#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	05:50:40 03 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	2_DO_CGATGT_L002_R1_001.fastq
SNP	1	65	NC_007779	66457	A	frequency=1
SNP	2	69	NC_007779	97880	T	frequency=1
SNP	3	80	NC_007779	167632	A	frequency=1
SNP	4	85	NC_007779	274547	G	frequency=1
DEL	5	595,610	NC_007779	274733	97240	frequency=1
SNP	6	104	NC_007779	547694	G	frequency=1
INS	7	105	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	107	NC_007779	556858	T	frequency=1
SNP	9	109	NC_007779	569996	C	frequency=1
DEL	10	596,615	NC_007779	654214	1199	frequency=1
SNP	11	145	NC_007779	749354	A	frequency=1
SNP	12	147	NC_007779	758440	A	frequency=1
SNP	13	160	NC_007779	887234	A	frequency=1
SNP	14	169	NC_007779	987574	T	frequency=1
SNP	15	211	NC_007779	1093686	C	frequency=1
SNP	16	213	NC_007779	1097580	T	frequency=1.975765e-01
SNP	17	220	NC_007779	1170573	T	frequency=1
DEL	18	598,620	NC_007779	1301041	1336	frequency=1
SNP	19	230	NC_007779	1318876	A	frequency=1
DEL	20	599,623	NC_007779	1413639	23060	frequency=1
SNP	21	246	NC_007779	1483588	A	frequency=1
DEL	22	248	NC_007779	1496775	1	frequency=1
SNP	23	262	NC_007779	1615814	A	frequency=1
DEL	24	266	NC_007779	1669599	1	frequency=1
SNP	25	286	NC_007779	1844073	A	frequency=1
SNP	26	294	NC_007779	1918872	A	frequency=1
SNP	27	300	NC_007779	1973476	A	frequency=1
SNP	28	303	NC_007779	2005401	T	frequency=1
SNP	29	313	NC_007779	2170094	A	frequency=1
SNP	30	315	NC_007779	2178210	C	frequency=3.479862e-02
DEL	31	601,630	NC_007779	2320795	1336	frequency=1
SNP	32	341	NC_007779	2406075	T	frequency=1
SNP	33	345	NC_007779	2416102	A	frequency=1
SNP	34	360	NC_007779	2538628	T	frequency=1
INS	35	635	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=7.248895e-01
SNP	36	393	NC_007779	2866111	G	frequency=1
SNP	37	405	NC_007779	3003330	A	frequency=1
SNP	38	409	NC_007779	3048743	T	frequency=8.616972e-02
SNP	39	410	NC_007779	3049815	T	frequency=1
SNP	40	452	NC_007779	3397813	G	frequency=1
DEL	41	642	NC_007779	3399027	3	frequency=1.068153e-01
DEL	42	604,644	NC_007779	3742936	1336	frequency=1
DEL	43	605,646	NC_007779	3746911	1199	frequency=1
DEL	44	510	NC_007779	3750122	1	frequency=1
DEL	45	606,649	NC_007779	3750591	1199	frequency=1
SNP	46	531	NC_007779	3898657	G	frequency=1
DEL	47	607,651	NC_007779	3958123	34	frequency=1
SNP	48	551	NC_007779	4090749	T	frequency=1
SNP	49	557	NC_007779	4165991	C	frequency=1
DEL	50	608,654	NC_007779	4310363	1199	frequency=1
DEL	51	572,573	NC_007779	4371271	2	frequency=1
SNP	52	582	NC_007779	4546535	A	frequency=1
RA	53	.	NC_007779	301	1	.	T	bias_e_value=4104380	bias_p_value=0.88336	fisher_strand_p_value=1	frequency=1.599979e-02	genotype_quality=1188.4	ks_quality_p_value=0.5577	log10_base_likelihood=-17.3082	log10_qual_likelihood_position_model=3.82195	log10_strand_likelihood_position_model=0.431996	new_cov=2/2	polymorphism_quality=12.0	quality=12.0	quality_position_model=3.88176e-15	ref_cov=110/136	reject=INDEL_HOMOPOLYMER	tot_cov=112/138
RA	54	.	NC_007779	302	0	T	.	bias_e_value=2712690	bias_p_value=0.583835	fisher_strand_p_value=0.256434	frequency=1.192188e-02	genotype_quality=993.7	ks_quality_p_value=0.939546	log10_base_likelihood=-6.88721	log10_qual_likelihood_position_model=4.35353	log10_strand_likelihood_position_model=0.768977	new_cov=0/3	polymorphism_quality=1.4	quality=1.4	quality_position_model=0.00189841	ref_cov=111/136	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/139
RA	55	.	NC_007779	5595	0	G	T	bias_e_value=0.0302686	bias_p_value=6.51452e-09	fisher_strand_p_value=2.83437e-10	frequency=7.155180e-02	genotype_quality=1071.2	ks_quality_p_value=1	log10_base_likelihood=-22.7392	log10_qual_likelihood_position_model=19.4395	log10_strand_likelihood_position_model=9.77954	new_cov=0/33	polymorphism_quality=17.5	quality=17.5	quality_position_model=Inf	ref_cov=164/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/184
RA	56	.	NC_007779	11143	0	G	T	bias_e_value=0.0139209	bias_p_value=2.9961e-09	fisher_strand_p_value=1.25911e-10	frequency=5.906820e-02	genotype_quality=1082.7	ks_quality_p_value=1	log10_base_likelihood=-13.7367	log10_qual_likelihood_position_model=23.9862	log10_strand_likelihood_position_model=9.89994	new_cov=0/30	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=164/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/159
RA	57	.	NC_007779	15382	0	A	G	bias_e_value=0.0159483	bias_p_value=3.43246e-09	fisher_strand_p_value=1.45114e-10	frequency=7.635784e-02	genotype_quality=700.7	ks_quality_p_value=1	log10_base_likelihood=-9.66519	log10_qual_likelihood_position_model=19.7445	log10_strand_likelihood_position_model=9.84617	new_cov=25/1	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=69/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/146
RA	58	.	NC_007779	17050	0	A	C	bias_e_value=0.00121329	bias_p_value=2.6113e-10	fisher_strand_p_value=9.91494e-12	frequency=9.292173e-02	genotype_quality=516.5	ks_quality_p_value=1	log10_base_likelihood=-7.08414	log10_qual_likelihood_position_model=21.5083	log10_strand_likelihood_position_model=11.0901	new_cov=0/35	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=86/63	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/98
RA	59	.	NC_007779	23556	0	A	.	bias_e_value=4097930	bias_p_value=0.881971	fisher_strand_p_value=0.597229	frequency=1.082134e-02	genotype_quality=1121.6	ks_quality_p_value=0.929844	log10_base_likelihood=-7.96473	log10_qual_likelihood_position_model=2.33721	log10_strand_likelihood_position_model=0.4614	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.66389e-07	ref_cov=148/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/128
RA	60	.	NC_007779	28427	0	C	A	bias_e_value=133.861	bias_p_value=2.881e-05	fisher_strand_p_value=2.04441e-06	frequency=4.475689e-02	genotype_quality=938.6	ks_quality_p_value=0.999363	log10_base_likelihood=-7.81767	log10_qual_likelihood_position_model=23.4726	log10_strand_likelihood_position_model=5.93403	new_cov=26/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=156/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=183/117
RA	61	.	NC_007779	29496	0	T	A	bias_e_value=5374.07	bias_p_value=0.00115663	fisher_strand_p_value=0.000114836	frequency=3.523827e-02	genotype_quality=784.1	ks_quality_p_value=1	log10_base_likelihood=-5.83418	log10_qual_likelihood_position_model=15.923	log10_strand_likelihood_position_model=3.93992	new_cov=0/10	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=141/90	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/100
RA	62	.	NC_007779	35004	0	G	T	bias_e_value=16.1833	bias_p_value=3.48304e-06	fisher_strand_p_value=2.12866e-07	frequency=4.176712e-02	genotype_quality=959.8	ks_quality_p_value=1	log10_base_likelihood=-11.0115	log10_qual_likelihood_position_model=16.979	log10_strand_likelihood_position_model=6.88178	new_cov=0/22	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=148/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/151
RA	63	.	NC_007779	47305	0	G	T	bias_e_value=0.0010158	bias_p_value=2.18625e-10	fisher_strand_p_value=8.24326e-12	frequency=8.805943e-02	genotype_quality=919.0	ks_quality_p_value=1	log10_base_likelihood=-21.3381	log10_qual_likelihood_position_model=26.2957	log10_strand_likelihood_position_model=11.0916	new_cov=1/32	polymorphism_quality=16.1	quality=16.1	quality_position_model=Inf	ref_cov=159/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/127
RA	64	.	NC_007779	48338	0	T	G	bias_e_value=24712.9	bias_p_value=0.0053188	fisher_strand_p_value=0.000636223	frequency=2.464962e-02	genotype_quality=552.5	ks_quality_p_value=1	log10_base_likelihood=-5.64223	log10_qual_likelihood_position_model=4.69642	log10_strand_likelihood_position_model=3.19639	new_cov=4/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=20/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=24/119
RA	65	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1271.3	new_cov=163/149	quality=1271.3	ref_cov=0/0	tot_cov=163/149
RA	66	.	NC_007779	70602	0	G	T	bias_e_value=0.00619217	bias_p_value=1.3327e-09	fisher_strand_p_value=5.40859e-11	frequency=6.657410e-02	genotype_quality=886.1	ks_quality_p_value=1	log10_base_likelihood=-13.82	log10_qual_likelihood_position_model=24.7897	log10_strand_likelihood_position_model=10.2669	new_cov=0/28	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=146/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/125
RA	67	.	NC_007779	75074	0	T	G	bias_e_value=1.01812e-31	bias_p_value=2.19124e-38	fisher_strand_p_value=2.37564e-40	frequency=1.915574e-01	genotype_quality=877.4	ks_quality_p_value=1	log10_base_likelihood=-53.6278	log10_qual_likelihood_position_model=57.218	log10_strand_likelihood_position_model=39.6242	new_cov=69/0	polymorphism_quality=48.6	quality=48.6	quality_position_model=Inf	ref_cov=37/188	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/188
RA	68	.	NC_007779	75079	0	C	T	bias_e_value=0.000192166	bias_p_value=4.13585e-11	fisher_strand_p_value=1.46403e-12	frequency=6.299639e-02	genotype_quality=881.9	ks_quality_p_value=1	log10_base_likelihood=-12.3058	log10_qual_likelihood_position_model=22.4628	log10_strand_likelihood_position_model=11.8386	new_cov=18/1	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=35/189	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=53/190
RA	69	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=1001.4	new_cov=110/134	quality=1001.4	ref_cov=0/0	tot_cov=110/134
RA	70	.	NC_007779	101246	0	T	G	bias_e_value=48227.1	bias_p_value=0.0103796	fisher_strand_p_value=0.00155127	frequency=2.753162e-02	genotype_quality=551.2	ks_quality_p_value=0.880928	log10_base_likelihood=-9.30671	log10_qual_likelihood_position_model=3.81003	log10_strand_likelihood_position_model=2.80931	new_cov=4/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=0.000188932	ref_cov=26/115	reject=POLYMORPHISM_STRAND	tot_cov=30/115
RA	71	.	NC_007779	107544	1	.	T	bias_e_value=2294500	bias_p_value=0.49383	fisher_strand_p_value=0.318103	frequency=1.568604e-02	genotype_quality=1236.7	ks_quality_p_value=0.575372	log10_base_likelihood=-17.4242	log10_qual_likelihood_position_model=2.5862	log10_strand_likelihood_position_model=0.740224	new_cov=3/1	polymorphism_quality=12.1	quality=12.1	quality_position_model=3.38303e-16	ref_cov=107/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/145
RA	72	.	NC_007779	119384	0	T	G	bias_e_value=1.05164e-10	bias_p_value=2.26338e-17	fisher_strand_p_value=5.25264e-19	frequency=9.430361e-02	genotype_quality=835.8	ks_quality_p_value=1	log10_base_likelihood=-15.663	log10_qual_likelihood_position_model=31.7549	log10_strand_likelihood_position_model=18.2796	new_cov=43/0	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=76/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/161
RA	73	.	NC_007779	150535	0	G	A	bias_e_value=74975	bias_p_value=0.0161364	fisher_strand_p_value=0.00227767	frequency=4.137611e-02	genotype_quality=771.4	ks_quality_p_value=1	log10_base_likelihood=-9.69556	log10_qual_likelihood_position_model=12.3933	log10_strand_likelihood_position_model=2.69609	new_cov=10/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=98/89	reject=POLYMORPHISM_STRAND	tot_cov=108/89
RA	74	.	NC_007779	150537	0	A	C	bias_e_value=129061	bias_p_value=0.027777	fisher_strand_p_value=0.00430839	frequency=2.905273e-02	genotype_quality=758.6	ks_quality_p_value=1	log10_base_likelihood=-8.97359	log10_qual_likelihood_position_model=12.2697	log10_strand_likelihood_position_model=2.43777	new_cov=9/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=99/90	reject=POLYMORPHISM_STRAND	tot_cov=108/90
RA	75	.	NC_007779	150546	0	A	C	bias_e_value=432777	bias_p_value=0.0931438	fisher_strand_p_value=0.0187081	frequency=3.470325e-02	genotype_quality=690.3	ks_quality_p_value=1	log10_base_likelihood=-10.9815	log10_qual_likelihood_position_model=10.0444	log10_strand_likelihood_position_model=1.79431	new_cov=7/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=93/78	reject=POLYMORPHISM_STRAND	tot_cov=100/78
RA	76	.	NC_007779	164574	0	T	G	bias_e_value=180.502	bias_p_value=3.88483e-05	fisher_strand_p_value=2.82718e-06	frequency=3.778076e-02	genotype_quality=456.1	ks_quality_p_value=0.997241	log10_base_likelihood=-7.1982	log10_qual_likelihood_position_model=7.509	log10_strand_likelihood_position_model=5.55598	new_cov=1/8	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=136/21	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/29
RA	77	.	NC_007779	164597	1	.	C	bias_e_value=2317770	bias_p_value=0.498839	fisher_strand_p_value=0.196504	frequency=1.369858e-02	genotype_quality=634.1	ks_quality_p_value=0.9465	log10_base_likelihood=-7.84531	log10_qual_likelihood_position_model=2.64448	log10_strand_likelihood_position_model=0.706628	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.33705e-06	ref_cov=63/81	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=65/81
RA	78	.	NC_007779	164601	0	T	C	bias_e_value=2602.07	bias_p_value=0.000560027	fisher_strand_p_value=5.38163e-05	frequency=7.030106e-02	genotype_quality=397.0	ks_quality_p_value=0.956996	log10_base_likelihood=-15.4724	log10_qual_likelihood_position_model=9.90697	log10_strand_likelihood_position_model=4.26909	new_cov=9/0	polymorphism_quality=10.1	quality=10.1	quality_position_model=0.00636638	ref_cov=36/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=46/81
RA	79	.	NC_007779	164603	0	A	C	bias_e_value=21280.9	bias_p_value=0.00458014	fisher_strand_p_value=0.000537474	frequency=4.890394e-02	genotype_quality=390.7	ks_quality_p_value=0.999067	log10_base_likelihood=-8.40081	log10_qual_likelihood_position_model=8.34217	log10_strand_likelihood_position_model=3.26964	new_cov=7/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=38/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=45/81
RA	80	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=1053.1	new_cov=134/124	quality=1053.1	ref_cov=0/0	tot_cov=134/125
RA	81	.	NC_007779	175694	0	T	G	bias_e_value=2.32631e-07	bias_p_value=5.00677e-14	fisher_strand_p_value=1.42294e-15	frequency=6.245708e-02	genotype_quality=889.8	ks_quality_p_value=1	log10_base_likelihood=-8.55123	log10_qual_likelihood_position_model=24.7595	log10_strand_likelihood_position_model=14.8468	new_cov=38/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=93/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/163
RA	82	.	NC_007779	207536	0	G	T	bias_e_value=0.0426489	bias_p_value=9.17904e-09	fisher_strand_p_value=4.05696e-10	frequency=8.367538e-02	genotype_quality=837.2	ks_quality_p_value=1	log10_base_likelihood=-18.9871	log10_qual_likelihood_position_model=25.9063	log10_strand_likelihood_position_model=9.64845	new_cov=0/34	polymorphism_quality=13.7	quality=13.7	quality_position_model=Inf	ref_cov=130/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/158
RA	83	.	NC_007779	221544	0	A	.	bias_e_value=4628910	bias_p_value=0.99625	fisher_strand_p_value=1	frequency=1.407814e-02	genotype_quality=846.6	ks_quality_p_value=0.914655	log10_base_likelihood=-8.64497	log10_qual_likelihood_position_model=1.42387	log10_strand_likelihood_position_model=0.391342	new_cov=1/2	polymorphism_quality=3.2	quality=3.2	quality_position_model=8.87748e-09	ref_cov=96/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=98/115
RA	84	.	NC_007779	229036	1	.	T	bias_e_value=2535700	bias_p_value=0.545742	fisher_strand_p_value=0.215171	frequency=9.295464e-03	genotype_quality=1042.8	ks_quality_p_value=1	log10_base_likelihood=-6.61489	log10_qual_likelihood_position_model=2.35322	log10_strand_likelihood_position_model=0.667217	new_cov=0/2	polymorphism_quality=1.1	quality=1.1	quality_position_model=2.05459e-05	ref_cov=115/98	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/100
RA	85	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1247.0	new_cov=146/142	quality=1247.0	ref_cov=0/0	tot_cov=146/142
RA	86	.	NC_007779	379236	1	.	G	bias_e_value=2596540	bias_p_value=0.558836	fisher_strand_p_value=1	frequency=1.843357e-02	genotype_quality=1030.2	ks_quality_p_value=0.223805	log10_base_likelihood=-18.0241	log10_qual_likelihood_position_model=2.52197	log10_strand_likelihood_position_model=0.432243	new_cov=3/1	polymorphism_quality=12.7	quality=12.7	quality_position_model=3.49234e-17	ref_cov=133/80	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/81
RA	87	.	NC_007779	379237	0	G	.	bias_e_value=2500780	bias_p_value=0.538226	fisher_strand_p_value=0.563353	frequency=1.298141e-02	genotype_quality=966.0	ks_quality_p_value=0.373326	log10_base_likelihood=-8.78529	log10_qual_likelihood_position_model=1.82003	log10_strand_likelihood_position_model=0.548642	new_cov=1/2	polymorphism_quality=3.3	quality=3.3	quality_position_model=2.36704e-08	ref_cov=139/89	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/91
RA	88	.	NC_007779	379266	0	G	C	bias_e_value=1640.58	bias_p_value=0.000353091	fisher_strand_p_value=3.16128e-05	frequency=4.652834e-02	genotype_quality=775.8	ks_quality_p_value=0.981421	log10_base_likelihood=-10.4105	log10_qual_likelihood_position_model=16.6755	log10_strand_likelihood_position_model=4.50014	new_cov=13/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=94/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=107/123
RA	89	.	NC_007779	387917	0	T	G	bias_e_value=0.0121734	bias_p_value=2.61999e-09	fisher_strand_p_value=1.0959e-10	frequency=5.969477e-02	genotype_quality=442.7	ks_quality_p_value=0.998825	log10_base_likelihood=-11.3595	log10_qual_likelihood_position_model=12.2146	log10_strand_likelihood_position_model=9.96023	new_cov=0/12	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=122/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/27
RA	90	.	NC_007779	387919	0	A	G	bias_e_value=1.8589e-05	bias_p_value=4.00078e-12	fisher_strand_p_value=1.32257e-13	frequency=1.002202e-01	genotype_quality=458.7	ks_quality_p_value=0.986377	log10_base_likelihood=-27.6131	log10_qual_likelihood_position_model=12.9714	log10_strand_likelihood_position_model=12.8786	new_cov=0/15	polymorphism_quality=22.4	quality=22.4	quality_position_model=0.00190586	ref_cov=121/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/27
RA	91	.	NC_007779	390218	0	T	G	bias_e_value=2570560	bias_p_value=0.553245	fisher_strand_p_value=0.232662	frequency=6.711006e-03	genotype_quality=1215.8	ks_quality_p_value=0.945964	log10_base_likelihood=-5.78309	log10_qual_likelihood_position_model=2.03742	log10_strand_likelihood_position_model=0.633274	new_cov=0/2	polymorphism_quality=0.2	quality=0.2	quality_position_model=6.65156e-05	ref_cov=154/142	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=154/144
RA	92	.	NC_007779	407306	0	C	A	bias_e_value=1.44695	bias_p_value=3.11418e-07	fisher_strand_p_value=1.64576e-08	frequency=6.084299e-02	genotype_quality=888.8	ks_quality_p_value=1	log10_base_likelihood=-12.3574	log10_qual_likelihood_position_model=16.9865	log10_strand_likelihood_position_model=7.81868	new_cov=26/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=130/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/143
RA	93	.	NC_007779	417763	0	G	T	bias_e_value=2.58642	bias_p_value=5.56658e-07	fisher_strand_p_value=3.0404e-08	frequency=4.456425e-02	genotype_quality=892.5	ks_quality_p_value=1	log10_base_likelihood=-7.63372	log10_qual_likelihood_position_model=18.4206	log10_strand_likelihood_position_model=7.51707	new_cov=0/20	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=149/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/118
RA	94	.	NC_007779	440767	0	G	T	bias_e_value=8.30094e-06	bias_p_value=1.78656e-12	fisher_strand_p_value=5.71774e-14	frequency=1.488252e-01	genotype_quality=677.0	ks_quality_p_value=0.99191	log10_base_likelihood=-38.7473	log10_qual_likelihood_position_model=25.375	log10_strand_likelihood_position_model=13.2498	new_cov=0/41	polymorphism_quality=33.6	quality=33.6	quality_position_model=0.261593	ref_cov=116/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/126
RA	95	.	NC_007779	468788	0	A	.	bias_e_value=3221550	bias_p_value=0.693353	fisher_strand_p_value=0.622278	frequency=1.458931e-02	genotype_quality=1099.3	ks_quality_p_value=0.526688	log10_base_likelihood=-11.0696	log10_qual_likelihood_position_model=2.88903	log10_strand_likelihood_position_model=0.595714	new_cov=1/3	polymorphism_quality=5.7	quality=5.7	quality_position_model=1.48466e-09	ref_cov=135/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/138
RA	96	.	NC_007779	474686	0	G	T	bias_e_value=0.0190339	bias_p_value=4.09655e-09	fisher_strand_p_value=1.74705e-10	frequency=7.648516e-02	genotype_quality=838.9	ks_quality_p_value=0.999131	log10_base_likelihood=-20.3197	log10_qual_likelihood_position_model=22.2819	log10_strand_likelihood_position_model=9.86889	new_cov=0/31	polymorphism_quality=15.0	quality=15.0	quality_position_model=Inf	ref_cov=139/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/144
RA	97	.	NC_007779	487248	0	C	A	bias_e_value=203.167	bias_p_value=4.37262e-05	fisher_strand_p_value=3.20306e-06	frequency=3.559208e-02	genotype_quality=1196.3	ks_quality_p_value=1	log10_base_likelihood=-6.57015	log10_qual_likelihood_position_model=16.3329	log10_strand_likelihood_position_model=5.49444	new_cov=0/14	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=193/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=193/138
RA	98	.	NC_007779	492774	0	C	A	bias_e_value=1528.9	bias_p_value=0.000329056	fisher_strand_p_value=2.87185e-05	frequency=3.150940e-02	genotype_quality=1074.6	ks_quality_p_value=1	log10_base_likelihood=-8.19997	log10_qual_likelihood_position_model=11.9981	log10_strand_likelihood_position_model=4.54184	new_cov=0/10	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=178/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=178/101
RA	99	.	NC_007779	506505	0	T	.	bias_e_value=3816600	bias_p_value=0.821423	fisher_strand_p_value=0.590111	frequency=9.366989e-03	genotype_quality=1300.1	ks_quality_p_value=0.788794	log10_base_likelihood=-7.87875	log10_qual_likelihood_position_model=2.15124	log10_strand_likelihood_position_model=0.475035	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.79362e-07	ref_cov=175/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=176/144
RA	100	.	NC_007779	513848	0	A	C	bias_e_value=4.46113e-23	bias_p_value=9.60139e-30	fisher_strand_p_value=1.3318e-31	frequency=1.986732e-01	genotype_quality=690.8	ks_quality_p_value=1	log10_base_likelihood=-34.0985	log10_qual_likelihood_position_model=43.3578	log10_strand_likelihood_position_model=30.8756	new_cov=0/64	polymorphism_quality=28.9	quality=28.9	quality_position_model=Inf	ref_cov=141/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/104
RA	101	.	NC_007779	522430	1	.	T	bias_e_value=3815980	bias_p_value=0.82129	fisher_strand_p_value=1	frequency=1.593590e-02	genotype_quality=1230.1	ks_quality_p_value=0.465302	log10_base_likelihood=-17.8126	log10_qual_likelihood_position_model=2.53644	log10_strand_likelihood_position_model=0.441725	new_cov=2/2	polymorphism_quality=12.5	quality=12.5	quality_position_model=6.0519e-17	ref_cov=142/105	reject=INDEL_HOMOPOLYMER	tot_cov=144/107
RA	102	.	NC_007779	524490	0	T	G	bias_e_value=0.00216511	bias_p_value=4.65982e-10	fisher_strand_p_value=1.81071e-11	frequency=6.435251e-02	genotype_quality=1055.1	ks_quality_p_value=1	log10_base_likelihood=-15.4381	log10_qual_likelihood_position_model=27.9202	log10_strand_likelihood_position_model=10.7422	new_cov=25/0	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=98/187	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/187
RA	103	.	NC_007779	539140	0	A	G	bias_e_value=1998940	bias_p_value=0.430219	fisher_strand_p_value=0.254191	frequency=1.050568e-02	genotype_quality=1120.6	ks_quality_p_value=0.581125	log10_base_likelihood=-5.57517	log10_qual_likelihood_position_model=3.07304	log10_strand_likelihood_position_model=0.788198	new_cov=0/3	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.00216068	ref_cov=128/152	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=128/155
RA	104	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=1350.4	new_cov=158/162	quality=1350.4	ref_cov=0/0	tot_cov=158/162
RA	105	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=1339.9	new_cov=159/150	quality=1339.9	ref_cov=0/0	tot_cov=159/150
RA	106	.	NC_007779	556653	0	A	C	bias_e_value=8.70416e-14	bias_p_value=1.87334e-20	fisher_strand_p_value=3.72116e-22	frequency=9.312057e-02	genotype_quality=863.4	ks_quality_p_value=1	log10_base_likelihood=-13.2609	log10_qual_likelihood_position_model=36.277	log10_strand_likelihood_position_model=21.4293	new_cov=0/41	polymorphism_quality=7.9	quality=7.9	quality_position_model=Inf	ref_cov=172/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/95
RA	107	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=1313.8	new_cov=172/149	quality=1313.8	ref_cov=0/0	tot_cov=172/149
RA	108	.	NC_007779	562819	0	T	C	bias_e_value=68641.4	bias_p_value=0.0147733	fisher_strand_p_value=0.00205548	frequency=4.440594e-02	genotype_quality=686.2	ks_quality_p_value=1	log10_base_likelihood=-6.47152	log10_qual_likelihood_position_model=17.5667	log10_strand_likelihood_position_model=2.82766	new_cov=0/13	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=76/110	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=76/123
RA	109	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1026.9	new_cov=116/119	quality=1026.9	ref_cov=0/0	tot_cov=116/119
RA	110	.	NC_007779	583702	1	.	T	bias_e_value=1193770	bias_p_value=0.256928	fisher_strand_p_value=0.137422	frequency=1.242256e-02	genotype_quality=792.4	ks_quality_p_value=0.511515	log10_base_likelihood=-8.72416	log10_qual_likelihood_position_model=1.36562	log10_strand_likelihood_position_model=0.861943	new_cov=0/2	polymorphism_quality=3.3	quality=3.3	quality_position_model=1.95748e-08	ref_cov=101/58	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=101/60
RA	111	.	NC_007779	593216	0	T	G	bias_e_value=5.76669e-12	bias_p_value=1.24113e-18	fisher_strand_p_value=2.69456e-20	frequency=7.620192e-02	genotype_quality=721.0	ks_quality_p_value=1	log10_base_likelihood=-12.3866	log10_qual_likelihood_position_model=28.8226	log10_strand_likelihood_position_model=19.5695	new_cov=28/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=26/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=54/158
RA	112	.	NC_007779	598799	0	T	G	bias_e_value=1.45492e-28	bias_p_value=3.13133e-35	fisher_strand_p_value=3.68868e-37	frequency=1.874046e-01	genotype_quality=711.3	ks_quality_p_value=1	log10_base_likelihood=-37.4287	log10_qual_likelihood_position_model=49.5276	log10_strand_likelihood_position_model=36.4331	new_cov=56/0	polymorphism_quality=32.3	quality=32.3	quality_position_model=Inf	ref_cov=20/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=76/156
RA	113	.	NC_007779	606687	1	.	T	bias_e_value=4561070	bias_p_value=0.981649	fisher_strand_p_value=1	frequency=1.102924e-02	genotype_quality=1345.0	ks_quality_p_value=0.814641	log10_base_likelihood=-12.7168	log10_qual_likelihood_position_model=1.73914	log10_strand_likelihood_position_model=0.421187	new_cov=2/1	polymorphism_quality=7.3	quality=7.3	quality_position_model=1.35317e-12	ref_cov=135/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/135
RA	114	.	NC_007779	606688	0	T	.	bias_e_value=114818	bias_p_value=0.0247114	fisher_strand_p_value=0.622258	frequency=1.448536e-02	genotype_quality=1111.6	ks_quality_p_value=0.00603045	log10_base_likelihood=-11.5328	log10_qual_likelihood_position_model=2.77734	log10_strand_likelihood_position_model=0.602077	new_cov=1/3	polymorphism_quality=6.1	quality=6.1	quality_position_model=3.87404e-10	ref_cov=137/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/138
RA	115	.	NC_007779	645970	0	T	G	bias_e_value=1.5801e-18	bias_p_value=3.40075e-25	fisher_strand_p_value=5.53337e-27	frequency=2.013373e-01	genotype_quality=631.2	ks_quality_p_value=1	log10_base_likelihood=-44.6349	log10_qual_likelihood_position_model=41.2262	log10_strand_likelihood_position_model=26.257	new_cov=46/0	polymorphism_quality=39.5	quality=39.5	quality_position_model=Inf	ref_cov=28/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/134
RA	116	.	NC_007779	645983	0	T	C	bias_e_value=2.52487	bias_p_value=5.43412e-07	fisher_strand_p_value=2.96393e-08	frequency=5.252314e-02	genotype_quality=735.0	ks_quality_p_value=1	log10_base_likelihood=-7.01854	log10_qual_likelihood_position_model=15.4822	log10_strand_likelihood_position_model=7.52813	new_cov=18/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=71/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=89/130
RA	117	.	NC_007779	646440	0	C	A	bias_e_value=1.60978e-09	bias_p_value=3.46462e-16	fisher_strand_p_value=8.65104e-18	frequency=7.507944e-02	genotype_quality=957.1	ks_quality_p_value=0.993885	log10_base_likelihood=-37.2223	log10_qual_likelihood_position_model=19.9122	log10_strand_likelihood_position_model=17.0629	new_cov=0/18	polymorphism_quality=32.1	quality=32.1	quality_position_model=0.146288	ref_cov=204/17	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=204/35
