2410289	1	.	A	bias_e_value=3318090	bias_p_value=0.71413	fisher_strand_p_value=1	frequency=7.220268e-03	genotype_quality=1361.0	ks_quality_p_value=0.346863	log10_base_likelihood=-8.16359	log10_qual_likelihood_position_model=1.83417	log10_strand_likelihood_position_model=0.300145	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.94649e-08	ref_cov=143/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/133
RA	342	.	NC_007779	2410314	1	.	C	bias_e_value=2572410	bias_p_value=0.553644	fisher_strand_p_value=0.247405	frequency=6.918907e-03	genotype_quality=1371.0	ks_quality_p_value=0.890662	log10_base_likelihood=-6.22639	log10_qual_likelihood_position_model=3.08778	log10_strand_likelihood_position_model=0.606592	new_cov=0/2	polymorphism_quality=0.7	quality=0.7	quality_position_model=0.000277367	ref_cov=145/142	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=145/144
RA	343	.	NC_007779	2410316	0	A	C	bias_e_value=4.09325e-05	bias_p_value=8.80964e-12	fisher_strand_p_value=2.95116e-13	frequency=8.225489e-02	genotype_quality=904.5	ks_quality_p_value=1	log10_base_likelihood=-20.6589	log10_qual_likelihood_position_model=31.5591	log10_strand_likelihood_position_model=12.5956	new_cov=0/39	polymorphism_quality=15.4	quality=15.4	quality_position_model=Inf	ref_cov=146/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/153
RA	344	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=1155.5	new_cov=119/173	quality=1155.5	ref_cov=0/0	tot_cov=119/174
RA	345	.	NC_007779	2417605	0	C	A	bias_e_value=3.26512e-06	bias_p_value=7.0273e-13	fisher_strand_p_value=3.04218e-14	frequency=9.580517e-02	genotype_quality=980.7	ks_quality_p_value=0.711545	log10_base_likelihood=-26.3012	log10_qual_likelihood_position_model=35.4994	log10_strand_likelihood_position_model=13.5168	new_cov=37/0	polymorphism_quality=21.1	quality=21.1	quality_position_model=Inf	ref_cov=109/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/169
RA	346	.	NC_007779	2468327	0	C	.	bias_e_value=4174920	bias_p_value=0.89854	fisher_strand_p_value=0.735765	frequency=3.225040e-02	genotype_quality=1149.8	ks_quality_p_value=0.794828	log10_base_likelihood=-29.2662	log10_qual_likelihood_position_model=3.83966	log10_strand_likelihood_position_model=0.647805	new_cov=3/6	polymorphism_quality=24.1	quality=24.1	quality_position_model=5.35299e-27	ref_cov=119/151	reject=INDEL_HOMOPOLYMER	tot_cov=122/157
RA	347	.	NC_007779	2475172	0	T	.	bias_e_value=3501910	bias_p_value=0.753693	fisher_strand_p_value=0.553947	frequency=1.647663e-02	genotype_quality=727.7	ks_quality_p_value=0.697297	log10_base_likelihood=-8.78633	log10_qual_likelihood_position_model=2.16712	log10_strand_likelihood_position_model=0.583743	new_cov=3/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=5.85952e-08	ref_cov=113/65	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/65
RA	348	.	NC_007779	2476279	0	C	G	bias_e_value=611392	bias_p_value=0.131586	fisher_strand_p_value=0.0289753	frequency=1.776791e-02	genotype_quality=840.8	ks_quality_p_value=1	log10_base_likelihood=-6.4521	log10_qual_likelihood_position_model=6.50989	log10_strand_likelihood_position_model=1.53797	new_cov=0/5	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=102/96	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=103/101
RA	349	.	NC_007779	2476287	0	T	G	bias_e_value=147402	bias_p_value=0.0317244	fisher_strand_p_value=0.00505998	frequency=3.032780e-02	genotype_quality=778.8	ks_quality_p_value=0.996838	log10_base_likelihood=-6.81146	log10_qual_likelihood_position_model=12.4046	log10_strand_likelihood_position_model=2.29585	new_cov=0/7	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=106/90	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=106/97
RA	350	.	NC_007779	2476289	0	A	T	bias_e_value=72562.4	bias_p_value=0.0156171	fisher_strand_p_value=0.0021926	frequency=3.179455e-02	genotype_quality=762.3	ks_quality_p_value=1	log10_base_likelihood=-7.2505	log10_qual_likelihood_position_model=12.6264	log10_strand_likelihood_position_model=2.65904	new_cov=0/8	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=104/86	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=104/94
RA	351	.	NC_007779	2478675	0	C	A	bias_e_value=0.594552	bias_p_value=1.27962e-07	fisher_strand_p_value=6.4431e-09	frequency=6.615114e-02	genotype_quality=888.3	ks_quality_p_value=1	log10_base_likelihood=-13.1737	log10_qual_likelihood_position_model=17.8835	log10_strand_likelihood_position_model=8.23086	new_cov=27/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=119/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/136
RA	352	.	NC_007779	2488915	1	.	A	bias_e_value=2269160	bias_p_value=0.488376	fisher_strand_p_value=1	frequency=1.255226e-02	genotype_quality=1181.8	ks_quality_p_value=0.179833	log10_base_likelihood=-13.2673	log10_qual_likelihood_position_model=1.99547	log10_strand_likelihood_position_model=0.411879	new_cov=2/1	polymorphism_quality=7.9	quality=7.9	quality_position_model=6.63665e-13	ref_cov=121/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/116
RA	353	.	NC_007779	2517218	0	A	C	bias_e_value=1.10492e-11	bias_p_value=2.37805e-18	fisher_strand_p_value=5.23849e-20	frequency=7.126045e-02	genotype_quality=773.2	ks_quality_p_value=1	log10_base_likelihood=-7.37263	log10_qual_likelihood_position_model=44.2255	log10_strand_likelihood_position_model=19.2808	new_cov=0/38	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=156/52	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/91
RA	354	.	NC_007779	2536601	0	T	G	bias_e_value=0.412731	bias_p_value=8.88295e-08	fisher_strand_p_value=4.38785e-09	frequency=5.902100e-02	genotype_quality=1016.4	ks_quality_p_value=1	log10_base_likelihood=-8.79118	log10_qual_likelihood_position_model=27.9814	log10_strand_likelihood_position_model=8.35775	new_cov=26/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=130/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/157
RA	355	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=1247.3	new_cov=151/154	quality=1247.3	ref_cov=0/0	tot_cov=151/154
RA	356	.	NC_007779	2539595	1	.	A	bias_e_value=2472230	bias_p_value=0.532083	fisher_strand_p_value=1	frequency=1.020432e-02	genotype_quality=1463.3	ks_quality_p_value=0.206398	log10_base_likelihood=-12.8635	log10_qual_likelihood_position_model=2.25101	log10_strand_likelihood_position_model=0.424489	new_cov=2/1	polymorphism_quality=7.5	quality=7.5	quality_position_model=3.21549e-12	ref_cov=145/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/147
RA	357	.	NC_007779	2556426	0	G	T	bias_e_value=0.000106368	bias_p_value=2.28928e-11	fisher_strand_p_value=9.17667e-13	frequency=7.976437e-02	genotype_quality=1001.0	ks_quality_p_value=0.864324	log10_base_likelihood=-19.4795	log10_qual_likelihood_position_model=34.2989	log10_strand_likelihood_position_model=12.0373	new_cov=0/35	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=166/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/156
RA	358	.	NC_007779	2577495	1	.	A	bias_e_value=2073950	bias_p_value=0.446363	fisher_strand_p_value=0.21515	frequency=7.041931e-03	genotype_quality=1405.8	ks_quality_p_value=0.726404	log10_base_likelihood=-8.1807	log10_qual_likelihood_position_model=1.41768	log10_strand_likelihood_position_model=0.66726	new_cov=0/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.07625e-08	ref_cov=152/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/132
RA	359	.	NC_007779	2577496	0	A	.	bias_e_value=668708	bias_p_value=0.143922	fisher_strand_p_value=1	frequency=1.033783e-02	genotype_quality=1146.5	ks_quality_p_value=0.0325175	log10_base_likelihood=-8.21143	log10_qual_likelihood_position_model=2.67257	log10_strand_likelihood_position_model=0.399816	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.97612e-07	ref_cov=152/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/136
RA	360	.	NC_007779	2601998	0	A	C	bias_e_value=3.73584e-11	bias_p_value=8.0404e-18	fisher_strand_p_value=1.82117e-19	frequency=9.297657e-02	genotype_quality=724.3	ks_quality_p_value=1	log10_base_likelihood=-22.7404	log10_qual_likelihood_position_model=26.3428	log10_strand_likelihood_position_model=18.7396	new_cov=0/23	polymorphism_quality=17.5	quality=17.5	quality_position_model=Inf	ref_cov=161/18	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/41
RA	361	.	NC_007779	2618382	1	.	C	bias_e_value=17297.9	bias_p_value=0.00372292	fisher_strand_p_value=0.000443459	frequency=1.212120e-02	genotype_quality=817.8	ks_quality_p_value=0.957929	log10_base_likelihood=-8.26363	log10_qual_likelihood_position_model=3.65418	log10_strand_likelihood_position_model=3.35315	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=0.00707501	ref_cov=161/2	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=161/4
RA	362	.	NC_007779	2618856	1	.	A	bias_e_value=4560480	bias_p_value=0.981522	fisher_strand_p_value=1	frequency=6.849289e-03	genotype_quality=1457.6	ks_quality_p_value=0.814026	log10_base_likelihood=-8.19307	log10_qual_likelihood_position_model=1.33754	log10_strand_likelihood_position_model=0.322314	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.79445e-08	ref_cov=112/178	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/179
RA	363	.	NC_007779	2623159	0	T	G	bias_e_value=2.69987e-22	bias_p_value=5.81076e-29	fisher_strand_p_value=8.26948e-31	frequency=1.671906e-01	genotype_quality=847.2	ks_quality_p_value=1	log10_base_likelihood=-33.5928	log10_qual_likelihood_position_model=47.3573	log10_strand_likelihood_position_model=30.0825	new_cov=70/0	polymorphism_quality=28.4	quality=28.4	quality_position_model=Inf	ref_cov=65/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/165
RA	364	.	NC_007779	2641345	0	T	G	bias_e_value=0.000683541	bias_p_value=1.47114e-10	fisher_strand_p_value=5.46219e-12	frequency=5.017900e-02	genotype_quality=638.7	ks_quality_p_value=1	log10_base_likelihood=-8.85669	log10_qual_likelihood_position_model=17.1757	log10_strand_likelihood_position_model=11.2626	new_cov=15/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=23/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=38/142
RA	365	.	NC_007779	2648595	0	A	C	bias_e_value=1.21125e-07	bias_p_value=2.6069e-14	fisher_strand_p_value=7.27014e-16	frequency=8.814907e-02	genotype_quality=644.4	ks_quality_p_value=1	log10_base_likelihood=-18.3318	log10_qual_likelihood_position_model=24.4827	log10_strand_likelihood_position_model=15.1385	new_cov=0/19	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=144/18	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/37
RA	366	.	NC_007779	2652909	0	T	C	bias_e_value=3647470	bias_p_value=0.785021	fisher_strand_p_value=0.62011	frequency=9.742737e-03	genotype_quality=1229.5	ks_quality_p_value=0.678548	log10_base_likelihood=-6.25097	log10_qual_likelihood_position_model=1.43196	log10_strand_likelihood_position_model=0.428886	new_cov=2/1	polymorphism_quality=0.7	quality=0.7	quality_position_model=3.00211e-06	ref_cov=150/154	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=152/155
RA	367	.	NC_007779	2676695	0	T	G	bias_e_value=2.56194e-06	bias_p_value=5.5139e-13	fisher_strand_p_value=1.68548e-14	frequency=5.627775e-02	genotype_quality=820.7	ks_quality_p_value=1	log10_base_likelihood=-7.59001	log10_qual_likelihood_position_model=42.8782	log10_strand_likelihood_position_model=13.7733	new_cov=37/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=85/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/140
RA	368	.	NC_007779	2712657	0	A	T	bias_e_value=3101550	bias_p_value=0.667528	fisher_strand_p_value=0.611893	frequency=9.729385e-03	genotype_quality=1239.8	ks_quality_p_value=0.498945	log10_base_likelihood=-7.54104	log10_qual_likelihood_position_model=1.39184	log10_strand_likelihood_position_model=0.439444	new_cov=1/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.27307e-07	ref_cov=158/147	reject=POLYMORPHISM_STRAND	tot_cov=159/149
RA	369	.	NC_007779	2733780	0	T	A	bias_e_value=4514030	bias_p_value=0.971526	fisher_strand_p_value=1	frequency=1.129346e-01	genotype_quality=1076.2	ks_quality_p_value=0.771055	log10_base_likelihood=-117.837	log10_qual_likelihood_position_model=5.87546	log10_strand_likelihood_position_model=0.847291	new_cov=18/16	polymorphism_quality=112.9	quality=112.9	quality_position_model=1.17524e-113	ref_cov=137/130	tot_cov=155/146
RA	370	.	NC_007779	2753432	1	.	A	bias_e_value=1966100	bias_p_value=0.42315	fisher_strand_p_value=0.503459	frequency=6.756783e-03	genotype_quality=1489.2	ks_quality_p_value=0.28611	log10_base_likelihood=-8.32744	log10_qual_likelihood_position_model=1.43057	log10_strand_likelihood_position_model=0.519411	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.59787e-08	ref_cov=161/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=163/133
RA	371	.	NC_007779	2771144	0	G	T	bias_e_value=610.589	bias_p_value=0.000131413	fisher_strand_p_value=1.12166e-05	frequency=4.221821e-02	genotype_quality=938.4	ks_quality_p_value=0.940313	log10_base_likelihood=-7.98479	log10_qual_likelihood_position_model=21.0805	log10_strand_likelihood_position_model=5.09477	new_cov=1/18	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=148/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/134
RA	372	.	NC_007779	2772064	1	.	T	bias_e_value=4637770	bias_p_value=0.998158	fisher_strand_p_value=1	frequency=8.546829e-03	genotype_quality=1172.2	ks_quality_p_value=0.939915	log10_base_likelihood=-8.56835	log10_qual_likelihood_position_model=1.43991	log10_strand_likelihood_position_model=0.302354	new_cov=1/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=8.95505e-09	ref_cov=106/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/127
RA	373	.	NC_007779	2816615	0	G	C	bias_e_value=2.29774	bias_p_value=4.94528e-07	fisher_strand_p_value=3.02882e-08	frequency=5.351591e-02	genotype_quality=806.3	ks_quality_p_value=0.885729	log10_base_likelihood=-11.4429	log10_qual_likelihood_position_model=21.2627	log10_strand_likelihood_position_model=7.51873	new_cov=17/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=76/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=93/150
RA	374	.	NC_007779	2817030	0	G	C	bias_e_value=1.57973e-08	bias_p_value=3.39996e-15	fisher_strand_p_value=1.30389e-16	frequency=1.049509e-01	genotype_quality=850.0	ks_quality_p_value=0.687078	log10_base_likelihood=-28.8498	log10_qual_likelihood_position_model=37.2538	log10_strand_likelihood_position_model=15.8848	new_cov=33/0	polymorphism_quality=23.6	quality=23.6	quality_position_model=Inf	ref_cov=67/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=100/169
RA	375	.	NC_007779	2833989	0	A	C	bias_e_value=1.72256e-23	bias_p_value=3.70736e-30	fisher_strand_p_value=5.07451e-32	frequency=1.712241e-01	genotype_quality=782.4	ks_quality_p_value=1	log10_base_likelihood=-34.3987	log10_qual_likelihood_position_model=48.1963	log10_strand_likelihood_position_model=31.2946	new_cov=0/58	polymorphism_quality=29.2	quality=29.2	quality_position_model=Inf	ref_cov=162/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/97
RA	376	.	NC_007779	2839296	0	A	G	bias_e_value=0.0964034	bias_p_value=2.07483e-08	fisher_strand_p_value=9.53006e-10	frequency=4.853821e-02	genotype_quality=741.6	ks_quality_p_value=1	log10_base_likelihood=-5.5717	log10_qual_likelihood_position_model=19.7907	log10_strand_likelihood_position_model=9.0209	new_cov=17/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=56/155	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/155
RA	377	.	NC_007779	2847445	0	G	T	bias_e_value=0.0838803	bias_p_value=1.8053e-08	fisher_strand_p_value=8.23691e-10	frequency=6.248951e-02	genotype_quality=991.2	ks_quality_p_value=1	log10_base_likelihood=-9.43257	log10_qual_likelihood_position_model=22.8004	log10_strand_likelihood_position_model=9.11194	new_cov=0/30	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=152/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/165
RA	378	.	NC_007779	2865228	0	A	G	bias_e_value=2528720	bias_p_value=0.544239	fisher_strand_p_value=0.22557	frequency=5.108261e-02	genotype_quality=1286.1	ks_quality_p_value=0.949567	log10_base_likelihood=-46.8225	log10_qual_likelihood_position_model=4.83965	log10_strand_likelihood_position_model=1.16182	new_cov=6/12	polymorphism_quality=41.7	quality=41.7	quality_position_model=3.79622e-43	ref_cov=170/164	tot_cov=176/176
RA	379	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1330.5	new_cov=147/156	quality=1330.5	ref_cov=0/0	tot_cov=148/156
RA	380	.	NC_007779	2868094	0	C	A	bias_e_value=6.12332e-08	bias_p_value=1.31788e-14	fisher_strand_p_value=3.6048e-16	frequency=1.167326e-01	genotype_quality=1017.4	ks_quality_p_value=1	log10_base_likelihood=-35.2466	log10_qual_likelihood_position_model=27.0736	log10_strand_likelihood_position_model=15.5802	new_cov=47/0	polymorphism_quality=30.1	quality=30.1	quality_position_model=Inf	ref_cov=121/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/165
RA	381	.	NC_007779	2895131	0	A	C	bias_e_value=8.71699e-08	bias_p_value=1.8761e-14	fisher_strand_p_value=5.18318e-16	frequency=7.037306e-02	genotype_quality=766.7	ks_quality_p_value=1	log10_base_likelihood=-7.04519	log10_qual_likelihood_position_model=38.5006	log10_strand_likelihood_position_model=15.2854	new_cov=0/34	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=141/61	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/95
RA	382	.	NC_007779	2898837	0	G	T	bias_e_value=0.000343001	bias_p_value=7.38218e-11	fisher_strand_p_value=2.66997e-12	frequency=6.899643e-02	genotype_quality=1027.2	ks_quality_p_value=1	log10_base_likelihood=-17.3589	log10_qual_likelihood_position_model=24.5293	log10_strand_likelihood_position_model=11.5735	new_cov=0/32	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=169/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/147
RA	383	.	NC_007779	2898953	1	.	A	bias_e_value=4319950	bias_p_value=0.929755	fisher_strand_p_value=1	frequency=8.230209e-03	genotype_quality=1206.8	ks_quality_p_value=0.649411	log10_base_likelihood=-8.37506	log10_qual_likelihood_position_model=1.4472	log10_strand_likelihood_position_model=0.302495	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.44182e-08	ref_cov=110/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/132