RA	118	.	NC_007779	657963	1	.	T	bias_e_value=3872240	bias_p_value=0.833397	fisher_strand_p_value=1	frequency=7.812500e-03	genotype_quality=1245.6	ks_quality_p_value=0.481491	log10_base_likelihood=-8.16925	log10_qual_likelihood_position_model=1.52877	log10_strand_likelihood_position_model=0.299436	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.83274e-08	ref_cov=129/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/126
RA	119	.	NC_007779	667452	0	G	T	bias_e_value=1096410	bias_p_value=0.235972	fisher_strand_p_value=0.0628165	frequency=2.302551e-02	genotype_quality=836.9	ks_quality_p_value=0.996027	log10_base_likelihood=-5.9623	log10_qual_likelihood_position_model=7.79329	log10_strand_likelihood_position_model=1.3692	new_cov=5/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=104/94	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=109/94
RA	120	.	NC_007779	686495	0	A	C	bias_e_value=1.01353e-12	bias_p_value=2.18135e-19	fisher_strand_p_value=4.55997e-21	frequency=7.999134e-02	genotype_quality=764.7	ks_quality_p_value=1	log10_base_likelihood=-13.2008	log10_qual_likelihood_position_model=29.6326	log10_strand_likelihood_position_model=20.341	new_cov=0/25	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=171/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/44
RA	121	.	NC_007779	687133	0	A	C	bias_e_value=0.000191729	bias_p_value=4.12645e-11	fisher_strand_p_value=1.46058e-12	frequency=6.485891e-02	genotype_quality=909.0	ks_quality_p_value=1	log10_base_likelihood=-14.6876	log10_qual_likelihood_position_model=29.8168	log10_strand_likelihood_position_model=11.8355	new_cov=0/26	polymorphism_quality=9.3	quality=9.3	quality_position_model=Inf	ref_cov=165/76	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/103
RA	122	.	NC_007779	697558	1	.	T	bias_e_value=2126130	bias_p_value=0.457594	fisher_strand_p_value=0.206312	frequency=7.168770e-03	genotype_quality=1375.9	ks_quality_p_value=0.787157	log10_base_likelihood=-8.36517	log10_qual_likelihood_position_model=1.83504	log10_strand_likelihood_position_model=0.685475	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=9.2301e-08	ref_cov=125/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/152
RA	123	.	NC_007779	704668	0	T	G	bias_e_value=4.15335e-08	bias_p_value=8.93899e-15	fisher_strand_p_value=2.41868e-16	frequency=7.092142e-02	genotype_quality=644.3	ks_quality_p_value=1	log10_base_likelihood=-9.73551	log10_qual_likelihood_position_model=27.1301	log10_strand_likelihood_position_model=15.6164	new_cov=29/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=40/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=69/133
RA	124	.	NC_007779	706386	0	T	.	bias_e_value=4626720	bias_p_value=0.995778	fisher_strand_p_value=1	frequency=2.196980e-02	genotype_quality=1088.5	ks_quality_p_value=0.909531	log10_base_likelihood=-17.9832	log10_qual_likelihood_position_model=3.3748	log10_strand_likelihood_position_model=0.515341	new_cov=3/3	polymorphism_quality=12.7	quality=12.7	quality_position_model=3.42045e-16	ref_cov=119/148	reject=INDEL_HOMOPOLYMER	tot_cov=122/151
RA	125	.	NC_007779	730056	0	A	C	bias_e_value=1887890	bias_p_value=0.406318	fisher_strand_p_value=1	frequency=8.584976e-03	genotype_quality=902.1	ks_quality_p_value=0.135491	log10_base_likelihood=-6.01079	log10_qual_likelihood_position_model=1.98466	log10_strand_likelihood_position_model=0.327327	new_cov=2/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=1.59491e-05	ref_cov=158/73	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=160/73
RA	126	.	NC_007779	730441	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	127	.	NC_007779	730442	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	128	.	NC_007779	730443	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	129	.	NC_007779	730444	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	130	.	NC_007779	730445	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	131	.	NC_007779	730449	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	132	.	NC_007779	730450	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	133	.	NC_007779	730451	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	134	.	NC_007779	730452	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	135	.	NC_007779	730454	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	136	.	NC_007779	730455	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	137	.	NC_007779	730458	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	138	.	NC_007779	730459	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	139	.	NC_007779	730460	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	140	.	NC_007779	730461	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	141	.	NC_007779	730463	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	142	.	NC_007779	730464	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	143	.	NC_007779	730465	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	144	.	NC_007779	730466	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	145	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=991.2	new_cov=102/139	quality=991.2	ref_cov=0/0	tot_cov=102/139
RA	146	.	NC_007779	752693	0	A	C	bias_e_value=5.2165e-08	bias_p_value=1.12271e-14	fisher_strand_p_value=3.05718e-16	frequency=5.700111e-02	genotype_quality=1019.6	ks_quality_p_value=1	log10_base_likelihood=-7.57857	log10_qual_likelihood_position_model=33.4019	log10_strand_likelihood_position_model=15.5147	new_cov=0/31	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=198/76	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=198/107
RA	147	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=1181.7	new_cov=142/145	quality=1181.7	ref_cov=0/0	tot_cov=142/145
RA	148	.	NC_007779	759019	0	C	G	bias_e_value=1.35771e-08	bias_p_value=2.9221e-15	fisher_strand_p_value=7.67659e-17	frequency=8.526993e-02	genotype_quality=706.7	ks_quality_p_value=0.998904	log10_base_likelihood=-26.456	log10_qual_likelihood_position_model=19.2667	log10_strand_likelihood_position_model=16.1148	new_cov=0/16	polymorphism_quality=21.2	quality=21.2	quality_position_model=Inf	ref_cov=154/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=154/25
RA	149	.	NC_007779	817515	0	G	T	bias_e_value=0.137148	bias_p_value=2.95176e-08	fisher_strand_p_value=1.37921e-09	frequency=5.092192e-02	genotype_quality=862.6	ks_quality_p_value=1	log10_base_likelihood=-7.15517	log10_qual_likelihood_position_model=20.1735	log10_strand_likelihood_position_model=8.86037	new_cov=0/26	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=142/106	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/133
RA	150	.	NC_007779	829769	0	G	T	bias_e_value=7166.27	bias_p_value=0.00154235	fisher_strand_p_value=0.000158159	frequency=2.973366e-02	genotype_quality=806.3	ks_quality_p_value=1	log10_base_likelihood=-6.50495	log10_qual_likelihood_position_model=11.9422	log10_strand_likelihood_position_model=3.82911	new_cov=0/14	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=110/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/132
RA	151	.	NC_007779	837857	0	A	.	bias_e_value=4550680	bias_p_value=0.979412	fisher_strand_p_value=1	frequency=1.030159e-02	genotype_quality=1171.6	ks_quality_p_value=0.804069	log10_base_likelihood=-8.12616	log10_qual_likelihood_position_model=1.42412	log10_strand_likelihood_position_model=0.372837	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.91361e-08	ref_cov=122/165	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/167
RA	152	.	NC_007779	839315	1	.	G	bias_e_value=2594860	bias_p_value=0.558475	fisher_strand_p_value=0.235533	frequency=6.896019e-03	genotype_quality=1451.1	ks_quality_p_value=0.949182	log10_base_likelihood=-7.90455	log10_qual_likelihood_position_model=2.51506	log10_strand_likelihood_position_model=0.627949	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.22955e-06	ref_cov=139/149	reject=POLYMORPHISM_STRAND	tot_cov=141/149
RA	153	.	NC_007779	848585	0	C	A	bias_e_value=6.93052	bias_p_value=1.49161e-06	fisher_strand_p_value=9.21112e-08	frequency=2.905083e-02	genotype_quality=1023.5	ks_quality_p_value=0.937981	log10_base_likelihood=-6.19054	log10_qual_likelihood_position_model=24.4113	log10_strand_likelihood_position_model=7.03569	new_cov=19/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=115/168	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/168
RA	154	.	NC_007779	853114	0	C	G	bias_e_value=73.8402	bias_p_value=1.58922e-05	fisher_strand_p_value=1.07815e-06	frequency=4.438210e-02	genotype_quality=757.3	ks_quality_p_value=1	log10_base_likelihood=-10.4498	log10_qual_likelihood_position_model=14.4882	log10_strand_likelihood_position_model=5.96732	new_cov=0/11	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=139/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/61
RA	155	.	NC_007779	854528	0	C	A	bias_e_value=796079	bias_p_value=0.171335	fisher_strand_p_value=0.040804	frequency=1.253986e-02	genotype_quality=1298.1	ks_quality_p_value=1	log10_base_likelihood=-7.05663	log10_qual_likelihood_position_model=7.80988	log10_strand_likelihood_position_model=1.451	new_cov=6/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=175/133	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=181/133
RA	156	.	NC_007779	854530	0	T	C	bias_e_value=506218	bias_p_value=0.10895	fisher_strand_p_value=0.022785	frequency=2.153587e-02	genotype_quality=1186.5	ks_quality_p_value=1	log10_base_likelihood=-10.2631	log10_qual_likelihood_position_model=11.0421	log10_strand_likelihood_position_model=1.94308	new_cov=8/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=169/130	reject=POLYMORPHISM_STRAND	tot_cov=177/130
RA	157	.	NC_007779	854535	0	T	A	bias_e_value=845502	bias_p_value=0.181972	fisher_strand_p_value=0.0441714	frequency=2.123928e-02	genotype_quality=1170.0	ks_quality_p_value=1	log10_base_likelihood=-12.292	log10_qual_likelihood_position_model=7.80508	log10_strand_likelihood_position_model=1.59472	new_cov=7/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=0.000114113	ref_cov=170/120	reject=POLYMORPHISM_STRAND	tot_cov=178/120
RA	158	.	NC_007779	868837	0	C	.	bias_e_value=3329200	bias_p_value=0.716522	fisher_strand_p_value=0.621336	frequency=9.735107e-03	genotype_quality=1267.9	ks_quality_p_value=0.5619	log10_base_likelihood=-8.5189	log10_qual_likelihood_position_model=1.08012	log10_strand_likelihood_position_model=0.427423	new_cov=1/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=5.77169e-09	ref_cov=154/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=155/153
RA	159	.	NC_007779	871317	0	T	.	bias_e_value=3546360	bias_p_value=0.76326	fisher_strand_p_value=0.5933	frequency=9.546280e-03	genotype_quality=1195.5	ks_quality_p_value=0.668234	log10_base_likelihood=-8.01009	log10_qual_likelihood_position_model=3.11875	log10_strand_likelihood_position_model=0.468887	new_cov=2/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.77738e-06	ref_cov=141/170	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/171
RA	160	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=891.0	new_cov=139/88	quality=891.0	ref_cov=0/0	tot_cov=139/88
RA	161	.	NC_007779	894943	0	T	G	bias_e_value=9.83478e-07	bias_p_value=2.11668e-13	fisher_strand_p_value=6.28069e-15	frequency=6.420755e-02	genotype_quality=862.8	ks_quality_p_value=1	log10_base_likelihood=-6.56206	log10_qual_likelihood_position_model=36.3117	log10_strand_likelihood_position_model=14.202	new_cov=35/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=83/155	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/155
RA	162	.	NC_007779	895911	0	C	A	bias_e_value=0.00641196	bias_p_value=1.38001e-09	fisher_strand_p_value=5.60884e-11	frequency=7.157993e-02	genotype_quality=899.7	ks_quality_p_value=1	log10_base_likelihood=-11.5809	log10_qual_likelihood_position_model=22.9352	log10_strand_likelihood_position_model=10.2511	new_cov=31/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=115/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/149
RA	163	.	NC_007779	904838	0	C	A	bias_e_value=6.8167e-14	bias_p_value=1.46711e-20	fisher_strand_p_value=3.33233e-22	frequency=1.631751e-01	genotype_quality=829.8	ks_quality_p_value=0.870226	log10_base_likelihood=-40.7144	log10_qual_likelihood_position_model=41.9548	log10_strand_likelihood_position_model=21.4773	new_cov=56/0	polymorphism_quality=35.6	quality=35.6	quality_position_model=Inf	ref_cov=79/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/150
RA	164	.	NC_007779	914008	0	C	T	bias_e_value=3033840	bias_p_value=0.652953	fisher_strand_p_value=0.333579	frequency=1.232815e-02	genotype_quality=1362.9	ks_quality_p_value=0.879014	log10_base_likelihood=-6.49273	log10_qual_likelihood_position_model=4.1477	log10_strand_likelihood_position_model=0.688691	new_cov=3/1	polymorphism_quality=1.0	quality=1.0	quality_position_model=0.00250345	ref_cov=143/174	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=146/175
RA	165	.	NC_007779	915697	0	G	T	bias_e_value=1129.8	bias_p_value=0.000243159	fisher_strand_p_value=2.0626e-05	frequency=3.058720e-02	genotype_quality=960.8	ks_quality_p_value=1	log10_base_likelihood=-7.82205	log10_qual_likelihood_position_model=12.5643	log10_strand_likelihood_position_model=4.87991	new_cov=0/16	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=145/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/151
RA	166	.	NC_007779	917407	0	C	A	bias_e_value=0.468215	bias_p_value=1.00771e-07	fisher_strand_p_value=5.5195e-09	frequency=4.382324e-02	genotype_quality=1047.3	ks_quality_p_value=0.907792	log10_base_likelihood=-8.77204	log10_qual_likelihood_position_model=27.2939	log10_strand_likelihood_position_model=8.2581	new_cov=23/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=122/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/172
RA	167	.	NC_007779	969494	0	C	A	bias_e_value=20.1731	bias_p_value=4.34174e-06	fisher_strand_p_value=2.69502e-07	frequency=6.646013e-02	genotype_quality=604.6	ks_quality_p_value=0.998913	log10_base_likelihood=-8.59664	log10_qual_likelihood_position_model=13.7142	log10_strand_likelihood_position_model=6.56944	new_cov=20/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=80/102	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/103
RA	168	.	NC_007779	975142	0	T	G	bias_e_value=4115.54	bias_p_value=0.00088576	fisher_strand_p_value=8.5434e-05	frequency=3.003693e-02	genotype_quality=521.4	ks_quality_p_value=1	log10_base_likelihood=-6.16343	log10_qual_likelihood_position_model=6.29065	log10_strand_likelihood_position_model=4.06837	new_cov=4/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=10/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=14/117
RA	169	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=999.2	new_cov=82/161	quality=999.2	ref_cov=0/0	tot_cov=82/161
RA	170	.	NC_007779	987916	0	T	G	bias_e_value=1.4379e-07	bias_p_value=3.0947e-14	fisher_strand_p_value=8.67321e-16	frequency=9.262037e-02	genotype_quality=549.4	ks_quality_p_value=1	log10_base_likelihood=-12.8744	log10_qual_likelihood_position_model=22.7989	log10_strand_likelihood_position_model=15.0618	new_cov=19/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=14/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=33/121
RA	171	.	NC_007779	991407	0	G	T	bias_e_value=6.92938	bias_p_value=1.49137e-06	fisher_strand_p_value=9.71715e-08	frequency=5.732679e-02	genotype_quality=932.6	ks_quality_p_value=0.88898	log10_base_likelihood=-12.3462	log10_qual_likelihood_position_model=26.5053	log10_strand_likelihood_position_model=7.03332	new_cov=0/24	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=139/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/157
RA	172	.	NC_007779	999606	0	A	T	bias_e_value=9843.83	bias_p_value=0.00211862	fisher_strand_p_value=0.000225447	frequency=6.417274e-02	genotype_quality=704.0	ks_quality_p_value=1	log10_base_likelihood=-19.2483	log10_qual_likelihood_position_model=13.0626	log10_strand_likelihood_position_model=3.70898	new_cov=13/0	polymorphism_quality=14.0	quality=14.0	quality_position_model=0.000318105	ref_cov=90/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/90
RA	173	.	NC_007779	999607	0	A	C	bias_e_value=9843.83	bias_p_value=0.00211862	fisher_strand_p_value=0.000225447	frequency=5.994034e-02	genotype_quality=679.3	ks_quality_p_value=1	log10_base_likelihood=-21.5936	log10_qual_likelihood_position_model=13.7931	log10_strand_likelihood_position_model=3.70898	new_cov=13/0	polymorphism_quality=16.3	quality=16.3	quality_position_model=6.16627e-06	ref_cov=90/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/90
RA	174	.	NC_007779	999613	0	A	T	bias_e_value=11329.6	bias_p_value=0.0024384	fisher_strand_p_value=0.000276845	frequency=6.676006e-02	genotype_quality=703.1	ks_quality_p_value=0.95323	log10_base_likelihood=-32.7696	log10_qual_likelihood_position_model=12.3327	log10_strand_likelihood_position_model=3.59359	new_cov=13/0	polymorphism_quality=27.6	quality=27.6	quality_position_model=5.57383e-19	ref_cov=92/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/89
RA	175	.	NC_007779	999623	0	A	T	bias_e_value=694811	bias_p_value=0.14954	fisher_strand_p_value=0.0341819	frequency=2.980709e-02	genotype_quality=709.3	ks_quality_p_value=0.999634	log10_base_likelihood=-10.3235	log10_qual_likelihood_position_model=6.98697	log10_strand_likelihood_position_model=1.56659	new_cov=6/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=0.00187324	ref_cov=96/82	reject=POLYMORPHISM_STRAND	tot_cov=102/82
RA	176	.	NC_007779	999625	0	T	C	bias_e_value=1154640	bias_p_value=0.248505	fisher_strand_p_value=0.067148	frequency=2.330589e-02	genotype_quality=701.4	ks_quality_p_value=1	log10_base_likelihood=-7.82453	log10_qual_likelihood_position_model=5.88276	log10_strand_likelihood_position_model=1.2908	new_cov=5/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=0.0378087	ref_cov=98/82	reject=POLYMORPHISM_STRAND	tot_cov=103/82
RA	177	.	NC_007779	999627	0	A	T	bias_e_value=1160880	bias_p_value=0.249849	fisher_strand_p_value=0.0681732	frequency=2.644730e-02	genotype_quality=709.8	ks_quality_p_value=0.992269	log10_base_likelihood=-7.88767	log10_qual_likelihood_position_model=6.9876	log10_strand_likelihood_position_model=1.27651	new_cov=5/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=97/80	reject=POLYMORPHISM_STRAND	tot_cov=102/80
RA	178	.	NC_007779	999628	0	A	G	bias_e_value=747768	bias_p_value=0.160937	fisher_strand_p_value=0.0375942	frequency=2.571201e-02	genotype_quality=652.4	ks_quality_p_value=1	log10_base_likelihood=-7.04171	log10_qual_likelihood_position_model=7.1783	log10_strand_likelihood_position_model=1.49528	new_cov=6/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=92/74	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=98/75
RA	179	.	NC_007779	1005047	0	T	G	bias_e_value=8.45674	bias_p_value=1.82009e-06	fisher_strand_p_value=1.06732e-07	frequency=2.088833e-02	genotype_quality=649.3	ks_quality_p_value=1	log10_base_likelihood=-6.25194	log10_qual_likelihood_position_model=11.3873	log10_strand_likelihood_position_model=6.97171	new_cov=8/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=18/144	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=26/144
RA	180	.	NC_007779	1005102	1	.	T	bias_e_value=2195560	bias_p_value=0.472537	fisher_strand_p_value=0.499455	frequency=8.968353e-03	genotype_quality=1095.4	ks_quality_p_value=0.341847	log10_base_likelihood=-8.66191	log10_qual_likelihood_position_model=1.99223	log10_strand_likelihood_position_model=0.55459	new_cov=0/2	polymorphism_quality=3.2	quality=3.2	quality_position_model=4.84798e-08	ref_cov=105/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/118
RA	181	.	NC_007779	1006080	0	C	A	bias_e_value=1.6986	bias_p_value=3.65579e-07	fisher_strand_p_value=1.94943e-08	frequency=7.097816e-02	genotype_quality=770.4	ks_quality_p_value=1	log10_base_likelihood=-12.6871	log10_qual_likelihood_position_model=19.5135	log10_strand_likelihood_position_model=7.81385	new_cov=25/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=105/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/124
RA	182	.	NC_007779	1008243	0	G	T	bias_e_value=1097.4	bias_p_value=0.000236187	fisher_strand_p_value=1.99807e-05	frequency=4.027081e-02	genotype_quality=876.7	ks_quality_p_value=1	log10_base_likelihood=-5.87221	log10_qual_likelihood_position_model=13.3368	log10_strand_likelihood_position_model=4.92331	new_cov=0/18	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=124/132	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/150
RA	183	.	NC_007779	1019390	1	.	A	bias_e_value=4488540	bias_p_value=0.966038	fisher_strand_p_value=1	frequency=7.781982e-03	genotype_quality=1266.0	ks_quality_p_value=0.750965	log10_base_likelihood=-7.62047	log10_qual_likelihood_position_model=2.01335	log10_strand_likelihood_position_model=0.299396	new_cov=1/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=3.32421e-07	ref_cov=129/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/127
RA	184	.	NC_007779	1050652	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	185	.	NC_007779	1050654	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	186	.	NC_007779	1050655	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	187	.	NC_007779	1050656	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	188	.	NC_007779	1050657	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	189	.	NC_007779	1050658	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	190	.	NC_007779	1050659	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	191	.	NC_007779	1050660	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	192	.	NC_007779	1050661	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	193	.	NC_007779	1050662	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	194	.	NC_007779	1050663	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	195	.	NC_007779	1050664	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	196	.	NC_007779	1050665	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	197	.	NC_007779	1050667	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	198	.	NC_007779	1050668	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	199	.	NC_007779	1050669	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	200	.	NC_007779	1050671	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	201	.	NC_007779	1050672	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	202	.	NC_007779	1050673	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	203	.	NC_007779	1050674	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	204	.	NC_007779	1050675	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	205	.	NC_007779	1050676	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	206	.	NC_007779	1050677	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	207	.	NC_007779	1050680	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	208	.	NC_007779	1050681	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	209	.	NC_007779	1050682	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	210	.	NC_007779	1070200	0	A	C	bias_e_value=0.0046726	bias_p_value=1.00565e-09	fisher_strand_p_value=4.03329e-11	frequency=5.387545e-02	genotype_quality=739.3	ks_quality_p_value=1	log10_base_likelihood=-8.99489	log10_qual_likelihood_position_model=17.7877	log10_strand_likelihood_position_model=10.3943	new_cov=0/13	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=163/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/37
RA	211	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1156.9	new_cov=116/145	quality=1156.9	ref_cov=0/0	tot_cov=116/145
RA	212	.	NC_007779	1097403	0	A	.	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=7.463455e-03	genotype_quality=1445.1	ks_quality_p_value=0.999061	log10_base_likelihood=-6.75344	log10_qual_likelihood_position_model=4.61139	log10_strand_likelihood_position_model=0.368664	new_cov=2/1	polymorphism_quality=1.2	quality=1.2	quality_position_model=0.00185688	ref_cov=233/165	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=235/166
RA	213	.	NC_007779	1097580	0	C	T	bias_e_value=631658	bias_p_value=0.135948	fisher_strand_p_value=0.410583	frequency=1.975765e-01	genotype_quality=864.4	ks_quality_p_value=0.073589	log10_base_likelihood=-197.246	log10_qual_likelihood_position_model=17.0965	log10_strand_likelihood_position_model=1.12503	new_cov=32/35	polymorphism_quality=192.5	quality=192.5	quality_position_model=1.13945e-181	ref_cov=114/158	tot_cov=146/193
RA	214	.	NC_007779	1116582	0	G	C	bias_e_value=6.8101e-18	bias_p_value=1.46569e-24	fisher_strand_p_value=2.44949e-26	frequency=1.498408e-01	genotype_quality=528.8	ks_quality_p_value=0.997719	log10_base_likelihood=-38.7295	log10_qual_likelihood_position_model=22.4696	log10_strand_likelihood_position_model=25.6109	new_cov=0/25	polymorphism_quality=33.6	quality=33.6	quality_position_model=Inf	ref_cov=133/3	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/28
RA	215	.	NC_007779	1119859	1	.	T	bias_e_value=4370660	bias_p_value=0.940669	fisher_strand_p_value=1	frequency=6.600380e-03	genotype_quality=1470.0	ks_quality_p_value=0.675931	log10_base_likelihood=-7.1854	log10_qual_likelihood_position_model=2.06935	log10_strand_likelihood_position_model=0.299826	new_cov=1/1	polymorphism_quality=1.7	quality=1.7	quality_position_model=1.0784e-06	ref_cov=147/154	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/155
RA	216	.	NC_007779	1120197	0	C	A	bias_e_value=4.0959	bias_p_value=8.81534e-07	fisher_strand_p_value=4.94631e-08	frequency=4.327393e-02	genotype_quality=806.9	ks_quality_p_value=1	log10_base_likelihood=-6.6488	log10_qual_likelihood_position_model=16.4628	log10_strand_likelihood_position_model=7.30572	new_cov=21/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=100/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/136
RA	217	.	NC_007779	1148417	0	C	A	bias_e_value=1440.55	bias_p_value=0.000310039	fisher_strand_p_value=3.19277e-05	frequency=3.850365e-02	genotype_quality=822.4	ks_quality_p_value=0.842709	log10_base_likelihood=-5.63677	log10_qual_likelihood_position_model=20.3894	log10_strand_likelihood_position_model=4.7446	new_cov=19/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=133/111	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/111
RA	218	.	NC_007779	1151485	0	C	A	bias_e_value=44.1566	bias_p_value=9.50355e-06	fisher_strand_p_value=6.21508e-07	frequency=4.930639e-02	genotype_quality=897.6	ks_quality_p_value=1	log10_base_likelihood=-10.38	log10_qual_likelihood_position_model=14.0626	log10_strand_likelihood_position_model=6.20655	new_cov=19/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=115/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/140
RA	219	.	NC_007779	1158848	0	T	G	bias_e_value=1.49761e-09	bias_p_value=3.2232e-16	fisher_strand_p_value=7.98433e-18	frequency=6.157446e-02	genotype_quality=815.6	ks_quality_p_value=1	log10_base_likelihood=-6.72752	log10_qual_likelihood_position_model=30.0187	log10_strand_likelihood_position_model=17.0978	new_cov=36/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=63/160	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/160
RA	220	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1171.0	new_cov=180/104	quality=1171.0	ref_cov=0/0	tot_cov=180/104
RA	221	.	NC_007779	1177683	0	A	G	bias_e_value=2.42154e-07	bias_p_value=5.21173e-14	fisher_strand_p_value=1.48293e-15	frequency=1.042514e-01	genotype_quality=741.2	ks_quality_p_value=1	log10_base_likelihood=-19.1995	log10_qual_likelihood_position_model=27.1629	log10_strand_likelihood_position_model=14.8289	new_cov=29/0	polymorphism_quality=13.9	quality=13.9	quality_position_model=Inf	ref_cov=56/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=85/158
RA	222	.	NC_007779	1213001	0	T	C	bias_e_value=4335560	bias_p_value=0.933115	fisher_strand_p_value=0.657878	frequency=2.293873e-02	genotype_quality=863.7	ks_quality_p_value=0.999131	log10_base_likelihood=-11.2294	log10_qual_likelihood_position_model=3.15029	log10_strand_likelihood_position_model=0.510942	new_cov=4/1	polymorphism_quality=5.8	quality=5.8	quality_position_model=1.54442e-09	ref_cov=136/76	reject=POLYMORPHISM_STRAND	tot_cov=140/77
RA	223	.	NC_007779	1213013	0	T	C	bias_e_value=4634980	bias_p_value=0.997556	fisher_strand_p_value=1	frequency=1.782131e-02	genotype_quality=895.6	ks_quality_p_value=0.930912	log10_base_likelihood=-9.00335	log10_qual_likelihood_position_model=2.66528	log10_strand_likelihood_position_model=0.429798	new_cov=3/1	polymorphism_quality=3.5	quality=3.5	quality_position_model=7.93209e-08	ref_cov=138/82	reject=POLYMORPHISM_STRAND	tot_cov=141/83
RA	224	.	NC_007779	1219648	0	G	T	bias_e_value=194.728	bias_p_value=4.191e-05	fisher_strand_p_value=3.12238e-06	frequency=5.509758e-02	genotype_quality=668.3	ks_quality_p_value=0.979942	log10_base_likelihood=-8.49749	log10_qual_likelihood_position_model=14.6421	log10_strand_likelihood_position_model=5.50551	new_cov=0/14	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=111/68	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/83
RA	225	.	NC_007779	1273399	0	T	G	bias_e_value=4.34398e-14	bias_p_value=9.34926e-21	fisher_strand_p_value=1.83133e-22	frequency=7.695913e-02	genotype_quality=850.2	ks_quality_p_value=1	log10_base_likelihood=-14.1578	log10_qual_likelihood_position_model=33.8695	log10_strand_likelihood_position_model=21.7372	new_cov=31/0	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=31/185	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=63/185