RA	384	.	NC_007779	2898954	0	A	.	bias_e_value=503850	bias_p_value=0.10844	fisher_strand_p_value=0.132991	frequency=2.810574e-02	genotype_quality=998.9	ks_quality_p_value=0.170315	log10_base_likelihood=-22.2247	log10_qual_likelihood_position_model=2.1671	log10_strand_likelihood_position_model=1.07001	new_cov=1/6	polymorphism_quality=17.0	quality=17.0	quality_position_model=3.77084e-21	ref_cov=111/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/137
RA	385	.	NC_007779	2899215	1	.	T	bias_e_value=4128540	bias_p_value=0.888559	fisher_strand_p_value=1	frequency=7.117271e-03	genotype_quality=1389.7	ks_quality_p_value=0.566727	log10_base_likelihood=-8.27709	log10_qual_likelihood_position_model=1.29489	log10_strand_likelihood_position_model=0.299531	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.25847e-08	ref_cov=138/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/142
RA	386	.	NC_007779	2911644	0	G	T	bias_e_value=0.266526	bias_p_value=5.73626e-08	fisher_strand_p_value=3.14936e-09	frequency=5.637836e-02	genotype_quality=958.2	ks_quality_p_value=0.879726	log10_base_likelihood=-12.4226	log10_qual_likelihood_position_model=29.4006	log10_strand_likelihood_position_model=8.54705	new_cov=0/28	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=148/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/159
RA	387	.	NC_007779	2926157	0	T	G	bias_e_value=1.85334e-12	bias_p_value=3.98882e-19	fisher_strand_p_value=8.44724e-21	frequency=5.251169e-02	genotype_quality=853.5	ks_quality_p_value=1	log10_base_likelihood=-7.16154	log10_qual_likelihood_position_model=27.1785	log10_strand_likelihood_position_model=20.0733	new_cov=26/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=26/190	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=52/190
RA	388	.	NC_007779	2939008	0	A	C	bias_e_value=0.240783	bias_p_value=5.18221e-08	fisher_strand_p_value=2.49014e-09	frequency=4.929161e-02	genotype_quality=988.7	ks_quality_p_value=1	log10_base_likelihood=-5.57814	log10_qual_likelihood_position_model=26.9476	log10_strand_likelihood_position_model=8.60378	new_cov=0/25	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=158/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/143
RA	389	.	NC_007779	2974959	1	.	A	bias_e_value=4632970	bias_p_value=0.997124	fisher_strand_p_value=1	frequency=7.220268e-03	genotype_quality=1384.5	ks_quality_p_value=0.925118	log10_base_likelihood=-8.02008	log10_qual_likelihood_position_model=1.78648	log10_strand_likelihood_position_model=0.302464	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=7.51173e-08	ref_cov=149/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/127
RA	390	.	NC_007779	2994664	0	T	.	bias_e_value=3692120	bias_p_value=0.79463	fisher_strand_p_value=1	frequency=1.320934e-02	genotype_quality=913.0	ks_quality_p_value=0.432047	log10_base_likelihood=-8.69046	log10_qual_likelihood_position_model=1.20718	log10_strand_likelihood_position_model=0.401084	new_cov=1/2	polymorphism_quality=3.2	quality=3.2	quality_position_model=4.87979e-09	ref_cov=106/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/120
RA	391	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=1346.2	new_cov=153/175	quality=1346.2	ref_cov=0/0	tot_cov=153/175
RA	392	.	NC_007779	3029385	0	C	A	bias_e_value=20.9961	bias_p_value=4.51886e-06	fisher_strand_p_value=2.82348e-07	frequency=2.593136e-02	genotype_quality=969.7	ks_quality_p_value=0.99499	log10_base_likelihood=-6.37933	log10_qual_likelihood_position_model=13.7035	log10_strand_likelihood_position_model=6.54922	new_cov=0/9	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=195/40	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=195/49
RA	393	.	NC_007779	3034413	0	A	C	bias_e_value=2.03243e-22	bias_p_value=4.37426e-29	fisher_strand_p_value=6.19973e-31	frequency=1.598468e-01	genotype_quality=813.5	ks_quality_p_value=1	log10_base_likelihood=-32.1915	log10_qual_likelihood_position_model=45.1914	log10_strand_likelihood_position_model=30.2076	new_cov=0/63	polymorphism_quality=27.0	quality=27.0	quality_position_model=Inf	ref_cov=166/53	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/116
RA	394	.	NC_007779	3035390	0	T	C	bias_e_value=2.75811e-08	bias_p_value=5.93611e-15	fisher_strand_p_value=1.58809e-16	frequency=1.352458e-01	genotype_quality=539.7	ks_quality_p_value=1	log10_base_likelihood=-28.737	log10_qual_likelihood_position_model=22.963	log10_strand_likelihood_position_model=15.7991	new_cov=0/33	polymorphism_quality=23.5	quality=23.5	quality_position_model=Inf	ref_cov=137/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/85
RA	395	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=1276.6	new_cov=160/156	quality=1276.6	ref_cov=0/0	tot_cov=160/156
RA	396	.	NC_007779	3059420	1	.	T	bias_e_value=939035	bias_p_value=0.202102	fisher_strand_p_value=0.236	frequency=5.970001e-03	genotype_quality=1688.1	ks_quality_p_value=0.215149	log10_base_likelihood=-8.14041	log10_qual_likelihood_position_model=2.06292	log10_strand_likelihood_position_model=0.627089	new_cov=0/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.36393e-07	ref_cov=172/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=172/163
RA	397	.	NC_007779	3082917	0	C	.	bias_e_value=645958	bias_p_value=0.139025	fisher_strand_p_value=0.498534	frequency=5.845070e-03	genotype_quality=1459.8	ks_quality_p_value=0.0623779	log10_base_likelihood=-5.66215	log10_qual_likelihood_position_model=1.54748	log10_strand_likelihood_position_model=0.603335	new_cov=0/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=2.5144e-05	ref_cov=171/169	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=171/171
RA	398	.	NC_007779	3084663	0	C	A	bias_e_value=0.661751	bias_p_value=1.42424e-07	fisher_strand_p_value=7.21228e-09	frequency=4.147911e-02	genotype_quality=1253.2	ks_quality_p_value=1	log10_base_likelihood=-8.15452	log10_qual_likelihood_position_model=23.1968	log10_strand_likelihood_position_model=8.15407	new_cov=28/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=170/176	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=198/176
RA	399	.	NC_007779	3088549	0	G	T	bias_e_value=1.34187	bias_p_value=2.88802e-07	fisher_strand_p_value=1.51985e-08	frequency=9.422255e-02	genotype_quality=840.3	ks_quality_p_value=1	log10_base_likelihood=-18.1869	log10_qual_likelihood_position_model=20.2517	log10_strand_likelihood_position_model=8.13448	new_cov=0/37	polymorphism_quality=12.9	quality=12.9	quality_position_model=Inf	ref_cov=113/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/190
RA	400	.	NC_007779	3110532	0	C	A	bias_e_value=575.526	bias_p_value=0.000123867	fisher_strand_p_value=9.96887e-06	frequency=2.304077e-02	genotype_quality=896.7	ks_quality_p_value=0.992127	log10_base_likelihood=-5.63567	log10_qual_likelihood_position_model=12.2952	log10_strand_likelihood_position_model=5.00135	new_cov=0/8	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=172/49	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/58
RA	401	.	NC_007779	3111877	0	A	.	bias_e_value=4329360	bias_p_value=0.93178	fisher_strand_p_value=1	frequency=1.048183e-02	genotype_quality=1149.2	ks_quality_p_value=0.654141	log10_base_likelihood=-8.07555	log10_qual_likelihood_position_model=2.58707	log10_strand_likelihood_position_model=0.372295	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.25595e-07	ref_cov=163/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/121
RA	402	.	NC_007779	3139985	0	A	.	deleted=1	frequency=1	genotype_quality=4.6	new_cov=1/0	quality=4.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	403	.	NC_007779	3139986	0	C	.	deleted=1	frequency=1	genotype_quality=4.6	new_cov=1/0	quality=4.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	404	.	NC_007779	3139987	0	T	.	deleted=1	frequency=1	genotype_quality=4.6	new_cov=1/0	quality=4.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	405	.	NC_007779	3152855	0	A	.	bias_e_value=509103	bias_p_value=0.109571	fisher_strand_p_value=0.0663158	frequency=1.542568e-02	genotype_quality=1292.6	ks_quality_p_value=0.346062	log10_base_likelihood=-14.8353	log10_qual_likelihood_position_model=3.5162	log10_strand_likelihood_position_model=1.31738	new_cov=5/0	polymorphism_quality=9.5	quality=9.5	quality_position_model=4.98176e-12	ref_cov=172/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=177/147
RA	406	.	NC_007779	3160153	0	G	C	bias_e_value=3.90393	bias_p_value=8.40219e-07	fisher_strand_p_value=4.70492e-08	frequency=5.151463e-02	genotype_quality=596.6	ks_quality_p_value=0.999183	log10_base_likelihood=-9.20696	log10_qual_likelihood_position_model=12.442	log10_strand_likelihood_position_model=7.32745	new_cov=9/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=18/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/126
RA	407	.	NC_007779	3188903	0	A	.	bias_e_value=3459210	bias_p_value=0.744504	fisher_strand_p_value=1	frequency=1.002598e-02	genotype_quality=1216.6	ks_quality_p_value=0.37673	log10_base_likelihood=-8.06273	log10_qual_likelihood_position_model=2.77013	log10_strand_likelihood_position_model=0.40421	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.07015e-07	ref_cov=155/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/142
RA	408	.	NC_007779	3195962	0	G	T	bias_e_value=11.6079	bias_p_value=2.4983e-06	fisher_strand_p_value=1.49453e-07	frequency=7.251406e-02	genotype_quality=826.4	ks_quality_p_value=1	log10_base_likelihood=-10.5234	log10_qual_likelihood_position_model=20.1426	log10_strand_likelihood_position_model=7.02394	new_cov=0/31	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=110/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/177
RA	409	.	NC_007779	3223274	0	G	T	bias_e_value=0.173076	bias_p_value=3.725e-08	fisher_strand_p_value=1.7606e-09	frequency=6.461668e-02	genotype_quality=922.9	ks_quality_p_value=1	log10_base_likelihood=-13.6439	log10_qual_likelihood_position_model=17.8467	log10_strand_likelihood_position_model=9.05537	new_cov=0/28	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=145/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/145
RA	410	.	NC_007779	3231285	0	C	A	bias_e_value=44.148	bias_p_value=9.50169e-06	fisher_strand_p_value=6.21377e-07	frequency=3.392792e-02	genotype_quality=1084.7	ks_quality_p_value=1	log10_base_likelihood=-6.09717	log10_qual_likelihood_position_model=15.1861	log10_strand_likelihood_position_model=6.20664	new_cov=0/13	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=186/86	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=186/99
RA	411	.	NC_007779	3231297	0	C	G	bias_e_value=15.3352	bias_p_value=3.30051e-06	fisher_strand_p_value=2.06326e-07	frequency=3.474903e-02	genotype_quality=999.9	ks_quality_p_value=0.974214	log10_base_likelihood=-6.0157	log10_qual_likelihood_position_model=20.0024	log10_strand_likelihood_position_model=6.68545	new_cov=0/14	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=175/80	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/94
RA	412	.	NC_007779	3231302	0	C	G	bias_e_value=0.458907	bias_p_value=9.87676e-08	fisher_strand_p_value=5.11154e-09	frequency=5.158854e-02	genotype_quality=993.2	ks_quality_p_value=0.959748	log10_base_likelihood=-9.21846	log10_qual_likelihood_position_model=22.7129	log10_strand_likelihood_position_model=8.29145	new_cov=0/20	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=173/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/118
RA	413	.	NC_007779	3231832	1	.	G	bias_e_value=4618.39	bias_p_value=0.000993986	fisher_strand_p_value=0.00011904	frequency=3.529453e-02	genotype_quality=1220.2	ks_quality_p_value=0.815422	log10_base_likelihood=-42.9195	log10_qual_likelihood_position_model=3.2956	log10_strand_likelihood_position_model=3.92431	new_cov=9/0	polymorphism_quality=37.8	quality=37.8	quality_position_model=5.365e-38	ref_cov=87/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=96/159
RA	414	.	NC_007779	3238322	0	T	C	bias_e_value=17551.2	bias_p_value=0.00377744	fisher_strand_p_value=0.000431832	frequency=4.545784e-02	genotype_quality=512.3	ks_quality_p_value=1	log10_base_likelihood=-7.43648	log10_qual_likelihood_position_model=10.7465	log10_strand_likelihood_position_model=3.36469	new_cov=9/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=61/90	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=70/90
RA	415	.	NC_007779	3256890	1	.	A	bias_e_value=4624410	bias_p_value=0.995282	fisher_strand_p_value=1	frequency=7.017136e-03	genotype_quality=1433.9	ks_quality_p_value=0.90445	log10_base_likelihood=-8.11453	log10_qual_likelihood_position_model=1.20025	log10_strand_likelihood_position_model=0.305366	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.49924e-08	ref_cov=158/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/126
RA	416	.	NC_007779	3256891	0	A	.	bias_e_value=3113560	bias_p_value=0.670111	fisher_strand_p_value=0.328503	frequency=1.388168e-02	genotype_quality=1181.5	ks_quality_p_value=0.93602	log10_base_likelihood=-11.3923	log10_qual_likelihood_position_model=2.27481	log10_strand_likelihood_position_model=0.703425	new_cov=1/3	polymorphism_quality=6.0	quality=6.0	quality_position_model=2.09397e-10	ref_cov=158/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/129
RA	417	.	NC_007779	3266843	0	C	G	bias_e_value=0.0592554	bias_p_value=1.27531e-08	fisher_strand_p_value=5.76258e-10	frequency=6.112719e-02	genotype_quality=827.9	ks_quality_p_value=0.993256	log10_base_likelihood=-7.81921	log10_qual_likelihood_position_model=21.0938	log10_strand_likelihood_position_model=9.23938	new_cov=0/18	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=152/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/76
RA	418	.	NC_007779	3280326	0	A	C	bias_e_value=4.29831e-15	bias_p_value=9.25098e-22	fisher_strand_p_value=1.73206e-23	frequency=9.301949e-02	genotype_quality=836.9	ks_quality_p_value=1	log10_base_likelihood=-11.2963	log10_qual_likelihood_position_model=35.6003	log10_strand_likelihood_position_model=22.7614	new_cov=0/51	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=164/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=164/119
RA	419	.	NC_007779	3287872	1	.	G	bias_e_value=1848170	bias_p_value=0.39777	fisher_strand_p_value=0.202742	frequency=7.220268e-03	genotype_quality=1373.2	ks_quality_p_value=0.647368	log10_base_likelihood=-8.01696	log10_qual_likelihood_position_model=3.40627	log10_strand_likelihood_position_model=0.693057	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=9.38761e-06	ref_cov=123/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/152
RA	420	.	NC_007779	3300073	0	T	G	bias_e_value=2.25482e-06	bias_p_value=4.8529e-13	fisher_strand_p_value=1.47748e-14	frequency=1.007962e-01	genotype_quality=782.4	ks_quality_p_value=1	log10_base_likelihood=-14.5955	log10_qual_likelihood_position_model=45.0115	log10_strand_likelihood_position_model=13.9291	new_cov=48/0	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=106/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/123
RA	421	.	NC_007779	3305552	1	.	C	bias_e_value=1461430	bias_p_value=0.314535	fisher_strand_p_value=0.111167	frequency=1.041508e-02	genotype_quality=1370.7	ks_quality_p_value=0.839028	log10_base_likelihood=-10.4801	log10_qual_likelihood_position_model=3.79615	log10_strand_likelihood_position_model=0.954026	new_cov=0/3	polymorphism_quality=5.1	quality=5.1	quality_position_model=1.21331e-07	ref_cov=149/136	reject=POLYMORPHISM_STRAND	tot_cov=149/139
RA	422	.	NC_007779	3325139	0	G	T	bias_e_value=37.2208	bias_p_value=8.01079e-06	fisher_strand_p_value=5.17698e-07	frequency=4.203796e-02	genotype_quality=1169.0	ks_quality_p_value=1	log10_base_likelihood=-10.7652	log10_qual_likelihood_position_model=18.0446	log10_strand_likelihood_position_model=6.534	new_cov=0/25	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=155/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/201
RA	423	.	NC_007779	3333429	1	.	A	bias_e_value=1490830	bias_p_value=0.320862	fisher_strand_p_value=0.184466	frequency=6.472588e-03	genotype_quality=1539.7	ks_quality_p_value=0.520178	log10_base_likelihood=-8.23381	log10_qual_likelihood_position_model=1.21359	log10_strand_likelihood_position_model=0.734084	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=3.22763e-08	ref_cov=131/176	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/176
RA	424	.	NC_007779	3333612	0	T	G	bias_e_value=0.000153013	bias_p_value=3.29319e-11	fisher_strand_p_value=1.15607e-12	frequency=4.772091e-02	genotype_quality=735.2	ks_quality_p_value=1	log10_base_likelihood=-10.6597	log10_qual_likelihood_position_model=18.1154	log10_strand_likelihood_position_model=11.937	new_cov=13/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=16/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=29/165
RA	425	.	NC_007779	3334554	0	G	C	bias_e_value=36769.9	bias_p_value=0.00791376	fisher_strand_p_value=0.00100097	frequency=1.526356e-02	genotype_quality=1459.7	ks_quality_p_value=0.999903	log10_base_likelihood=-8.83609	log10_qual_likelihood_position_model=7.54193	log10_strand_likelihood_position_model=2.99958	new_cov=6/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=108/241	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=114/241
RA	426	.	NC_007779	3357279	0	C	A	bias_e_value=3.39713	bias_p_value=7.31143e-07	fisher_strand_p_value=5.67198e-08	frequency=3.019047e-02	genotype_quality=975.4	ks_quality_p_value=0.715335	log10_base_likelihood=-7.08118	log10_qual_likelihood_position_model=26.5755	log10_strand_likelihood_position_model=7.24627	new_cov=21/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=126/166	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/166
RA	427	.	NC_007779	3392267	0	C	A	bias_e_value=0.0182734	bias_p_value=3.93286e-09	fisher_strand_p_value=1.67275e-10	frequency=4.618263e-02	genotype_quality=1201.0	ks_quality_p_value=1	log10_base_likelihood=-10.9791	log10_qual_likelihood_position_model=21.191	log10_strand_likelihood_position_model=9.77657	new_cov=27/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=133/191	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/191