RA	226	.	NC_007779	1280617	0	G	T	bias_e_value=12571.4	bias_p_value=0.00270567	fisher_strand_p_value=0.000296569	frequency=3.266335e-02	genotype_quality=932.7	ks_quality_p_value=1	log10_base_likelihood=-8.2835	log10_qual_likelihood_position_model=12.4864	log10_strand_likelihood_position_model=3.66792	new_cov=0/16	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=115/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/173
RA	227	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=105.4	new_cov=17/13	quality=105.4	ref_cov=0/0	tot_cov=17/13
RA	228	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=35.7	new_cov=7/5	quality=35.7	ref_cov=0/0	tot_cov=7/5
RA	229	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=57.0	new_cov=16/8	quality=57.0	ref_cov=0/0	tot_cov=16/8
RA	230	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1263.5	new_cov=144/165	quality=1263.5	ref_cov=0/0	tot_cov=144/165
RA	231	.	NC_007779	1324681	1	.	A	bias_e_value=2795410	bias_p_value=0.601639	fisher_strand_p_value=0.498419	frequency=7.246017e-03	genotype_quality=1367.8	ks_quality_p_value=0.508956	log10_base_likelihood=-8.22757	log10_qual_likelihood_position_model=1.49285	log10_strand_likelihood_position_model=0.584895	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.4635e-08	ref_cov=139/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/135
RA	232	.	NC_007779	1339548	0	G	.	bias_e_value=3682690	bias_p_value=0.792602	fisher_strand_p_value=0.498771	frequency=8.542061e-03	genotype_quality=1008.0	ks_quality_p_value=0.861393	log10_base_likelihood=-5.57634	log10_qual_likelihood_position_model=0.914273	log10_strand_likelihood_position_model=0.567427	new_cov=2/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=6.1205e-06	ref_cov=120/112	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/112
RA	233	.	NC_007779	1352913	1	.	T	bias_e_value=423372	bias_p_value=0.0911197	fisher_strand_p_value=0.0193328	frequency=1.570702e-02	genotype_quality=917.7	ks_quality_p_value=0.941462	log10_base_likelihood=-12.9933	log10_qual_likelihood_position_model=2.10822	log10_strand_likelihood_position_model=1.71371	new_cov=3/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=3.51378e-11	ref_cov=49/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=52/139
RA	234	.	NC_007779	1371749	1	.	T	bias_e_value=1048050	bias_p_value=0.225565	fisher_strand_p_value=0.214489	frequency=1.807213e-02	genotype_quality=1590.3	ks_quality_p_value=0.274385	log10_base_likelihood=-27.1171	log10_qual_likelihood_position_model=3.50567	log10_strand_likelihood_position_model=1.0347	new_cov=1/5	polymorphism_quality=21.9	quality=21.9	quality_position_model=8.9219e-25	ref_cov=165/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/166
RA	235	.	NC_007779	1375289	0	G	T	bias_e_value=0.0416166	bias_p_value=8.95688e-09	fisher_strand_p_value=3.95429e-10	frequency=9.965658e-02	genotype_quality=894.1	ks_quality_p_value=1	log10_base_likelihood=-23.1461	log10_qual_likelihood_position_model=26.5369	log10_strand_likelihood_position_model=9.45193	new_cov=1/38	polymorphism_quality=17.9	quality=17.9	quality_position_model=Inf	ref_cov=133/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/165
RA	236	.	NC_007779	1378219	0	A	C	bias_e_value=2.10426e-10	bias_p_value=4.52886e-17	fisher_strand_p_value=1.06863e-18	frequency=1.171880e-01	genotype_quality=706.5	ks_quality_p_value=1	log10_base_likelihood=-11.3643	log10_qual_likelihood_position_model=48.2169	log10_strand_likelihood_position_model=17.9712	new_cov=0/47	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=125/66	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=125/114
RA	237	.	NC_007779	1380725	0	C	A	bias_e_value=134.824	bias_p_value=2.90173e-05	fisher_strand_p_value=2.05894e-06	frequency=3.379154e-02	genotype_quality=974.2	ks_quality_p_value=1	log10_base_likelihood=-5.81823	log10_qual_likelihood_position_model=15.6678	log10_strand_likelihood_position_model=5.98739	new_cov=19/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=129/148	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/148
RA	238	.	NC_007779	1404189	0	C	A	bias_e_value=1109.39	bias_p_value=0.000238767	fisher_strand_p_value=2.02193e-05	frequency=2.807426e-02	genotype_quality=893.4	ks_quality_p_value=1	log10_base_likelihood=-6.12201	log10_qual_likelihood_position_model=12.3521	log10_strand_likelihood_position_model=4.69423	new_cov=14/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=118/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/146
RA	239	.	NC_007779	1405508	0	G	T	bias_e_value=0.0350072	bias_p_value=7.53437e-09	fisher_strand_p_value=3.57419e-10	frequency=7.045317e-02	genotype_quality=597.9	ks_quality_p_value=0.923265	log10_base_likelihood=-19.9501	log10_qual_likelihood_position_model=13.6816	log10_strand_likelihood_position_model=9.44682	new_cov=11/0	polymorphism_quality=14.7	quality=14.7	quality_position_model=Inf	ref_cov=15/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=26/129
RA	240	.	NC_007779	1409137	0	G	T	bias_e_value=1.90756e-13	bias_p_value=4.10552e-20	fisher_strand_p_value=8.28691e-22	frequency=2.074671e-01	genotype_quality=658.6	ks_quality_p_value=1	log10_base_likelihood=-56.4687	log10_qual_likelihood_position_model=28.6438	log10_strand_likelihood_position_model=21.3382	new_cov=0/61	polymorphism_quality=51.4	quality=51.4	quality_position_model=2.00416e-08	ref_cov=126/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/134
RA	241	.	NC_007779	1411975	0	A	.	bias_e_value=1728140	bias_p_value=0.371937	fisher_strand_p_value=0.619911	frequency=1.016140e-02	genotype_quality=1188.8	ks_quality_p_value=0.191682	log10_base_likelihood=-8.05836	log10_qual_likelihood_position_model=2.31319	log10_strand_likelihood_position_model=0.429009	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.2578e-07	ref_cov=144/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/149
RA	242	.	NC_007779	1412694	0	C	A	bias_e_value=0.000105817	bias_p_value=2.27742e-11	fisher_strand_p_value=7.88906e-13	frequency=6.985760e-02	genotype_quality=957.0	ks_quality_p_value=1	log10_base_likelihood=-16.8298	log10_qual_likelihood_position_model=21.0324	log10_strand_likelihood_position_model=12.103	new_cov=30/0	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=94/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/167
RA	243	.	NC_007779	1437441	0	G	A	bias_e_value=0.00667623	bias_p_value=1.43688e-09	fisher_strand_p_value=5.85002e-11	frequency=5.566597e-02	genotype_quality=828.4	ks_quality_p_value=1	log10_base_likelihood=-8.84295	log10_qual_likelihood_position_model=20.7097	log10_strand_likelihood_position_model=10.2328	new_cov=0/14	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=172/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=172/46
RA	244	.	NC_007779	1457034	0	T	A	bias_e_value=391762	bias_p_value=0.0843164	fisher_strand_p_value=0.0165229	frequency=2.521038e-02	genotype_quality=852.2	ks_quality_p_value=1	log10_base_likelihood=-7.05362	log10_qual_likelihood_position_model=9.65634	log10_strand_likelihood_position_model=1.89221	new_cov=7/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=113/101	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=121/101
RA	245	.	NC_007779	1457036	0	A	C	bias_e_value=239043	bias_p_value=0.0514477	fisher_strand_p_value=0.00901123	frequency=2.345657e-02	genotype_quality=864.3	ks_quality_p_value=1	log10_base_likelihood=-8.9484	log10_qual_likelihood_position_model=9.73889	log10_strand_likelihood_position_model=2.12051	new_cov=8/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=118/103	reject=POLYMORPHISM_STRAND	tot_cov=126/103
RA	246	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=819.4	new_cov=124/82	quality=819.4	ref_cov=0/0	tot_cov=124/82
RA	247	.	NC_007779	1493621	1	.	C	bias_e_value=1841630	bias_p_value=0.396362	fisher_strand_p_value=0.139644	frequency=8.331299e-03	genotype_quality=1154.7	ks_quality_p_value=0.934918	log10_base_likelihood=-6.28939	log10_qual_likelihood_position_model=3.45758	log10_strand_likelihood_position_model=0.854977	new_cov=0/2	polymorphism_quality=0.8	quality=0.8	quality_position_model=0.0011093	ref_cov=150/88	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/90
RA	248	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1313.8	new_cov=99/164	quality=1313.8	ref_cov=0/0	tot_cov=99/164
RA	249	.	NC_007779	1504851	0	C	A	bias_e_value=1739.91	bias_p_value=0.00037447	fisher_strand_p_value=3.30914e-05	frequency=7.079697e-02	genotype_quality=610.3	ks_quality_p_value=1	log10_base_likelihood=-10.3591	log10_qual_likelihood_position_model=14.9319	log10_strand_likelihood_position_model=4.72165	new_cov=23/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=119/79	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/79
RA	250	.	NC_007779	1507752	0	A	C	bias_e_value=0.628137	bias_p_value=1.3519e-07	fisher_strand_p_value=6.82695e-09	frequency=5.425262e-02	genotype_quality=663.1	ks_quality_p_value=1	log10_base_likelihood=-6.00066	log10_qual_likelihood_position_model=19.3189	log10_strand_likelihood_position_model=8.16577	new_cov=0/18	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=122/57	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/75
RA	251	.	NC_007779	1512495	0	A	.	bias_e_value=4013270	bias_p_value=0.863749	fisher_strand_p_value=0.617208	frequency=1.249313e-02	genotype_quality=971.0	ks_quality_p_value=0.851766	log10_base_likelihood=-8.39172	log10_qual_likelihood_position_model=1.75812	log10_strand_likelihood_position_model=0.431637	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.94292e-08	ref_cov=116/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/122
RA	252	.	NC_007779	1515709	0	A	G	bias_e_value=8.1887e-06	bias_p_value=1.7624e-12	fisher_strand_p_value=5.5923e-14	frequency=1.438789e-01	genotype_quality=617.8	ks_quality_p_value=1	log10_base_likelihood=-23.653	log10_qual_likelihood_position_model=42.2485	log10_strand_likelihood_position_model=13.2591	new_cov=41/0	polymorphism_quality=18.4	quality=18.4	quality_position_model=Inf	ref_cov=84/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/115
RA	253	.	NC_007779	1526885	0	G	T	bias_e_value=35.3217	bias_p_value=7.60205e-06	fisher_strand_p_value=4.89512e-07	frequency=3.674412e-02	genotype_quality=1000.5	ks_quality_p_value=1	log10_base_likelihood=-9.93395	log10_qual_likelihood_position_model=14.7644	log10_strand_likelihood_position_model=6.31024	new_cov=0/17	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=170/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/135
RA	254	.	NC_007779	1527474	0	G	A	bias_e_value=266.998	bias_p_value=5.74642e-05	fisher_strand_p_value=4.30239e-06	frequency=5.424786e-02	genotype_quality=893.1	ks_quality_p_value=1	log10_base_likelihood=-9.60309	log10_qual_likelihood_position_model=20.1595	log10_strand_likelihood_position_model=5.56021	new_cov=0/18	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=132/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/136
RA	255	.	NC_007779	1527479	0	C	A	bias_e_value=15624.9	bias_p_value=0.00336285	fisher_strand_p_value=0.00038331	frequency=3.046227e-02	genotype_quality=1004.8	ks_quality_p_value=0.988125	log10_base_likelihood=-5.57112	log10_qual_likelihood_position_model=18.6408	log10_strand_likelihood_position_model=3.66225	new_cov=0/12	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=136/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=136/139
RA	256	.	NC_007779	1533124	0	C	A	bias_e_value=250937	bias_p_value=0.0540075	fisher_strand_p_value=0.00955826	frequency=1.921463e-02	genotype_quality=1020.2	ks_quality_p_value=1	log10_base_likelihood=-6.62886	log10_qual_likelihood_position_model=9.64215	log10_strand_likelihood_position_model=2.01962	new_cov=0/6	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=127/105	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=127/111
RA	257	.	NC_007779	1537499	0	A	G	bias_e_value=0.00092208	bias_p_value=1.98453e-10	fisher_strand_p_value=7.45443e-12	frequency=8.241892e-02	genotype_quality=809.6	ks_quality_p_value=1	log10_base_likelihood=-12.3069	log10_qual_likelihood_position_model=22.7992	log10_strand_likelihood_position_model=11.1276	new_cov=32/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=103/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/146
RA	258	.	NC_007779	1552377	0	A	C	bias_e_value=1.60482e-09	bias_p_value=3.45394e-16	fisher_strand_p_value=8.57096e-18	frequency=1.162043e-01	genotype_quality=642.3	ks_quality_p_value=1	log10_base_likelihood=-12.7404	log10_qual_likelihood_position_model=33.9673	log10_strand_likelihood_position_model=17.067	new_cov=0/40	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=119/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/92
RA	259	.	NC_007779	1554570	0	C	.	bias_e_value=2179970	bias_p_value=0.469181	fisher_strand_p_value=0.499371	frequency=8.193016e-03	genotype_quality=886.9	ks_quality_p_value=0.338115	log10_base_likelihood=-5.73808	log10_qual_likelihood_position_model=1.7241	log10_strand_likelihood_position_model=0.558408	new_cov=0/2	polymorphism_quality=0.2	quality=0.2	quality_position_model=2.87964e-05	ref_cov=115/126	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=116/128
RA	260	.	NC_007779	1584342	0	A	.	bias_e_value=2048730	bias_p_value=0.440934	fisher_strand_p_value=0.155179	frequency=1.341629e-02	genotype_quality=612.4	ks_quality_p_value=0.98838	log10_base_likelihood=-5.7376	log10_qual_likelihood_position_model=1.5239	log10_strand_likelihood_position_model=0.809168	new_cov=2/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=3.26061e-05	ref_cov=57/90	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=59/90
RA	261	.	NC_007779	1595839	0	C	.	bias_e_value=3525050	bias_p_value=0.758673	fisher_strand_p_value=0.501502	frequency=9.896278e-03	genotype_quality=846.6	ks_quality_p_value=0.780731	log10_base_likelihood=-5.70459	log10_qual_likelihood_position_model=0.562052	log10_strand_likelihood_position_model=0.529728	new_cov=0/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=1.7573e-06	ref_cov=92/108	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=92/110
RA	262	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=887.6	new_cov=100/131	quality=887.6	ref_cov=0/0	tot_cov=100/131
RA	263	.	NC_007779	1628027	0	G	T	bias_e_value=1066.68	bias_p_value=0.000229576	fisher_strand_p_value=2.66657e-05	frequency=1.147733e-01	genotype_quality=376.6	ks_quality_p_value=0.726424	log10_base_likelihood=-22.5063	log10_qual_likelihood_position_model=14.768	log10_strand_likelihood_position_model=4.69903	new_cov=15/0	polymorphism_quality=17.2	quality=17.2	quality_position_model=7.95639e-05	ref_cov=49/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=64/60
RA	264	.	NC_007779	1651009	0	T	G	bias_e_value=1.70771e-07	bias_p_value=3.67539e-14	fisher_strand_p_value=1.0352e-15	frequency=1.721816e-01	genotype_quality=403.5	ks_quality_p_value=1	log10_base_likelihood=-22.6518	log10_qual_likelihood_position_model=23.8625	log10_strand_likelihood_position_model=14.985	new_cov=26/0	polymorphism_quality=17.4	quality=17.4	quality_position_model=Inf	ref_cov=18/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=44/84
RA	265	.	NC_007779	1660545	0	G	T	bias_e_value=3.20357	bias_p_value=6.89485e-07	fisher_strand_p_value=3.8161e-08	frequency=6.389427e-02	genotype_quality=810.1	ks_quality_p_value=0.999199	log10_base_likelihood=-12.6348	log10_qual_likelihood_position_model=17.5538	log10_strand_likelihood_position_model=7.60569	new_cov=0/24	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=127/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/131
RA	266	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=1129.1	new_cov=116/108	quality=1129.1	ref_cov=0/0	tot_cov=117/108
RA	267	.	NC_007779	1669781	0	G	A	bias_e_value=210827	bias_p_value=0.045375	fisher_strand_p_value=0.00774167	frequency=2.653313e-02	genotype_quality=950.4	ks_quality_p_value=1	log10_base_likelihood=-6.04776	log10_qual_likelihood_position_model=10.6411	log10_strand_likelihood_position_model=2.24303	new_cov=0/8	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=112/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=113/127
RA	268	.	NC_007779	1669785	0	T	G	bias_e_value=1781970	bias_p_value=0.383522	fisher_strand_p_value=0.124746	frequency=1.025295e-02	genotype_quality=943.4	ks_quality_p_value=0.996618	log10_base_likelihood=-5.83862	log10_qual_likelihood_position_model=4.34524	log10_strand_likelihood_position_model=1.11043	new_cov=0/4	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.0884061	ref_cov=115/126	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=115/130
RA	269	.	NC_007779	1669786	0	G	A	bias_e_value=31407.8	bias_p_value=0.00675969	fisher_strand_p_value=0.000835867	frequency=3.621578e-02	genotype_quality=983.2	ks_quality_p_value=1	log10_base_likelihood=-8.18455	log10_qual_likelihood_position_model=14.5586	log10_strand_likelihood_position_model=3.23418	new_cov=0/11	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=119/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/129
RA	270	.	NC_007779	1677110	0	G	T	bias_e_value=0.0194217	bias_p_value=4.18001e-09	fisher_strand_p_value=2.48939e-10	frequency=9.276915e-02	genotype_quality=693.8	ks_quality_p_value=0.716116	log10_base_likelihood=-15.3525	log10_qual_likelihood_position_model=28.1454	log10_strand_likelihood_position_model=9.71793	new_cov=0/30	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=113/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/117
RA	271	.	NC_007779	1693217	0	C	A	bias_e_value=29428.5	bias_p_value=0.0063337	fisher_strand_p_value=0.000780889	frequency=2.964973e-02	genotype_quality=948.6	ks_quality_p_value=0.993826	log10_base_likelihood=-6.25502	log10_qual_likelihood_position_model=11.9323	log10_strand_likelihood_position_model=3.29921	new_cov=14/1	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=133/138	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/139
RA	272	.	NC_007779	1705204	0	A	C	bias_e_value=6161.79	bias_p_value=0.00132616	fisher_strand_p_value=0.000133685	frequency=6.551743e-02	genotype_quality=835.0	ks_quality_p_value=1	log10_base_likelihood=-18.469	log10_qual_likelihood_position_model=26.3584	log10_strand_likelihood_position_model=3.96719	new_cov=20/1	polymorphism_quality=13.2	quality=13.2	quality_position_model=Inf	ref_cov=120/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/100
RA	273	.	NC_007779	1705209	1	.	T	bias_e_value=1958490	bias_p_value=0.421514	fisher_strand_p_value=0.144072	frequency=1.817894e-02	genotype_quality=1050.1	ks_quality_p_value=0.993958	log10_base_likelihood=-14.9861	log10_qual_likelihood_position_model=4.66539	log10_strand_likelihood_position_model=0.935809	new_cov=4/0	polymorphism_quality=9.6	quality=9.6	quality_position_model=2.12552e-11	ref_cov=125/91	reject=POLYMORPHISM_STRAND	tot_cov=129/91
RA	274	.	NC_007779	1705210	0	G	T	bias_e_value=101106	bias_p_value=0.0217603	fisher_strand_p_value=0.00323094	frequency=4.688263e-02	genotype_quality=846.8	ks_quality_p_value=1	log10_base_likelihood=-14.1839	log10_qual_likelihood_position_model=14.339	log10_strand_likelihood_position_model=2.59798	new_cov=11/0	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=120/91	reject=POLYMORPHISM_STRAND	tot_cov=131/92
RA	275	.	NC_007779	1705224	0	G	T	bias_e_value=67171.1	bias_p_value=0.0144568	fisher_strand_p_value=0.00200444	frequency=4.927731e-02	genotype_quality=889.7	ks_quality_p_value=1	log10_base_likelihood=-12.7832	log10_qual_likelihood_position_model=15.343	log10_strand_likelihood_position_model=2.92846	new_cov=13/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=124/89	reject=POLYMORPHISM_STRAND	tot_cov=137/89
RA	276	.	NC_007779	1713510	0	A	C	bias_e_value=4.00283e-06	bias_p_value=8.61504e-13	fisher_strand_p_value=2.67102e-14	frequency=7.394981e-02	genotype_quality=820.3	ks_quality_p_value=1	log10_base_likelihood=-9.66025	log10_qual_likelihood_position_model=40.7386	log10_strand_likelihood_position_model=13.5733	new_cov=0/37	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=141/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/126
RA	277	.	NC_007779	1716031	1	.	T	bias_e_value=2915060	bias_p_value=0.62739	fisher_strand_p_value=0.497952	frequency=8.771896e-03	genotype_quality=1106.1	ks_quality_p_value=0.548181	log10_base_likelihood=-8.44554	log10_qual_likelihood_position_model=1.74829	log10_strand_likelihood_position_model=0.588805	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=4.92526e-08	ref_cov=114/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/112
RA	278	.	NC_007779	1716032	0	T	.	bias_e_value=4642640	bias_p_value=0.999205	fisher_strand_p_value=1	frequency=1.286697e-02	genotype_quality=938.2	ks_quality_p_value=0.960388	log10_base_likelihood=-8.20709	log10_qual_likelihood_position_model=1.98657	log10_strand_likelihood_position_model=0.415001	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.01325e-07	ref_cov=117/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/114
RA	279	.	NC_007779	1759412	0	T	.	bias_e_value=2256170	bias_p_value=0.48558	fisher_strand_p_value=0.257399	frequency=1.171112e-02	genotype_quality=1011.8	ks_quality_p_value=0.692338	log10_base_likelihood=-8.31441	log10_qual_likelihood_position_model=1.46244	log10_strand_likelihood_position_model=0.76277	new_cov=0/3	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.15611e-08	ref_cov=113/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/143
RA	280	.	NC_007779	1763744	0	C	A	bias_e_value=0.000119582	bias_p_value=2.57368e-11	fisher_strand_p_value=8.95461e-13	frequency=8.371067e-02	genotype_quality=866.0	ks_quality_p_value=1	log10_base_likelihood=-24.5968	log10_qual_likelihood_position_model=19.0261	log10_strand_likelihood_position_model=12.048	new_cov=32/0	polymorphism_quality=19.4	quality=19.4	quality_position_model=Inf	ref_cov=100/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/160
RA	281	.	NC_007779	1766499	0	T	A	bias_e_value=766.939	bias_p_value=0.000165063	fisher_strand_p_value=1.3517e-05	frequency=6.235027e-02	genotype_quality=528.5	ks_quality_p_value=1	log10_base_likelihood=-6.14936	log10_qual_likelihood_position_model=10.3921	log10_strand_likelihood_position_model=4.86912	new_cov=0/13	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=97/64	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=97/77
RA	282	.	NC_007779	1781198	0	T	.	bias_e_value=3998240	bias_p_value=0.860516	fisher_strand_p_value=0.622391	frequency=1.378536e-02	genotype_quality=1171.2	ks_quality_p_value=0.836653	log10_base_likelihood=-11.2697	log10_qual_likelihood_position_model=2.67152	log10_strand_likelihood_position_model=0.602076	new_cov=3/1	polymorphism_quality=5.9	quality=5.9	quality_position_model=5.61658e-10	ref_cov=142/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/145
RA	283	.	NC_007779	1793859	0	T	.	bias_e_value=4553060	bias_p_value=0.979926	fisher_strand_p_value=1	frequency=1.175308e-02	genotype_quality=1039.3	ks_quality_p_value=0.80644	log10_base_likelihood=-7.86031	log10_qual_likelihood_position_model=2.59977	log10_strand_likelihood_position_model=0.403631	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=9.78124e-07	ref_cov=132/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/121
RA	284	.	NC_007779	1832491	0	G	T	bias_e_value=0.000229401	bias_p_value=4.93725e-11	fisher_strand_p_value=1.76471e-12	frequency=7.278061e-02	genotype_quality=991.0	ks_quality_p_value=0.996845	log10_base_likelihood=-12.4604	log10_qual_likelihood_position_model=25.1135	log10_strand_likelihood_position_model=11.7533	new_cov=0/33	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=162/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/145
RA	285	.	NC_007779	1840899	0	G	T	bias_e_value=0.0360554	bias_p_value=7.75998e-09	fisher_strand_p_value=3.40634e-10	frequency=6.737041e-02	genotype_quality=811.1	ks_quality_p_value=0.999117	log10_base_likelihood=-11.1196	log10_qual_likelihood_position_model=22.633	log10_strand_likelihood_position_model=9.46771	new_cov=0/26	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=138/92	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/119
RA	286	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=1097.2	new_cov=146/124	quality=1097.2	ref_cov=0/0	tot_cov=146/124
RA	287	.	NC_007779	1844628	0	A	G	bias_e_value=0.0482664	bias_p_value=1.03881e-08	fisher_strand_p_value=4.61775e-10	frequency=5.983925e-02	genotype_quality=530.2	ks_quality_p_value=1	log10_base_likelihood=-7.26105	log10_qual_likelihood_position_model=14.9223	log10_strand_likelihood_position_model=9.33557	new_cov=12/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=18/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=30/121
RA	288	.	NC_007779	1861399	0	A	C	bias_e_value=3.28725e-11	bias_p_value=7.07493e-18	fisher_strand_p_value=1.59775e-19	frequency=1.262827e-01	genotype_quality=579.1	ks_quality_p_value=1	log10_base_likelihood=-15.3167	log10_qual_likelihood_position_model=31.4024	log10_strand_likelihood_position_model=18.7965	new_cov=0/36	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=119/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/70
RA	289	.	NC_007779	1864105	1	.	T	bias_e_value=4598680	bias_p_value=0.989744	fisher_strand_p_value=1	frequency=7.967949e-03	genotype_quality=1253.4	ks_quality_p_value=0.860238	log10_base_likelihood=-8.02798	log10_qual_likelihood_position_model=2.30346	log10_strand_likelihood_position_model=0.302347	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.52882e-07	ref_cov=114/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/136
RA	290	.	NC_007779	1870486	0	A	.	bias_e_value=3122010	bias_p_value=0.671931	fisher_strand_p_value=1	frequency=9.166718e-03	genotype_quality=1327.3	ks_quality_p_value=0.309032	log10_base_likelihood=-7.98973	log10_qual_likelihood_position_model=1.28858	log10_strand_likelihood_position_model=0.387085	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=3.02032e-08	ref_cov=146/178	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/180
RA	291	.	NC_007779	1879404	0	A	C	bias_e_value=1.1088e-11	bias_p_value=2.3864e-18	fisher_strand_p_value=5.25731e-20	frequency=7.829809e-02	genotype_quality=820.5	ks_quality_p_value=1	log10_base_likelihood=-11.9264	log10_qual_likelihood_position_model=29.8127	log10_strand_likelihood_position_model=19.2792	new_cov=0/27	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=176/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=176/56
RA	292	.	NC_007779	1906477	1	.	G	bias_e_value=1030650	bias_p_value=0.221819	fisher_strand_p_value=0.057587	frequency=1.214123e-02	genotype_quality=1190.0	ks_quality_p_value=0.999104	log10_base_likelihood=-10.4505	log10_qual_likelihood_position_model=4.66225	log10_strand_likelihood_position_model=1.23968	new_cov=3/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=2.05066e-06	ref_cov=93/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=96/151
RA	293	.	NC_007779	1906488	0	G	T	bias_e_value=5.90324	bias_p_value=1.27052e-06	fisher_strand_p_value=7.28735e-08	frequency=5.082321e-02	genotype_quality=843.6	ks_quality_p_value=1	log10_base_likelihood=-9.70154	log10_qual_likelihood_position_model=14.3997	log10_strand_likelihood_position_model=7.13743	new_cov=15/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=67/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/149
RA	294	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=1113.8	new_cov=138/147	quality=1113.8	ref_cov=0/0	tot_cov=138/147
RA	295	.	NC_007779	1920746	0	G	T	bias_e_value=6.80095	bias_p_value=1.46372e-06	fisher_strand_p_value=8.46851e-08	frequency=5.867434e-02	genotype_quality=929.1	ks_quality_p_value=1	log10_base_likelihood=-16.0311	log10_qual_likelihood_position_model=16.5941	log10_strand_likelihood_position_model=7.08448	new_cov=1/22	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=155/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/125
RA	296	.	NC_007779	1933780	1	.	A	bias_e_value=3125500	bias_p_value=0.672681	fisher_strand_p_value=0.501191	frequency=1.015186e-02	genotype_quality=957.8	ks_quality_p_value=0.617869	log10_base_likelihood=-8.56809	log10_qual_likelihood_position_model=1.11543	log10_strand_likelihood_position_model=0.532033	new_cov=0/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=7.15662e-09	ref_cov=90/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=90/107
RA	297	.	NC_007779	1941891	0	T	.	bias_e_value=4080140	bias_p_value=0.878143	fisher_strand_p_value=0.617751	frequency=1.161957e-02	genotype_quality=1042.1	ks_quality_p_value=0.888523	log10_base_likelihood=-8.20664	log10_qual_likelihood_position_model=1.98439	log10_strand_likelihood_position_model=0.431226	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.04885e-07	ref_cov=130/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/127
RA	298	.	NC_007779	1956118	0	C	A	bias_e_value=8289.16	bias_p_value=0.00178402	fisher_strand_p_value=0.000190519	frequency=3.378201e-02	genotype_quality=579.6	ks_quality_p_value=0.976478	log10_base_likelihood=-8.05369	log10_qual_likelihood_position_model=6.93438	log10_strand_likelihood_position_model=3.72006	new_cov=0/5	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=118/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/28