RA	428	.	NC_007779	3397405	0	A	C	bias_e_value=5.51332e-13	bias_p_value=1.1866e-19	fisher_strand_p_value=2.44867e-21	frequency=6.359243e-02	genotype_quality=886.5	ks_quality_p_value=1	log10_base_likelihood=-6.78147	log10_qual_likelihood_position_model=35.6485	log10_strand_likelihood_position_model=20.6111	new_cov=0/46	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=172/73	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=172/119
RA	429	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1364.3	new_cov=151/162	quality=1364.3	ref_cov=0/0	tot_cov=151/162
RA	430	.	NC_007779	3407746	0	C	A	bias_e_value=641.466	bias_p_value=0.000138059	fisher_strand_p_value=1.11284e-05	frequency=3.747940e-02	genotype_quality=1039.8	ks_quality_p_value=1	log10_base_likelihood=-6.4277	log10_qual_likelihood_position_model=18.7065	log10_strand_likelihood_position_model=5.07136	new_cov=17/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=142/149	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/149
RA	431	.	NC_007779	3414615	0	C	A	bias_e_value=0.0601144	bias_p_value=1.2938e-08	fisher_strand_p_value=5.81494e-10	frequency=7.116747e-02	genotype_quality=970.1	ks_quality_p_value=0.999258	log10_base_likelihood=-15.6541	log10_qual_likelihood_position_model=19.8399	log10_strand_likelihood_position_model=9.34897	new_cov=32/0	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=134/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/144
RA	432	.	NC_007779	3421203	0	T	C	bias_e_value=0.00114132	bias_p_value=2.45639e-10	fisher_strand_p_value=9.3043e-12	frequency=4.949999e-02	genotype_quality=830.7	ks_quality_p_value=1	log10_base_likelihood=-6.21627	log10_qual_likelihood_position_model=18.6917	log10_strand_likelihood_position_model=11.0313	new_cov=0/22	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=172/68	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/90
RA	433	.	NC_007779	3423128	1	.	G	bias_e_value=3846380	bias_p_value=0.827831	fisher_strand_p_value=0.49878	frequency=8.333206e-03	genotype_quality=877.7	ks_quality_p_value=0.950231	log10_base_likelihood=-8.03448	log10_qual_likelihood_position_model=2.24274	log10_strand_likelihood_position_model=0.568277	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.06608e-07	ref_cov=123/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/115
RA	434	.	NC_007779	3431259	0	T	G	bias_e_value=64261.4	bias_p_value=0.0138306	fisher_strand_p_value=0.00190405	frequency=3.141403e-02	genotype_quality=982.8	ks_quality_p_value=1	log10_base_likelihood=-9.92877	log10_qual_likelihood_position_model=15.2682	log10_strand_likelihood_position_model=2.78794	new_cov=0/12	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=105/142	reject=POLYMORPHISM_STRAND	tot_cov=105/154
RA	435	.	NC_007779	3436272	0	T	A	bias_e_value=4113920	bias_p_value=0.885412	fisher_strand_p_value=0.612451	frequency=9.137154e-03	genotype_quality=1277.1	ks_quality_p_value=0.916372	log10_base_likelihood=-5.60724	log10_qual_likelihood_position_model=3.40211	log10_strand_likelihood_position_model=0.438825	new_cov=2/1	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.00189065	ref_cov=154/165	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=156/166
RA	436	.	NC_007779	3439587	0	A	C	bias_e_value=14934.3	bias_p_value=0.00321421	fisher_strand_p_value=0.000359952	frequency=3.793240e-02	genotype_quality=818.6	ks_quality_p_value=1	log10_base_likelihood=-7.71035	log10_qual_likelihood_position_model=13.2129	log10_strand_likelihood_position_model=3.69855	new_cov=12/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=101/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/111
RA	437	.	NC_007779	3439592	0	G	.	bias_e_value=1059710	bias_p_value=0.228075	fisher_strand_p_value=0.0597409	frequency=2.176762e-02	genotype_quality=893.6	ks_quality_p_value=1	log10_base_likelihood=-10.7717	log10_qual_likelihood_position_model=7.70806	log10_strand_likelihood_position_model=1.51504	new_cov=5/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=0.00330179	ref_cov=108/112	reject=POLYMORPHISM_STRAND	tot_cov=117/112
RA	438	.	NC_007779	3439598	1	.	T	bias_e_value=1920040	bias_p_value=0.413238	fisher_strand_p_value=0.139469	frequency=2.083302e-02	genotype_quality=925.1	ks_quality_p_value=0.99646	log10_base_likelihood=-15.9027	log10_qual_likelihood_position_model=6.18304	log10_strand_likelihood_position_model=0.961984	new_cov=4/0	polymorphism_quality=10.6	quality=10.6	quality_position_model=9.31229e-11	ref_cov=107/81	reject=POLYMORPHISM_STRAND	tot_cov=111/81
RA	439	.	NC_007779	3439601	0	G	T	bias_e_value=161088	bias_p_value=0.0346698	fisher_strand_p_value=0.00560654	frequency=4.708767e-02	genotype_quality=770.3	ks_quality_p_value=1	log10_base_likelihood=-12.4749	log10_qual_likelihood_position_model=12.2608	log10_strand_likelihood_position_model=2.46185	new_cov=10/0	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=106/85	reject=POLYMORPHISM_STRAND	tot_cov=116/85
RA	440	.	NC_007779	3439607	0	G	T	bias_e_value=851115	bias_p_value=0.18318	fisher_strand_p_value=0.0445592	frequency=2.625275e-02	genotype_quality=892.6	ks_quality_p_value=1	log10_base_likelihood=-6.88276	log10_qual_likelihood_position_model=9.28077	log10_strand_likelihood_position_model=1.53022	new_cov=7/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=129/87	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=136/87
RA	441	.	NC_007779	3440270	0	C	A	bias_e_value=0.0177614	bias_p_value=3.82268e-09	fisher_strand_p_value=1.62383e-10	frequency=6.905699e-02	genotype_quality=898.2	ks_quality_p_value=1	log10_base_likelihood=-11.3954	log10_qual_likelihood_position_model=21.1264	log10_strand_likelihood_position_model=9.83006	new_cov=34/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=131/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/140
RA	442	.	NC_007779	3441442	0	C	A	bias_e_value=3.92406	bias_p_value=8.44549e-07	fisher_strand_p_value=4.72675e-08	frequency=4.643536e-02	genotype_quality=1000.9	ks_quality_p_value=1	log10_base_likelihood=-13.0806	log10_qual_likelihood_position_model=19.3332	log10_strand_likelihood_position_model=7.5317	new_cov=24/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=134/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/155
RA	443	.	NC_007779	3449822	0	G	T	bias_e_value=1730050	bias_p_value=0.372348	fisher_strand_p_value=0.121151	frequency=1.753902e-02	genotype_quality=1461.3	ks_quality_p_value=0.982404	log10_base_likelihood=-14.2828	log10_qual_likelihood_position_model=3.10307	log10_strand_likelihood_position_model=1.0397	new_cov=1/5	polymorphism_quality=8.9	quality=8.9	quality_position_model=3.5992e-12	ref_cov=170/165	reject=POLYMORPHISM_STRAND	tot_cov=171/170
RA	444	.	NC_007779	3449851	0	G	A	bias_e_value=3499210	bias_p_value=0.753112	fisher_strand_p_value=0.389599	frequency=1.361036e-01	genotype_quality=876.6	ks_quality_p_value=0.989879	log10_base_likelihood=-99.833	log10_qual_likelihood_position_model=14.3488	log10_strand_likelihood_position_model=1.02317	new_cov=16/22	polymorphism_quality=94.9	quality=94.9	quality_position_model=6.06166e-87	ref_cov=120/121	tot_cov=136/143
RA	445	.	NC_007779	3450056	0	C	A	bias_e_value=4546120	bias_p_value=0.978431	fisher_strand_p_value=0.899642	frequency=2.230201e-01	genotype_quality=1074.5	ks_quality_p_value=0.888826	log10_base_likelihood=-252.055	log10_qual_likelihood_position_model=13.4672	log10_strand_likelihood_position_model=1.00828	new_cov=42/39	polymorphism_quality=247.3	quality=247.3	quality_position_model=2.75598e-240	ref_cov=150/132	tot_cov=192/171
RA	446	.	NC_007779	3451634	0	T	A	bias_e_value=1112740	bias_p_value=0.239487	fisher_strand_p_value=1	frequency=9.391785e-03	genotype_quality=1276.4	ks_quality_p_value=0.0638398	log10_base_likelihood=-7.4024	log10_qual_likelihood_position_model=2.49957	log10_strand_likelihood_position_model=0.423242	new_cov=1/2	polymorphism_quality=1.9	quality=1.9	quality_position_model=2.42067e-06	ref_cov=158/158	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=159/160
RA	447	.	NC_007779	3475527	0	T	G	bias_e_value=8.94634e-09	bias_p_value=1.92546e-15	fisher_strand_p_value=4.99663e-17	frequency=8.936977e-02	genotype_quality=917.2	ks_quality_p_value=1	log10_base_likelihood=-16.9619	log10_qual_likelihood_position_model=37.4765	log10_strand_likelihood_position_model=16.3013	new_cov=44/0	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=98/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/161
RA	448	.	NC_007779	3475533	0	C	T	bias_e_value=0.00520455	bias_p_value=1.12014e-09	fisher_strand_p_value=4.51278e-11	frequency=8.417416e-02	genotype_quality=991.1	ks_quality_p_value=1	log10_base_likelihood=-21.4653	log10_qual_likelihood_position_model=39.6486	log10_strand_likelihood_position_model=10.3456	new_cov=30/0	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=121/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=151/165
RA	449	.	NC_007779	3478395	1	.	T	bias_e_value=1323670	bias_p_value=0.284884	fisher_strand_p_value=0.623085	frequency=1.273918e-02	genotype_quality=1510.9	ks_quality_p_value=0.130194	log10_base_likelihood=-17.421	log10_qual_likelihood_position_model=2.74424	log10_strand_likelihood_position_model=0.580295	new_cov=3/1	polymorphism_quality=12.1	quality=12.1	quality_position_model=3.39337e-16	ref_cov=158/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=161/153
RA	450	.	NC_007779	3499066	0	A	C	bias_e_value=7.9126e-07	bias_p_value=1.70298e-13	fisher_strand_p_value=5.01977e-15	frequency=9.285927e-02	genotype_quality=800.8	ks_quality_p_value=1	log10_base_likelihood=-16.5262	log10_qual_likelihood_position_model=32.876	log10_strand_likelihood_position_model=14.2993	new_cov=0/27	polymorphism_quality=11.2	quality=11.2	quality_position_model=Inf	ref_cov=156/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/79
RA	451	.	NC_007779	3519465	1	.	A	bias_e_value=1981430	bias_p_value=0.426451	fisher_strand_p_value=0.501673	frequency=5.865097e-03	genotype_quality=1718.3	ks_quality_p_value=0.290535	log10_base_likelihood=-8.12495	log10_qual_likelihood_position_model=2.18571	log10_strand_likelihood_position_model=0.536964	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.65194e-07	ref_cov=182/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=184/157
RA	452	.	NC_007779	3523734	0	G	T	bias_e_value=3.92914e-05	bias_p_value=8.45643e-12	fisher_strand_p_value=2.82883e-13	frequency=7.482672e-02	genotype_quality=1030.9	ks_quality_p_value=1	log10_base_likelihood=-15.7872	log10_qual_likelihood_position_model=33.6412	log10_strand_likelihood_position_model=12.568	new_cov=0/40	polymorphism_quality=10.4	quality=10.4	quality_position_model=Inf	ref_cov=158/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/171
RA	453	.	NC_007779	3526752	1	.	T	bias_e_value=3168970	bias_p_value=0.682037	fisher_strand_p_value=0.498833	frequency=7.352829e-03	genotype_quality=1368.6	ks_quality_p_value=0.636969	log10_base_likelihood=-8.28133	log10_qual_likelihood_position_model=0.904696	log10_strand_likelihood_position_model=0.572191	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=9.42682e-09	ref_cov=139/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/131
RA	454	.	NC_007779	3540340	0	T	G	bias_e_value=843885	bias_p_value=0.181624	fisher_strand_p_value=0.503591	frequency=5.908012e-03	genotype_quality=1337.1	ks_quality_p_value=0.0874914	log10_base_likelihood=-5.94029	log10_qual_likelihood_position_model=1.6169	log10_strand_likelihood_position_model=0.519862	new_cov=0/2	polymorphism_quality=0.4	quality=0.4	quality_position_model=1.23739e-05	ref_cov=152/184	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=153/186
RA	455	.	NC_007779	3543547	0	A	C	bias_e_value=3.73914e-13	bias_p_value=8.04751e-20	fisher_strand_p_value=1.64722e-21	frequency=1.779099e-01	genotype_quality=766.6	ks_quality_p_value=1	log10_base_likelihood=-37.1148	log10_qual_likelihood_position_model=54.4531	log10_strand_likelihood_position_model=20.9021	new_cov=0/67	polymorphism_quality=32.0	quality=32.0	quality_position_model=Inf	ref_cov=129/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/159
RA	456	.	NC_007779	3545388	0	T	G	bias_e_value=1.50816e-05	bias_p_value=3.24591e-12	fisher_strand_p_value=1.051e-13	frequency=4.655647e-02	genotype_quality=961.9	ks_quality_p_value=1	log10_base_likelihood=-5.77444	log10_qual_likelihood_position_model=28.8815	log10_strand_likelihood_position_model=12.9784	new_cov=37/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=116/167	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/167
RA	457	.	NC_007779	3576400	1	.	A	bias_e_value=4594500	bias_p_value=0.988845	fisher_strand_p_value=1	frequency=1.212120e-02	genotype_quality=1624.0	ks_quality_p_value=0.854403	log10_base_likelihood=-17.1317	log10_qual_likelihood_position_model=2.02694	log10_strand_likelihood_position_model=0.423357	new_cov=2/2	polymorphism_quality=11.8	quality=11.8	quality_position_model=8.65195e-17	ref_cov=162/164	reject=INDEL_HOMOPOLYMER	tot_cov=164/166
RA	458	.	NC_007779	3576401	0	A	.	bias_e_value=4609770	bias_p_value=0.99213	fisher_strand_p_value=1	frequency=1.182175e-02	genotype_quality=1373.0	ks_quality_p_value=0.877193	log10_base_likelihood=-10.3322	log10_qual_likelihood_position_model=4.08328	log10_strand_likelihood_position_model=0.423663	new_cov=2/2	polymorphism_quality=4.9	quality=4.9	quality_position_model=9.66687e-08	ref_cov=164/170	reject=INDEL_HOMOPOLYMER	tot_cov=166/172
RA	459	.	NC_007779	3580297	0	G	T	bias_e_value=0.894141	bias_p_value=1.9244e-07	fisher_strand_p_value=9.90412e-09	frequency=5.034351e-02	genotype_quality=1234.4	ks_quality_p_value=1	log10_base_likelihood=-12.883	log10_qual_likelihood_position_model=18.6612	log10_strand_likelihood_position_model=8.03879	new_cov=0/27	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=179/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/195
RA	460	.	NC_007779	3592154	0	A	C	bias_e_value=1260790	bias_p_value=0.271351	fisher_strand_p_value=0.239047	frequency=6.824493e-03	genotype_quality=1184.7	ks_quality_p_value=0.317114	log10_base_likelihood=-5.80148	log10_qual_likelihood_position_model=2.02566	log10_strand_likelihood_position_model=0.621516	new_cov=2/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=6.00368e-05	ref_cov=142/150	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=144/151
RA	461	.	NC_007779	3609441	0	T	G	bias_e_value=1.99623e-11	bias_p_value=4.29636e-18	fisher_strand_p_value=9.59206e-20	frequency=6.505060e-02	genotype_quality=936.3	ks_quality_p_value=1	log10_base_likelihood=-7.9794	log10_qual_likelihood_position_model=34.1965	log10_strand_likelihood_position_model=19.0181	new_cov=43/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=78/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/175
RA	462	.	NC_007779	3620038	0	G	T	bias_e_value=0.262629	bias_p_value=5.65239e-08	fisher_strand_p_value=2.72803e-09	frequency=4.310226e-02	genotype_quality=997.2	ks_quality_p_value=1	log10_base_likelihood=-5.6251	log10_qual_likelihood_position_model=21.0055	log10_strand_likelihood_position_model=8.56415	new_cov=0/23	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=172/115	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/140
RA	463	.	NC_007779	3627545	0	T	.	bias_e_value=4134240	bias_p_value=0.889787	fisher_strand_p_value=1	frequency=9.029388e-03	genotype_quality=1317.0	ks_quality_p_value=0.568897	log10_base_likelihood=-8.04059	log10_qual_likelihood_position_model=1.65997	log10_strand_likelihood_position_model=0.396445	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=6.62041e-08	ref_cov=176/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=178/154
RA	464	.	NC_007779	3651641	0	G	C	bias_e_value=12062.3	bias_p_value=0.0025961	fisher_strand_p_value=0.000283119	frequency=2.656364e-02	genotype_quality=1396.0	ks_quality_p_value=1	log10_base_likelihood=-10.7623	log10_qual_likelihood_position_model=14.9281	log10_strand_likelihood_position_model=3.54803	new_cov=11/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=152/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/174
RA	465	.	NC_007779	3653996	1	.	G	bias_e_value=4641900	bias_p_value=0.999046	fisher_strand_p_value=1	frequency=1.286125e-02	genotype_quality=1528.9	ks_quality_p_value=0.956643	log10_base_likelihood=-17.2989	log10_qual_likelihood_position_model=3.98276	log10_strand_likelihood_position_model=0.438797	new_cov=3/1	polymorphism_quality=12.0	quality=12.0	quality_position_model=5.87223e-15	ref_cov=190/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=193/118
RA	466	.	NC_007779	3659516	0	C	A	bias_e_value=0.192335	bias_p_value=4.13951e-08	fisher_strand_p_value=1.96681e-09	frequency=4.941130e-02	genotype_quality=1183.9	ks_quality_p_value=1	log10_base_likelihood=-15.6537	log10_qual_likelihood_position_model=19.2426	log10_strand_likelihood_position_model=8.70624	new_cov=23/0	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=127/193	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/193
RA	467	.	NC_007779	3665059	0	C	A	bias_e_value=0.441264	bias_p_value=9.49704e-08	fisher_strand_p_value=4.70754e-09	frequency=4.402161e-02	genotype_quality=1097.0	ks_quality_p_value=1	log10_base_likelihood=-8.53381	log10_qual_likelihood_position_model=20.1854	log10_strand_likelihood_position_model=8.32721	new_cov=25/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=139/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/175
RA	468	.	NC_007779	3677212	0	C	G	bias_e_value=0.0113387	bias_p_value=2.44035e-09	fisher_strand_p_value=1.01641e-10	frequency=5.383015e-02	genotype_quality=769.3	ks_quality_p_value=1	log10_base_likelihood=-12.7762	log10_qual_likelihood_position_model=15.9538	log10_strand_likelihood_position_model=9.99293	new_cov=0/12	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=164/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/34