RA	299	.	NC_007779	1971508	0	A	C	bias_e_value=0.000859589	bias_p_value=1.85004e-10	fisher_strand_p_value=6.93569e-12	frequency=5.263376e-02	genotype_quality=710.8	ks_quality_p_value=0.999215	log10_base_likelihood=-12.2995	log10_qual_likelihood_position_model=15.9113	log10_strand_likelihood_position_model=11.1589	new_cov=0/14	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=159/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=159/37
RA	300	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=1135.2	new_cov=132/151	quality=1135.2	ref_cov=1/0	tot_cov=133/151
RA	301	.	NC_007779	1993894	0	A	C	bias_e_value=54.6258	bias_p_value=1.17568e-05	fisher_strand_p_value=7.80488e-07	frequency=5.563116e-02	genotype_quality=920.6	ks_quality_p_value=1	log10_base_likelihood=-13.2559	log10_qual_likelihood_position_model=23.5663	log10_strand_likelihood_position_model=6.14856	new_cov=0/23	polymorphism_quality=7.9	quality=7.9	quality_position_model=Inf	ref_cov=124/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/157
RA	302	.	NC_007779	2004055	0	A	C	bias_e_value=4.24254e-24	bias_p_value=9.13094e-31	fisher_strand_p_value=1.22598e-32	frequency=1.957707e-01	genotype_quality=821.0	ks_quality_p_value=1	log10_base_likelihood=-50.8412	log10_qual_likelihood_position_model=48.5055	log10_strand_likelihood_position_model=31.9115	new_cov=0/72	polymorphism_quality=45.8	quality=45.8	quality_position_model=Inf	ref_cov=162/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/130
RA	303	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=1372.2	new_cov=178/156	quality=1372.2	ref_cov=0/0	tot_cov=178/156
RA	304	.	NC_007779	2014008	0	T	.	bias_e_value=756252	bias_p_value=0.162763	fisher_strand_p_value=0.077782	frequency=1.180267e-02	genotype_quality=1036.8	ks_quality_p_value=0.490499	log10_base_likelihood=-8.10046	log10_qual_likelihood_position_model=2.80139	log10_strand_likelihood_position_model=1.10912	new_cov=3/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.86296e-06	ref_cov=106/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/145
RA	305	.	NC_007779	2027359	0	T	A	bias_e_value=1063600	bias_p_value=0.228912	fisher_strand_p_value=0.0601192	frequency=1.821041e-02	genotype_quality=1017.6	ks_quality_p_value=0.998654	log10_base_likelihood=-6.44706	log10_qual_likelihood_position_model=7.6351	log10_strand_likelihood_position_model=1.51365	new_cov=0/5	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=130/126	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=130/131
RA	306	.	NC_007779	2032185	0	G	C	bias_e_value=399.97	bias_p_value=8.60829e-05	fisher_strand_p_value=6.66333e-06	frequency=5.379868e-02	genotype_quality=510.2	ks_quality_p_value=1	log10_base_likelihood=-10.7387	log10_qual_likelihood_position_model=9.76253	log10_strand_likelihood_position_model=5.17631	new_cov=8/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=25/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=33/101
RA	307	.	NC_007779	2082881	0	A	.	bias_e_value=3306480	bias_p_value=0.711632	fisher_strand_p_value=1	frequency=1.254368e-02	genotype_quality=960.6	ks_quality_p_value=0.344511	log10_base_likelihood=-8.22763	log10_qual_likelihood_position_model=2.17859	log10_strand_likelihood_position_model=0.400617	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.47361e-07	ref_cov=111/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/126
RA	308	.	NC_007779	2095582	0	G	T	bias_e_value=0.0139226	bias_p_value=2.99647e-09	fisher_strand_p_value=1.26009e-10	frequency=6.511259e-02	genotype_quality=1044.0	ks_quality_p_value=0.999347	log10_base_likelihood=-15.8636	log10_qual_likelihood_position_model=21.8898	log10_strand_likelihood_position_model=10.096	new_cov=0/34	polymorphism_quality=10.5	quality=10.5	quality_position_model=Inf	ref_cov=160/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/180
RA	309	.	NC_007779	2099403	1	.	A	bias_e_value=3663920	bias_p_value=0.788562	fisher_strand_p_value=0.52003	frequency=6.492615e-03	genotype_quality=1513.3	ks_quality_p_value=0.817044	log10_base_likelihood=-7.55565	log10_qual_likelihood_position_model=3.16951	log10_strand_likelihood_position_model=0.439004	new_cov=0/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=8.74115e-06	ref_cov=122/184	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/186
RA	310	.	NC_007779	2106207	0	T	.	bias_e_value=3223100	bias_p_value=0.693687	fisher_strand_p_value=0.510148	frequency=1.306438e-02	genotype_quality=620.1	ks_quality_p_value=0.643043	log10_base_likelihood=-5.62168	log10_qual_likelihood_position_model=2.04847	log10_strand_likelihood_position_model=0.472662	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=6.84727e-05	ref_cov=87/64	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=89/64
RA	311	.	NC_007779	2122820	0	G	.	bias_e_value=932643	bias_p_value=0.200727	fisher_strand_p_value=0.229984	frequency=8.579254e-03	genotype_quality=989.3	ks_quality_p_value=0.218773	log10_base_likelihood=-5.64205	log10_qual_likelihood_position_model=1.82975	log10_strand_likelihood_position_model=0.638303	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=5.72162e-05	ref_cov=110/121	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/121
RA	312	.	NC_007779	2156661	0	C	A	bias_e_value=4.95216	bias_p_value=1.06582e-06	fisher_strand_p_value=6.04864e-08	frequency=6.541538e-02	genotype_quality=911.9	ks_quality_p_value=1	log10_base_likelihood=-13.5441	log10_qual_likelihood_position_model=21.7866	log10_strand_likelihood_position_model=7.3314	new_cov=31/1	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=137/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/136
RA	313	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1101.9	new_cov=99/167	quality=1101.9	ref_cov=0/0	tot_cov=99/167
RA	314	.	NC_007779	2174678	0	C	G	bias_e_value=290.123	bias_p_value=6.24413e-05	fisher_strand_p_value=4.73152e-06	frequency=4.588509e-02	genotype_quality=704.2	ks_quality_p_value=0.994751	log10_base_likelihood=-8.77283	log10_qual_likelihood_position_model=12.3538	log10_strand_likelihood_position_model=5.325	new_cov=0/10	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=131/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/59
RA	315	.	NC_007779	2178210	0	A	C	bias_e_value=4646290	bias_p_value=0.999992	fisher_strand_p_value=1	frequency=3.479862e-02	genotype_quality=1125.1	ks_quality_p_value=0.995983	log10_base_likelihood=-30.7145	log10_qual_likelihood_position_model=7.19754	log10_strand_likelihood_position_model=0.6058	new_cov=5/5	polymorphism_quality=25.5	quality=25.5	quality_position_model=4.10107e-25	ref_cov=132/145	tot_cov=137/150
RA	316	.	NC_007779	2200801	1	.	A	bias_e_value=3710890	bias_p_value=0.79867	fisher_strand_p_value=0.510285	frequency=7.407188e-03	genotype_quality=1341.2	ks_quality_p_value=0.856176	log10_base_likelihood=-8.30392	log10_qual_likelihood_position_model=1.07139	log10_strand_likelihood_position_model=0.47766	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.06033e-08	ref_cov=114/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/156
RA	317	.	NC_007779	2202934	0	G	T	bias_e_value=87.9943	bias_p_value=1.89384e-05	fisher_strand_p_value=1.30417e-06	frequency=3.874016e-02	genotype_quality=851.8	ks_quality_p_value=0.9979	log10_base_likelihood=-6.2865	log10_qual_likelihood_position_model=15.3082	log10_strand_likelihood_position_model=5.88467	new_cov=0/17	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=140/106	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/123
RA	318	.	NC_007779	2212417	0	G	T	bias_e_value=94.5975	bias_p_value=2.03596e-05	fisher_strand_p_value=1.40726e-06	frequency=3.318119e-02	genotype_quality=740.5	ks_quality_p_value=0.999532	log10_base_likelihood=-6.72603	log10_qual_likelihood_position_model=10.8183	log10_strand_likelihood_position_model=5.85163	new_cov=8/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=30/151	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=38/151
RA	319	.	NC_007779	2213136	0	G	T	bias_e_value=0.000236929	bias_p_value=5.09926e-11	fisher_strand_p_value=1.81904e-12	frequency=1.033583e-01	genotype_quality=693.1	ks_quality_p_value=1	log10_base_likelihood=-31.9402	log10_qual_likelihood_position_model=24.7754	log10_strand_likelihood_position_model=11.7402	new_cov=22/0	polymorphism_quality=26.8	quality=26.8	quality_position_model=Inf	ref_cov=44/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=66/133
RA	320	.	NC_007779	2222886	0	T	G	bias_e_value=1255.57	bias_p_value=0.000270228	fisher_strand_p_value=2.32044e-05	frequency=2.215672e-02	genotype_quality=767.1	ks_quality_p_value=0.997599	log10_base_likelihood=-5.74844	log10_qual_likelihood_position_model=7.28059	log10_strand_likelihood_position_model=4.63443	new_cov=5/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=20/171	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=25/171
RA	321	.	NC_007779	2226024	0	C	A	bias_e_value=0.0996049	bias_p_value=2.14373e-08	fisher_strand_p_value=9.86206e-10	frequency=5.854368e-02	genotype_quality=925.1	ks_quality_p_value=1	log10_base_likelihood=-7.0602	log10_qual_likelihood_position_model=23.0994	log10_strand_likelihood_position_model=9.11035	new_cov=29/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=122/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/145
RA	322	.	NC_007779	2249963	0	T	G	bias_e_value=1.10392e-06	bias_p_value=2.3759e-13	fisher_strand_p_value=7.07487e-15	frequency=1.291480e-01	genotype_quality=692.0	ks_quality_p_value=1	log10_base_likelihood=-16.8728	log10_qual_likelihood_position_model=42.041	log10_strand_likelihood_position_model=14.3361	new_cov=48/0	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=90/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=138/112
RA	323	.	NC_007779	2254201	0	G	T	bias_e_value=22.4343	bias_p_value=4.82839e-06	fisher_strand_p_value=3.01501e-07	frequency=3.106308e-02	genotype_quality=999.5	ks_quality_p_value=1	log10_base_likelihood=-5.62123	log10_qual_likelihood_position_model=15.3872	log10_strand_likelihood_position_model=6.52071	new_cov=0/18	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=162/115	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/133
RA	324	.	NC_007779	2266892	0	G	T	bias_e_value=40.9339	bias_p_value=8.80995e-06	fisher_strand_p_value=6.18843e-07	frequency=5.982733e-02	genotype_quality=886.6	ks_quality_p_value=0.926099	log10_base_likelihood=-13.9968	log10_qual_likelihood_position_model=16.4477	log10_strand_likelihood_position_model=6.28663	new_cov=0/23	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=126/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/155
RA	325	.	NC_007779	2271208	1	.	C	bias_e_value=2418280	bias_p_value=0.520471	fisher_strand_p_value=0.216378	frequency=8.968353e-03	genotype_quality=1078.7	ks_quality_p_value=0.920248	log10_base_likelihood=-7.78696	log10_qual_likelihood_position_model=2.88848	log10_strand_likelihood_position_model=0.664787	new_cov=0/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=4.37614e-06	ref_cov=119/102	reject=POLYMORPHISM_STRAND	tot_cov=119/104
RA	326	.	NC_007779	2271592	0	G	T	bias_e_value=2.22597	bias_p_value=4.79082e-07	fisher_strand_p_value=2.5942e-08	frequency=5.202055e-02	genotype_quality=896.6	ks_quality_p_value=1	log10_base_likelihood=-8.62093	log10_qual_likelihood_position_model=19.7444	log10_strand_likelihood_position_model=7.586	new_cov=0/21	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=132/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/112
RA	327	.	NC_007779	2278635	0	C	A	bias_e_value=7.9638	bias_p_value=1.714e-06	fisher_strand_p_value=1.00136e-07	frequency=3.627300e-02	genotype_quality=909.0	ks_quality_p_value=1	log10_base_likelihood=-7.15558	log10_qual_likelihood_position_model=15.4205	log10_strand_likelihood_position_model=6.99941	new_cov=20/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=110/149	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/149
RA	328	.	NC_007779	2287403	1	.	A	bias_e_value=3935140	bias_p_value=0.846934	fisher_strand_p_value=0.50052	frequency=5.640030e-03	genotype_quality=1776.2	ks_quality_p_value=1	log10_base_likelihood=-6.05857	log10_qual_likelihood_position_model=3.45333	log10_strand_likelihood_position_model=0.550779	new_cov=0/2	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.000912401	ref_cov=166/186	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/188
RA	329	.	NC_007779	2296314	1	.	T	bias_e_value=1715550	bias_p_value=0.369228	fisher_strand_p_value=0.517127	frequency=6.557465e-03	genotype_quality=1501.4	ks_quality_p_value=0.227328	log10_base_likelihood=-8.09313	log10_qual_likelihood_position_model=2.45663	log10_strand_likelihood_position_model=0.449423	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.43585e-07	ref_cov=180/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=182/123
RA	330	.	NC_007779	2306988	1	.	G	bias_e_value=1652580	bias_p_value=0.355675	fisher_strand_p_value=0.114244	frequency=6.993294e-03	genotype_quality=1432.7	ks_quality_p_value=0.974285	log10_base_likelihood=-8.11296	log10_qual_likelihood_position_model=1.66471	log10_strand_likelihood_position_model=0.942168	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.06967e-07	ref_cov=95/189	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=97/189
RA	331	.	NC_007779	2307309	0	T	C	bias_e_value=0.93116	bias_p_value=2.00408e-07	fisher_strand_p_value=1.03369e-08	frequency=3.754520e-02	genotype_quality=899.9	ks_quality_p_value=1	log10_base_likelihood=-5.94226	log10_qual_likelihood_position_model=14.6987	log10_strand_likelihood_position_model=7.98561	new_cov=0/14	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=194/64	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=194/78
RA	332	.	NC_007779	2331120	0	T	G	bias_e_value=4.69351e-12	bias_p_value=1.01015e-18	fisher_strand_p_value=2.18313e-20	frequency=1.049542e-01	genotype_quality=714.5	ks_quality_p_value=1	log10_base_likelihood=-10.7518	log10_qual_likelihood_position_model=29.5662	log10_strand_likelihood_position_model=19.6609	new_cov=45/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=58/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/138
RA	333	.	NC_007779	2332580	0	A	C	bias_e_value=4.96588e-08	bias_p_value=1.06877e-14	fisher_strand_p_value=2.90629e-16	frequency=1.315203e-01	genotype_quality=679.9	ks_quality_p_value=1	log10_base_likelihood=-13.6389	log10_qual_likelihood_position_model=32.0473	log10_strand_likelihood_position_model=15.5805	new_cov=1/47	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=120/70	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/117
RA	334	.	NC_007779	2344586	0	C	A	bias_e_value=0.469598	bias_p_value=1.01069e-07	fisher_strand_p_value=5.02614e-09	frequency=5.077028e-02	genotype_quality=810.1	ks_quality_p_value=1	log10_base_likelihood=-5.85107	log10_qual_likelihood_position_model=23.6121	log10_strand_likelihood_position_model=8.29877	new_cov=24/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=93/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/128
RA	335	.	NC_007779	2348480	0	G	T	bias_e_value=0.00123495	bias_p_value=2.65791e-10	fisher_strand_p_value=1.0099e-11	frequency=5.709219e-02	genotype_quality=1002.9	ks_quality_p_value=1	log10_base_likelihood=-9.14139	log10_qual_likelihood_position_model=29.6014	log10_strand_likelihood_position_model=10.9957	new_cov=0/27	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=161/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/117
RA	336	.	NC_007779	2353815	0	A	C	bias_e_value=1.58987e-12	bias_p_value=3.42176e-19	fisher_strand_p_value=7.2224e-21	frequency=1.029630e-01	genotype_quality=786.6	ks_quality_p_value=1	log10_base_likelihood=-18.5882	log10_qual_likelihood_position_model=34.9889	log10_strand_likelihood_position_model=20.1413	new_cov=0/38	polymorphism_quality=13.3	quality=13.3	quality_position_model=Inf	ref_cov=156/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/86
RA	337	.	NC_007779	2354291	0	A	C	bias_e_value=1.8071	bias_p_value=3.8893e-07	fisher_strand_p_value=2.0812e-08	frequency=4.034805e-02	genotype_quality=1007.7	ks_quality_p_value=1	log10_base_likelihood=-5.62602	log10_qual_likelihood_position_model=21.6002	log10_strand_likelihood_position_model=7.68169	new_cov=0/22	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=167/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=167/146
RA	338	.	NC_007779	2368771	0	C	.	bias_e_value=3580150	bias_p_value=0.770533	fisher_strand_p_value=0.497634	frequency=9.846687e-03	genotype_quality=857.5	ks_quality_p_value=0.812665	log10_base_likelihood=-5.66716	log10_qual_likelihood_position_model=0.880293	log10_strand_likelihood_position_model=0.59141	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=4.79883e-06	ref_cov=101/100	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=103/100
RA	339	.	NC_007779	2368772	0	G	.	bias_e_value=3400930	bias_p_value=0.731959	fisher_strand_p_value=0.497561	frequency=9.751320e-03	genotype_quality=853.8	ks_quality_p_value=0.731768	log10_base_likelihood=-5.69173	log10_qual_likelihood_position_model=0.988927	log10_strand_likelihood_position_model=0.599947	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=6.0003e-06	ref_cov=101/102	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=103/102
RA	340	.	NC_007779	2373239	0	A	C	bias_e_value=3.71946e-08	bias_p_value=8.00515e-15	fisher_strand_p_value=2.15938e-16	frequency=8.977890e-02	genotype_quality=733.8	ks_quality_p_value=1	log10_base_likelihood=-13.4883	log10_qual_likelihood_position_model=29.947	log10_strand_likelihood_position_model=15.6657	new_cov=0/35	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=139/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/95
RA	341	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=1080.4	new_cov=133/134	quality=1080.4	ref_cov=0/0	tot_cov=133/134
RA	342	.	NC_007779	2409404	0	A	C	bias_e_value=5.95438	bias_p_value=1.28152e-06	fisher_strand_p_value=7.35435e-08	frequency=5.068874e-02	genotype_quality=695.8	ks_quality_p_value=1	log10_base_likelihood=-6.46584	log10_qual_likelihood_position_model=17.7008	log10_strand_likelihood_position_model=7.13346	new_cov=0/17	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=125/68	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/85
RA	343	.	NC_007779	2410316	0	A	C	bias_e_value=0.216764	bias_p_value=4.66527e-08	fisher_strand_p_value=2.22991e-09	frequency=6.885338e-02	genotype_quality=823.4	ks_quality_p_value=1	log10_base_likelihood=-18.6522	log10_qual_likelihood_position_model=25.1989	log10_strand_likelihood_position_model=8.71408	new_cov=0/28	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=130/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=130/138
RA	344	.	NC_007779	2410326	1	.	C	bias_e_value=2792140	bias_p_value=0.600934	fisher_strand_p_value=0.25316	frequency=1.108456e-02	genotype_quality=1323.3	ks_quality_p_value=1	log10_base_likelihood=-6.62806	log10_qual_likelihood_position_model=6.5111	log10_strand_likelihood_position_model=0.796213	new_cov=0/3	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=123/144	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=123/147
RA	345	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=971.7	new_cov=115/127	quality=971.7	ref_cov=0/0	tot_cov=115/127
RA	346	.	NC_007779	2417605	0	C	A	bias_e_value=0.0209567	bias_p_value=4.51038e-09	fisher_strand_p_value=4.053e-10	frequency=1.289997e-01	genotype_quality=676.8	ks_quality_p_value=0.476223	log10_base_likelihood=-33.3623	log10_qual_likelihood_position_model=35.4812	log10_strand_likelihood_position_model=9.45819	new_cov=37/0	polymorphism_quality=28.2	quality=28.2	quality_position_model=Inf	ref_cov=104/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/98
RA	347	.	NC_007779	2418070	1	.	A	bias_e_value=1715330	bias_p_value=0.369178	fisher_strand_p_value=0.199264	frequency=7.781982e-03	genotype_quality=1278.9	ks_quality_p_value=0.589842	log10_base_likelihood=-8.28975	log10_qual_likelihood_position_model=1.9947	log10_strand_likelihood_position_model=0.70057	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.67599e-07	ref_cov=113/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/142
RA	348	.	NC_007779	2446437	0	A	C	bias_e_value=107.881	bias_p_value=2.32185e-05	fisher_strand_p_value=1.61992e-06	frequency=4.119587e-02	genotype_quality=991.7	ks_quality_p_value=1	log10_base_likelihood=-5.87656	log10_qual_likelihood_position_model=23.3252	log10_strand_likelihood_position_model=5.83199	new_cov=0/20	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=141/137	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/157
RA	349	.	NC_007779	2459734	0	T	.	bias_e_value=2509570	bias_p_value=0.540118	fisher_strand_p_value=0.328354	frequency=1.645374e-02	genotype_quality=970.9	ks_quality_p_value=0.644213	log10_base_likelihood=-11.7233	log10_qual_likelihood_position_model=2.38446	log10_strand_likelihood_position_model=0.702251	new_cov=1/3	polymorphism_quality=6.3	quality=6.3	quality_position_model=1.23889e-10	ref_cov=133/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/109
RA	350	.	NC_007779	2465370	0	C	A	bias_e_value=30.4506	bias_p_value=6.55368e-06	fisher_strand_p_value=4.18044e-07	frequency=5.196619e-02	genotype_quality=637.3	ks_quality_p_value=0.999274	log10_base_likelihood=-12.2287	log10_qual_likelihood_position_model=11.7013	log10_strand_likelihood_position_model=6.37878	new_cov=0/9	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=127/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/35
RA	351	.	NC_007779	2468326	1	.	C	bias_e_value=1559670	bias_p_value=0.335677	fisher_strand_p_value=0.498113	frequency=1.249981e-02	genotype_quality=761.8	ks_quality_p_value=0.205506	log10_base_likelihood=-9.39165	log10_qual_likelihood_position_model=2.24715	log10_strand_likelihood_position_model=0.56216	new_cov=2/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=1.59688e-08	ref_cov=82/76	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=84/76
RA	352	.	NC_007779	2468327	0	C	.	bias_e_value=3749400	bias_p_value=0.806959	fisher_strand_p_value=1	frequency=4.320431e-02	genotype_quality=656.2	ks_quality_p_value=0.447044	log10_base_likelihood=-24.496	log10_qual_likelihood_position_model=3.17168	log10_strand_likelihood_position_model=0.536516	new_cov=4/3	polymorphism_quality=19.3	quality=19.3	quality_position_model=5.71443e-23	ref_cov=81/74	reject=INDEL_HOMOPOLYMER	tot_cov=85/77
RA	353	.	NC_007779	2475172	0	T	.	bias_e_value=4477250	bias_p_value=0.963609	fisher_strand_p_value=1	frequency=1.638699e-02	genotype_quality=494.3	ks_quality_p_value=0.742642	log10_base_likelihood=-5.91032	log10_qual_likelihood_position_model=1.24487	log10_strand_likelihood_position_model=0.346846	new_cov=1/1	polymorphism_quality=0.4	quality=0.4	quality_position_model=3.56633e-06	ref_cov=80/40	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=81/41
RA	354	.	NC_007779	2476279	0	C	G	bias_e_value=568172	bias_p_value=0.122284	fisher_strand_p_value=0.0264144	frequency=2.363777e-02	genotype_quality=745.5	ks_quality_p_value=0.998786	log10_base_likelihood=-7.49783	log10_qual_likelihood_position_model=6.76172	log10_strand_likelihood_position_model=1.57816	new_cov=0/5	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=94/85	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=94/90
RA	355	.	NC_007779	2476287	0	T	G	bias_e_value=330871	bias_p_value=0.0712112	fisher_strand_p_value=0.0134055	frequency=2.382851e-02	genotype_quality=693.2	ks_quality_p_value=1	log10_base_likelihood=-7.83259	log10_qual_likelihood_position_model=8.41166	log10_strand_likelihood_position_model=1.87272	new_cov=0/6	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=92/84	reject=POLYMORPHISM_STRAND	tot_cov=92/90
RA	356	.	NC_007779	2476289	0	A	T	bias_e_value=601884	bias_p_value=0.12954	fisher_strand_p_value=0.0286756	frequency=3.268242e-02	genotype_quality=688.8	ks_quality_p_value=0.990359	log10_base_likelihood=-9.1492	log10_qual_likelihood_position_model=8.84486	log10_strand_likelihood_position_model=1.82879	new_cov=0/6	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=89/84	reject=POLYMORPHISM_STRAND	tot_cov=89/90
RA	357	.	NC_007779	2478675	0	C	A	bias_e_value=51.0135	bias_p_value=1.09793e-05	fisher_strand_p_value=7.25348e-07	frequency=5.351353e-02	genotype_quality=691.2	ks_quality_p_value=1	log10_base_likelihood=-8.04691	log10_qual_likelihood_position_model=13.4725	log10_strand_likelihood_position_model=6.13945	new_cov=16/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=72/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=88/114
RA	358	.	NC_007779	2517218	0	A	C	bias_e_value=1.01391e-09	bias_p_value=2.18218e-16	fisher_strand_p_value=5.35254e-18	frequency=7.787561e-02	genotype_quality=657.5	ks_quality_p_value=1	log10_base_likelihood=-6.27629	log10_qual_likelihood_position_model=39.9813	log10_strand_likelihood_position_model=17.2714	new_cov=0/36	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=132/48	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=132/84
RA	359	.	NC_007779	2536601	0	T	G	bias_e_value=8.89444	bias_p_value=1.91429e-06	fisher_strand_p_value=1.1261e-07	frequency=5.625963e-02	genotype_quality=971.4	ks_quality_p_value=1	log10_base_likelihood=-9.05887	log10_qual_likelihood_position_model=25.5771	log10_strand_likelihood_position_model=7.23746	new_cov=24/1	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=117/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/160
RA	360	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=1362.5	new_cov=152/183	quality=1362.5	ref_cov=0/0	tot_cov=152/183
RA	361	.	NC_007779	2556426	0	G	T	bias_e_value=6.09155e-06	bias_p_value=1.31105e-12	fisher_strand_p_value=8.24664e-14	frequency=8.226061e-02	genotype_quality=952.8	ks_quality_p_value=0.499616	log10_base_likelihood=-15.9044	log10_qual_likelihood_position_model=40.2451	log10_strand_likelihood_position_model=13.0837	new_cov=0/39	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=160/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/157
RA	362	.	NC_007779	2577495	1	.	A	bias_e_value=176827	bias_p_value=0.0380572	fisher_strand_p_value=0.208374	frequency=7.092476e-03	genotype_quality=1393.3	ks_quality_p_value=0.0300768	log10_base_likelihood=-8.24438	log10_qual_likelihood_position_model=2.36493	log10_strand_likelihood_position_model=0.681156	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=4.31841e-07	ref_cov=153/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/129
RA	363	.	NC_007779	2581401	1	.	A	bias_e_value=1855250	bias_p_value=0.399293	fisher_strand_p_value=0.21801	frequency=7.547379e-03	genotype_quality=1316.7	ks_quality_p_value=0.605474	log10_base_likelihood=-8.2892	log10_qual_likelihood_position_model=1.09542	log10_strand_likelihood_position_model=0.661523	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.79853e-08	ref_cov=122/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/141
RA	364	.	NC_007779	2581900	0	G	T	bias_e_value=36.1147	bias_p_value=7.77274e-06	fisher_strand_p_value=5.01269e-07	frequency=3.129578e-02	genotype_quality=1078.7	ks_quality_p_value=1	log10_base_likelihood=-5.71336	log10_qual_likelihood_position_model=18.1089	log10_strand_likelihood_position_model=6.32164	new_cov=0/22	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=156/155	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/177
RA	365	.	NC_007779	2601998	0	A	C	bias_e_value=3.33633e-14	bias_p_value=7.18056e-21	fisher_strand_p_value=1.39915e-22	frequency=1.565366e-01	genotype_quality=576.2	ks_quality_p_value=1	log10_base_likelihood=-35.7148	log10_qual_likelihood_position_model=31.6136	log10_strand_likelihood_position_model=21.8541	new_cov=0/30	polymorphism_quality=30.6	quality=30.6	quality_position_model=Inf	ref_cov=126/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/45
RA	366	.	NC_007779	2604001	0	T	G	bias_e_value=0.000150886	bias_p_value=3.24742e-11	fisher_strand_p_value=1.13943e-12	frequency=6.686163e-02	genotype_quality=812.1	ks_quality_p_value=1	log10_base_likelihood=-12.0098	log10_qual_likelihood_position_model=24.0961	log10_strand_likelihood_position_model=11.9433	new_cov=31/0	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=84/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/142
RA	367	.	NC_007779	2614764	1	.	A	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=6.733894e-03	genotype_quality=1488.2	ks_quality_p_value=0.999589	log10_base_likelihood=-7.45846	log10_qual_likelihood_position_model=2.95282	log10_strand_likelihood_position_model=0.29957	new_cov=1/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=4.67758e-06	ref_cov=147/148	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/149
RA	368	.	NC_007779	2618856	1	.	A	bias_e_value=3284430	bias_p_value=0.706886	fisher_strand_p_value=0.504806	frequency=6.919861e-03	genotype_quality=1443.2	ks_quality_p_value=0.673692	log10_base_likelihood=-7.98622	log10_qual_likelihood_position_model=1.71078	log10_strand_likelihood_position_model=0.509344	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.11306e-07	ref_cov=128/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/161