RA	469	.	NC_007779	3686205	0	A	.	bias_e_value=4148820	bias_p_value=0.892924	fisher_strand_p_value=0.687681	frequency=1.947212e-02	genotype_quality=1233.1	ks_quality_p_value=0.835428	log10_base_likelihood=-17.6871	log10_qual_likelihood_position_model=3.95718	log10_strand_likelihood_position_model=0.581556	new_cov=4/2	polymorphism_quality=12.4	quality=12.4	quality_position_model=3.11465e-15	ref_cov=159/143	reject=INDEL_HOMOPOLYMER	tot_cov=163/145
RA	470	.	NC_007779	3688850	0	A	C	bias_e_value=0.000488701	bias_p_value=1.0518e-10	fisher_strand_p_value=3.85535e-12	frequency=8.963585e-02	genotype_quality=705.3	ks_quality_p_value=1	log10_base_likelihood=-6.86244	log10_qual_likelihood_position_model=23.1551	log10_strand_likelihood_position_model=11.4139	new_cov=0/30	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=126/75	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/106
RA	471	.	NC_007779	3688858	0	A	C	bias_e_value=1.99572e-09	bias_p_value=4.29527e-16	fisher_strand_p_value=1.07182e-17	frequency=1.107140e-01	genotype_quality=677.2	ks_quality_p_value=1	log10_base_likelihood=-14.7546	log10_qual_likelihood_position_model=30.5997	log10_strand_likelihood_position_model=16.9699	new_cov=0/45	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=124/68	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/115
RA	472	.	NC_007779	3701118	0	G	T	bias_e_value=5.46299	bias_p_value=1.17576e-06	fisher_strand_p_value=6.71223e-08	frequency=4.086018e-02	genotype_quality=1035.5	ks_quality_p_value=1	log10_base_likelihood=-7.06639	log10_qual_likelihood_position_model=21.805	log10_strand_likelihood_position_model=7.18501	new_cov=1/21	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=176/108	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=177/129
RA	473	.	NC_007779	3711109	0	C	A	bias_e_value=0.0207113	bias_p_value=4.45755e-09	fisher_strand_p_value=1.90652e-10	frequency=7.204056e-02	genotype_quality=969.7	ks_quality_p_value=1	log10_base_likelihood=-11.8949	log10_qual_likelihood_position_model=24.172	log10_strand_likelihood_position_model=9.7555	new_cov=34/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=140/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/147
RA	474	.	NC_007779	3726951	0	C	A	bias_e_value=353641	bias_p_value=0.0761118	fisher_strand_p_value=0.0145531	frequency=1.841640e-02	genotype_quality=1266.4	ks_quality_p_value=1	log10_base_likelihood=-7.18773	log10_qual_likelihood_position_model=5.27849	log10_strand_likelihood_position_model=1.83705	new_cov=0/6	polymorphism_quality=1.7	quality=1.7	quality_position_model=0.360713	ref_cov=151/144	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=151/150
RA	475	.	NC_007779	3727557	0	A	G	bias_e_value=0.000207559	bias_p_value=4.46715e-11	fisher_strand_p_value=1.58579e-12	frequency=4.785872e-02	genotype_quality=830.9	ks_quality_p_value=1	log10_base_likelihood=-6.26469	log10_qual_likelihood_position_model=19.1667	log10_strand_likelihood_position_model=11.7998	new_cov=18/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=45/191	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=63/191
RA	476	.	NC_007779	3728146	1	.	T	bias_e_value=499737	bias_p_value=0.107555	fisher_strand_p_value=0.0224312	frequency=1.530552e-02	genotype_quality=958.8	ks_quality_p_value=0.999366	log10_base_likelihood=-12.3451	log10_qual_likelihood_position_model=3.91585	log10_strand_likelihood_position_model=1.64915	new_cov=3/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=9.98714e-09	ref_cov=53/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=56/140
RA	477	.	NC_007779	3728155	0	T	C	bias_e_value=10.7356	bias_p_value=2.31056e-06	fisher_strand_p_value=1.37851e-07	frequency=4.525661e-02	genotype_quality=599.2	ks_quality_p_value=0.997734	log10_base_likelihood=-11.4697	log10_qual_likelihood_position_model=8.94308	log10_strand_likelihood_position_model=6.86059	new_cov=8/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=19/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=27/145
RA	478	.	NC_007779	3728157	0	A	C	bias_e_value=21.4636	bias_p_value=4.61946e-06	fisher_strand_p_value=2.87608e-07	frequency=3.211308e-02	genotype_quality=563.9	ks_quality_p_value=1	log10_base_likelihood=-8.05206	log10_qual_likelihood_position_model=9.75227	log10_strand_likelihood_position_model=6.5412	new_cov=8/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=22/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=30/147
RA	479	.	NC_007779	3731042	0	T	.	bias_e_value=3712680	bias_p_value=0.799057	fisher_strand_p_value=0.676011	frequency=1.581573e-02	genotype_quality=1224.5	ks_quality_p_value=0.646973	log10_base_likelihood=-14.6412	log10_qual_likelihood_position_model=2.41787	log10_strand_likelihood_position_model=0.517498	new_cov=3/2	polymorphism_quality=9.3	quality=9.3	quality_position_model=9.1276e-14	ref_cov=149/160	reject=INDEL_HOMOPOLYMER	tot_cov=153/163
RA	480	.	NC_007779	3732310	0	G	T	bias_e_value=0.000566736	bias_p_value=1.21975e-10	fisher_strand_p_value=4.49631e-12	frequency=8.026600e-02	genotype_quality=1100.2	ks_quality_p_value=1	log10_base_likelihood=-20.4992	log10_qual_likelihood_position_model=25.244	log10_strand_likelihood_position_model=11.3553	new_cov=1/36	polymorphism_quality=15.2	quality=15.2	quality_position_model=Inf	ref_cov=178/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/161
RA	481	.	NC_007779	3750122	0	C	.	bias_e_value=188857	bias_p_value=0.0406464	fisher_strand_p_value=0.311669	frequency=9.748602e-01	genotype_quality=1751.8	ks_quality_p_value=0.0217593	log10_base_likelihood=-41.4953	log10_qual_likelihood_position_model=6.91447	log10_strand_likelihood_position_model=0.901778	new_cov=159/190	polymorphism_quality=36.4	quality=36.4	quality_position_model=5.7891e-36	ref_cov=6/3	tot_cov=165/193
RA	482	.	NC_007779	3750123	0	C	T	bias_e_value=3114260	bias_p_value=0.670261	fisher_strand_p_value=0.312102	frequency=2.501774e-02	genotype_quality=1452.5	ks_quality_p_value=0.985616	log10_base_likelihood=-17.5471	log10_qual_likelihood_position_model=6.25227	log10_strand_likelihood_position_model=0.897524	new_cov=6/3	polymorphism_quality=12.2	quality=12.2	quality_position_model=1.96651e-12	ref_cov=159/189	tot_cov=165/193
RA	483	.	NC_007779	3758414	0	G	T	bias_e_value=4.88468	bias_p_value=1.0513e-06	fisher_strand_p_value=5.9613e-08	frequency=4.175091e-02	genotype_quality=1078.3	ks_quality_p_value=1	log10_base_likelihood=-8.0743	log10_qual_likelihood_position_model=21.9026	log10_strand_likelihood_position_model=7.24002	new_cov=0/25	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=160/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/181
RA	484	.	NC_007779	3772840	0	A	.	bias_e_value=4610820	bias_p_value=0.992358	fisher_strand_p_value=1	frequency=9.309769e-03	genotype_quality=1317.6	ks_quality_p_value=0.878945	log10_base_likelihood=-8.11664	log10_qual_likelihood_position_model=1.1325	log10_strand_likelihood_position_model=0.383781	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.52998e-08	ref_cov=142/177	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/179
RA	485	.	NC_007779	3788380	0	G	T	bias_e_value=0.00377431	bias_p_value=8.12321e-10	fisher_strand_p_value=3.22911e-11	frequency=9.515572e-02	genotype_quality=1006.7	ks_quality_p_value=1	log10_base_likelihood=-26.9495	log10_qual_likelihood_position_model=22.9138	log10_strand_likelihood_position_model=10.7278	new_cov=0/41	polymorphism_quality=21.7	quality=21.7	quality_position_model=Inf	ref_cov=140/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/190
RA	486	.	NC_007779	3813810	0	T	G	bias_e_value=7.16042e-16	bias_p_value=1.54109e-22	fisher_strand_p_value=2.79001e-24	frequency=1.047783e-01	genotype_quality=785.1	ks_quality_p_value=1	log10_base_likelihood=-13.3277	log10_qual_likelihood_position_model=36.3441	log10_strand_likelihood_position_model=23.5544	new_cov=47/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=50/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=97/157
RA	487	.	NC_007779	3824606	1	.	T	bias_e_value=3766790	bias_p_value=0.810701	fisher_strand_p_value=1	frequency=9.614944e-03	genotype_quality=1522.8	ks_quality_p_value=0.451723	log10_base_likelihood=-12.796	log10_qual_likelihood_position_model=1.88264	log10_strand_likelihood_position_model=0.403862	new_cov=1/2	polymorphism_quality=7.4	quality=7.4	quality_position_model=1.51099e-12	ref_cov=147/162	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/164
RA	488	.	NC_007779	3841756	0	A	.	bias_e_value=3529320	bias_p_value=0.759593	fisher_strand_p_value=1	frequency=1.110458e-02	genotype_quality=1107.6	ks_quality_p_value=0.392521	log10_base_likelihood=-8.37624	log10_qual_likelihood_position_model=1.99731	log10_strand_likelihood_position_model=0.395489	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=6.63205e-08	ref_cov=143/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/125
RA	489	.	NC_007779	3855276	1	.	T	bias_e_value=3483080	bias_p_value=0.749642	fisher_strand_p_value=0.652048	frequency=1.351357e-02	genotype_quality=1456.6	ks_quality_p_value=0.585894	log10_base_likelihood=-17.56	log10_qual_likelihood_position_model=1.70205	log10_strand_likelihood_position_model=0.459716	new_cov=2/2	polymorphism_quality=12.2	quality=12.2	quality_position_model=1.62259e-17	ref_cov=176/116	reject=INDEL_HOMOPOLYMER	tot_cov=178/118
RA	490	.	NC_007779	3859254	1	.	T	bias_e_value=358135	bias_p_value=0.077079	fisher_strand_p_value=0.0193212	frequency=1.520920e-02	genotype_quality=1291.1	ks_quality_p_value=0.765075	log10_base_likelihood=-17.7571	log10_qual_likelihood_position_model=1.5817	log10_strand_likelihood_position_model=1.71397	new_cov=4/0	polymorphism_quality=12.4	quality=12.4	quality_position_model=1.44632e-16	ref_cov=95/164	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/164
RA	491	.	NC_007779	3859258	1	.	T	bias_e_value=551817	bias_p_value=0.118764	fisher_strand_p_value=0.0261779	frequency=1.712513e-02	genotype_quality=1092.8	ks_quality_p_value=0.971009	log10_base_likelihood=-10.8335	log10_qual_likelihood_position_model=4.39286	log10_strand_likelihood_position_model=1.58207	new_cov=3/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=9.74239e-07	ref_cov=66/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=70/161
RA	492	.	NC_007779	3859258	2	.	C	bias_e_value=1279410	bias_p_value=0.275358	fisher_strand_p_value=0.089083	frequency=1.291180e-02	genotype_quality=1100.7	ks_quality_p_value=0.868457	log10_base_likelihood=-9.08493	log10_qual_likelihood_position_model=2.97338	log10_strand_likelihood_position_model=1.05021	new_cov=2/0	polymorphism_quality=3.6	quality=3.6	quality_position_model=5.99317e-07	ref_cov=67/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=70/161
RA	493	.	NC_007779	3859258	3	.	C	bias_e_value=1180800	bias_p_value=0.254135	fisher_strand_p_value=0.0909091	frequency=8.658409e-03	genotype_quality=1109.9	ks_quality_p_value=0.761689	log10_base_likelihood=-8.71309	log10_qual_likelihood_position_model=2.54925	log10_strand_likelihood_position_model=1.04139	new_cov=2/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=5.17771e-07	ref_cov=68/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=70/161
RA	494	.	NC_007779	3859263	0	T	C	bias_e_value=7.07508e-07	bias_p_value=1.52272e-13	fisher_strand_p_value=4.47325e-15	frequency=8.977556e-02	genotype_quality=698.9	ks_quality_p_value=1	log10_base_likelihood=-34.1934	log10_qual_likelihood_position_model=19.5265	log10_strand_likelihood_position_model=14.3494	new_cov=22/0	polymorphism_quality=29.0	quality=29.0	quality_position_model=0.111598	ref_cov=38/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=60/171
RA	495	.	NC_007779	3859265	0	A	C	bias_e_value=0.000455997	bias_p_value=9.81413e-11	fisher_strand_p_value=3.58789e-12	frequency=6.921005e-02	genotype_quality=628.2	ks_quality_p_value=1	log10_base_likelihood=-18.6864	log10_qual_likelihood_position_model=14.5832	log10_strand_likelihood_position_model=11.4541	new_cov=21/2	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=38/167	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=59/170
RA	496	.	NC_007779	3859270	0	G	C	bias_e_value=0.00529824	bias_p_value=1.1403e-09	fisher_strand_p_value=4.59746e-11	frequency=6.244564e-02	genotype_quality=880.4	ks_quality_p_value=1	log10_base_likelihood=-25.9957	log10_qual_likelihood_position_model=15.02	log10_strand_likelihood_position_model=10.3375	new_cov=15/0	polymorphism_quality=20.8	quality=20.8	quality_position_model=0.039277	ref_cov=37/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=52/174
RA	497	.	NC_007779	3859271	0	G	C	bias_e_value=4210.39	bias_p_value=0.000906175	fisher_strand_p_value=8.76163e-05	frequency=2.460766e-02	genotype_quality=906.6	ks_quality_p_value=1	log10_base_likelihood=-10.1944	log10_qual_likelihood_position_model=7.00576	log10_strand_likelihood_position_model=4.05742	new_cov=6/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=43/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/174
RA	498	.	NC_007779	3859275	0	T	C	bias_e_value=20.0351	bias_p_value=4.31204e-06	fisher_strand_p_value=2.67246e-07	frequency=2.993202e-02	genotype_quality=829.0	ks_quality_p_value=1	log10_base_likelihood=-7.32993	log10_qual_likelihood_position_model=11.9486	log10_strand_likelihood_position_model=6.57309	new_cov=10/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=44/175	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=54/175
RA	499	.	NC_007779	3859383	0	A	G	bias_e_value=1.94184	bias_p_value=4.17931e-07	fisher_strand_p_value=2.24552e-08	frequency=3.815556e-02	genotype_quality=577.2	ks_quality_p_value=1	log10_base_likelihood=-6.79571	log10_qual_likelihood_position_model=11.4061	log10_strand_likelihood_position_model=7.64868	new_cov=0/7	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=146/9	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/16
RA	500	.	NC_007779	3866109	0	G	T	bias_e_value=0.0221778	bias_p_value=4.77319e-09	fisher_strand_p_value=2.04778e-10	frequency=5.284548e-02	genotype_quality=959.1	ks_quality_p_value=1	log10_base_likelihood=-12.5056	log10_qual_likelihood_position_model=19.357	log10_strand_likelihood_position_model=9.98975	new_cov=0/31	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=169/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/169
RA	501	.	NC_007779	3868635	0	A	.	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=1.073456e-02	genotype_quality=1133.7	ks_quality_p_value=0.999922	log10_base_likelihood=-7.12164	log10_qual_likelihood_position_model=4.42871	log10_strand_likelihood_position_model=0.40673	new_cov=2/1	polymorphism_quality=1.6	quality=1.6	quality_position_model=0.000510846	ref_cov=143/132	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/133
RA	502	.	NC_007779	3891907	0	T	.	bias_e_value=1456270	bias_p_value=0.313424	fisher_strand_p_value=0.336727	frequency=1.350689e-02	genotype_quality=1175.4	ks_quality_p_value=0.275606	log10_base_likelihood=-11.6103	log10_qual_likelihood_position_model=2.08939	log10_strand_likelihood_position_model=0.679171	new_cov=1/3	polymorphism_quality=6.2	quality=6.2	quality_position_model=7.63862e-11	ref_cov=159/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/136
RA	503	.	NC_007779	3893880	0	G	T	bias_e_value=0.000428145	bias_p_value=9.21468e-11	fisher_strand_p_value=3.36071e-12	frequency=7.587099e-02	genotype_quality=945.9	ks_quality_p_value=1	log10_base_likelihood=-16.9122	log10_qual_likelihood_position_model=26.2526	log10_strand_likelihood_position_model=11.6395	new_cov=0/36	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=158/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/162
RA	504	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1439.3	new_cov=156/175	quality=1439.3	ref_cov=0/0	tot_cov=156/175
RA	505	.	NC_007779	3900680	0	T	G	bias_e_value=2.17757e-15	bias_p_value=4.68663e-22	fisher_strand_p_value=8.66242e-24	frequency=1.023335e-01	genotype_quality=788.6	ks_quality_p_value=1	log10_base_likelihood=-24.4752	log10_qual_likelihood_position_model=31.3098	log10_strand_likelihood_position_model=23.0624	new_cov=27/0	polymorphism_quality=19.2	quality=19.2	quality_position_model=Inf	ref_cov=16/177	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=43/177
RA	506	.	NC_007779	3900687	0	G	T	bias_e_value=0.199043	bias_p_value=4.28388e-08	fisher_strand_p_value=2.03889e-09	frequency=4.113960e-02	genotype_quality=943.2	ks_quality_p_value=1	log10_base_likelihood=-7.95062	log10_qual_likelihood_position_model=17.6094	log10_strand_likelihood_position_model=8.69061	new_cov=12/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=36/182	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=48/182
RA	507	.	NC_007779	3900690	1	.	C	bias_e_value=886382	bias_p_value=0.19077	fisher_strand_p_value=0.0509842	frequency=8.584023e-03	genotype_quality=1150.2	ks_quality_p_value=0.922256	log10_base_likelihood=-8.43188	log10_qual_likelihood_position_model=4.43181	log10_strand_likelihood_position_model=1.29256	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=0.000179779	ref_cov=51/180	reject=POLYMORPHISM_STRAND	tot_cov=53/180
RA	508	.	NC_007779	3910746	0	C	A	bias_e_value=0.00189896	bias_p_value=4.08701e-10	fisher_strand_p_value=1.58101e-11	frequency=8.737421e-02	genotype_quality=1008.7	ks_quality_p_value=0.999209	log10_base_likelihood=-23.0065	log10_qual_likelihood_position_model=31.9869	log10_strand_likelihood_position_model=10.8397	new_cov=41/0	polymorphism_quality=17.8	quality=17.8	quality_position_model=Inf	ref_cov=155/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=197/147
RA	509	.	NC_007779	3930443	0	T	G	bias_e_value=1.26234e-14	bias_p_value=2.71686e-21	fisher_strand_p_value=5.19356e-23	frequency=8.458757e-02	genotype_quality=744.6	ks_quality_p_value=1	log10_base_likelihood=-7.81124	log10_qual_likelihood_position_model=38.025	log10_strand_likelihood_position_model=22.2845	new_cov=45/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=50/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/152
RA	510	.	NC_007779	3933153	0	G	T	bias_e_value=4555.75	bias_p_value=0.000980504	fisher_strand_p_value=9.58954e-05	frequency=2.793694e-02	genotype_quality=1085.3	ks_quality_p_value=0.997025	log10_base_likelihood=-7.2514	log10_qual_likelihood_position_model=14.9916	log10_strand_likelihood_position_model=4.22223	new_cov=1/15	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=170/133	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/148