RA	369	.	NC_007779	2618857	0	A	.	bias_e_value=4092930	bias_p_value=0.880896	fisher_strand_p_value=0.633321	frequency=1.373863e-02	genotype_quality=1195.9	ks_quality_p_value=0.873975	log10_base_likelihood=-11.3739	log10_qual_likelihood_position_model=1.36	log10_strand_likelihood_position_model=0.508783	new_cov=1/3	polymorphism_quality=6.0	quality=6.0	quality_position_model=1.60177e-11	ref_cov=127/160	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/163
RA	370	.	NC_007779	2623159	0	T	G	bias_e_value=1.39614e-24	bias_p_value=3.00482e-31	fisher_strand_p_value=3.97434e-33	frequency=1.931467e-01	genotype_quality=757.8	ks_quality_p_value=1	log10_base_likelihood=-41.6281	log10_qual_likelihood_position_model=45.9603	log10_strand_likelihood_position_model=32.4007	new_cov=68/0	polymorphism_quality=36.5	quality=36.5	quality_position_model=Inf	ref_cov=46/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/154
RA	371	.	NC_007779	2625320	1	.	G	bias_e_value=2671860	bias_p_value=0.575046	fisher_strand_p_value=0.241268	frequency=7.811546e-03	genotype_quality=1256.0	ks_quality_p_value=0.973236	log10_base_likelihood=-7.16131	log10_qual_likelihood_position_model=2.91169	log10_strand_likelihood_position_model=0.6175	new_cov=2/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=1.87502e-05	ref_cov=124/130	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/130
RA	372	.	NC_007779	2641345	0	T	G	bias_e_value=6.42457e-08	bias_p_value=1.38272e-14	fisher_strand_p_value=3.78726e-16	frequency=7.112694e-02	genotype_quality=662.7	ks_quality_p_value=1	log10_base_likelihood=-11.1772	log10_qual_likelihood_position_model=23.1919	log10_strand_likelihood_position_model=15.4217	new_cov=19/0	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=18/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=37/150
RA	373	.	NC_007779	2650773	0	T	.	bias_e_value=4178120	bias_p_value=0.899229	fisher_strand_p_value=1	frequency=1.055622e-02	genotype_quality=1117.7	ks_quality_p_value=0.586094	log10_base_likelihood=-8.1972	log10_qual_likelihood_position_model=1.78989	log10_strand_likelihood_position_model=0.397978	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=6.23558e-08	ref_cov=131/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/152
RA	374	.	NC_007779	2672817	0	A	C	bias_e_value=5.07297e-07	bias_p_value=1.09182e-13	fisher_strand_p_value=3.17544e-15	frequency=5.139494e-02	genotype_quality=799.4	ks_quality_p_value=1	log10_base_likelihood=-6.71728	log10_qual_likelihood_position_model=28.5846	log10_strand_likelihood_position_model=14.4982	new_cov=0/33	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=151/70	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=151/103
RA	375	.	NC_007779	2676695	0	T	G	bias_e_value=2.1219e-08	bias_p_value=4.56683e-15	fisher_strand_p_value=1.21303e-16	frequency=8.166265e-02	genotype_quality=671.7	ks_quality_p_value=1	log10_base_likelihood=-11.1197	log10_qual_likelihood_position_model=38.7808	log10_strand_likelihood_position_model=15.9161	new_cov=34/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=49/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=83/127
RA	376	.	NC_007779	2690409	1	.	C	bias_e_value=2190590	bias_p_value=0.471467	fisher_strand_p_value=0.170132	frequency=8.027077e-03	genotype_quality=1214.3	ks_quality_p_value=1	log10_base_likelihood=-5.6002	log10_qual_likelihood_position_model=3.41044	log10_strand_likelihood_position_model=0.769214	new_cov=0/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.00460023	ref_cov=146/101	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=146/103
RA	377	.	NC_007779	2703542	0	G	T	bias_e_value=0.131227	bias_p_value=2.82431e-08	fisher_strand_p_value=1.31681e-09	frequency=4.181767e-02	genotype_quality=1004.3	ks_quality_p_value=1	log10_base_likelihood=-6.59526	log10_qual_likelihood_position_model=18.4887	log10_strand_likelihood_position_model=8.88048	new_cov=0/24	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=167/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/136
RA	378	.	NC_007779	2708935	0	A	C	bias_e_value=261.56	bias_p_value=5.62938e-05	fisher_strand_p_value=4.20776e-06	frequency=4.684496e-02	genotype_quality=796.5	ks_quality_p_value=1	log10_base_likelihood=-7.36539	log10_qual_likelihood_position_model=17.4882	log10_strand_likelihood_position_model=5.56615	new_cov=0/18	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=127/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/131
RA	379	.	NC_007779	2733192	0	C	.	bias_e_value=3870780	bias_p_value=0.833084	fisher_strand_p_value=0.613142	frequency=1.070881e-02	genotype_quality=1181.5	ks_quality_p_value=0.784586	log10_base_likelihood=-8.6271	log10_qual_likelihood_position_model=0.87082	log10_strand_likelihood_position_model=0.437451	new_cov=2/1	polymorphism_quality=3.2	quality=3.2	quality_position_model=2.78616e-09	ref_cov=134/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/144
RA	380	.	NC_007779	2753432	1	.	A	bias_e_value=2266440	bias_p_value=0.487792	fisher_strand_p_value=1	frequency=1.265812e-02	genotype_quality=1168.7	ks_quality_p_value=0.179492	log10_base_likelihood=-13.2015	log10_qual_likelihood_position_model=1.84617	log10_strand_likelihood_position_model=0.382572	new_cov=2/1	polymorphism_quality=7.8	quality=7.8	quality_position_model=5.0931e-13	ref_cov=130/104	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/105
RA	381	.	NC_007779	2757983	1	.	A	bias_e_value=3834950	bias_p_value=0.82537	fisher_strand_p_value=1	frequency=8.474350e-03	genotype_quality=1173.5	ks_quality_p_value=0.470676	log10_base_likelihood=-7.98005	log10_qual_likelihood_position_model=1.53126	log10_strand_likelihood_position_model=0.301187	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.48713e-08	ref_cov=125/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/110
RA	382	.	NC_007779	2771858	0	G	T	bias_e_value=4645210	bias_p_value=0.999758	fisher_strand_p_value=1	frequency=9.490013e-03	genotype_quality=1360.8	ks_quality_p_value=0.978064	log10_base_likelihood=-5.59318	log10_qual_likelihood_position_model=3.08959	log10_strand_likelihood_position_model=0.361978	new_cov=1/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.000733204	ref_cov=124/187	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=125/189
RA	383	.	NC_007779	2791171	0	G	T	bias_e_value=1.68953	bias_p_value=3.63627e-07	fisher_strand_p_value=1.93843e-08	frequency=3.938007e-02	genotype_quality=1269.9	ks_quality_p_value=1	log10_base_likelihood=-7.96912	log10_qual_likelihood_position_model=20.2158	log10_strand_likelihood_position_model=7.71255	new_cov=0/24	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=191/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=191/186
RA	384	.	NC_007779	2791635	0	C	T	bias_e_value=8.79475e-06	bias_p_value=1.89284e-12	fisher_strand_p_value=6.02523e-14	frequency=7.297134e-02	genotype_quality=879.4	ks_quality_p_value=0.999176	log10_base_likelihood=-12.9686	log10_qual_likelihood_position_model=21.9299	log10_strand_likelihood_position_model=13.22	new_cov=0/28	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=173/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/102
RA	385	.	NC_007779	2797644	0	C	A	bias_e_value=2887.35	bias_p_value=0.000621425	fisher_strand_p_value=5.77572e-05	frequency=2.857590e-02	genotype_quality=1041.2	ks_quality_p_value=1	log10_base_likelihood=-6.67661	log10_qual_likelihood_position_model=8.86607	log10_strand_likelihood_position_model=4.23839	new_cov=0/9	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=180/87	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=180/96
RA	386	.	NC_007779	2816615	0	G	C	bias_e_value=22.208	bias_p_value=4.77968e-06	fisher_strand_p_value=3.17752e-07	frequency=5.000544e-02	genotype_quality=656.4	ks_quality_p_value=0.938651	log10_base_likelihood=-8.32978	log10_qual_likelihood_position_model=17.0979	log10_strand_likelihood_position_model=6.49791	new_cov=13/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=51/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=64/125
RA	387	.	NC_007779	2817030	0	G	C	bias_e_value=0.002852	bias_p_value=6.13818e-10	fisher_strand_p_value=3.63658e-11	frequency=8.581400e-02	genotype_quality=668.3	ks_quality_p_value=0.663274	log10_base_likelihood=-15.7956	log10_qual_likelihood_position_model=28.3006	log10_strand_likelihood_position_model=10.4393	new_cov=22/0	polymorphism_quality=10.5	quality=10.5	quality_position_model=Inf	ref_cov=55/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=77/131
RA	388	.	NC_007779	2833989	0	A	C	bias_e_value=2.33634e-15	bias_p_value=5.02836e-22	fisher_strand_p_value=9.30637e-24	frequency=8.198166e-02	genotype_quality=818.8	ks_quality_p_value=1	log10_base_likelihood=-14.705	log10_qual_likelihood_position_model=33.9461	log10_strand_likelihood_position_model=23.0312	new_cov=0/29	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=182/21	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=182/50
RA	389	.	NC_007779	2839296	0	A	G	bias_e_value=0.0615835	bias_p_value=1.32542e-08	fisher_strand_p_value=5.95939e-10	frequency=7.261944e-02	genotype_quality=641.1	ks_quality_p_value=1	log10_base_likelihood=-10.7636	log10_qual_likelihood_position_model=16.7642	log10_strand_likelihood_position_model=9.2248	new_cov=20/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=58/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=78/129
RA	390	.	NC_007779	2847445	0	G	T	bias_e_value=0.00309992	bias_p_value=6.67176e-10	fisher_strand_p_value=2.6307e-11	frequency=8.216381e-02	genotype_quality=993.9	ks_quality_p_value=1	log10_base_likelihood=-18.3103	log10_qual_likelihood_position_model=22.5581	log10_strand_likelihood_position_model=10.6854	new_cov=0/36	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=151/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/172
RA	391	.	NC_007779	2861528	0	G	T	bias_e_value=49.5955	bias_p_value=1.06741e-05	fisher_strand_p_value=7.50212e-07	frequency=3.668118e-02	genotype_quality=1012.8	ks_quality_p_value=0.938112	log10_base_likelihood=-8.00475	log10_qual_likelihood_position_model=23.0418	log10_strand_likelihood_position_model=6.12482	new_cov=0/18	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=155/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/139
RA	392	.	NC_007779	2862783	1	.	T	bias_e_value=3945830	bias_p_value=0.849235	fisher_strand_p_value=0.503891	frequency=7.688522e-03	genotype_quality=1298.5	ks_quality_p_value=0.99994	log10_base_likelihood=-6.00243	log10_qual_likelihood_position_model=4.52724	log10_strand_likelihood_position_model=0.514575	new_cov=0/2	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.0156714	ref_cov=116/142	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=116/144
RA	393	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1157.4	new_cov=113/150	quality=1157.4	ref_cov=0/1	tot_cov=113/151
RA	394	.	NC_007779	2868094	0	C	A	bias_e_value=3.06603	bias_p_value=6.59882e-07	fisher_strand_p_value=3.63998e-08	frequency=8.392143e-02	genotype_quality=801.0	ks_quality_p_value=1	log10_base_likelihood=-13.3794	log10_qual_likelihood_position_model=19.6953	log10_strand_likelihood_position_model=7.46316	new_cov=27/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=110/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/110
RA	395	.	NC_007779	2895131	0	A	C	bias_e_value=3.47473e-07	bias_p_value=7.47843e-14	fisher_strand_p_value=2.15064e-15	frequency=6.579494e-02	genotype_quality=786.3	ks_quality_p_value=1	log10_base_likelihood=-6.74523	log10_qual_likelihood_position_model=32.6345	log10_strand_likelihood_position_model=14.6674	new_cov=0/27	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=153/48	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/75
RA	396	.	NC_007779	2898837	0	G	T	bias_e_value=1.38074	bias_p_value=2.97168e-07	fisher_strand_p_value=1.56635e-08	frequency=6.801510e-02	genotype_quality=905.6	ks_quality_p_value=1	log10_base_likelihood=-15.8569	log10_qual_likelihood_position_model=23.2895	log10_strand_likelihood_position_model=7.86896	new_cov=1/27	polymorphism_quality=10.5	quality=10.5	quality_position_model=Inf	ref_cov=141/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/135
RA	397	.	NC_007779	2898953	1	.	A	bias_e_value=2167540	bias_p_value=0.466506	fisher_strand_p_value=0.228901	frequency=8.196831e-03	genotype_quality=1204.0	ks_quality_p_value=0.731077	log10_base_likelihood=-7.93409	log10_qual_likelihood_position_model=2.0406	log10_strand_likelihood_position_model=0.640352	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.7876e-07	ref_cov=127/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/117
RA	398	.	NC_007779	2926157	0	T	G	bias_e_value=1.40416e-11	bias_p_value=3.02209e-18	fisher_strand_p_value=6.69336e-20	frequency=7.106590e-02	genotype_quality=623.3	ks_quality_p_value=1	log10_base_likelihood=-6.38996	log10_qual_likelihood_position_model=26.1222	log10_strand_likelihood_position_model=19.1744	new_cov=24/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=15/140	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=39/140
RA	399	.	NC_007779	2939008	0	A	C	bias_e_value=4.48861	bias_p_value=9.66054e-07	fisher_strand_p_value=5.45022e-08	frequency=3.959846e-02	genotype_quality=958.3	ks_quality_p_value=1	log10_base_likelihood=-5.89457	log10_qual_likelihood_position_model=20.8761	log10_strand_likelihood_position_model=7.26359	new_cov=0/18	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=166/99	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=166/117
RA	400	.	NC_007779	2940225	0	G	T	bias_e_value=4645.11	bias_p_value=0.000999738	fisher_strand_p_value=9.77332e-05	frequency=3.693390e-02	genotype_quality=981.8	ks_quality_p_value=0.999566	log10_base_likelihood=-9.90784	log10_qual_likelihood_position_model=13.3892	log10_strand_likelihood_position_model=4.22536	new_cov=1/17	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=145/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/151
RA	401	.	NC_007779	2942972	0	G	T	bias_e_value=6.72396	bias_p_value=1.44715e-06	fisher_strand_p_value=9.79918e-08	frequency=3.181171e-02	genotype_quality=1060.7	ks_quality_p_value=0.853826	log10_base_likelihood=-5.99637	log10_qual_likelihood_position_model=17.9424	log10_strand_likelihood_position_model=7.00881	new_cov=0/18	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=179/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/133
RA	402	.	NC_007779	2945991	1	.	A	bias_e_value=1007890	bias_p_value=0.216923	fisher_strand_p_value=1	frequency=1.000023e-02	genotype_quality=1475.0	ks_quality_p_value=0.0558294	log10_base_likelihood=-12.6685	log10_qual_likelihood_position_model=2.38712	log10_strand_likelihood_position_model=0.375853	new_cov=2/1	polymorphism_quality=7.3	quality=7.3	quality_position_model=6.24578e-12	ref_cov=169/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=171/129
RA	403	.	NC_007779	2953753	0	C	.	bias_e_value=4646330	bias_p_value=0.999999	fisher_strand_p_value=1	frequency=9.951591e-03	genotype_quality=1253.4	ks_quality_p_value=0.998923	log10_base_likelihood=-7.61559	log10_qual_likelihood_position_model=2.49328	log10_strand_likelihood_position_model=0.405527	new_cov=1/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.369e-06	ref_cov=142/155	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/158
RA	404	.	NC_007779	2974960	0	A	.	bias_e_value=2224330	bias_p_value=0.478729	fisher_strand_p_value=0.382178	frequency=1.864910e-02	genotype_quality=1090.1	ks_quality_p_value=0.455967	log10_base_likelihood=-14.8106	log10_qual_likelihood_position_model=3.26478	log10_strand_likelihood_position_model=0.691221	new_cov=4/1	polymorphism_quality=9.5	quality=9.5	quality_position_model=6.72057e-13	ref_cov=143/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/121
RA	405	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=854.2	new_cov=108/100	quality=854.2	ref_cov=0/0	tot_cov=108/100
RA	406	.	NC_007779	3034413	0	A	C	bias_e_value=1.83492e-11	bias_p_value=3.94918e-18	fisher_strand_p_value=8.80003e-20	frequency=1.153831e-01	genotype_quality=664.1	ks_quality_p_value=1	log10_base_likelihood=-18.7878	log10_qual_likelihood_position_model=30.2354	log10_strand_likelihood_position_model=19.0583	new_cov=1/35	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=144/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/70
RA	407	.	NC_007779	3035390	0	T	C	bias_e_value=0.000576764	bias_p_value=1.24133e-10	fisher_strand_p_value=4.57894e-12	frequency=1.127005e-01	genotype_quality=520.8	ks_quality_p_value=1	log10_base_likelihood=-19.6203	log10_qual_likelihood_position_model=20.1456	log10_strand_likelihood_position_model=11.3392	new_cov=0/24	polymorphism_quality=14.3	quality=14.3	quality_position_model=Inf	ref_cov=120/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/73
RA	408	.	NC_007779	3044705	1	.	T	bias_e_value=786594	bias_p_value=0.169294	fisher_strand_p_value=0.0427581	frequency=1.129913e-02	genotype_quality=840.8	ks_quality_p_value=0.939411	log10_base_likelihood=-8.29589	log10_qual_likelihood_position_model=2.28937	log10_strand_likelihood_position_model=1.36898	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.65593e-06	ref_cov=35/140	reject=POLYMORPHISM_STRAND	tot_cov=37/140
RA	409	.	NC_007779	3048743	0	C	T	bias_e_value=881015	bias_p_value=0.189615	fisher_strand_p_value=0.0471991	frequency=8.616972e-02	genotype_quality=902.6	ks_quality_p_value=0.988221	log10_base_likelihood=-55.1805	log10_qual_likelihood_position_model=7.77074	log10_strand_likelihood_position_model=1.62855	new_cov=6/16	polymorphism_quality=50.1	quality=50.1	quality_position_model=3.93111e-48	ref_cov=116/117	tot_cov=122/133
RA	410	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=996.6	new_cov=126/122	quality=996.6	ref_cov=0/0	tot_cov=126/122
RA	411	.	NC_007779	3059420	1	.	T	bias_e_value=4093430	bias_p_value=0.881002	fisher_strand_p_value=0.589761	frequency=9.771347e-03	genotype_quality=1521.1	ks_quality_p_value=0.938833	log10_base_likelihood=-11.8189	log10_qual_likelihood_position_model=2.85553	log10_strand_likelihood_position_model=0.475552	new_cov=1/2	polymorphism_quality=6.4	quality=6.4	quality_position_model=1.7596e-10	ref_cov=168/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=169/138
RA	412	.	NC_007779	3074129	0	G	T	bias_e_value=66.5438	bias_p_value=1.43218e-05	fisher_strand_p_value=9.6431e-07	frequency=3.705311e-02	genotype_quality=821.3	ks_quality_p_value=1	log10_base_likelihood=-5.92385	log10_qual_likelihood_position_model=15.3166	log10_strand_likelihood_position_model=6.01578	new_cov=0/18	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=129/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/120
RA	413	.	NC_007779	3084663	0	C	A	bias_e_value=21.2252	bias_p_value=4.56817e-06	fisher_strand_p_value=2.84204e-07	frequency=4.421520e-02	genotype_quality=966.0	ks_quality_p_value=1	log10_base_likelihood=-6.83906	log10_qual_likelihood_position_model=16.3663	log10_strand_likelihood_position_model=6.61296	new_cov=22/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=129/140	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/140
RA	414	.	NC_007779	3088549	0	G	T	bias_e_value=9.25556	bias_p_value=1.99201e-06	fisher_strand_p_value=1.17474e-07	frequency=6.613636e-02	genotype_quality=853.6	ks_quality_p_value=1	log10_base_likelihood=-12.666	log10_qual_likelihood_position_model=20.6622	log10_strand_likelihood_position_model=6.96937	new_cov=0/29	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=118/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/174
RA	415	.	NC_007779	3095244	0	A	.	bias_e_value=2592480	bias_p_value=0.557962	fisher_strand_p_value=0.569527	frequency=9.139061e-03	genotype_quality=1331.7	ks_quality_p_value=0.391942	log10_base_likelihood=-7.97865	log10_qual_likelihood_position_model=2.23467	log10_strand_likelihood_position_model=0.52776	new_cov=2/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.13721e-07	ref_cov=132/193	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/194
RA	416	.	NC_007779	3105663	1	.	T	bias_e_value=3152280	bias_p_value=0.678445	fisher_strand_p_value=0.611092	frequency=1.260471e-02	genotype_quality=1152.4	ks_quality_p_value=0.514851	log10_base_likelihood=-12.6857	log10_qual_likelihood_position_model=2.55369	log10_strand_likelihood_position_model=0.439608	new_cov=2/1	polymorphism_quality=7.3	quality=7.3	quality_position_model=1.03098e-11	ref_cov=113/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/123
RA	417	.	NC_007779	3110532	0	C	A	bias_e_value=35.7837	bias_p_value=7.7015e-06	fisher_strand_p_value=4.9636e-07	frequency=4.496861e-02	genotype_quality=770.0	ks_quality_p_value=1	log10_base_likelihood=-11.7261	log10_qual_likelihood_position_model=13.7708	log10_strand_likelihood_position_model=6.3042	new_cov=0/11	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=145/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/59
RA	418	.	NC_007779	3124070	0	G	.	bias_e_value=3427890	bias_p_value=0.737762	fisher_strand_p_value=0.576626	frequency=9.197235e-03	genotype_quality=1365.4	ks_quality_p_value=0.641469	log10_base_likelihood=-8.46876	log10_qual_likelihood_position_model=1.58622	log10_strand_likelihood_position_model=0.506068	new_cov=2/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.60395e-08	ref_cov=136/186	reject=POLYMORPHISM_STRAND	tot_cov=139/187
RA	419	.	NC_007779	3124071	0	C	.	bias_e_value=3636210	bias_p_value=0.782598	fisher_strand_p_value=0.575543	frequency=9.310722e-03	genotype_quality=1351.0	ks_quality_p_value=0.726246	log10_base_likelihood=-8.32621	log10_qual_likelihood_position_model=1.4066	log10_strand_likelihood_position_model=0.509004	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.40113e-08	ref_cov=134/185	reject=POLYMORPHISM_STRAND	tot_cov=136/186
RA	420	.	NC_007779	3147621	0	G	T	bias_e_value=71.6531	bias_p_value=1.54214e-05	fisher_strand_p_value=1.04393e-06	frequency=4.373932e-02	genotype_quality=803.8	ks_quality_p_value=1	log10_base_likelihood=-7.64452	log10_qual_likelihood_position_model=12.8966	log10_strand_likelihood_position_model=5.98133	new_cov=0/18	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=136/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/128
RA	421	.	NC_007779	3152854	1	.	A	bias_e_value=4178690	bias_p_value=0.899352	fisher_strand_p_value=0.618271	frequency=1.079082e-02	genotype_quality=1371.3	ks_quality_p_value=0.948329	log10_base_likelihood=-12.874	log10_qual_likelihood_position_model=3.06698	log10_strand_likelihood_position_model=0.430834	new_cov=2/1	polymorphism_quality=7.5	quality=7.5	quality_position_model=2.16955e-11	ref_cov=135/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/141
RA	422	.	NC_007779	3152855	0	A	.	bias_e_value=2748560	bias_p_value=0.591555	fisher_strand_p_value=1	frequency=1.407337e-02	genotype_quality=1142.3	ks_quality_p_value=0.246399	log10_base_likelihood=-10.9551	log10_qual_likelihood_position_model=3.43258	log10_strand_likelihood_position_model=0.423285	new_cov=2/2	polymorphism_quality=5.5	quality=5.5	quality_position_model=4.68666e-09	ref_cov=137/143	reject=INDEL_HOMOPOLYMER	tot_cov=139/145
RA	423	.	NC_007779	3160153	0	G	C	bias_e_value=0.000333511	bias_p_value=7.17793e-11	fisher_strand_p_value=2.5966e-12	frequency=7.888460e-02	genotype_quality=559.1	ks_quality_p_value=0.998753	log10_base_likelihood=-15.3057	log10_qual_likelihood_position_model=15.9214	log10_strand_likelihood_position_model=11.5856	new_cov=13/0	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=12/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=25/126
RA	424	.	NC_007779	3162929	0	G	C	bias_e_value=207984	bias_p_value=0.044763	fisher_strand_p_value=0.00777885	frequency=3.041458e-02	genotype_quality=874.7	ks_quality_p_value=0.979062	log10_base_likelihood=-7.40087	log10_qual_likelihood_position_model=12.2485	log10_strand_likelihood_position_model=2.22145	new_cov=9/1	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=111/130	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=121/131
RA	425	.	NC_007779	3195962	0	G	T	bias_e_value=14.8304	bias_p_value=3.19185e-06	fisher_strand_p_value=1.93968e-07	frequency=5.396891e-02	genotype_quality=783.0	ks_quality_p_value=1	log10_base_likelihood=-8.08487	log10_qual_likelihood_position_model=18.1404	log10_strand_likelihood_position_model=6.72935	new_cov=0/23	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=118/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/134
RA	426	.	NC_007779	3223274	0	G	T	bias_e_value=0.299903	bias_p_value=6.45461e-08	fisher_strand_p_value=3.13632e-09	frequency=6.728458e-02	genotype_quality=865.2	ks_quality_p_value=1	log10_base_likelihood=-12.0459	log10_qual_likelihood_position_model=16.7339	log10_strand_likelihood_position_model=8.50358	new_cov=0/26	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=135/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/133
RA	427	.	NC_007779	3231439	1	.	A	bias_e_value=4644130	bias_p_value=0.999527	fisher_strand_p_value=1	frequency=6.756783e-03	genotype_quality=1478.4	ks_quality_p_value=0.969406	log10_base_likelihood=-8.39702	log10_qual_likelihood_position_model=2.5609	log10_strand_likelihood_position_model=0.302924	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.93996e-07	ref_cov=160/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=161/135
RA	428	.	NC_007779	3231832	1	.	G	bias_e_value=1102190	bias_p_value=0.237218	fisher_strand_p_value=0.0653051	frequency=1.351357e-02	genotype_quality=1103.7	ks_quality_p_value=0.964963	log10_base_likelihood=-13.0815	log10_qual_likelihood_position_model=1.72997	log10_strand_likelihood_position_model=1.18505	new_cov=3/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=3.38232e-12	ref_cov=87/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=90/132
RA	429	.	NC_007779	3238315	1	.	T	bias_e_value=1840780	bias_p_value=0.396179	fisher_strand_p_value=0.130608	frequency=2.298832e-02	genotype_quality=783.0	ks_quality_p_value=0.998919	log10_base_likelihood=-17.5061	log10_qual_likelihood_position_model=3.27501	log10_strand_likelihood_position_model=1.02723	new_cov=4/0	polymorphism_quality=12.2	quality=12.2	quality_position_model=2.73535e-15	ref_cov=93/77	reject=POLYMORPHISM_STRAND	tot_cov=97/77
RA	430	.	NC_007779	3238317	1	.	T	bias_e_value=3933580	bias_p_value=0.846599	fisher_strand_p_value=0.500036	frequency=1.197243e-02	genotype_quality=742.4	ks_quality_p_value=1	log10_base_likelihood=-6.08616	log10_qual_likelihood_position_model=2.76158	log10_strand_likelihood_position_model=0.539192	new_cov=2/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.00014839	ref_cov=88/77	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=90/77
RA	431	.	NC_007779	3238317	2	.	C	bias_e_value=3772590	bias_p_value=0.81195	fisher_strand_p_value=0.500036	frequency=1.197529e-02	genotype_quality=747.6	ks_quality_p_value=0.90653	log10_base_likelihood=-7.68364	log10_qual_likelihood_position_model=3.2387	log10_strand_likelihood_position_model=0.539192	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=9.66159e-06	ref_cov=88/77	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=90/77
RA	432	.	NC_007779	3238322	0	T	C	bias_e_value=285711	bias_p_value=0.0614917	fisher_strand_p_value=0.0111962	frequency=4.523277e-02	genotype_quality=508.7	ks_quality_p_value=1	log10_base_likelihood=-6.855	log10_qual_likelihood_position_model=11.1024	log10_strand_likelihood_position_model=2.17536	new_cov=8/1	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=64/88	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=72/89
RA	433	.	NC_007779	3238324	0	A	C	bias_e_value=190080	bias_p_value=0.0409098	fisher_strand_p_value=0.0068345	frequency=2.752495e-02	genotype_quality=484.2	ks_quality_p_value=1	log10_base_likelihood=-7.1999	log10_qual_likelihood_position_model=5.71563	log10_strand_likelihood_position_model=2.16529	new_cov=6/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=66/90	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=72/90
RA	434	.	NC_007779	3258468	0	G	T	bias_e_value=68.0855	bias_p_value=1.46536e-05	fisher_strand_p_value=9.88285e-07	frequency=3.854465e-02	genotype_quality=982.3	ks_quality_p_value=1	log10_base_likelihood=-6.02261	log10_qual_likelihood_position_model=18.8462	log10_strand_likelihood_position_model=6.19523	new_cov=0/24	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=135/154	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/178
RA	435	.	NC_007779	3266843	0	C	G	bias_e_value=606.73	bias_p_value=0.000130583	fisher_strand_p_value=1.04965e-05	frequency=3.989887e-02	genotype_quality=758.9	ks_quality_p_value=0.997918	log10_base_likelihood=-6.73209	log10_qual_likelihood_position_model=12.5371	log10_strand_likelihood_position_model=4.97896	new_cov=0/10	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=134/57	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/67
RA	436	.	NC_007779	3270337	0	C	.	bias_e_value=1376230	bias_p_value=0.296198	fisher_strand_p_value=0.247233	frequency=1.114750e-02	genotype_quality=1093.3	ks_quality_p_value=0.34654	log10_base_likelihood=-8.77003	log10_qual_likelihood_position_model=1.55398	log10_strand_likelihood_position_model=0.898237	new_cov=3/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=2.99355e-08	ref_cov=132/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/134
RA	437	.	NC_007779	3280326	0	A	C	bias_e_value=4.28116e-15	bias_p_value=9.21407e-22	fisher_strand_p_value=1.72502e-23	frequency=1.223197e-01	genotype_quality=890.0	ks_quality_p_value=1	log10_base_likelihood=-24.0625	log10_qual_likelihood_position_model=39.6353	log10_strand_likelihood_position_model=22.7632	new_cov=0/59	polymorphism_quality=18.8	quality=18.8	quality_position_model=Inf	ref_cov=162/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=162/146
RA	438	.	NC_007779	3293230	1	.	A	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=6.191254e-03	genotype_quality=1618.0	ks_quality_p_value=0.999961	log10_base_likelihood=-7.40826	log10_qual_likelihood_position_model=2.38157	log10_strand_likelihood_position_model=0.300021	new_cov=1/1	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.33691e-06	ref_cov=156/165	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/166
RA	439	.	NC_007779	3300073	0	T	G	bias_e_value=6.93637e-06	bias_p_value=1.49287e-12	fisher_strand_p_value=4.71142e-14	frequency=5.335379e-02	genotype_quality=821.0	ks_quality_p_value=1	log10_base_likelihood=-5.58581	log10_qual_likelihood_position_model=39.2401	log10_strand_likelihood_position_model=13.3268	new_cov=36/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=90/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/145
RA	440	.	NC_007779	3317267	1	.	T	bias_e_value=2872150	bias_p_value=0.618155	fisher_strand_p_value=0.500433	frequency=6.919861e-03	genotype_quality=1437.0	ks_quality_p_value=0.531393	log10_base_likelihood=-7.76749	log10_qual_likelihood_position_model=2.1879	log10_strand_likelihood_position_model=0.548078	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=6.43698e-07	ref_cov=152/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/135
RA	441	.	NC_007779	3331383	1	.	G	bias_e_value=1898380	bias_p_value=0.408576	fisher_strand_p_value=0.143023	frequency=9.259224e-03	genotype_quality=1068.7	ks_quality_p_value=0.955255	log10_base_likelihood=-7.94627	log10_qual_likelihood_position_model=3.28668	log10_strand_likelihood_position_model=0.844593	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.2035e-05	ref_cov=80/134	reject=POLYMORPHISM_STRAND	tot_cov=82/134
RA	442	.	NC_007779	3333612	0	T	G	bias_e_value=22.8673	bias_p_value=4.92157e-06	fisher_strand_p_value=3.07712e-07	frequency=4.653549e-02	genotype_quality=645.2	ks_quality_p_value=1	log10_base_likelihood=-13.9582	log10_qual_likelihood_position_model=10.9627	log10_strand_likelihood_position_model=6.51186	new_cov=8/0	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=21/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=29/140
RA	443	.	NC_007779	3338299	1	.	T	bias_e_value=3114730	bias_p_value=0.670364	fisher_strand_p_value=0.501077	frequency=6.756783e-03	genotype_quality=1475.8	ks_quality_p_value=0.614077	log10_base_likelihood=-8.11923	log10_qual_likelihood_position_model=1.53051	log10_strand_likelihood_position_model=0.54106	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.69179e-08	ref_cov=157/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/137
RA	444	.	NC_007779	3350708	0	A	C	bias_e_value=0.0414688	bias_p_value=8.92507e-09	fisher_strand_p_value=3.9396e-10	frequency=5.202579e-02	genotype_quality=850.2	ks_quality_p_value=1	log10_base_likelihood=-5.76361	log10_qual_likelihood_position_model=23.4838	log10_strand_likelihood_position_model=9.40455	new_cov=0/28	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=139/105	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/133
RA	445	.	NC_007779	3357279	0	C	A	bias_e_value=0.449108	bias_p_value=9.66585e-08	fisher_strand_p_value=6.93034e-09	frequency=4.405308e-02	genotype_quality=874.4	ks_quality_p_value=0.691976	log10_base_likelihood=-7.7337	log10_qual_likelihood_position_model=29.4953	log10_strand_likelihood_position_model=8.15925	new_cov=23/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=107/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/150
RA	446	.	NC_007779	3379905	0	A	.	bias_e_value=1368020	bias_p_value=0.294431	fisher_strand_p_value=0.101943	frequency=1.089859e-02	genotype_quality=1102.7	ks_quality_p_value=0.833389	log10_base_likelihood=-7.82372	log10_qual_likelihood_position_model=2.11205	log10_strand_likelihood_position_model=0.991643	new_cov=0/3	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.35837e-06	ref_cov=146/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/129
RA	447	.	NC_007779	3380462	0	G	T	bias_e_value=239.495	bias_p_value=5.15449e-05	fisher_strand_p_value=3.82557e-06	frequency=3.899670e-02	genotype_quality=812.4	ks_quality_p_value=1	log10_base_likelihood=-6.87625	log10_qual_likelihood_position_model=18.2232	log10_strand_likelihood_position_model=5.56173	new_cov=0/22	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=110/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/150
RA	448	.	NC_007779	3385700	1	.	T	bias_e_value=4625020	bias_p_value=0.995413	fisher_strand_p_value=1	frequency=7.462502e-03	genotype_quality=1318.7	ks_quality_p_value=0.905762	log10_base_likelihood=-8.06281	log10_qual_likelihood_position_model=1.01391	log10_strand_likelihood_position_model=0.300012	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.07548e-08	ref_cov=128/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/139
RA	449	.	NC_007779	3389914	0	A	C	bias_e_value=5.67544e-05	bias_p_value=1.22149e-11	fisher_strand_p_value=4.13879e-13	frequency=7.717419e-02	genotype_quality=772.1	ks_quality_p_value=1	log10_base_likelihood=-10.074	log10_qual_likelihood_position_model=25.7085	log10_strand_likelihood_position_model=12.3831	new_cov=0/33	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=135/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/115
RA	450	.	NC_007779	3392267	0	C	A	bias_e_value=0.0218255	bias_p_value=4.69737e-09	fisher_strand_p_value=2.01381e-10	frequency=4.943275e-02	genotype_quality=1053.0	ks_quality_p_value=1	log10_base_likelihood=-10.0272	log10_qual_likelihood_position_model=19.8595	log10_strand_likelihood_position_model=9.69598	new_cov=25/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=110/177	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/177
RA	451	.	NC_007779	3397405	0	A	C	bias_e_value=6.15721e-09	bias_p_value=1.32518e-15	fisher_strand_p_value=3.40499e-17	frequency=1.020517e-01	genotype_quality=707.9	ks_quality_p_value=1	log10_base_likelihood=-13.4363	log10_qual_likelihood_position_model=32.9281	log10_strand_likelihood_position_model=16.4679	new_cov=0/40	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=135/66	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=135/106
RA	452	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1105.6	new_cov=132/124	quality=1105.6	ref_cov=0/0	tot_cov=132/124
RA	453	.	NC_007779	3412753	0	C	T	bias_e_value=6.12196e-05	bias_p_value=1.31759e-11	fisher_strand_p_value=4.4763e-13	frequency=6.212950e-02	genotype_quality=882.7	ks_quality_p_value=1	log10_base_likelihood=-8.37142	log10_qual_likelihood_position_model=25.1984	log10_strand_likelihood_position_model=12.3491	new_cov=0/22	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=172/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/76
RA	454	.	NC_007779	3412772	0	A	C	bias_e_value=2.85987e-09	bias_p_value=6.15511e-16	fisher_strand_p_value=1.55019e-17	frequency=4.986858e-02	genotype_quality=766.0	ks_quality_p_value=1	log10_base_likelihood=-5.7527	log10_qual_likelihood_position_model=27.0752	log10_strand_likelihood_position_model=16.8096	new_cov=0/25	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=164/32	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/57
RA	455	.	NC_007779	3421203	0	T	C	bias_e_value=0.000372645	bias_p_value=8.02019e-11	fisher_strand_p_value=2.90977e-12	frequency=7.510662e-02	genotype_quality=742.0	ks_quality_p_value=1	log10_base_likelihood=-9.03087	log10_qual_likelihood_position_model=20.1704	log10_strand_likelihood_position_model=11.5361	new_cov=0/24	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=152/63	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/87
RA	456	.	NC_007779	3429289	0	A	G	bias_e_value=3525070	bias_p_value=0.758678	fisher_strand_p_value=0.62835	frequency=1.357460e-02	genotype_quality=1158.6	ks_quality_p_value=0.62313	log10_base_likelihood=-8.74365	log10_qual_likelihood_position_model=1.64647	log10_strand_likelihood_position_model=0.531152	new_cov=1/3	polymorphism_quality=3.3	quality=3.3	quality_position_model=1.65991e-08	ref_cov=133/157	reject=POLYMORPHISM_STRAND	tot_cov=134/160
RA	457	.	NC_007779	3431060	0	C	A	bias_e_value=3753.23	bias_p_value=0.000807783	fisher_strand_p_value=7.71544e-05	frequency=4.977655e-02	genotype_quality=774.4	ks_quality_p_value=1	log10_base_likelihood=-8.17759	log10_qual_likelihood_position_model=12.7481	log10_strand_likelihood_position_model=4.384	new_cov=0/14	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=105/92	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/106
RA	458	.	NC_007779	3431245	1	.	A	bias_e_value=2916220	bias_p_value=0.627639	fisher_strand_p_value=0.274293	frequency=1.303291e-02	genotype_quality=1112.8	ks_quality_p_value=0.995871	log10_base_likelihood=-8.07608	log10_qual_likelihood_position_model=5.5232	log10_strand_likelihood_position_model=0.678905	new_cov=0/3	polymorphism_quality=2.6	quality=2.6	quality_position_model=0.00143847	ref_cov=93/134	reject=POLYMORPHISM_STRAND	tot_cov=93/137
RA	459	.	NC_007779	3431250	0	T	.	bias_e_value=2803850	bias_p_value=0.603455	fisher_strand_p_value=0.26107	frequency=1.092148e-02	genotype_quality=1069.2	ks_quality_p_value=0.97675	log10_base_likelihood=-6.53295	log10_qual_likelihood_position_model=5.22452	log10_strand_likelihood_position_model=0.741157	new_cov=0/3	polymorphism_quality=1.0	quality=1.0	quality_position_model=0.0486779	ref_cov=118/152	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=118/156
RA	460	.	NC_007779	3431251	0	G	.	bias_e_value=2771170	bias_p_value=0.596422	fisher_strand_p_value=0.255113	frequency=1.092052e-02	genotype_quality=1146.0	ks_quality_p_value=0.979527	log10_base_likelihood=-6.47345	log10_qual_likelihood_position_model=5.62724	log10_strand_likelihood_position_model=0.780228	new_cov=0/3	polymorphism_quality=0.9	quality=0.9	quality_position_model=0.378279	ref_cov=123/148	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=123/151
RA	461	.	NC_007779	3431254	0	C	.	bias_e_value=2317930	bias_p_value=0.498874	fisher_strand_p_value=0.253298	frequency=1.110458e-02	genotype_quality=1087.8	ks_quality_p_value=0.734359	log10_base_likelihood=-8.46085	log10_qual_likelihood_position_model=2.54083	log10_strand_likelihood_position_model=0.794665	new_cov=0/3	polymorphism_quality=3.0	quality=3.0	quality_position_model=5.14177e-07	ref_cov=121/142	reject=POLYMORPHISM_STRAND	tot_cov=122/148
RA	462	.	NC_007779	3439598	1	.	T	bias_e_value=2830440	bias_p_value=0.609176	fisher_strand_p_value=0.259899	frequency=1.562405e-02	genotype_quality=926.8	ks_quality_p_value=0.997358	log10_base_likelihood=-11.2867	log10_qual_likelihood_position_model=4.08267	log10_strand_likelihood_position_model=0.742854	new_cov=3/0	polymorphism_quality=5.9	quality=5.9	quality_position_model=2.12927e-08	ref_cov=106/83	reject=POLYMORPHISM_STRAND	tot_cov=109/83
RA	463	.	NC_007779	3439601	0	G	T	bias_e_value=90788	bias_p_value=0.0195397	fisher_strand_p_value=0.00284786	frequency=4.703665e-02	genotype_quality=773.8	ks_quality_p_value=1	log10_base_likelihood=-8.74369	log10_qual_likelihood_position_model=13.8342	log10_strand_likelihood_position_model=2.72321	new_cov=11/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=106/86	reject=POLYMORPHISM_STRAND	tot_cov=117/86
RA	464	.	NC_007779	3439607	0	G	T	bias_e_value=36113	bias_p_value=0.00777237	fisher_strand_p_value=0.000980429	frequency=5.333614e-02	genotype_quality=812.0	ks_quality_p_value=1	log10_base_likelihood=-8.97169	log10_qual_likelihood_position_model=16.248	log10_strand_likelihood_position_model=3.3118	new_cov=14/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=110/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/85
RA	465	.	NC_007779	3475527	0	T	G	bias_e_value=5.22044e-12	bias_p_value=1.12356e-18	fisher_strand_p_value=2.43394e-20	frequency=1.114278e-01	genotype_quality=816.1	ks_quality_p_value=1	log10_base_likelihood=-14.9223	log10_qual_likelihood_position_model=38.3246	log10_strand_likelihood_position_model=19.6137	new_cov=51/0	polymorphism_quality=9.6	quality=9.6	quality_position_model=Inf	ref_cov=78/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/146
RA	466	.	NC_007779	3475533	0	C	T	bias_e_value=4.90408	bias_p_value=1.05547e-06	fisher_strand_p_value=5.9864e-08	frequency=7.848597e-02	genotype_quality=918.8	ks_quality_p_value=1	log10_base_likelihood=-14.891	log10_qual_likelihood_position_model=36.6141	log10_strand_likelihood_position_model=7.34922	new_cov=25/1	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=114/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/151
RA	467	.	NC_007779	3499066	0	A	C	bias_e_value=0.118603	bias_p_value=2.55262e-08	fisher_strand_p_value=1.18428e-09	frequency=6.081963e-02	genotype_quality=864.8	ks_quality_p_value=1	log10_base_likelihood=-11.3868	log10_qual_likelihood_position_model=24.724	log10_strand_likelihood_position_model=8.92654	new_cov=0/17	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=164/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/78
RA	468	.	NC_007779	3519466	0	A	.	bias_e_value=1924480	bias_p_value=0.414193	fisher_strand_p_value=0.258242	frequency=1.098156e-02	genotype_quality=1102.4	ks_quality_p_value=0.540037	log10_base_likelihood=-8.18417	log10_qual_likelihood_position_model=1.39498	log10_strand_likelihood_position_model=0.758189	new_cov=3/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.92215e-08	ref_cov=150/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/120
RA	469	.	NC_007779	3521019	1	.	G	bias_e_value=2648430	bias_p_value=0.570004	fisher_strand_p_value=0.241467	frequency=7.631302e-03	genotype_quality=1266.7	ks_quality_p_value=0.958096	log10_base_likelihood=-6.57243	log10_qual_likelihood_position_model=3.45473	log10_strand_likelihood_position_model=0.617142	new_cov=2/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=0.000299847	ref_cov=127/133	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/133
RA	470	.	NC_007779	3523734	0	G	T	bias_e_value=0.0603191	bias_p_value=1.29821e-08	fisher_strand_p_value=5.83134e-10	frequency=9.430027e-02	genotype_quality=718.6	ks_quality_p_value=1	log10_base_likelihood=-14.5615	log10_qual_likelihood_position_model=24.3694	log10_strand_likelihood_position_model=9.49481	new_cov=0/31	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=108/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/122
RA	471	.	NC_007779	3543547	0	A	C	bias_e_value=5.3713e-15	bias_p_value=1.15603e-21	fisher_strand_p_value=2.17368e-23	frequency=1.986585e-01	genotype_quality=710.4	ks_quality_p_value=1	log10_base_likelihood=-33.6938	log10_qual_likelihood_position_model=53.3154	log10_strand_likelihood_position_model=22.7154	new_cov=0/69	polymorphism_quality=28.5	quality=28.5	quality_position_model=Inf	ref_cov=124/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/146
RA	472	.	NC_007779	3550877	0	C	A	bias_e_value=95.2643	bias_p_value=2.05031e-05	fisher_strand_p_value=1.41725e-06	frequency=4.070663e-02	genotype_quality=1038.6	ks_quality_p_value=1	log10_base_likelihood=-10.4394	log10_qual_likelihood_position_model=17.4777	log10_strand_likelihood_position_model=6.02902	new_cov=23/1	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=134/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/152
RA	473	.	NC_007779	3553973	1	.	C	bias_e_value=3620340	bias_p_value=0.779183	fisher_strand_p_value=0.541388	frequency=7.066727e-03	genotype_quality=1366.9	ks_quality_p_value=0.764871	log10_base_likelihood=-7.70107	log10_qual_likelihood_position_model=3.82285	log10_strand_likelihood_position_model=0.379513	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=2.59285e-05	ref_cov=181/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=183/100
RA	474	.	NC_007779	3560478	0	G	T	bias_e_value=65.3081	bias_p_value=1.40558e-05	fisher_strand_p_value=9.45124e-07	frequency=3.922749e-02	genotype_quality=1090.7	ks_quality_p_value=1	log10_base_likelihood=-11.6849	log10_qual_likelihood_position_model=19.801	log10_strand_likelihood_position_model=6.11434	new_cov=0/26	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=136/176	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/202
RA	475	.	NC_007779	3566189	1	.	T	bias_e_value=815124	bias_p_value=0.175434	fisher_strand_p_value=0.0454513	frequency=1.197624e-02	genotype_quality=819.4	ks_quality_p_value=0.926083	log10_base_likelihood=-8.12783	log10_qual_likelihood_position_model=2.9657	log10_strand_likelihood_position_model=1.34245	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.18994e-05	ref_cov=34/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=36/131
RA	476	.	NC_007779	3566193	1	.	C	bias_e_value=21983.6	bias_p_value=0.00473139	fisher_strand_p_value=0.000562903	frequency=2.054691e-02	genotype_quality=698.8	ks_quality_p_value=0.989708	log10_base_likelihood=-11.9379	log10_qual_likelihood_position_model=5.22881	log10_strand_likelihood_position_model=3.24957	new_cov=3/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=2.8521e-05	ref_cov=10/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=13/133
RA	477	.	NC_007779	3566927	1	.	A	bias_e_value=859411	bias_p_value=0.184965	fisher_strand_p_value=0.221863	frequency=5.934715e-03	genotype_quality=1678.2	ks_quality_p_value=0.203433	log10_base_likelihood=-7.98882	log10_qual_likelihood_position_model=1.77705	log10_strand_likelihood_position_model=0.653915	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.82906e-07	ref_cov=157/178	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/178
RA	478	.	NC_007779	3576400	1	.	A	bias_e_value=2991580	bias_p_value=0.643858	fisher_strand_p_value=0.680413	frequency=1.893902e-02	genotype_quality=1268.3	ks_quality_p_value=0.420161	log10_base_likelihood=-22.5508	log10_qual_likelihood_position_model=2.42582	log10_strand_likelihood_position_model=0.508775	new_cov=2/3	polymorphism_quality=17.3	quality=17.3	quality_position_model=8.72784e-22	ref_cov=132/127	reject=INDEL_HOMOPOLYMER	tot_cov=134/130
RA	479	.	NC_007779	3580297	0	G	T	bias_e_value=31.9305	bias_p_value=6.87219e-06	fisher_strand_p_value=4.39463e-07	frequency=4.626560e-02	genotype_quality=969.1	ks_quality_p_value=1	log10_base_likelihood=-10.2281	log10_qual_likelihood_position_model=18.2644	log10_strand_likelihood_position_model=6.3879	new_cov=0/24	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=133/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/169
RA	480	.	NC_007779	3609441	0	T	G	bias_e_value=2.51727e-11	bias_p_value=5.41776e-18	fisher_strand_p_value=1.21601e-19	frequency=7.273579e-02	genotype_quality=957.8	ks_quality_p_value=1	log10_base_likelihood=-10.4695	log10_qual_likelihood_position_model=33.0124	log10_strand_likelihood_position_model=18.9151	new_cov=42/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=80/183	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/184
RA	481	.	NC_007779	3688858	0	A	C	bias_e_value=3.34493e-07	bias_p_value=7.19907e-14	fisher_strand_p_value=2.06797e-15	frequency=1.115375e-01	genotype_quality=558.5	ks_quality_p_value=1	log10_base_likelihood=-10.1977	log10_qual_likelihood_position_model=26.6544	log10_strand_likelihood_position_model=14.6845	new_cov=0/32	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=106/41	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=106/73
RA	482	.	NC_007779	3694746	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	483	.	NC_007779	3694747	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	484	.	NC_007779	3694748	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	485	.	NC_007779	3694750	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	486	.	NC_007779	3694752	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	487	.	NC_007779	3694754	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	488	.	NC_007779	3694755	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	489	.	NC_007779	3694757	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	490	.	NC_007779	3694758	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	491	.	NC_007779	3694759	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	492	.	NC_007779	3694761	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	493	.	NC_007779	3694762	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	494	.	NC_007779	3694763	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	495	.	NC_007779	3694764	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	496	.	NC_007779	3694765	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	497	.	NC_007779	3694766	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	498	.	NC_007779	3694767	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	499	.	NC_007779	3694768	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	500	.	NC_007779	3694769	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	501	.	NC_007779	3694770	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	502	.	NC_007779	3694772	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	503	.	NC_007779	3694773	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	504	.	NC_007779	3701118	0	G	T	bias_e_value=101.373	bias_p_value=2.18179e-05	fisher_strand_p_value=1.51513e-06	frequency=5.657291e-02	genotype_quality=650.9	ks_quality_p_value=1	log10_base_likelihood=-7.6664	log10_qual_likelihood_position_model=16.4213	log10_strand_likelihood_position_model=5.81955	new_cov=0/18	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=102/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/101
RA	505	.	NC_007779	3712339	1	.	T	bias_e_value=3943700	bias_p_value=0.848776	fisher_strand_p_value=0.504252	frequency=9.130478e-03	genotype_quality=1082.8	ks_quality_p_value=0.997898	log10_base_likelihood=-6.47389	log10_qual_likelihood_position_model=4.07684	log10_strand_likelihood_position_model=0.509755	new_cov=2/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=0.0013908	ref_cov=120/97	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=122/97
RA	506	.	NC_007779	3714367	0	G	.	bias_e_value=1022360	bias_p_value=0.220036	fisher_strand_p_value=0.498047	frequency=8.329391e-03	genotype_quality=1037.9	ks_quality_p_value=0.11427	log10_base_likelihood=-5.84916	log10_qual_likelihood_position_model=1.15309	log10_strand_likelihood_position_model=0.589464	new_cov=2/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=5.94621e-06	ref_cov=120/118	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/118
RA	507	.	NC_007779	3728146	1	.	T	bias_e_value=1254810	bias_p_value=0.270064	fisher_strand_p_value=0.0893718	frequency=1.369858e-02	genotype_quality=708.0	ks_quality_p_value=0.842625	log10_base_likelihood=-8.59308	log10_qual_likelihood_position_model=1.88481	log10_strand_likelihood_position_model=1.0488	new_cov=2/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=1.43529e-07	ref_cov=42/102	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=44/102
RA	508	.	NC_007779	3731041	1	.	T	bias_e_value=1501420	bias_p_value=0.32314	fisher_strand_p_value=0.198218	frequency=9.302139e-03	genotype_quality=1054.4	ks_quality_p_value=0.489004	log10_base_likelihood=-8.24246	log10_qual_likelihood_position_model=1.59467	log10_strand_likelihood_position_model=0.702857	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.26888e-08	ref_cov=119/94	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/96
RA	509	.	NC_007779	3732310	0	G	T	bias_e_value=4.72621	bias_p_value=1.01719e-06	fisher_strand_p_value=5.75649e-08	frequency=7.421970e-02	genotype_quality=701.7	ks_quality_p_value=1	log10_base_likelihood=-12.6263	log10_qual_likelihood_position_model=15.7631	log10_strand_likelihood_position_model=7.23984	new_cov=0/21	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=116/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/106
RA	510	.	NC_007779	3750122	0	C	.	bias_e_value=9444.99	bias_p_value=0.00203278	fisher_strand_p_value=0.00756666	frequency=1	genotype_quality=1386.9	ks_quality_p_value=0.0284476	log10_base_likelihood=-36.6701	log10_qual_likelihood_position_model=7.98852	log10_strand_likelihood_position_model=2.28176	new_cov=136/142	polymorphism_changed_to_consensus=1	polymorphism_quality=31.5	quality=31.5	quality_position_model=1.24158e-28	ref_cov=0/8	tot_cov=136/150
RA	511	.	NC_007779	3750123	0	C	T	bias_e_value=201823	bias_p_value=0.0434372	fisher_strand_p_value=0.00764281	frequency=2.805710e-02	genotype_quality=1157.1	ks_quality_p_value=0.961055	log10_base_likelihood=-15.2295	log10_qual_likelihood_position_model=9.13395	log10_strand_likelihood_position_model=2.26944	new_cov=0/8	polymorphism_quality=9.9	quality=9.9	quality_position_model=1.17151e-05	ref_cov=135/142	reject=POLYMORPHISM_STRAND	tot_cov=136/150
RA	512	.	NC_007779	3763528	0	A	C	bias_e_value=19.1687	bias_p_value=4.12555e-06	fisher_strand_p_value=2.54943e-07	frequency=2.453136e-02	genotype_quality=640.9	ks_quality_p_value=1	log10_base_likelihood=-6.23164	log10_qual_likelihood_position_model=7.69393	log10_strand_likelihood_position_model=6.59356	new_cov=0/5	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=156/5	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/10
RA	513	.	NC_007779	3783054	0	G	.	bias_e_value=3994510	bias_p_value=0.859713	fisher_strand_p_value=0.622496	frequency=9.961128e-03	genotype_quality=1284.7	ks_quality_p_value=0.834541	log10_base_likelihood=-8.44012	log10_qual_likelihood_position_model=2.60508	log10_strand_likelihood_position_model=0.425983	new_cov=2/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.60929e-07	ref_cov=148/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/151
RA	514	.	NC_007779	3788380	0	G	T	bias_e_value=2.19775	bias_p_value=4.73008e-07	fisher_strand_p_value=2.55944e-08	frequency=5.744505e-02	genotype_quality=1093.4	ks_quality_p_value=1	log10_base_likelihood=-17.4634	log10_qual_likelihood_position_model=16.5705	log10_strand_likelihood_position_model=7.60888	new_cov=0/26	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=157/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/177
RA	515	.	NC_007779	3812429	0	G	T	bias_e_value=0.530709	bias_p_value=1.14221e-07	fisher_strand_p_value=5.71681e-09	frequency=5.083370e-02	genotype_quality=933.7	ks_quality_p_value=1	log10_base_likelihood=-6.90556	log10_qual_likelihood_position_model=20.1874	log10_strand_likelihood_position_model=8.24285	new_cov=0/25	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=144/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/139
RA	516	.	NC_007779	3813810	0	T	G	bias_e_value=5.43214e-12	bias_p_value=1.16912e-18	fisher_strand_p_value=2.53488e-20	frequency=1.069064e-01	genotype_quality=694.4	ks_quality_p_value=1	log10_base_likelihood=-12.3806	log10_qual_likelihood_position_model=33.9691	log10_strand_likelihood_position_model=19.596	new_cov=45/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=55/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/132
RA	517	.	NC_007779	3845596	0	G	T	bias_e_value=354.976	bias_p_value=7.63992e-05	fisher_strand_p_value=5.96467e-06	frequency=3.545189e-02	genotype_quality=997.4	ks_quality_p_value=0.98164	log10_base_likelihood=-7.7022	log10_qual_likelihood_position_model=16.1172	log10_strand_likelihood_position_model=5.22441	new_cov=0/16	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=154/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/146
RA	518	.	NC_007779	3859254	1	.	T	bias_e_value=1256480	bias_p_value=0.270424	fisher_strand_p_value=0.144185	frequency=7.936478e-03	genotype_quality=1249.7	ks_quality_p_value=0.523257	log10_base_likelihood=-8.4431	log10_qual_likelihood_position_model=1.55804	log10_strand_likelihood_position_model=0.841079	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=5.74188e-08	ref_cov=94/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=96/156
RA	519	.	NC_007779	3859258	1	.	T	bias_e_value=72718.8	bias_p_value=0.0156508	fisher_strand_p_value=0.00219855	frequency=2.241230e-02	genotype_quality=1034.0	ks_quality_p_value=0.999794	log10_base_likelihood=-15.04	log10_qual_likelihood_position_model=8.21137	log10_strand_likelihood_position_model=2.65786	new_cov=5/0	polymorphism_quality=9.7	quality=9.7	quality_position_model=5.09334e-06	ref_cov=62/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=67/156
RA	520	.	NC_007779	3859258	2	.	C	bias_e_value=198966	bias_p_value=0.0428222	fisher_strand_p_value=0.00731755	frequency=2.221775e-02	genotype_quality=1040.7	ks_quality_p_value=0.9867	log10_base_likelihood=-15.7987	log10_qual_likelihood_position_model=6.13607	log10_strand_likelihood_position_model=2.13563	new_cov=4/0	polymorphism_quality=10.5	quality=10.5	quality_position_model=1.7024e-09	ref_cov=62/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=67/156