RA	511	.	NC_007779	3934876	0	C	T	bias_e_value=4252320	bias_p_value=0.9152	fisher_strand_p_value=0.628009	frequency=1.121426e-02	genotype_quality=1471.5	ks_quality_p_value=0.983326	log10_base_likelihood=-5.80056	log10_qual_likelihood_position_model=5.07093	log10_strand_likelihood_position_model=0.535521	new_cov=3/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.183379	ref_cov=187/160	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=191/161
RA	512	.	NC_007779	3952095	1	.	G	bias_e_value=285736	bias_p_value=0.0614972	fisher_strand_p_value=0.011547	frequency=1.639366e-02	genotype_quality=1209.1	ks_quality_p_value=0.96973	log10_base_likelihood=-17.2336	log10_qual_likelihood_position_model=2.49938	log10_strand_likelihood_position_model=1.93753	new_cov=4/0	polymorphism_quality=11.9	quality=11.9	quality_position_model=7.09222e-15	ref_cov=77/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=81/163
RA	513	.	NC_007779	3975445	1	.	A	bias_e_value=3472160	bias_p_value=0.74729	fisher_strand_p_value=1	frequency=1.144981e-02	genotype_quality=1299.1	ks_quality_p_value=0.379595	log10_base_likelihood=-12.9404	log10_qual_likelihood_position_model=1.68975	log10_strand_likelihood_position_model=0.421005	new_cov=2/1	polymorphism_quality=7.6	quality=7.6	quality_position_model=7.12591e-13	ref_cov=130/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/130
RA	514	.	NC_007779	3976303	1	.	A	bias_e_value=2418250	bias_p_value=0.520465	fisher_strand_p_value=0.1997	frequency=6.733894e-03	genotype_quality=1500.8	ks_quality_p_value=0.997082	log10_base_likelihood=-8.11005	log10_qual_likelihood_position_model=1.38968	log10_strand_likelihood_position_model=0.699623	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=6.06842e-08	ref_cov=164/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=164/133
RA	515	.	NC_007779	3985602	0	A	G	bias_e_value=4645900	bias_p_value=0.999907	fisher_strand_p_value=1	frequency=9.464264e-03	genotype_quality=1268.9	ks_quality_p_value=0.986358	log10_base_likelihood=-5.57273	log10_qual_likelihood_position_model=2.42376	log10_strand_likelihood_position_model=0.407655	new_cov=1/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.000165402	ref_cov=150/162	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=151/164
RA	516	.	NC_007779	4000535	1	.	A	bias_e_value=4213730	bias_p_value=0.906894	fisher_strand_p_value=1	frequency=6.711006e-03	genotype_quality=1491.6	ks_quality_p_value=0.600782	log10_base_likelihood=-8.22589	log10_qual_likelihood_position_model=1.33123	log10_strand_likelihood_position_model=0.307466	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.57858e-08	ref_cov=168/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=169/129
RA	517	.	NC_007779	4023064	1	.	G	bias_e_value=1423510	bias_p_value=0.306372	fisher_strand_p_value=0.0946573	frequency=1.321602e-02	genotype_quality=1133.8	ks_quality_p_value=0.949293	log10_base_likelihood=-12.6876	log10_qual_likelihood_position_model=1.76573	log10_strand_likelihood_position_model=1.02385	new_cov=3/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=6.35696e-12	ref_cov=101/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/123
RA	518	.	NC_007779	4023068	0	T	G	bias_e_value=0.440359	bias_p_value=9.47756e-08	fisher_strand_p_value=4.69738e-09	frequency=5.435324e-02	genotype_quality=611.3	ks_quality_p_value=1	log10_base_likelihood=-6.68756	log10_qual_likelihood_position_model=16.2491	log10_strand_likelihood_position_model=8.32814	new_cov=14/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=35/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/124
RA	519	.	NC_007779	4029633	0	T	G	bias_e_value=8.29209e-17	bias_p_value=1.78465e-23	fisher_strand_p_value=3.10748e-25	frequency=1.587443e-01	genotype_quality=714.5	ks_quality_p_value=1	log10_base_likelihood=-31.4551	log10_qual_likelihood_position_model=39.7713	log10_strand_likelihood_position_model=24.5076	new_cov=44/0	polymorphism_quality=26.3	quality=26.3	quality_position_model=Inf	ref_cov=35/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/145
RA	520	.	NC_007779	4031691	1	.	T	bias_e_value=32960.1	bias_p_value=0.00709378	fisher_strand_p_value=0.00134695	frequency=2.066135e-02	genotype_quality=1172.8	ks_quality_p_value=0.6557	log10_base_likelihood=-22.4194	log10_qual_likelihood_position_model=3.8176	log10_strand_likelihood_position_model=2.87065	new_cov=5/0	polymorphism_quality=17.2	quality=17.2	quality_position_model=7.46056e-18	ref_cov=61/176	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=66/176
RA	521	.	NC_007779	4037805	0	G	T	bias_e_value=965.046	bias_p_value=0.000207701	fisher_strand_p_value=1.73647e-05	frequency=2.914906e-02	genotype_quality=978.6	ks_quality_p_value=1	log10_base_likelihood=-6.41879	log10_qual_likelihood_position_model=14.4485	log10_strand_likelihood_position_model=4.76033	new_cov=0/15	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=142/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/139
RA	522	.	NC_007779	4052978	0	G	T	bias_e_value=2.3074e-05	bias_p_value=4.96608e-12	fisher_strand_p_value=1.6312e-13	frequency=7.637119e-02	genotype_quality=1093.3	ks_quality_p_value=1	log10_base_likelihood=-23.0102	log10_qual_likelihood_position_model=24.7403	log10_strand_likelihood_position_model=12.7944	new_cov=1/37	polymorphism_quality=17.8	quality=17.8	quality_position_model=Inf	ref_cov=192/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=193/156
RA	523	.	NC_007779	4055100	0	G	T	bias_e_value=0.0158249	bias_p_value=3.40588e-09	fisher_strand_p_value=1.4532e-10	frequency=6.097984e-02	genotype_quality=976.3	ks_quality_p_value=0.990514	log10_base_likelihood=-13.0745	log10_qual_likelihood_position_model=28.0674	log10_strand_likelihood_position_model=9.83768	new_cov=22/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=86/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/175
RA	524	.	NC_007779	4055329	0	T	G	bias_e_value=1.16474e-15	bias_p_value=2.5068e-22	fisher_strand_p_value=4.57943e-24	frequency=9.101772e-02	genotype_quality=735.0	ks_quality_p_value=1	log10_base_likelihood=-17.2864	log10_qual_likelihood_position_model=30.0433	log10_strand_likelihood_position_model=23.3392	new_cov=30/0	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=20/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=50/171
RA	525	.	NC_007779	4059484	1	.	T	bias_e_value=3601600	bias_p_value=0.775149	fisher_strand_p_value=1	frequency=6.873131e-03	genotype_quality=1433.9	ks_quality_p_value=0.409544	log10_base_likelihood=-8.02089	log10_qual_likelihood_position_model=2.0342	log10_strand_likelihood_position_model=0.299581	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.34371e-07	ref_cov=146/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/144
RA	526	.	NC_007779	4059485	0	T	.	bias_e_value=3140420	bias_p_value=0.675892	fisher_strand_p_value=1	frequency=1.002693e-02	genotype_quality=1214.5	ks_quality_p_value=0.312421	log10_base_likelihood=-8.3305	log10_qual_likelihood_position_model=2.6597	log10_strand_likelihood_position_model=0.420193	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.81052e-07	ref_cov=149/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/148
RA	527	.	NC_007779	4062114	0	T	G	bias_e_value=1.85201e-16	bias_p_value=3.98596e-23	fisher_strand_p_value=7.04072e-25	frequency=1.188745e-01	genotype_quality=781.1	ks_quality_p_value=1	log10_base_likelihood=-21.5632	log10_qual_likelihood_position_model=37.6506	log10_strand_likelihood_position_model=24.1524	new_cov=45/0	polymorphism_quality=16.3	quality=16.3	quality_position_model=Inf	ref_cov=45/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=92/162
RA	528	.	NC_007779	4064463	0	G	T	bias_e_value=0.292005	bias_p_value=6.28463e-08	fisher_strand_p_value=3.04957e-09	frequency=8.048058e-02	genotype_quality=913.1	ks_quality_p_value=1	log10_base_likelihood=-18.4923	log10_qual_likelihood_position_model=20.3813	log10_strand_likelihood_position_model=8.79723	new_cov=1/33	polymorphism_quality=13.2	quality=13.2	quality_position_model=Inf	ref_cov=145/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/160
RA	529	.	NC_007779	4080051	0	T	C	bias_e_value=1966590	bias_p_value=0.423256	fisher_strand_p_value=0.626378	frequency=1.286888e-02	genotype_quality=1189.7	ks_quality_p_value=0.230052	log10_base_likelihood=-8.69873	log10_qual_likelihood_position_model=2.83125	log10_strand_likelihood_position_model=0.544151	new_cov=1/3	polymorphism_quality=3.2	quality=3.2	quality_position_model=3.20252e-07	ref_cov=143/163	reject=POLYMORPHISM_STRAND	tot_cov=145/166
RA	530	.	NC_007779	4087368	1	.	T	bias_e_value=2398910	bias_p_value=0.516301	fisher_strand_p_value=1	frequency=7.518768e-03	genotype_quality=1333.3	ks_quality_p_value=0.196547	log10_base_likelihood=-8.22522	log10_qual_likelihood_position_model=1.18613	log10_strand_likelihood_position_model=0.300279	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.10149e-08	ref_cov=126/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/139
RA	531	.	NC_007779	4087369	0	T	.	bias_e_value=4646290	bias_p_value=0.999991	fisher_strand_p_value=1	frequency=1.126575e-02	genotype_quality=1078.1	ks_quality_p_value=0.995806	log10_base_likelihood=-7.74579	log10_qual_likelihood_position_model=2.50249	log10_strand_likelihood_position_model=0.405913	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.025e-06	ref_cov=126/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/139
RA	532	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1378.6	new_cov=170/171	quality=1378.6	ref_cov=0/0	tot_cov=170/171
RA	533	.	NC_007779	4098730	0	G	T	bias_e_value=9.57768e-05	bias_p_value=2.06134e-11	fisher_strand_p_value=7.1151e-13	frequency=9.028149e-02	genotype_quality=890.8	ks_quality_p_value=1	log10_base_likelihood=-19.4895	log10_qual_likelihood_position_model=24.0398	log10_strand_likelihood_position_model=12.2194	new_cov=0/38	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=149/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/155
RA	534	.	NC_007779	4108257	0	G	A	bias_e_value=1401500	bias_p_value=0.301635	fisher_strand_p_value=0.12829	frequency=1.229382e-02	genotype_quality=1391.6	ks_quality_p_value=0.685171	log10_base_likelihood=-7.71254	log10_qual_likelihood_position_model=1.50024	log10_strand_likelihood_position_model=1.06696	new_cov=0/4	polymorphism_quality=2.2	quality=2.2	quality_position_model=4.90168e-07	ref_cov=148/172	reject=POLYMORPHISM_STRAND	tot_cov=148/176
RA	535	.	NC_007779	4115400	0	T	C	bias_e_value=0.19177	bias_p_value=4.12734e-08	fisher_strand_p_value=1.96074e-09	frequency=4.434395e-02	genotype_quality=754.1	ks_quality_p_value=1	log10_base_likelihood=-5.8711	log10_qual_likelihood_position_model=17.0257	log10_strand_likelihood_position_model=8.70758	new_cov=0/18	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=154/66	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/84
RA	536	.	NC_007779	4124346	0	A	.	bias_e_value=4224970	bias_p_value=0.909312	fisher_strand_p_value=1	frequency=9.308815e-03	genotype_quality=1301.9	ks_quality_p_value=0.605565	log10_base_likelihood=-7.89063	log10_qual_likelihood_position_model=2.38987	log10_strand_likelihood_position_model=0.406843	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=5.54369e-07	ref_cov=166/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=168/154
RA	537	.	NC_007779	4124974	0	G	T	bias_e_value=5.40664e-07	bias_p_value=1.16364e-13	fisher_strand_p_value=3.39078e-15	frequency=1.145020e-01	genotype_quality=964.6	ks_quality_p_value=1	log10_base_likelihood=-29.3187	log10_qual_likelihood_position_model=28.2284	log10_strand_likelihood_position_model=14.5396	new_cov=0/49	polymorphism_quality=24.1	quality=24.1	quality_position_model=Inf	ref_cov=150/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/178
RA	538	.	NC_007779	4128669	1	.	T	bias_e_value=3712410	bias_p_value=0.798998	fisher_strand_p_value=0.500792	frequency=7.193565e-03	genotype_quality=1377.0	ks_quality_p_value=0.873195	log10_base_likelihood=-7.847	log10_qual_likelihood_position_model=1.57055	log10_strand_likelihood_position_model=0.543077	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.20338e-07	ref_cov=129/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/149
RA	539	.	NC_007779	4128670	0	T	.	bias_e_value=3848650	bias_p_value=0.82832	fisher_strand_p_value=0.625808	frequency=1.432228e-02	genotype_quality=1095.0	ks_quality_p_value=0.758399	log10_base_likelihood=-10.9344	log10_qual_likelihood_position_model=3.45717	log10_strand_likelihood_position_model=0.546269	new_cov=1/3	polymorphism_quality=5.5	quality=5.5	quality_position_model=6.98346e-09	ref_cov=129/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/149
RA	540	.	NC_007779	4138115	1	.	G	bias_e_value=3760920	bias_p_value=0.80944	fisher_strand_p_value=0.498582	frequency=7.407188e-03	genotype_quality=1346.6	ks_quality_p_value=0.902839	log10_base_likelihood=-8.60747	log10_qual_likelihood_position_model=1.80269	log10_strand_likelihood_position_model=0.578222	new_cov=0/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=3.71887e-08	ref_cov=131/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/139
RA	541	.	NC_007779	4148399	0	A	C	bias_e_value=1.64245e-07	bias_p_value=3.53494e-14	fisher_strand_p_value=9.94517e-16	frequency=6.790543e-02	genotype_quality=810.2	ks_quality_p_value=1	log10_base_likelihood=-9.1831	log10_qual_likelihood_position_model=27.4947	log10_strand_likelihood_position_model=15.0024	new_cov=0/32	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=157/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/98
RA	542	.	NC_007779	4148399	1	.	C	bias_e_value=464761	bias_p_value=0.100027	fisher_strand_p_value=0.0204581	frequency=1.572609e-02	genotype_quality=1179.3	ks_quality_p_value=1	log10_base_likelihood=-9.84114	log10_qual_likelihood_position_model=4.01952	log10_strand_likelihood_position_model=1.68913	new_cov=0/4	polymorphism_quality=4.4	quality=4.4	quality_position_model=5.58612e-06	ref_cov=157/93	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/97
RA	543	.	NC_007779	4152489	0	G	T	bias_e_value=4054.09	bias_p_value=0.000872536	fisher_strand_p_value=8.40547e-05	frequency=3.641891e-02	genotype_quality=1121.6	ks_quality_p_value=0.99963	log10_base_likelihood=-12.0224	log10_qual_likelihood_position_model=15.6694	log10_strand_likelihood_position_model=4.38524	new_cov=1/19	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=157/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/182
RA	544	.	NC_007779	4157323	0	C	A	bias_e_value=101.236	bias_p_value=2.17884e-05	fisher_strand_p_value=1.65663e-06	frequency=3.770638e-02	genotype_quality=968.7	ks_quality_p_value=0.913254	log10_base_likelihood=-9.96729	log10_qual_likelihood_position_model=23.5547	log10_strand_likelihood_position_model=5.78077	new_cov=18/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=124/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/146
RA	545	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1223.6	new_cov=133/152	quality=1223.6	ref_cov=0/0	tot_cov=133/152
RA	546	.	NC_007779	4174730	0	T	.	bias_e_value=4411580	bias_p_value=0.949476	fisher_strand_p_value=1	frequency=1.086140e-02	genotype_quality=1115.0	ks_quality_p_value=0.69945	log10_base_likelihood=-8.13254	log10_qual_likelihood_position_model=2.59437	log10_strand_likelihood_position_model=0.41519	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.17116e-07	ref_cov=139/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/135
RA	547	.	NC_007779	4197139	0	T	G	bias_e_value=1.89291e-20	bias_p_value=4.07399e-27	fisher_strand_p_value=6.177e-29	frequency=1.226802e-01	genotype_quality=784.5	ks_quality_p_value=1	log10_base_likelihood=-23.6386	log10_qual_likelihood_position_model=40.4175	log10_strand_likelihood_position_model=28.2092	new_cov=36/0	polymorphism_quality=18.4	quality=18.4	quality_position_model=Inf	ref_cov=18/176	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=54/176
RA	548	.	NC_007779	4200197	0	A	G	bias_e_value=1408590	bias_p_value=0.303163	fisher_strand_p_value=0.206836	frequency=3.607302e-01	genotype_quality=316.1	ks_quality_p_value=0.428019	log10_base_likelihood=-348.172	log10_qual_likelihood_position_model=9.38015	log10_strand_likelihood_position_model=1.3721	new_cov=44/51	polymorphism_quality=inf	quality=inf	quality_position_model=0	ref_cov=100/83	tot_cov=156/147
RA	549	.	NC_007779	4200494	0	T	G	bias_e_value=0.000841991	bias_p_value=1.81216e-10	fisher_strand_p_value=6.78291e-12	frequency=5.402708e-02	genotype_quality=969.6	ks_quality_p_value=1	log10_base_likelihood=-7.35117	log10_qual_likelihood_position_model=42.4634	log10_strand_likelihood_position_model=11.3722	new_cov=35/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=120/153	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/153
RA	550	.	NC_007779	4207565	0	C	A	bias_e_value=0.793919	bias_p_value=1.7087e-07	fisher_strand_p_value=8.73765e-09	frequency=7.707357e-02	genotype_quality=900.6	ks_quality_p_value=1	log10_base_likelihood=-17.5624	log10_qual_likelihood_position_model=23.243	log10_strand_likelihood_position_model=8.1853	new_cov=32/0	polymorphism_quality=12.2	quality=12.2	quality_position_model=Inf	ref_cov=141/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/126
RA	551	.	NC_007779	4214442	0	T	.	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	552	.	NC_007779	4214446	0	C	T	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	553	.	NC_007779	4218761	0	C	G	bias_e_value=30177	bias_p_value=0.00649479	fisher_strand_p_value=0.000798608	frequency=4.451084e-02	genotype_quality=995.9	ks_quality_p_value=1	log10_base_likelihood=-13.5218	log10_qual_likelihood_position_model=16.2684	log10_strand_likelihood_position_model=3.21366	new_cov=0/13	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=105/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/143