RA	521	.	NC_007779	3859258	3	.	C	bias_e_value=485291	bias_p_value=0.104446	fisher_strand_p_value=0.0262713	frequency=1.345253e-02	genotype_quality=1058.7	ks_quality_p_value=0.822276	log10_base_likelihood=-12.4607	log10_qual_likelihood_position_model=3.57966	log10_strand_likelihood_position_model=1.58052	new_cov=3/0	polymorphism_quality=7.1	quality=7.1	quality_position_model=2.90955e-09	ref_cov=64/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=67/156
RA	522	.	NC_007779	3859258	4	.	C	bias_e_value=1211320	bias_p_value=0.260704	fisher_strand_p_value=0.0893225	frequency=8.968353e-03	genotype_quality=1067.2	ks_quality_p_value=0.802947	log10_base_likelihood=-7.94647	log10_qual_likelihood_position_model=2.79157	log10_strand_likelihood_position_model=1.04904	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.95691e-06	ref_cov=65/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=67/156
RA	523	.	NC_007779	3859263	0	T	C	bias_e_value=0.00833898	bias_p_value=1.79474e-09	fisher_strand_p_value=7.37664e-11	frequency=5.923033e-02	genotype_quality=743.0	ks_quality_p_value=1	log10_base_likelihood=-16.8472	log10_qual_likelihood_position_model=18.7174	log10_strand_likelihood_position_model=10.1321	new_cov=16/0	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=43/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=60/169
RA	524	.	NC_007779	3859265	0	A	C	bias_e_value=35.9998	bias_p_value=7.74801e-06	fisher_strand_p_value=4.99564e-07	frequency=4.979849e-02	genotype_quality=628.5	ks_quality_p_value=1	log10_base_likelihood=-18.1525	log10_qual_likelihood_position_model=9.31814	log10_strand_likelihood_position_model=6.31819	new_cov=13/2	polymorphism_quality=12.8	quality=12.8	quality_position_model=0.000288475	ref_cov=45/165	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=60/171
RA	525	.	NC_007779	3859270	0	G	C	bias_e_value=842.932	bias_p_value=0.000181419	fisher_strand_p_value=1.49826e-05	frequency=3.048229e-02	genotype_quality=836.0	ks_quality_p_value=1	log10_base_likelihood=-12.2468	log10_qual_likelihood_position_model=6.78608	log10_strand_likelihood_position_model=4.82441	new_cov=7/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=0.0394962	ref_cov=39/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=46/167
RA	526	.	NC_007779	3859383	0	A	G	bias_e_value=17.1603	bias_p_value=3.6933e-06	fisher_strand_p_value=2.26674e-07	frequency=2.900600e-02	genotype_quality=633.5	ks_quality_p_value=0.99959	log10_base_likelihood=-6.44343	log10_qual_likelihood_position_model=8.23637	log10_strand_likelihood_position_model=6.6446	new_cov=0/6	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=158/10	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=159/16
RA	527	.	NC_007779	3870179	0	G	.	bias_e_value=778739	bias_p_value=0.167603	fisher_strand_p_value=0.0897279	frequency=1.249409e-02	genotype_quality=1004.3	ks_quality_p_value=0.441809	log10_base_likelihood=-8.78073	log10_qual_likelihood_position_model=2.58766	log10_strand_likelihood_position_model=1.04707	new_cov=3/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=4.89396e-07	ref_cov=105/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/132
RA	528	.	NC_007779	3873375	0	T	.	bias_e_value=3983280	bias_p_value=0.857297	fisher_strand_p_value=0.627426	frequency=1.350021e-02	genotype_quality=1189.6	ks_quality_p_value=0.822133	log10_base_likelihood=-10.5484	log10_qual_likelihood_position_model=3.55272	log10_strand_likelihood_position_model=0.536556	new_cov=1/3	polymorphism_quality=5.1	quality=5.1	quality_position_model=2.1397e-08	ref_cov=135/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/160
RA	529	.	NC_007779	3893880	0	G	T	bias_e_value=0.00804084	bias_p_value=1.73058e-09	fisher_strand_p_value=7.10182e-11	frequency=7.886887e-02	genotype_quality=819.0	ks_quality_p_value=1	log10_base_likelihood=-17.024	log10_qual_likelihood_position_model=25.3349	log10_strand_likelihood_position_model=10.1486	new_cov=0/30	polymorphism_quality=11.7	quality=11.7	quality_position_model=Inf	ref_cov=138/102	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/134
RA	530	.	NC_007779	3895373	0	T	G	bias_e_value=0.22787	bias_p_value=4.9043e-08	fisher_strand_p_value=2.35006e-09	frequency=5.088806e-02	genotype_quality=821.0	ks_quality_p_value=1	log10_base_likelihood=-8.38516	log10_qual_likelihood_position_model=29.5818	log10_strand_likelihood_position_model=8.62892	new_cov=26/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=108/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/139
RA	531	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1160.4	new_cov=116/151	quality=1160.4	ref_cov=0/0	tot_cov=116/151
RA	532	.	NC_007779	3900676	1	.	G	bias_e_value=2378190	bias_p_value=0.511842	fisher_strand_p_value=0.196944	frequency=7.873535e-03	genotype_quality=1268.5	ks_quality_p_value=0.984129	log10_base_likelihood=-7.96484	log10_qual_likelihood_position_model=1.68738	log10_strand_likelihood_position_model=0.705658	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.76919e-07	ref_cov=111/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/141
RA	533	.	NC_007779	3900680	0	T	G	bias_e_value=1.38146e-16	bias_p_value=2.97322e-23	fisher_strand_p_value=5.2243e-25	frequency=1.006575e-01	genotype_quality=620.4	ks_quality_p_value=1	log10_base_likelihood=-18.5943	log10_qual_likelihood_position_model=25.3841	log10_strand_likelihood_position_model=24.282	new_cov=21/0	polymorphism_quality=13.3	quality=13.3	quality_position_model=Inf	ref_cov=2/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=23/149
RA	534	.	NC_007779	3910746	0	C	A	bias_e_value=0.000417074	bias_p_value=8.97641e-11	fisher_strand_p_value=3.27056e-12	frequency=1.118951e-01	genotype_quality=787.3	ks_quality_p_value=1	log10_base_likelihood=-25.7139	log10_qual_likelihood_position_model=27.7338	log10_strand_likelihood_position_model=11.5163	new_cov=36/0	polymorphism_quality=20.5	quality=20.5	quality_position_model=Inf	ref_cov=97/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/125
RA	535	.	NC_007779	3930443	0	T	G	bias_e_value=1.10454e-06	bias_p_value=2.37724e-13	fisher_strand_p_value=7.07897e-15	frequency=6.225777e-02	genotype_quality=654.7	ks_quality_p_value=1	log10_base_likelihood=-6.68844	log10_qual_likelihood_position_model=22.7784	log10_strand_likelihood_position_model=14.15	new_cov=30/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=52/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/131
RA	536	.	NC_007779	3952095	1	.	G	bias_e_value=30467.9	bias_p_value=0.00655742	fisher_strand_p_value=0.00100097	frequency=3.375530e-02	genotype_quality=1133.7	ks_quality_p_value=0.806611	log10_base_likelihood=-37.7962	log10_qual_likelihood_position_model=3.15971	log10_strand_likelihood_position_model=2.99958	new_cov=8/0	polymorphism_quality=32.6	quality=32.6	quality_position_model=6.57903e-34	ref_cov=94/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=102/135
RA	537	.	NC_007779	3986830	0	T	.	bias_e_value=3327840	bias_p_value=0.716229	fisher_strand_p_value=1	frequency=1.795673e-02	genotype_quality=674.4	ks_quality_p_value=0.34885	log10_base_likelihood=-8.88532	log10_qual_likelihood_position_model=1.5	log10_strand_likelihood_position_model=0.357352	new_cov=2/1	polymorphism_quality=3.4	quality=3.4	quality_position_model=5.54884e-09	ref_cov=100/64	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=102/65
RA	538	.	NC_007779	4023068	0	T	G	bias_e_value=0.000258559	bias_p_value=5.5648e-11	fisher_strand_p_value=1.99155e-12	frequency=5.598545e-02	genotype_quality=653.0	ks_quality_p_value=1	log10_base_likelihood=-8.18644	log10_qual_likelihood_position_model=18.5772	log10_strand_likelihood_position_model=11.7008	new_cov=18/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=31/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/139
RA	539	.	NC_007779	4029633	0	T	G	bias_e_value=3.60761e-14	bias_p_value=7.76442e-21	fisher_strand_p_value=1.51527e-22	frequency=1.172071e-01	genotype_quality=710.8	ks_quality_p_value=1	log10_base_likelihood=-18.8392	log10_qual_likelihood_position_model=36.6467	log10_strand_likelihood_position_model=21.8195	new_cov=38/0	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=35/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/146
RA	540	.	NC_007779	4031691	1	.	T	bias_e_value=147654	bias_p_value=0.0317785	fisher_strand_p_value=0.00570102	frequency=1.834869e-02	genotype_quality=1059.2	ks_quality_p_value=0.886545	log10_base_likelihood=-17.9347	log10_qual_likelihood_position_model=1.91016	log10_strand_likelihood_position_model=2.24405	new_cov=4/0	polymorphism_quality=12.6	quality=12.6	quality_position_model=7.10204e-16	ref_cov=57/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=61/157
RA	541	.	NC_007779	4036507	0	G	T	bias_e_value=17.5844	bias_p_value=3.78458e-06	fisher_strand_p_value=2.80266e-07	frequency=4.201412e-02	genotype_quality=1119.9	ks_quality_p_value=0.829754	log10_base_likelihood=-8.85674	log10_qual_likelihood_position_model=26.4984	log10_strand_likelihood_position_model=6.76253	new_cov=0/24	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=161/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/189
RA	542	.	NC_007779	4055100	0	G	T	bias_e_value=0.0708706	bias_p_value=1.5253e-08	fisher_strand_p_value=7.08713e-10	frequency=5.933237e-02	genotype_quality=986.3	ks_quality_p_value=0.974127	log10_base_likelihood=-14.4748	log10_qual_likelihood_position_model=26.2133	log10_strand_likelihood_position_model=9.14953	new_cov=22/0	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=99/177	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/177
RA	543	.	NC_007779	4055329	0	T	G	bias_e_value=8.47317e-16	bias_p_value=1.82362e-22	fisher_strand_p_value=3.31179e-24	frequency=8.312559e-02	genotype_quality=865.6	ks_quality_p_value=1	log10_base_likelihood=-15.4517	log10_qual_likelihood_position_model=31.9469	log10_strand_likelihood_position_model=23.4799	new_cov=36/0	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=38/193	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/193
RA	544	.	NC_007779	4059484	1	.	T	bias_e_value=4637350	bias_p_value=0.998068	fisher_strand_p_value=1	frequency=7.843018e-03	genotype_quality=1252.4	ks_quality_p_value=0.938484	log10_base_likelihood=-8.12851	log10_qual_likelihood_position_model=2.40997	log10_strand_likelihood_position_model=0.301741	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.56152e-07	ref_cov=136/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/118
RA	545	.	NC_007779	4059485	0	T	.	bias_e_value=1120890	bias_p_value=0.241241	fisher_strand_p_value=0.687044	frequency=2.315807e-02	genotype_quality=1037.1	ks_quality_p_value=0.093849	log10_base_likelihood=-18.2688	log10_qual_likelihood_position_model=2.91657	log10_strand_likelihood_position_model=0.581532	new_cov=4/2	polymorphism_quality=13.0	quality=13.0	quality_position_model=7.02331e-17	ref_cov=133/120	reject=INDEL_HOMOPOLYMER	tot_cov=137/122
RA	546	.	NC_007779	4062114	0	T	G	bias_e_value=1.49862e-15	bias_p_value=3.22538e-22	fisher_strand_p_value=5.91989e-24	frequency=1.550574e-01	genotype_quality=684.2	ks_quality_p_value=1	log10_base_likelihood=-27.5792	log10_qual_likelihood_position_model=39.631	log10_strand_likelihood_position_model=23.2277	new_cov=50/0	polymorphism_quality=22.4	quality=22.4	quality_position_model=Inf	ref_cov=47/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/135
RA	547	.	NC_007779	4064463	0	G	T	bias_e_value=0.00966977	bias_p_value=2.08116e-09	fisher_strand_p_value=8.60849e-11	frequency=1.080842e-01	genotype_quality=758.0	ks_quality_p_value=1	log10_base_likelihood=-18.3876	log10_qual_likelihood_position_model=25.4094	log10_strand_likelihood_position_model=10.1139	new_cov=0/41	polymorphism_quality=13.1	quality=13.1	quality_position_model=Inf	ref_cov=108/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/162
RA	548	.	NC_007779	4074542	0	C	A	bias_e_value=2890.95	bias_p_value=0.000622201	fisher_strand_p_value=5.81785e-05	frequency=3.090477e-02	genotype_quality=872.3	ks_quality_p_value=0.994126	log10_base_likelihood=-6.02766	log10_qual_likelihood_position_model=14.6836	log10_strand_likelihood_position_model=4.23524	new_cov=0/11	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=144/95	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/106
RA	549	.	NC_007779	4076934	0	A	C	bias_e_value=736.08	bias_p_value=0.000158422	fisher_strand_p_value=1.29257e-05	frequency=3.068733e-02	genotype_quality=953.0	ks_quality_p_value=1	log10_base_likelihood=-6.86918	log10_qual_likelihood_position_model=14.4388	log10_strand_likelihood_position_model=4.88854	new_cov=0/13	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=161/110	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=161/123
RA	550	.	NC_007779	4087369	0	T	.	bias_e_value=2054550	bias_p_value=0.442188	fisher_strand_p_value=0.24891	frequency=1.012707e-02	genotype_quality=1198.8	ks_quality_p_value=0.618878	log10_base_likelihood=-7.99562	log10_qual_likelihood_position_model=1.90253	log10_strand_likelihood_position_model=0.850981	new_cov=3/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=3.88878e-07	ref_cov=151/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/142
RA	551	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1257.9	new_cov=161/148	quality=1257.9	ref_cov=0/0	tot_cov=161/148
RA	552	.	NC_007779	4098730	0	G	T	bias_e_value=0.00398444	bias_p_value=8.57545e-10	fisher_strand_p_value=3.41654e-11	frequency=3.735828e-02	genotype_quality=1009.7	ks_quality_p_value=1	log10_base_likelihood=-7.24196	log10_qual_likelihood_position_model=21.5581	log10_strand_likelihood_position_model=10.4664	new_cov=0/26	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=185/108	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=185/135
RA	553	.	NC_007779	4124974	0	G	T	bias_e_value=0.0221617	bias_p_value=4.76971e-09	fisher_strand_p_value=2.04622e-10	frequency=7.486153e-02	genotype_quality=875.6	ks_quality_p_value=1	log10_base_likelihood=-15.0519	log10_qual_likelihood_position_model=18.6389	log10_strand_likelihood_position_model=9.68905	new_cov=0/28	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=139/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/128
RA	554	.	NC_007779	4148399	0	A	C	bias_e_value=3.72661e-07	bias_p_value=8.02053e-14	fisher_strand_p_value=2.31133e-15	frequency=8.023357e-02	genotype_quality=773.5	ks_quality_p_value=1	log10_base_likelihood=-13.9335	log10_qual_likelihood_position_model=26.7901	log10_strand_likelihood_position_model=14.6361	new_cov=0/31	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=148/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/91
RA	555	.	NC_007779	4148715	0	G	T	bias_e_value=42268.7	bias_p_value=0.00909722	fisher_strand_p_value=0.0011795	frequency=7.099724e-02	genotype_quality=536.2	ks_quality_p_value=0.995566	log10_base_likelihood=-7.64068	log10_qual_likelihood_position_model=16.1444	log10_strand_likelihood_position_model=3.13688	new_cov=15/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=94/63	reject=POLYMORPHISM_STRAND	tot_cov=109/63
RA	556	.	NC_007779	4157323	0	C	A	bias_e_value=292.902	bias_p_value=6.30395e-05	fisher_strand_p_value=4.90127e-06	frequency=4.408836e-02	genotype_quality=783.0	ks_quality_p_value=0.970251	log10_base_likelihood=-8.70831	log10_qual_likelihood_position_model=18.2864	log10_strand_likelihood_position_model=5.30969	new_cov=16/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=98/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/122
RA	557	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=927.4	new_cov=105/109	quality=927.4	ref_cov=0/0	tot_cov=105/110
RA	558	.	NC_007779	4197139	0	T	G	bias_e_value=5.69915e-11	bias_p_value=1.22659e-17	fisher_strand_p_value=2.80572e-19	frequency=1.361604e-01	genotype_quality=518.1	ks_quality_p_value=1	log10_base_likelihood=-23.868	log10_qual_likelihood_position_model=25.6283	log10_strand_likelihood_position_model=18.552	new_cov=23/0	polymorphism_quality=18.6	quality=18.6	quality_position_model=Inf	ref_cov=11/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=34/118
RA	559	.	NC_007779	4218761	0	C	G	bias_e_value=265584	bias_p_value=0.05716	fisher_strand_p_value=0.0102413	frequency=3.433323e-02	genotype_quality=846.8	ks_quality_p_value=1	log10_base_likelihood=-9.78865	log10_qual_likelihood_position_model=12.1856	log10_strand_likelihood_position_model=2.03933	new_cov=0/8	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=93/112	reject=POLYMORPHISM_STRAND	tot_cov=93/120
RA	560	.	NC_007779	4218769	0	T	G	bias_e_value=148010	bias_p_value=0.0318552	fisher_strand_p_value=0.00506872	frequency=2.060223e-02	genotype_quality=761.6	ks_quality_p_value=1	log10_base_likelihood=-5.92576	log10_qual_likelihood_position_model=10.7375	log10_strand_likelihood_position_model=2.34099	new_cov=0/9	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=91/106	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=91/115
RA	561	.	NC_007779	4220019	0	A	C	bias_e_value=0.010702	bias_p_value=2.30333e-09	fisher_strand_p_value=9.56935e-11	frequency=6.649256e-02	genotype_quality=687.7	ks_quality_p_value=1	log10_base_likelihood=-6.53269	log10_qual_likelihood_position_model=36.5194	log10_strand_likelihood_position_model=10.0357	new_cov=0/32	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=110/88	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/121
RA	562	.	NC_007779	4224248	1	.	T	bias_e_value=2710580	bias_p_value=0.583382	fisher_strand_p_value=0.240613	frequency=8.400917e-03	genotype_quality=1191.1	ks_quality_p_value=1	log10_base_likelihood=-6.97527	log10_qual_likelihood_position_model=2.91882	log10_strand_likelihood_position_model=0.618681	new_cov=0/2	polymorphism_quality=1.5	quality=1.5	quality_position_model=3.00713e-05	ref_cov=121/115	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=121/117
RA	563	.	NC_007779	4224824	1	.	T	bias_e_value=4643350	bias_p_value=0.999358	fisher_strand_p_value=1	frequency=7.299423e-03	genotype_quality=1369.8	ks_quality_p_value=0.964369	log10_base_likelihood=-8.29147	log10_qual_likelihood_position_model=1.83569	log10_strand_likelihood_position_model=0.300577	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=4.40675e-08	ref_cov=143/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/130
RA	564	.	NC_007779	4227183	0	T	G	bias_e_value=2.93094e-11	bias_p_value=6.30808e-18	fisher_strand_p_value=1.42081e-19	frequency=6.689358e-02	genotype_quality=909.8	ks_quality_p_value=1	log10_base_likelihood=-7.31626	log10_qual_likelihood_position_model=35.1573	log10_strand_likelihood_position_model=18.8475	new_cov=41/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=73/175	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/175
RA	565	.	NC_007779	4288183	0	A	C	bias_e_value=537595	bias_p_value=0.115703	fisher_strand_p_value=0.235486	frequency=6.192207e-03	genotype_quality=1299.4	ks_quality_p_value=0.104419	log10_base_likelihood=-5.97055	log10_qual_likelihood_position_model=1.53134	log10_strand_likelihood_position_model=0.628034	new_cov=2/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=1.21467e-05	ref_cov=155/166	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=157/166
RA	566	.	NC_007779	4289840	0	G	T	bias_e_value=0.0380558	bias_p_value=8.1905e-09	fisher_strand_p_value=3.60324e-10	frequency=5.343580e-02	genotype_quality=1038.5	ks_quality_p_value=0.999398	log10_base_likelihood=-12.3453	log10_qual_likelihood_position_model=20.2551	log10_strand_likelihood_position_model=9.52507	new_cov=0/33	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=161/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/187
RA	567	.	NC_007779	4292321	0	C	A	bias_e_value=0.0681036	bias_p_value=1.46575e-08	fisher_strand_p_value=6.62171e-10	frequency=3.344536e-02	genotype_quality=1269.5	ks_quality_p_value=1	log10_base_likelihood=-9.82391	log10_qual_likelihood_position_model=23.1116	log10_strand_likelihood_position_model=9.17903	new_cov=25/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=143/207	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/207
RA	568	.	NC_007779	4321435	0	G	C	bias_e_value=1.92552	bias_p_value=4.14418e-07	fisher_strand_p_value=2.24552e-08	frequency=4.301548e-02	genotype_quality=666.5	ks_quality_p_value=0.991119	log10_base_likelihood=-13.8974	log10_qual_likelihood_position_model=10.6279	log10_strand_likelihood_position_model=7.64868	new_cov=7/0	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=9/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/146
RA	569	.	NC_007779	4337469	0	A	C	bias_e_value=5.26846e-10	bias_p_value=1.1339e-16	fisher_strand_p_value=2.73624e-18	frequency=1.322713e-01	genotype_quality=642.8	ks_quality_p_value=1	log10_base_likelihood=-17.3916	log10_qual_likelihood_position_model=35.329	log10_strand_likelihood_position_model=17.5628	new_cov=0/43	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=118/55	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/98
RA	570	.	NC_007779	4348529	0	T	G	bias_e_value=3.37782e-05	bias_p_value=7.26987e-12	fisher_strand_p_value=2.41925e-13	frequency=5.496836e-02	genotype_quality=742.3	ks_quality_p_value=1	log10_base_likelihood=-6.67377	log10_qual_likelihood_position_model=28.684	log10_strand_likelihood_position_model=12.6163	new_cov=24/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=50/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=74/146
RA	571	.	NC_007779	4351353	0	T	G	bias_e_value=6.74202e-13	bias_p_value=1.45104e-19	fisher_strand_p_value=3.00713e-21	frequency=1.227808e-01	genotype_quality=672.9	ks_quality_p_value=1	log10_base_likelihood=-13.4076	log10_qual_likelihood_position_model=47.8682	log10_strand_likelihood_position_model=20.5218	new_cov=48/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=53/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/127
RA	572	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=888.5	new_cov=88/87	quality=888.5	ref_cov=0/0	tot_cov=88/87
RA	573	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=888.5	new_cov=88/87	quality=888.5	ref_cov=0/0	tot_cov=88/87
RA	574	.	NC_007779	4414724	1	.	T	bias_e_value=2650350	bias_p_value=0.570417	fisher_strand_p_value=1	frequency=1.321602e-02	genotype_quality=1110.5	ks_quality_p_value=0.231632	log10_base_likelihood=-13.0674	log10_qual_likelihood_position_model=3.39207	log10_strand_likelihood_position_model=0.349661	new_cov=1/2	polymorphism_quality=7.7	quality=7.7	quality_position_model=2.44349e-11	ref_cov=72/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=73/154
RA	575	.	NC_007779	4429120	0	G	T	bias_e_value=0.00911212	bias_p_value=1.96114e-09	fisher_strand_p_value=1.46739e-10	frequency=4.426575e-02	genotype_quality=981.6	ks_quality_p_value=0.55141	log10_base_likelihood=-6.20827	log10_qual_likelihood_position_model=32.9276	log10_strand_likelihood_position_model=9.83346	new_cov=0/28	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=167/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/148
RA	576	.	NC_007779	4455463	0	T	G	bias_e_value=1.04913	bias_p_value=2.25798e-07	fisher_strand_p_value=1.17226e-08	frequency=5.391836e-02	genotype_quality=788.7	ks_quality_p_value=1	log10_base_likelihood=-8.61029	log10_qual_likelihood_position_model=24.9029	log10_strand_likelihood_position_model=7.94029	new_cov=19/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=65/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/150
RA	577	.	NC_007779	4479134	0	G	T	bias_e_value=27.3058	bias_p_value=5.87685e-06	fisher_strand_p_value=3.72156e-07	frequency=5.214357e-02	genotype_quality=727.1	ks_quality_p_value=0.999151	log10_base_likelihood=-8.18229	log10_qual_likelihood_position_model=19.6352	log10_strand_likelihood_position_model=6.45682	new_cov=0/24	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=110/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/140
RA	578	.	NC_007779	4494104	0	C	A	bias_e_value=27629.3	bias_p_value=0.00594647	fisher_strand_p_value=0.000722261	frequency=2.134323e-02	genotype_quality=989.7	ks_quality_p_value=1	log10_base_likelihood=-6.07424	log10_qual_likelihood_position_model=9.54369	log10_strand_likelihood_position_model=3.14131	new_cov=9/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=115/148	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/148
RA	579	.	NC_007779	4509629	1	.	T	bias_e_value=4501020	bias_p_value=0.968725	fisher_strand_p_value=1	frequency=1.363659e-02	genotype_quality=1087.2	ks_quality_p_value=0.760557	log10_base_likelihood=-12.9639	log10_qual_likelihood_position_model=1.46156	log10_strand_likelihood_position_model=0.389474	new_cov=1/2	polymorphism_quality=7.6	quality=7.6	quality_position_model=3.6662e-13	ref_cov=99/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=100/120
RA	580	.	NC_007779	4540870	0	T	G	bias_e_value=9.19934e-14	bias_p_value=1.97991e-20	fisher_strand_p_value=3.93728e-22	frequency=1.025801e-01	genotype_quality=665.9	ks_quality_p_value=1	log10_base_likelihood=-10.2712	log10_qual_likelihood_position_model=31.6919	log10_strand_likelihood_position_model=21.4048	new_cov=41/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=39/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/136
RA	581	.	NC_007779	4540877	0	A	T	bias_e_value=3.10616e-11	bias_p_value=6.68518e-18	fisher_strand_p_value=1.50776e-19	frequency=1.582851e-01	genotype_quality=614.8	ks_quality_p_value=1	log10_base_likelihood=-30.4401	log10_qual_likelihood_position_model=27.0628	log10_strand_likelihood_position_model=18.8217	new_cov=36/0	polymorphism_quality=25.2	quality=25.2	quality_position_model=Inf	ref_cov=41/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=77/136
RA	582	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=633.3	new_cov=88/66	quality=633.3	ref_cov=0/0	tot_cov=88/66
RA	583	.	NC_007779	4554525	1	.	T	bias_e_value=708711	bias_p_value=0.152531	fisher_strand_p_value=0.202596	frequency=8.849144e-03	genotype_quality=1085.4	ks_quality_p_value=0.173048	log10_base_likelihood=-8.44232	log10_qual_likelihood_position_model=2.37184	log10_strand_likelihood_position_model=0.693369	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.81623e-07	ref_cov=100/124	reject=POLYMORPHISM_STRAND	tot_cov=102/124
RA	584	.	NC_007779	4561440	1	.	T	bias_e_value=4553610	bias_p_value=0.980044	fisher_strand_p_value=1	frequency=1.754379e-02	genotype_quality=1102.6	ks_quality_p_value=0.806991	log10_base_likelihood=-17.3636	log10_qual_likelihood_position_model=3.58501	log10_strand_likelihood_position_model=0.420294	new_cov=3/1	polymorphism_quality=12.0	quality=12.0	quality_position_model=1.90607e-15	ref_cov=143/81	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/82
RA	585	.	NC_007779	4573184	0	T	G	bias_e_value=1.66005e-05	bias_p_value=3.57281e-12	fisher_strand_p_value=1.16058e-13	frequency=6.192207e-02	genotype_quality=929.8	ks_quality_p_value=1	log10_base_likelihood=-8.87535	log10_qual_likelihood_position_model=32.9036	log10_strand_likelihood_position_model=13.0014	new_cov=50/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=145/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=196/139
RA	586	.	NC_007779	4576471	0	G	T	bias_e_value=145307	bias_p_value=0.0312735	fisher_strand_p_value=0.00500712	frequency=3.802681e-02	genotype_quality=580.8	ks_quality_p_value=0.990362	log10_base_likelihood=-5.99429	log10_qual_likelihood_position_model=9.01325	log10_strand_likelihood_position_model=2.34391	new_cov=0/9	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=78/90	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=78/99
RA	587	.	NC_007779	4583431	0	T	.	bias_e_value=3252050	bias_p_value=0.699918	fisher_strand_p_value=0.62439	frequency=1.960182e-02	genotype_quality=805.6	ks_quality_p_value=0.534409	log10_base_likelihood=-12.1289	log10_qual_likelihood_position_model=1.90829	log10_strand_likelihood_position_model=0.549176	new_cov=1/3	polymorphism_quality=6.7	quality=6.7	quality_position_model=1.08309e-11	ref_cov=94/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=96/108
RA	588	.	NC_007779	4584556	0	C	A	bias_e_value=9.79621	bias_p_value=2.10838e-06	fisher_strand_p_value=1.24853e-07	frequency=4.920721e-02	genotype_quality=874.4	ks_quality_p_value=0.999417	log10_base_likelihood=-7.81808	log10_qual_likelihood_position_model=20.4158	log10_strand_likelihood_position_model=6.9036	new_cov=19/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=101/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/145
RA	589	.	NC_007779	4599760	0	C	A	bias_e_value=0.0011308	bias_p_value=2.43374e-10	fisher_strand_p_value=9.21515e-12	frequency=5.776119e-02	genotype_quality=1065.2	ks_quality_p_value=1	log10_base_likelihood=-10.9856	log10_qual_likelihood_position_model=21.7138	log10_strand_likelihood_position_model=11.0355	new_cov=28/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=109/182	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/182
RA	590	.	NC_007779	4610781	0	A	C	bias_e_value=0.378783	bias_p_value=8.1523e-08	fisher_strand_p_value=4.00906e-09	frequency=3.676414e-02	genotype_quality=882.1	ks_quality_p_value=1	log10_base_likelihood=-7.85401	log10_qual_likelihood_position_model=21.4089	log10_strand_likelihood_position_model=8.39696	new_cov=0/22	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=151/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/118