RA	554	.	NC_007779	4218769	0	T	G	bias_e_value=50373.8	bias_p_value=0.0108416	fisher_strand_p_value=0.00143688	frequency=2.532864e-02	genotype_quality=862.4	ks_quality_p_value=1	log10_base_likelihood=-5.80188	log10_qual_likelihood_position_model=14.738	log10_strand_likelihood_position_model=3.04183	new_cov=0/12	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=101/121	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=102/133
RA	555	.	NC_007779	4218770	0	C	A	bias_e_value=156217	bias_p_value=0.0336215	fisher_strand_p_value=0.00540502	frequency=2.984428e-02	genotype_quality=937.5	ks_quality_p_value=1	log10_base_likelihood=-7.66601	log10_qual_likelihood_position_model=12.2653	log10_strand_likelihood_position_model=2.30817	new_cov=0/9	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=103/123	reject=POLYMORPHISM_STRAND	tot_cov=103/132
RA	556	.	NC_007779	4220019	0	A	C	bias_e_value=6.03772e-09	bias_p_value=1.29946e-15	fisher_strand_p_value=3.33718e-17	frequency=9.196472e-02	genotype_quality=899.2	ks_quality_p_value=1	log10_base_likelihood=-12.1473	log10_qual_likelihood_position_model=50.5874	log10_strand_likelihood_position_model=16.4766	new_cov=0/48	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=151/102	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/150
RA	557	.	NC_007779	4226513	0	C	A	bias_e_value=64.9374	bias_p_value=1.39761e-05	fisher_strand_p_value=9.39374e-07	frequency=4.387665e-02	genotype_quality=961.0	ks_quality_p_value=1	log10_base_likelihood=-10.4834	log10_qual_likelihood_position_model=16.0541	log10_strand_likelihood_position_model=6.02716	new_cov=19/0	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=124/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/144
RA	558	.	NC_007779	4227183	0	T	G	bias_e_value=2.2574e-12	bias_p_value=4.85845e-19	fisher_strand_p_value=1.0333e-20	frequency=5.169964e-02	genotype_quality=1064.2	ks_quality_p_value=1	log10_base_likelihood=-8.73237	log10_qual_likelihood_position_model=35.1371	log10_strand_likelihood_position_model=19.9858	new_cov=44/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=89/204	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/204
RA	559	.	NC_007779	4271772	0	G	T	bias_e_value=1381.98	bias_p_value=0.000297434	fisher_strand_p_value=2.57104e-05	frequency=2.732372e-02	genotype_quality=1220.3	ks_quality_p_value=1	log10_base_likelihood=-7.33167	log10_qual_likelihood_position_model=16.6445	log10_strand_likelihood_position_model=4.73751	new_cov=1/17	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=181/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=182/164
RA	560	.	NC_007779	4304641	0	T	G	bias_e_value=4.2288e-06	bias_p_value=9.10137e-13	fisher_strand_p_value=2.82677e-14	frequency=6.896019e-02	genotype_quality=787.4	ks_quality_p_value=1	log10_base_likelihood=-10.3179	log10_qual_likelihood_position_model=24.7656	log10_strand_likelihood_position_model=13.5487	new_cov=34/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=79/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/144
RA	561	.	NC_007779	4316403	0	T	.	bias_e_value=2687790	bias_p_value=0.578476	fisher_strand_p_value=0.610356	frequency=9.252548e-03	genotype_quality=1318.8	ks_quality_p_value=0.388604	log10_base_likelihood=-8.1459	log10_qual_likelihood_position_model=2.38337	log10_strand_likelihood_position_model=0.441717	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=3.22176e-07	ref_cov=167/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=168/156
RA	562	.	NC_007779	4318992	0	T	G	bias_e_value=4.3553e-05	bias_p_value=9.37362e-12	fisher_strand_p_value=3.14686e-13	frequency=3.066921e-02	genotype_quality=741.2	ks_quality_p_value=1	log10_base_likelihood=-7.60952	log10_qual_likelihood_position_model=16.4633	log10_strand_likelihood_position_model=12.5021	new_cov=0/12	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=202/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=203/26
RA	563	.	NC_007779	4318994	0	A	G	bias_e_value=2.27874e-07	bias_p_value=4.90439e-14	fisher_strand_p_value=1.393e-15	frequency=5.300093e-02	genotype_quality=785.0	ks_quality_p_value=1	log10_base_likelihood=-16.97	log10_qual_likelihood_position_model=14.4957	log10_strand_likelihood_position_model=14.856	new_cov=0/13	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=200/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=200/22
RA	564	.	NC_007779	4321435	0	G	C	bias_e_value=14.4457	bias_p_value=3.10904e-06	fisher_strand_p_value=1.887e-07	frequency=3.543663e-02	genotype_quality=685.1	ks_quality_p_value=0.999548	log10_base_likelihood=-10.1567	log10_qual_likelihood_position_model=7.94651	log10_strand_likelihood_position_model=6.72423	new_cov=6/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=9/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/151
RA	565	.	NC_007779	4328528	0	T	.	bias_e_value=4632790	bias_p_value=0.997085	fisher_strand_p_value=1	frequency=8.945465e-03	genotype_quality=1294.7	ks_quality_p_value=0.924623	log10_base_likelihood=-7.63837	log10_qual_likelihood_position_model=2.35235	log10_strand_likelihood_position_model=0.417028	new_cov=1/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=9.50195e-07	ref_cov=163/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=164/171
RA	566	.	NC_007779	4337469	0	A	C	bias_e_value=1.25199e-15	bias_p_value=2.69458e-22	fisher_strand_p_value=4.92909e-24	frequency=1.560173e-01	genotype_quality=714.0	ks_quality_p_value=1	log10_base_likelihood=-26.4901	log10_qual_likelihood_position_model=38.9155	log10_strand_likelihood_position_model=23.3072	new_cov=0/51	polymorphism_quality=21.3	quality=21.3	quality_position_model=Inf	ref_cov=138/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=138/101
RA	567	.	NC_007779	4346527	0	C	G	bias_e_value=560347	bias_p_value=0.1206	fisher_strand_p_value=0.0268886	frequency=3.876114e-02	genotype_quality=1181.3	ks_quality_p_value=0.963985	log10_base_likelihood=-28.4468	log10_qual_likelihood_position_model=11.0116	log10_strand_likelihood_position_model=1.76773	new_cov=4/10	polymorphism_quality=23.2	quality=23.2	quality_position_model=8.65542e-18	ref_cov=177/120	tot_cov=181/131
RA	568	.	NC_007779	4346883	0	T	A	bias_e_value=2490850	bias_p_value=0.536089	fisher_strand_p_value=0.754802	frequency=3.321552e-02	genotype_quality=1163.0	ks_quality_p_value=0.276823	log10_base_likelihood=-30.5035	log10_qual_likelihood_position_model=3.89603	log10_strand_likelihood_position_model=0.636053	new_cov=4/6	polymorphism_quality=25.3	quality=25.3	quality_position_model=3.3564e-28	ref_cov=137/154	tot_cov=141/160
RA	569	.	NC_007779	4347339	0	C	T	bias_e_value=2343680	bias_p_value=0.504416	fisher_strand_p_value=0.716329	frequency=2.840519e-02	genotype_quality=1150.6	ks_quality_p_value=0.264298	log10_base_likelihood=-17.478	log10_qual_likelihood_position_model=3.16507	log10_strand_likelihood_position_model=0.63696	new_cov=4/4	polymorphism_quality=12.2	quality=12.2	quality_position_model=9.06801e-16	ref_cov=107/166	tot_cov=111/170
RA	570	.	NC_007779	4348529	0	T	G	bias_e_value=2.78992e-09	bias_p_value=6.00455e-16	fisher_strand_p_value=1.5113e-17	frequency=8.095932e-02	genotype_quality=866.6	ks_quality_p_value=1	log10_base_likelihood=-9.19004	log10_qual_likelihood_position_model=44.7513	log10_strand_likelihood_position_model=16.8206	new_cov=40/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=79/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/161
RA	571	.	NC_007779	4351353	0	T	G	bias_e_value=5.7472e-12	bias_p_value=1.23693e-18	fisher_strand_p_value=2.68525e-20	frequency=6.940603e-02	genotype_quality=906.1	ks_quality_p_value=1	log10_base_likelihood=-6.30259	log10_qual_likelihood_position_model=49.8342	log10_strand_likelihood_position_model=19.571	new_cov=42/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=69/172	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/172
RA	572	.	NC_007779	4357170	1	.	A	bias_e_value=4548590	bias_p_value=0.978964	fisher_strand_p_value=1	frequency=7.547379e-03	genotype_quality=1319.8	ks_quality_p_value=0.802023	log10_base_likelihood=-8.27765	log10_qual_likelihood_position_model=1.17349	log10_strand_likelihood_position_model=0.318511	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=9.85662e-09	ref_cov=104/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/160
RA	573	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=1217.8	new_cov=115/123	quality=1217.8	ref_cov=0/0	tot_cov=115/123
RA	574	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=1217.8	new_cov=115/123	quality=1217.8	ref_cov=0/0	tot_cov=115/123
RA	575	.	NC_007779	4371461	0	T	C	bias_e_value=2516900	bias_p_value=0.541696	fisher_strand_p_value=0.283212	frequency=2.350426e-02	genotype_quality=1328.7	ks_quality_p_value=0.750489	log10_base_likelihood=-19.1108	log10_qual_likelihood_position_model=3.99776	log10_strand_likelihood_position_model=0.966353	new_cov=2/6	polymorphism_quality=13.8	quality=13.8	quality_position_model=3.01762e-16	ref_cov=168/164	tot_cov=171/170
RA	576	.	NC_007779	4371467	0	G	T	bias_e_value=2062390	bias_p_value=0.443875	fisher_strand_p_value=0.632495	frequency=5.001068e-02	genotype_quality=1528.6	ks_quality_p_value=0.244979	log10_base_likelihood=-47.849	log10_qual_likelihood_position_model=5.09248	log10_strand_likelihood_position_model=0.794192	new_cov=8/10	polymorphism_quality=42.8	quality=42.8	quality_position_model=2.70474e-44	ref_cov=177/166	reject=SURROUNDING_HOMOPOLYMER	tot_cov=187/179
RA	577	.	NC_007779	4414724	1	.	T	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=7.603645e-03	genotype_quality=1322.5	ks_quality_p_value=0.999767	log10_base_likelihood=-7.62324	log10_qual_likelihood_position_model=2.88401	log10_strand_likelihood_position_model=0.306267	new_cov=0/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=2.70804e-06	ref_cov=78/183	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=78/185
RA	578	.	NC_007779	4429120	0	G	T	bias_e_value=0.00142853	bias_p_value=3.07454e-10	fisher_strand_p_value=1.86469e-11	frequency=6.591272e-02	genotype_quality=916.0	ks_quality_p_value=0.63011	log10_base_likelihood=-8.914	log10_qual_likelihood_position_model=31.7887	log10_strand_likelihood_position_model=10.7294	new_cov=0/31	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=153/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/141
RA	579	.	NC_007779	4455463	0	T	G	bias_e_value=0.00870449	bias_p_value=1.87341e-09	fisher_strand_p_value=7.71415e-11	frequency=4.036331e-02	genotype_quality=938.4	ks_quality_p_value=1	log10_base_likelihood=-6.2457	log10_qual_likelihood_position_model=25.8063	log10_strand_likelihood_position_model=10.1127	new_cov=20/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=71/179	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/179
RA	580	.	NC_007779	4484645	0	T	.	bias_e_value=1176890	bias_p_value=0.253295	fisher_strand_p_value=0.080267	frequency=9.764671e-03	genotype_quality=1239.6	ks_quality_p_value=0.85876	log10_base_likelihood=-8.1503	log10_qual_likelihood_position_model=1.91252	log10_strand_likelihood_position_model=1.09546	new_cov=0/3	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.93729e-07	ref_cov=174/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=174/133
RA	581	.	NC_007779	4510865	1	.	A	bias_e_value=4633160	bias_p_value=0.997164	fisher_strand_p_value=1	frequency=6.756783e-03	genotype_quality=1487.2	ks_quality_p_value=0.925644	log10_base_likelihood=-8.16876	log10_qual_likelihood_position_model=1.33689	log10_strand_likelihood_position_model=0.307564	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.83279e-08	ref_cov=127/167	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/168
RA	582	.	NC_007779	4512816	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	583	.	NC_007779	4512817	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	584	.	NC_007779	4512818	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	585	.	NC_007779	4512819	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	586	.	NC_007779	4512820	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	587	.	NC_007779	4512821	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	588	.	NC_007779	4512822	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	589	.	NC_007779	4512823	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	590	.	NC_007779	4512825	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	591	.	NC_007779	4512826	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	592	.	NC_007779	4512827	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	593	.	NC_007779	4512828	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	594	.	NC_007779	4512829	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	595	.	NC_007779	4512830	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	596	.	NC_007779	4512831	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	597	.	NC_007779	4512832	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	598	.	NC_007779	4512833	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	599	.	NC_007779	4512834	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	600	.	NC_007779	4512835	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	601	.	NC_007779	4512836	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	602	.	NC_007779	4512837	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	603	.	NC_007779	4512838	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	604	.	NC_007779	4512839	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	605	.	NC_007779	4512840	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	606	.	NC_007779	4512841	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	607	.	NC_007779	4512842	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	608	.	NC_007779	4512845	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	609	.	NC_007779	4512846	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	610	.	NC_007779	4512848	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	611	.	NC_007779	4512849	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	612	.	NC_007779	4512850	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	613	.	NC_007779	4512851	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	614	.	NC_007779	4512852	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	615	.	NC_007779	4512854	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	616	.	NC_007779	4512856	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	617	.	NC_007779	4512857	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	618	.	NC_007779	4512858	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	619	.	NC_007779	4515952	0	G	T	bias_e_value=0.123201	bias_p_value=2.65158e-08	fisher_strand_p_value=1.23248e-09	frequency=6.894970e-02	genotype_quality=897.1	ks_quality_p_value=1	log10_base_likelihood=-13.5006	log10_qual_likelihood_position_model=33.2139	log10_strand_likelihood_position_model=9.0097	new_cov=0/33	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=137/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/173
RA	620	.	NC_007779	4540870	0	T	G	bias_e_value=1.55244e-15	bias_p_value=3.34122e-22	fisher_strand_p_value=6.13656e-24	frequency=9.112120e-02	genotype_quality=794.0	ks_quality_p_value=1	log10_base_likelihood=-10.5144	log10_qual_likelihood_position_model=35.7431	log10_strand_likelihood_position_model=23.2121	new_cov=43/0	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=46/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=90/165
RA	621	.	NC_007779	4540877	0	A	T	bias_e_value=1.0424e-07	bias_p_value=2.24348e-14	fisher_strand_p_value=6.22982e-16	frequency=1.075115e-01	genotype_quality=757.6	ks_quality_p_value=1	log10_base_likelihood=-21.6905	log10_qual_likelihood_position_model=22.5275	log10_strand_likelihood_position_model=15.2055	new_cov=31/0	polymorphism_quality=16.4	quality=16.4	quality_position_model=Inf	ref_cov=63/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/164
RA	622	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=931.4	new_cov=135/92	quality=931.4	ref_cov=0/0	tot_cov=135/92
RA	623	.	NC_007779	4553745	0	C	A	bias_e_value=98.1542	bias_p_value=2.11251e-05	fisher_strand_p_value=1.46551e-06	frequency=2.963161e-02	genotype_quality=1064.8	ks_quality_p_value=0.998625	log10_base_likelihood=-6.16694	log10_qual_likelihood_position_model=18.0558	log10_strand_likelihood_position_model=5.83401	new_cov=17/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=134/172	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/172
RA	624	.	NC_007779	4554525	1	.	T	bias_e_value=1384920	bias_p_value=0.298067	fisher_strand_p_value=0.0909973	frequency=1.200008e-02	genotype_quality=1204.9	ks_quality_p_value=0.949898	log10_base_likelihood=-12.7193	log10_qual_likelihood_position_model=2.56883	log10_strand_likelihood_position_model=1.04097	new_cov=3/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=4.06498e-11	ref_cov=110/137	reject=POLYMORPHISM_STRAND	tot_cov=113/137
RA	625	.	NC_007779	4554532	0	T	C	bias_e_value=8.58038	bias_p_value=1.8467e-06	fisher_strand_p_value=1.10174e-07	frequency=6.131077e-02	genotype_quality=707.4	ks_quality_p_value=0.983812	log10_base_likelihood=-18.5963	log10_qual_likelihood_position_model=13.235	log10_strand_likelihood_position_model=6.95792	new_cov=15/0	polymorphism_quality=13.3	quality=13.3	quality_position_model=Inf	ref_cov=66/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=81/141
RA	626	.	NC_007779	4554534	0	A	C	bias_e_value=1699.86	bias_p_value=0.000365851	fisher_strand_p_value=3.22569e-05	frequency=4.340458e-02	genotype_quality=657.9	ks_quality_p_value=1	log10_base_likelihood=-12.3019	log10_qual_likelihood_position_model=14.2036	log10_strand_likelihood_position_model=4.50765	new_cov=12/1	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=69/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=82/139
RA	627	.	NC_007779	4554538	0	T	C	bias_e_value=10539.3	bias_p_value=0.0022683	fisher_strand_p_value=0.000243432	frequency=2.226162e-02	genotype_quality=744.2	ks_quality_p_value=0.999681	log10_base_likelihood=-7.03188	log10_qual_likelihood_position_model=7.56745	log10_strand_likelihood_position_model=3.61362	new_cov=7/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=60/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=67/146
RA	628	.	NC_007779	4561440	1	.	T	bias_e_value=2642090	bias_p_value=0.56864	fisher_strand_p_value=1	frequency=9.569168e-03	genotype_quality=1039.9	ks_quality_p_value=0.230418	log10_base_likelihood=-8.27097	log10_qual_likelihood_position_model=2.05388	log10_strand_likelihood_position_model=0.3235	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=8.21444e-08	ref_cov=128/79	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/80
RA	629	.	NC_007779	4561441	0	T	.	bias_e_value=4605810	bias_p_value=0.991279	fisher_strand_p_value=1	frequency=1.859665e-02	genotype_quality=840.8	ks_quality_p_value=0.870875	log10_base_likelihood=-11.8104	log10_qual_likelihood_position_model=2.15214	log10_strand_likelihood_position_model=0.439997	new_cov=3/1	polymorphism_quality=6.4	quality=6.4	quality_position_model=3.14649e-11	ref_cov=130/81	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/82
RA	630	.	NC_007779	4573184	0	T	G	bias_e_value=0.000517074	bias_p_value=1.11286e-10	fisher_strand_p_value=4.08796e-12	frequency=5.975962e-02	genotype_quality=888.2	ks_quality_p_value=1	log10_base_likelihood=-7.32903	log10_qual_likelihood_position_model=28.0215	log10_strand_likelihood_position_model=11.5842	new_cov=40/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=131/143	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/144
RA	631	.	NC_007779	4578176	0	A	G	bias_e_value=1.99817e-06	bias_p_value=4.30054e-13	fisher_strand_p_value=1.30436e-14	frequency=6.833792e-02	genotype_quality=864.6	ks_quality_p_value=1	log10_base_likelihood=-13.347	log10_qual_likelihood_position_model=24.8419	log10_strand_likelihood_position_model=13.8846	new_cov=21/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=43/192	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=64/192
RA	632	.	NC_007779	4583431	0	T	.	bias_e_value=1868210	bias_p_value=0.402082	fisher_strand_p_value=0.660772	frequency=2.221394e-02	genotype_quality=892.4	ks_quality_p_value=0.201856	log10_base_likelihood=-15.101	log10_qual_likelihood_position_model=3.60021	log10_strand_likelihood_position_model=0.552294	new_cov=3/2	polymorphism_quality=9.8	quality=9.8	quality_position_model=5.3915e-13	ref_cov=99/121	reject=INDEL_HOMOPOLYMER	tot_cov=102/123
RA	633	.	NC_007779	4584556	0	C	A	bias_e_value=454.786	bias_p_value=9.78807e-05	fisher_strand_p_value=7.65913e-06	frequency=3.840828e-02	genotype_quality=876.5	ks_quality_p_value=1	log10_base_likelihood=-6.13765	log10_qual_likelihood_position_model=22.5918	log10_strand_likelihood_position_model=5.14975	new_cov=18/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=129/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/129
RA	634	.	NC_007779	4584731	0	G	T	bias_e_value=1.06452	bias_p_value=2.29109e-07	fisher_strand_p_value=1.1904e-08	frequency=4.125309e-02	genotype_quality=1067.2	ks_quality_p_value=1	log10_base_likelihood=-8.91417	log10_qual_likelihood_position_model=14.9475	log10_strand_likelihood_position_model=7.92431	new_cov=0/19	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=190/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=191/128
RA	635	.	NC_007779	4599760	0	C	A	bias_e_value=1.64068e-06	bias_p_value=3.53113e-13	fisher_strand_p_value=1.06443e-14	frequency=7.749176e-02	genotype_quality=1150.4	ks_quality_p_value=1	log10_base_likelihood=-24.1317	log10_qual_likelihood_position_model=24.8774	log10_strand_likelihood_position_model=13.9729	new_cov=37/0	polymorphism_quality=18.9	quality=18.9	quality_position_model=Inf	ref_cov=123/196	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/196
RA	636	.	NC_007779	4601746	1	.	T	bias_e_value=237688	bias_p_value=0.0511561	fisher_strand_p_value=0.58539	frequency=9.966850e-03	genotype_quality=1496.7	ks_quality_p_value=0.0152879	log10_base_likelihood=-12.9748	log10_qual_likelihood_position_model=2.33462	log10_strand_likelihood_position_model=0.484503	new_cov=1/2	polymorphism_quality=7.6	quality=7.6	quality_position_model=3.46926e-12	ref_cov=167/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=168/133
RA	637	.	NC_007779	4610766	1	.	G	bias_e_value=4133780	bias_p_value=0.889686	fisher_strand_p_value=1	frequency=2.205849e-02	genotype_quality=1309.7	ks_quality_p_value=0.568718	log10_base_likelihood=-27.7594	log10_qual_likelihood_position_model=3.13434	log10_strand_likelihood_position_model=0.519213	new_cov=4/2	polymorphism_quality=22.5	quality=22.5	quality_position_model=2.55485e-26	ref_cov=154/112	reject=INDEL_HOMOPOLYMER	tot_cov=158/114
RA	638	.	NC_007779	4610781	0	A	C	bias_e_value=7.18976e-06	bias_p_value=1.54741e-12	fisher_strand_p_value=4.88925e-14	frequency=7.507038e-02	genotype_quality=966.7	ks_quality_p_value=1	log10_base_likelihood=-19.7488	log10_qual_likelihood_position_model=31.0727	log10_strand_likelihood_position_model=13.3108	new_cov=0/36	polymorphism_quality=14.5	quality=14.5	quality_position_model=Inf	ref_cov=165/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/142
RA	639	.	NC_007779	4610781	1	.	C	bias_e_value=1441160	bias_p_value=0.310172	fisher_strand_p_value=0.103135	frequency=1.030540e-02	genotype_quality=1338.6	ks_quality_p_value=0.886613	log10_base_likelihood=-10.7973	log10_qual_likelihood_position_model=2.96489	log10_strand_likelihood_position_model=0.986596	new_cov=0/3	polymorphism_quality=5.4	quality=5.4	quality_position_model=8.54585e-09	ref_cov=154/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/137
RA	640	.	NC_007779	4611002	1	.	G	bias_e_value=509986	bias_p_value=0.109761	fisher_strand_p_value=0.247606	frequency=9.836197e-03	genotype_quality=1518.3	ks_quality_p_value=0.0928886	log10_base_likelihood=-12.7273	log10_qual_likelihood_position_model=3.0794	log10_strand_likelihood_position_model=0.89456	new_cov=3/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=9.40805e-11	ref_cov=151/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/151
RA	641	.	NC_007779	4613456	0	C	A	bias_e_value=427.739	bias_p_value=9.20595e-05	fisher_strand_p_value=7.16633e-06	frequency=3.508282e-02	genotype_quality=877.1	ks_quality_p_value=1	log10_base_likelihood=-7.59827	log10_qual_likelihood_position_model=16.5856	log10_strand_likelihood_position_model=5.18728	new_cov=18/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=134/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/135
RA	642	.	NC_007779	4635770	0	G	T	bias_e_value=2343.54	bias_p_value=0.000504386	fisher_strand_p_value=4.58989e-05	frequency=3.326416e-02	genotype_quality=815.3	ks_quality_p_value=1	log10_base_likelihood=-5.84715	log10_qual_likelihood_position_model=10.6683	log10_strand_likelihood_position_model=4.46918	new_cov=0/15	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=132/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/141
RA	643	.	NC_007779	4636470	0	C	G	bias_e_value=0.00847874	bias_p_value=1.82483e-09	fisher_strand_p_value=7.50562e-11	frequency=5.904388e-02	genotype_quality=808.6	ks_quality_p_value=1	log10_base_likelihood=-8.63367	log10_qual_likelihood_position_model=16.5459	log10_strand_likelihood_position_model=10.1246	new_cov=18/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=50/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=68/157
RA	644	.	NC_007779	4642868	0	C	.	bias_e_value=3415590	bias_p_value=0.735114	fisher_strand_p_value=1	frequency=8.373260e-03	genotype_quality=1537.9	ks_quality_p_value=0.367235	log10_base_likelihood=-8.02311	log10_qual_likelihood_position_model=2.5269	log10_strand_likelihood_position_model=0.398377	new_cov=2/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.49187e-07	ref_cov=189/166	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=191/167
MC	645	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=304	right_inside_cov=0	right_outside_cov=304
MC	646	.	NC_007779	654214	655412	1196	0	left_inside_cov=0	left_outside_cov=304	right_inside_cov=0	right_outside_cov=306
MC	647	.	NC_007779	1288310	1288520	71	61	left_inside_cov=233	left_outside_cov=237	right_inside_cov=233	right_outside_cov=235
MC	648	.	NC_007779	1301041	1302376	1327	0	left_inside_cov=0	left_outside_cov=279	right_inside_cov=0	right_outside_cov=274
MC	649	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=364	right_inside_cov=0	right_outside_cov=361
MC	650	.	NC_007779	2176983	2178208	0	0	left_inside_cov=0	left_outside_cov=350	right_inside_cov=0	right_outside_cov=253
MC	651	.	NC_007779	2320795	2322130	1329	0	left_inside_cov=0	left_outside_cov=324	right_inside_cov=0	right_outside_cov=326
MC	652	.	NC_007779	3128831	3147473	1171	0	left_inside_cov=232	left_outside_cov=235	right_inside_cov=0	right_outside_cov=301
MC	653	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=302	right_inside_cov=0	right_outside_cov=475
MC	654	.	NC_007779	3742936	3744271	1327	0	left_inside_cov=0	left_outside_cov=363	right_inside_cov=0	right_outside_cov=363
MC	655	.	NC_007779	3746911	3748109	0	1197	left_inside_cov=0	left_outside_cov=359	right_inside_cov=0	right_outside_cov=359
MC	656	.	NC_007779	4310363	4311561	0	1197	left_inside_cov=0	left_outside_cov=361	right_inside_cov=1	right_outside_cov=364
JC	657	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=127	coverage_plus=181	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1__1__NC_007779__4646332__-1__0____101__101__0__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=93	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=310	pos_hash_score=144	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=308
JC	658	.	NC_007779	273179	1	NC_007779	657843	1	0	alignment_overlap=0	coverage_minus=110	coverage_plus=108	flanking_left=101	flanking_right=101	frequency=8.257576e-01	junction_possible_overlap_registers=90	key=NC_007779__273179__1__NC_007779__657843__1__0____101__101__1__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.75	new_junction_frequency=8.257576e-01	new_junction_read_count=218	pos_hash_score=125	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.16	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=46	side_2_redundant=0	total_non_overlap_reads=218
JC	659	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=8	coverage_minus=118	coverage_plus=133	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371965__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=87	max_min_left=46	max_min_left_minus=46	max_min_left_plus=45	max_min_right=46	max_min_right_minus=46	max_min_right_plus=45	max_pos_hash_score=160	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=245	pos_hash_score=122	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=2	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=251
JC	660	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=100	coverage_plus=106	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=32	max_min_left_plus=33	max_min_right=34	max_min_right_minus=33	max_min_right_plus=34	max_pos_hash_score=114	max_right=62	max_right_minus=62	max_right_plus=62	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.12	new_junction_frequency=1.000000e+00	new_junction_read_count=206	pos_hash_score=96	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=206	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	661	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=180	coverage_plus=130	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=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.07	new_junction_frequency=NA	new_junction_read_count=310	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=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	662	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=146	coverage_plus=141	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=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=48	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=NA	new_junction_read_count=289	pos_hash_score=136	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=287
JC	663	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=120	coverage_plus=143	flanking_left=101	flanking_right=101	frequency=8.774466e-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=91	max_left_plus=92	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=174	max_right=92	max_right_minus=92	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.94	new_junction_frequency=8.774466e-01	new_junction_read_count=263	pos_hash_score=133	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.13	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=38	side_2_redundant=0	total_non_overlap_reads=263
JC	664	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=143	coverage_plus=105	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=47	max_min_right=48	max_min_right_minus=47	max_min_right_plus=48	max_pos_hash_score=170	max_right=90	max_right_minus=90	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=248	pos_hash_score=132	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=248
JC	665	.	NC_007779	654213	1	NC_007779	657846	-1	0	alignment_overlap=0	coverage_minus=89	coverage_plus=123	flanking_left=101	flanking_right=101	frequency=8.255814e-01	junction_possible_overlap_registers=90	key=NC_007779__654213__1__NC_007779__657846__-1__0____101__101__1__0	max_left=91	max_left_minus=89	max_left_plus=91	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=46	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.73	new_junction_frequency=8.255814e-01	new_junction_read_count=213	pos_hash_score=125	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.16	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=45	side_2_redundant=0	total_non_overlap_reads=212
JC	666	.	NC_007779	655407	-1	NC_007779	656438	-1	0	alignment_overlap=0	coverage_minus=1	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.239669e-02	junction_possible_overlap_registers=90	key=NC_007779__655407__-1__NC_007779__656438__-1__0____101__101__1__0	max_left=82	max_left_minus=58	max_left_plus=82	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=43	max_min_right_minus=43	max_min_right_plus=39	max_pos_hash_score=180	max_right=43	max_right_minus=43	max_right_plus=39	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.01	new_junction_frequency=1.239669e-02	new_junction_read_count=3	pos_hash_score=3	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=0.82	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=239	side_2_redundant=0	total_non_overlap_reads=3
JC	667	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=15	coverage_plus=18	flanking_left=101	flanking_right=101	frequency=1.476877e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=75	max_left_minus=74	max_left_plus=75	max_min_left=40	max_min_left_minus=40	max_min_left_plus=40	max_min_right=36	max_min_right_minus=36	max_min_right_plus=31	max_pos_hash_score=148	max_right=78	max_right_minus=78	max_right_plus=74	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.14	new_junction_frequency=1.476877e-01	new_junction_read_count=33	pos_hash_score=29	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.76	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=220	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.84	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=200	side_2_redundant=0	total_non_overlap_reads=33
JC	668	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=18	coverage_plus=12	flanking_left=101	flanking_right=101	frequency=1.392040e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=78	max_left_minus=78	max_left_plus=76	max_min_left=42	max_min_left_minus=42	max_min_left_plus=40	max_min_right=38	max_min_right_minus=38	max_min_right_plus=26	max_pos_hash_score=148	max_right=78	max_right_minus=78	max_right_plus=76	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.13	new_junction_frequency=1.392040e-01	new_junction_read_count=30	pos_hash_score=28	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.72	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=208	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.84	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=200	side_2_redundant=0	total_non_overlap_reads=30
JC	669	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=119	coverage_plus=136	flanking_left=101	flanking_right=101	frequency=9.924483e-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=86	max_right_minus=86	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=9.924483e-01	new_junction_read_count=257	pos_hash_score=120	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=2	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=255
JC	670	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=132	coverage_plus=114	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1221495__-1__NC_007779__1302369__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=88	max_right_minus=88	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.85	new_junction_frequency=1.000000e+00	new_junction_read_count=246	pos_hash_score=120	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=246
JC	671	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=118	coverage_plus=118	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=83	key=NC_007779__1301040__-1__NC_007779__1302370__1__7____101__101__0__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=47	max_min_right_minus=47	max_min_right_plus=44	max_pos_hash_score=166	max_right=88	max_right_minus=88	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=237	pos_hash_score=129	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=236
JC	672	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=127	coverage_plus=118	flanking_left=101	flanking_right=101	frequency=8.650451e-01	junction_possible_overlap_registers=86	key=NC_007779__1305037__-1__NC_007779__2519719__1__4____101__101__0__1	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.88	new_junction_frequency=8.650451e-01	new_junction_read_count=245	pos_hash_score=132	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.14	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=40	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=245
JC	673	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=117	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1397758__1__NC_007779__1672777__1__0____101__101__1__0	max_left=89	max_left_minus=89	max_left_plus=89	max_min_left=50	max_min_left_minus=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=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.79	new_junction_frequency=1.000000e+00	new_junction_read_count=230	pos_hash_score=124	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=230
JC	674	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=115	coverage_plus=108	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=66	max_left_plus=69	max_min_left=37	max_min_left_minus=37	max_min_left_plus=37	max_min_right=36	max_min_right_minus=36	max_min_right_plus=36	max_pos_hash_score=128	max_right=69	max_right_minus=69	max_right_plus=68	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=223	pos_hash_score=95	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=223
JC	675	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=127	coverage_plus=134	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=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=85	max_right_minus=84	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=1.000000e+00	new_junction_read_count=262	pos_hash_score=125	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=261
JC	676	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=149	coverage_plus=139	flanking_left=101	flanking_right=101	frequency=9.696970e-01	junction_possible_overlap_registers=90	key=NC_007779__1907280__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	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=0.99	new_junction_frequency=9.696970e-01	new_junction_read_count=288	pos_hash_score=142	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.03	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=9	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=288
JC	677	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=138	coverage_plus=130	flanking_left=101	flanking_right=101	frequency=9.307958e-01	junction_possible_overlap_registers=90	key=NC_007779__1907288__-1__NC_007779__2411458__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=9.307958e-01	new_junction_read_count=269	pos_hash_score=137	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.07	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=20	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=268
JC	678	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=60	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1980091__1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=41	max_min_right=49	max_min_right_minus=49	max_min_right_plus=43	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=0.63	new_junction_frequency=1.000000e+00	new_junction_read_count=182	pos_hash_score=108	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=182
JC	679	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=183	coverage_plus=143	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=49	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=326	pos_hash_score=149	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=326
JC	680	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=134	coverage_plus=102	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=89	max_right_minus=85	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=1.000000e+00	new_junction_read_count=237	pos_hash_score=126	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=236
JC	681	.	NC_007779	2319506	1	NC_007779	2322124	-1	0	alignment_overlap=0	coverage_minus=23	coverage_plus=31	flanking_left=101	flanking_right=101	frequency=1.894737e-01	junction_possible_overlap_registers=90	key=NC_007779__2319506__1__NC_007779__2322124__-1__0____101__101__0__1	max_left=92	max_left_minus=92	max_left_plus=88	max_min_left=50	max_min_left_minus=37	max_min_left_plus=50	max_min_right=48	max_min_right_minus=44	max_min_right_plus=48	max_pos_hash_score=180	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.19	new_junction_frequency=1.894737e-01	new_junction_read_count=54	pos_hash_score=50	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.80	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=231	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=54
JC	682	.	NC_007779	2319510	-1	NC_007779	2320794	1	0	alignment_overlap=0	coverage_minus=25	coverage_plus=26	flanking_left=101	flanking_right=101	frequency=1.770833e-01	junction_possible_overlap_registers=90	key=NC_007779__2319510__-1__NC_007779__2320794__1__0____101__101__0__1	max_left=94	max_left_minus=91	max_left_plus=94	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=47	max_min_right_minus=45	max_min_right_plus=47	max_pos_hash_score=180	max_right=86	max_right_minus=86	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.18	new_junction_frequency=1.770833e-01	new_junction_read_count=51	pos_hash_score=49	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.82	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=237	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=51
JC	683	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=136	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=84	key=NC_007779__2320794__-1__NC_007779__2322125__1__6____101__101__0__0	max_left=89	max_left_minus=89	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=45	max_min_right=46	max_min_right_minus=46	max_min_right_plus=46	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=269	pos_hash_score=130	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=268
JC	684	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=96	coverage_plus=158	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=0.88	new_junction_frequency=1.000000e+00	new_junction_read_count=254	pos_hash_score=118	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=254
JC	685	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=165	coverage_plus=162	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2322124__-1__NC_007779__2589830__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=330	pos_hash_score=150	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=327
JC	686	.	NC_007779	2411458	-1	NC_007779	2412235	1	0	alignment_overlap=9	coverage_minus=4	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=2.005683e-02	junction_possible_overlap_registers=81	key=NC_007779__2411458__-1__NC_007779__2412226__1__9____101__101__0__0	max_left=81	max_left_minus=81	max_left_plus=52	max_min_left=42	max_min_left_minus=33	max_min_left_plus=42	max_min_right=40	max_min_right_minus=13	max_min_right_plus=40	max_pos_hash_score=162	max_right=73	max_right_minus=73	max_right_plus=50	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=2.005683e-02	new_junction_read_count=6	pos_hash_score=6	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.13	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=327	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.12	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=292	side_2_redundant=0	total_non_overlap_reads=6
JC	687	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=128	coverage_plus=151	flanking_left=101	flanking_right=101	frequency=9.491525e-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=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=0.97	new_junction_frequency=9.491525e-01	new_junction_read_count=280	pos_hash_score=142	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.05	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=15	side_2_redundant=0	total_non_overlap_reads=279
JC	688	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=119	coverage_plus=121	flanking_left=101	flanking_right=101	frequency=9.678715e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=49	max_min_right_minus=49	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=0.83	new_junction_frequency=9.678715e-01	new_junction_read_count=241	pos_hash_score=125	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.03	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=8	side_2_redundant=0	total_non_overlap_reads=240
JC	689	.	NC_007779	2865225	1	NC_007779	2865278	-1	-38	alignment_overlap=-38	coverage_minus=5	coverage_plus=10	flanking_left=101	flanking_right=101	frequency=8.876907e-02	junction_possible_overlap_registers=52	key=NC_007779__2865225__1__NC_007779__2865278__-1__-38__TGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA__101__101__0__0	max_left=45	max_left_minus=35	max_left_plus=45	max_min_left=30	max_min_left_minus=27	max_min_left_plus=30	max_min_right=30	max_min_right_minus=28	max_min_right_plus=30	max_pos_hash_score=104	max_right=42	max_right_minus=42	max_right_plus=41	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.09	new_junction_frequency=8.876907e-02	new_junction_read_count=15	pos_hash_score=13	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=278	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.88	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=255	side_2_redundant=0	total_non_overlap_reads=15	unique_read_sequence=TGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA
JC	690	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=26	coverage_plus=28	flanking_left=101	flanking_right=101	frequency=2.146338e-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=86	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=46	max_min_right_minus=24	max_min_right_plus=46	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.25	new_junction_frequency=2.146338e-01	new_junction_read_count=69	pos_hash_score=47	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.93	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=271	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.89	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=246	side_2_redundant=0	total_non_overlap_reads=54
JC	691	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=145	coverage_plus=137	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3147474__1__NC_007779__3262328__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	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=87	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=1.000000e+00	new_junction_read_count=282	pos_hash_score=134	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=282
JC	692	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=162	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=9.802836e-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=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=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.03	new_junction_frequency=9.802836e-01	new_junction_read_count=295	pos_hash_score=142	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=0.02	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=6	side_2_redundant=0	total_non_overlap_reads=291
JC	693	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=138	coverage_plus=126	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=88	max_min_left=47	max_min_left_minus=45	max_min_left_plus=47	max_min_right=47	max_min_right_minus=47	max_min_right_plus=45	max_pos_hash_score=168	max_right=89	max_right_minus=88	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=265	pos_hash_score=127	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=264	unique_read_sequence=CTTTGC
JC	694	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=88	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0	max_left=85	max_left_minus=84	max_left_plus=85	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.70	new_junction_frequency=1.000000e+00	new_junction_read_count=203	pos_hash_score=115	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=201
JC	695	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=142	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=94	max_left_minus=94	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=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=291	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=0.00	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=290
JC	696	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=174	coverage_plus=136	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=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=310	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=310
JC	697	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=133	coverage_plus=168	flanking_left=101	flanking_right=101	frequency=9.934722e-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=84	max_right_minus=81	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=9.934722e-01	new_junction_read_count=301	pos_hash_score=131	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=2	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=301
JC	698	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=150	coverage_plus=136	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=85	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=1.09	new_junction_frequency=1.000000e+00	new_junction_read_count=287	pos_hash_score=130	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=286
JC	699	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=172	coverage_plus=137	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=93	max_left_minus=93	max_left_plus=89	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=313	pos_hash_score=132	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=309
JC	700	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=162	coverage_plus=147	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3746910__-1__NC_007779__3748106__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=47	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.12	new_junction_frequency=1.000000e+00	new_junction_read_count=309	pos_hash_score=147	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=309
JC	701	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=144	coverage_plus=120	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=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=283	pos_hash_score=132	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=264
JC	702	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=154	coverage_plus=141	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3748105__-1__NC_007779__3748643__1__0____101__101__1__0	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=94	max_right_minus=94	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=295	pos_hash_score=150	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=295
JC	703	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=158	coverage_plus=161	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=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=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.15	new_junction_frequency=1.000000e+00	new_junction_read_count=320	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=319
JC	704	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=161	coverage_plus=130	flanking_left=101	flanking_right=101	frequency=9.800850e-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=93	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=93	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=9.800850e-01	new_junction_read_count=292	pos_hash_score=139	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=291
JC	705	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=145	coverage_plus=133	flanking_left=101	flanking_right=101	frequency=9.964681e-01	junction_possible_overlap_registers=88	key=NC_007779__3958122__-1__NC_007779__3958155__1__2____101__101__0__0	max_left=92	max_left_minus=92	max_left_plus=92	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=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=9.964681e-01	new_junction_read_count=279	pos_hash_score=142	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=1	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=88	side_2_read_count=1	side_2_redundant=0	total_non_overlap_reads=278
JC	706	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=127	coverage_plus=132	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=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=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=260	pos_hash_score=131	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=259
JC	707	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=164	coverage_plus=174	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3988379__-1__NC_007779__4009199__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=48	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=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=339	pos_hash_score=150	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=338
JC	708	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=146	coverage_plus=153	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=90	max_left_plus=91	max_min_left=47	max_min_left_minus=47	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=89	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=300	pos_hash_score=137	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=299
JC	709	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=146	coverage_plus=146	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=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=1.03	new_junction_frequency=1.000000e+00	new_junction_read_count=299	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=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=292
JC	710	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=146	coverage_plus=170	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=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=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.13	new_junction_frequency=1.000000e+00	new_junction_read_count=328	pos_hash_score=143	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=316
JC	711	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=165	coverage_plus=188	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=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.22	new_junction_frequency=1.000000e+00	new_junction_read_count=354	pos_hash_score=152	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=353
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