RA	591	.	NC_007779	4613456	0	C	A	bias_e_value=16.0084	bias_p_value=3.44538e-06	fisher_strand_p_value=2.10416e-07	frequency=5.893707e-02	genotype_quality=786.2	ks_quality_p_value=1	log10_base_likelihood=-8.3399	log10_qual_likelihood_position_model=19.2009	log10_strand_likelihood_position_model=6.88786	new_cov=24/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=117/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/121
RA	592	.	NC_007779	4635770	0	G	T	bias_e_value=993.274	bias_p_value=0.000213776	fisher_strand_p_value=1.79198e-05	frequency=4.298019e-02	genotype_quality=778.8	ks_quality_p_value=1	log10_base_likelihood=-8.33432	log10_qual_likelihood_position_model=13.1289	log10_strand_likelihood_position_model=4.86097	new_cov=0/20	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=112/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/159
RA	593	.	NC_007779	4636470	0	C	G	bias_e_value=4.87706e-09	bias_p_value=1.04966e-15	fisher_strand_p_value=2.68058e-17	frequency=9.494066e-02	genotype_quality=841.3	ks_quality_p_value=1	log10_base_likelihood=-16.1789	log10_qual_likelihood_position_model=25.9449	log10_strand_likelihood_position_model=16.5718	new_cov=28/0	polymorphism_quality=10.8	quality=10.8	quality_position_model=Inf	ref_cov=44/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=72/168
RA	594	.	NC_007779	4642414	1	.	A	bias_e_value=3141980	bias_p_value=0.676229	fisher_strand_p_value=0.377009	frequency=1.945496e-02	genotype_quality=1229.8	ks_quality_p_value=0.82945	log10_base_likelihood=-22.5509	log10_qual_likelihood_position_model=3.73379	log10_strand_likelihood_position_model=0.717678	new_cov=4/1	polymorphism_quality=17.3	quality=17.3	quality_position_model=2.98385e-20	ref_cov=134/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/119
MC	595	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=298	right_inside_cov=0	right_outside_cov=300
MC	596	.	NC_007779	654214	655412	1193	0	left_inside_cov=0	left_outside_cov=275	right_inside_cov=0	right_outside_cov=275
MC	597	.	NC_007779	1288334	1288495	65	36	left_inside_cov=160	left_outside_cov=163	right_inside_cov=156	right_outside_cov=163
MC	598	.	NC_007779	1301041	1302376	1328	0	left_inside_cov=0	left_outside_cov=299	right_inside_cov=0	right_outside_cov=301
MC	599	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=310	right_inside_cov=0	right_outside_cov=308
MC	600	.	NC_007779	2176983	2178208	0	0	left_inside_cov=0	left_outside_cov=300	right_inside_cov=0	right_outside_cov=343
MC	601	.	NC_007779	2320795	2322130	1327	0	left_inside_cov=0	left_outside_cov=238	right_inside_cov=0	right_outside_cov=241
MC	602	.	NC_007779	3128845	3147473	1157	0	left_inside_cov=158	left_outside_cov=163	right_inside_cov=0	right_outside_cov=429
MC	603	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=304	right_inside_cov=0	right_outside_cov=320
MC	604	.	NC_007779	3742936	3744271	1325	0	left_inside_cov=0	left_outside_cov=251	right_inside_cov=0	right_outside_cov=251
MC	605	.	NC_007779	3746911	3748109	0	0	left_inside_cov=0	left_outside_cov=287	right_inside_cov=0	right_outside_cov=287
MC	606	.	NC_007779	3750591	3751789	1194	0	left_inside_cov=1	left_outside_cov=301	right_inside_cov=0	right_outside_cov=300
MC	607	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=326	right_inside_cov=0	right_outside_cov=326
MC	608	.	NC_007779	4310363	4311561	0	0	left_inside_cov=0	left_outside_cov=346	right_inside_cov=0	right_outside_cov=345
JC	609	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=142	coverage_plus=144	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=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=286	pos_hash_score=140	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=286
JC	610	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=10	coverage_minus=124	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371963__1__10____101__101__0__0	max_left=85	max_left_minus=84	max_left_plus=85	max_min_left=45	max_min_left_minus=43	max_min_left_plus=45	max_min_right=45	max_min_right_minus=45	max_min_right_plus=45	max_pos_hash_score=160	max_right=85	max_right_minus=85	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.03	new_junction_frequency=1.000000e+00	new_junction_read_count=237	pos_hash_score=127	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=10	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=80	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=237
JC	611	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=84	coverage_plus=94	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=57	key=NC_007779__289856__1__NC_007779__2176982__-1__-33__CTATTGCAATACCGCATTGTGAGGCGATTCATG__101__101__1__0	max_left=62	max_left_minus=62	max_left_plus=62	max_min_left=33	max_min_left_minus=33	max_min_left_plus=33	max_min_right=34	max_min_right_minus=34	max_min_right_plus=34	max_pos_hash_score=114	max_right=62	max_right_minus=62	max_right_plus=62	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=178	pos_hash_score=94	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=178	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	612	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=100	coverage_plus=64	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=90	key=NC_007779__380484__1__NC_007779__381407__-1__0____101__101__1__1	max_left=90	max_left_minus=90	max_left_plus=90	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	max_pos_hash_score=180	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.63	new_junction_frequency=NA	new_junction_read_count=164	pos_hash_score=103	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=164
JC	613	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=77	coverage_plus=109	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=88	key=NC_007779__381401__1__NC_007779__381814__-1__2____101__101__1__1	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=47	max_min_left_plus=49	max_min_right=49	max_min_right_minus=47	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.74	new_junction_frequency=NA	new_junction_read_count=187	pos_hash_score=110	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=186
JC	614	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=128	coverage_plus=136	flanking_left=101	flanking_right=101	frequency=9.579100e-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=46	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=90	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=9.579100e-01	new_junction_read_count=264	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=0.05	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=12	side_2_redundant=0	total_non_overlap_reads=264
JC	615	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=116	coverage_plus=110	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=89	max_min_left=47	max_min_left_minus=45	max_min_left_plus=47	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=170	max_right=90	max_right_minus=90	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=1.000000e+00	new_junction_read_count=228	pos_hash_score=126	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=226
JC	616	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=31	coverage_plus=29	flanking_left=101	flanking_right=101	frequency=3.179650e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=77	max_left_minus=77	max_left_plus=75	max_min_left=41	max_min_left_minus=38	max_min_left_plus=41	max_min_right=41	max_min_right_minus=41	max_min_right_plus=41	max_pos_hash_score=148	max_right=76	max_right_minus=74	max_right_plus=76	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.28	new_junction_frequency=3.179650e-01	new_junction_read_count=60	pos_hash_score=49	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.56	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=144	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.65	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=139	side_2_redundant=0	total_non_overlap_reads=60
JC	617	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=22	coverage_plus=28	flanking_left=101	flanking_right=101	frequency=2.837148e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=79	max_left_minus=75	max_left_plus=79	max_min_left=41	max_min_left_minus=41	max_min_left_plus=38	max_min_right=42	max_min_right_minus=42	max_min_right_plus=40	max_pos_hash_score=148	max_right=79	max_right_minus=79	max_right_plus=73	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.23	new_junction_frequency=2.837148e-01	new_junction_read_count=50	pos_hash_score=41	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.53	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=138	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.65	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=139	side_2_redundant=0	total_non_overlap_reads=50
JC	618	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=63	coverage_plus=91	flanking_left=101	flanking_right=101	frequency=9.937313e-01	junction_possible_overlap_registers=88	key=NC_007779__1221489__1__NC_007779__1301039__1__2____101__101__0__1	max_left=93	max_left_minus=92	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=48	max_pos_hash_score=176	max_right=84	max_right_minus=82	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.61	new_junction_frequency=9.937313e-01	new_junction_read_count=155	pos_hash_score=94	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=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=154
JC	619	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=74	coverage_plus=55	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=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.50	new_junction_frequency=1.000000e+00	new_junction_read_count=129	pos_hash_score=91	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=129
JC	620	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=106	coverage_plus=137	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=87	max_left_plus=88	max_min_left=46	max_min_left_minus=44	max_min_left_plus=46	max_min_right=47	max_min_right_minus=46	max_min_right_plus=47	max_pos_hash_score=166	max_right=88	max_right_minus=88	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.03	new_junction_frequency=1.000000e+00	new_junction_read_count=246	pos_hash_score=123	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=243
JC	621	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=127	coverage_plus=140	flanking_left=101	flanking_right=101	frequency=9.394792e-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=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=48	max_min_right_minus=46	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=1.08	new_junction_frequency=9.394792e-01	new_junction_read_count=267	pos_hash_score=135	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.07	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=18	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=267
JC	622	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1397758__1__NC_007779__1672777__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=254	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=254
JC	623	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=97	coverage_plus=100	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=68	max_left_plus=69	max_min_left=37	max_min_left_minus=37	max_min_left_plus=37	max_min_right=37	max_min_right_minus=35	max_min_right_plus=37	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=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=197	pos_hash_score=94	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=197
JC	624	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=112	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1672780__-1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=85	max_right_minus=85	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=237	pos_hash_score=118	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=236
JC	625	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=107	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=9.653680e-01	junction_possible_overlap_registers=90	key=NC_007779__1907280__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=87	max_right_minus=87	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=9.653680e-01	new_junction_read_count=223	pos_hash_score=119	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=8	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=220
JC	626	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=100	coverage_plus=89	flanking_left=101	flanking_right=101	frequency=9.452736e-01	junction_possible_overlap_registers=90	key=NC_007779__1907288__-1__NC_007779__2411458__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=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=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.73	new_junction_frequency=9.452736e-01	new_junction_read_count=190	pos_hash_score=116	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=11	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=189
JC	627	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=112	coverage_plus=45	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=48	max_min_left_minus=48	max_min_left_plus=34	max_min_right=49	max_min_right_minus=49	max_min_right_plus=38	max_pos_hash_score=180	max_right=91	max_right_minus=91	max_right_plus=67	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.61	new_junction_frequency=1.000000e+00	new_junction_read_count=158	pos_hash_score=81	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=157
JC	628	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=137	coverage_plus=107	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=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=178	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=246	pos_hash_score=126	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=244
JC	629	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=112	coverage_plus=140	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=94	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=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=1.000000e+00	new_junction_read_count=252	pos_hash_score=132	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=252
JC	630	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=89	coverage_plus=109	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=46	max_min_right=47	max_min_right_minus=45	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=1.000000e+00	new_junction_read_count=198	pos_hash_score=113	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=198
JC	631	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=64	coverage_plus=149	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2320794__1__NC_007779__2589834__-1__0____101__101__1__0	max_left=85	max_left_minus=85	max_left_plus=84	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=1.000000e+00	new_junction_read_count=213	pos_hash_score=109	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=213
JC	632	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=147	coverage_plus=147	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=1.13	new_junction_frequency=1.000000e+00	new_junction_read_count=294	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=294
JC	633	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=90	coverage_plus=81	flanking_left=101	flanking_right=101	frequency=9.560440e-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=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=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.67	new_junction_frequency=9.560440e-01	new_junction_read_count=174	pos_hash_score=107	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.03	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=8	side_2_redundant=0	total_non_overlap_reads=171
JC	634	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=62	coverage_plus=85	flanking_left=101	flanking_right=101	frequency=9.865772e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=90	max_left_minus=86	max_left_plus=90	max_min_left=49	max_min_left_minus=49	max_min_left_plus=48	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=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.57	new_junction_frequency=9.865772e-01	new_junction_read_count=147	pos_hash_score=94	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.01	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=2	side_2_redundant=0	total_non_overlap_reads=147
JC	635	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=160	coverage_plus=145	flanking_left=101	flanking_right=101	frequency=7.248895e-01	junction_possible_overlap_registers=86	key=NC_007779__2865229__1__NC_007779__2865278__-1__4____101__101__0__0	max_left=91	max_left_minus=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.23	new_junction_frequency=7.248895e-01	new_junction_read_count=306	pos_hash_score=143	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.50	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=129	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.44	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=109	side_2_redundant=0	total_non_overlap_reads=305
JC	636	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=155	coverage_plus=148	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=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=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=303	pos_hash_score=146	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=303
JC	637	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=134	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=9.817511e-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=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=9.817511e-01	new_junction_read_count=266	pos_hash_score=135	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=5	side_2_redundant=0	total_non_overlap_reads=266
JC	638	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=137	coverage_plus=128	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=84	key=NC_007779__3261133__-1__NC_007779__3748109__-1__-6__CTTTGC__101__101__0__1	max_left=89	max_left_minus=89	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=266	pos_hash_score=130	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=265	unique_read_sequence=CTTTGC
JC	639	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=100	coverage_plus=112	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0	max_left=85	max_left_minus=85	max_left_plus=85	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=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=1.000000e+00	new_junction_read_count=212	pos_hash_score=112	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=212
JC	640	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=122	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=92	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=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=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=270	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=270
JC	641	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=167	coverage_plus=134	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=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=302	pos_hash_score=142	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=301
JC	642	.	NC_007779	3399026	-1	NC_007779	3399030	1	0	alignment_overlap=0	coverage_minus=2	coverage_plus=1	flanking_left=101	flanking_right=101	frequency=1.068153e-01	junction_possible_overlap_registers=90	key=NC_007779__3399026__-1__NC_007779__3399030__1__0____101__101__0__0	max_left=77	max_left_minus=77	max_left_plus=26	max_min_left=26	max_min_left_minus=0	max_min_left_plus=26	max_min_right=41	max_min_right_minus=41	max_min_right_plus=0	max_pos_hash_score=162	max_right=75	max_right_minus=41	max_right_plus=75	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.13	new_junction_frequency=1.068153e-01	new_junction_read_count=33	pos_hash_score=3	side_1_annotate_key=gene	side_1_continuation=9	side_1_coverage=1.04	side_1_overlap=0	side_1_possible_overlap_registers=81	side_1_read_count=242	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.09	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=283	side_2_redundant=0	total_non_overlap_reads=3
JC	643	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=104	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=9.916188e-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=83	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=9.916188e-01	new_junction_read_count=234	pos_hash_score=120	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=233
JC	644	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=106	coverage_plus=99	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=86	max_left_minus=86	max_left_plus=86	max_min_left=46	max_min_left_minus=46	max_min_left_plus=42	max_min_right=46	max_min_right_minus=46	max_min_right_plus=46	max_pos_hash_score=164	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.87	new_junction_frequency=1.000000e+00	new_junction_read_count=206	pos_hash_score=116	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=205
JC	645	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=133	coverage_plus=94	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=90	max_left_minus=90	max_left_plus=88	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.88	new_junction_frequency=1.000000e+00	new_junction_read_count=227	pos_hash_score=131	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=227
JC	646	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=3	coverage_minus=112	coverage_plus=134	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3746910__-1__NC_007779__3748107__1__3____101__101__0__0	max_left=92	max_left_minus=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=172	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=243	pos_hash_score=137	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=3	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=1	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=246
JC	647	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=121	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=49	max_pos_hash_score=180	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=257	pos_hash_score=130	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=243
JC	648	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=124	coverage_plus=129	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=95	max_left_plus=95	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=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=255	pos_hash_score=128	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=253
JC	649	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=123	coverage_plus=146	flanking_left=101	flanking_right=101	frequency=9.982270e-01	junction_possible_overlap_registers=86	key=NC_007779__3750590__-1__NC_007779__3751786__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=46	max_min_left_plus=48	max_min_right=48	max_min_right_minus=45	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=1.09	new_junction_frequency=9.982270e-01	new_junction_read_count=269	pos_hash_score=135	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=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=86	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=269
JC	650	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=133	coverage_plus=103	flanking_left=101	flanking_right=101	frequency=9.835155e-01	junction_possible_overlap_registers=89	key=NC_007779__3903279__-1__NC_007779__4504191__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=9.835155e-01	new_junction_read_count=236	pos_hash_score=122	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=4	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=236
JC	651	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=125	coverage_plus=161	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=88	key=NC_007779__3958122__-1__NC_007779__3958155__1__2____101__101__0__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=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=1.13	new_junction_frequency=1.000000e+00	new_junction_read_count=286	pos_hash_score=143	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=88	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=286
JC	652	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=150	coverage_plus=139	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=292	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=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=289
JC	653	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=162	coverage_plus=180	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=94	max_left_plus=95	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.32	new_junction_frequency=1.000000e+00	new_junction_read_count=342	pos_hash_score=149	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=342
JC	654	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=166	coverage_plus=139	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__4310362__-1__NC_007779__4311558__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=48	max_min_right_minus=46	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=1.23	new_junction_frequency=1.000000e+00	new_junction_read_count=305	pos_hash_score=138	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=305
JC	655	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=129	coverage_plus=116	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=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=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=248	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=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=245
JC	656	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=111	coverage_plus=135	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4311557__-1__NC_007779__4353543__-1__0____101__101__1__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	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=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=261	pos_hash_score=131	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=246
JC	657	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=132	coverage_plus=132	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=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=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=266	pos_hash_score=133	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=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
JC	658	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=125	coverage_plus=155	flanking_left=101	flanking_right=101	frequency=9.729168e-01	junction_possible_overlap_registers=88	key=NC_007779__4355066__-1__NC_007779__4504191__-1__2____101__101__0__1	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=47	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=9.729168e-01	new_junction_read_count=281	pos_hash_score=142	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.03	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=8	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=280
JC	659	.	NC_007779	4547362	1	NC_007779	4547676	1	0	alignment_overlap=9	coverage_minus=13	coverage_plus=7	flanking_left=101	flanking_right=101	frequency=1.222494e-01	junction_possible_overlap_registers=81	key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0	max_left=85	max_left_minus=85	max_left_plus=82	max_min_left=45	max_min_left_minus=27	max_min_left_plus=45	max_min_right=29	max_min_right_minus=29	max_min_right_plus=26	max_pos_hash_score=162	max_right=86	max_right_minus=86	max_right_plus=71	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.09	new_junction_frequency=1.222494e-01	new_junction_read_count=20	pos_hash_score=16	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.57	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=148	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.66	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=154	side_2_redundant=0	total_non_overlap_reads=20
JC	660	.	NC_007779	4547370	-1	NC_007779	4547666	-1	0	alignment_overlap=9	coverage_minus=10	coverage_plus=8	flanking_left=101	flanking_right=101	frequency=1.098566e-01	junction_possible_overlap_registers=81	key=NC_007779__4547370__-1__NC_007779__4547675__-1__9____101__101__0__0	max_left=84	max_left_minus=84	max_left_plus=78	max_min_left=43	max_min_left_minus=43	max_min_left_plus=25	max_min_right=46	max_min_right_minus=24	max_min_right_plus=46	max_pos_hash_score=162	max_right=85	max_right_minus=85	max_right_plus=67	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.08	new_junction_frequency=1.098566e-01	new_junction_read_count=18	pos_hash_score=17	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.59	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=153	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.66	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=154	side_2_redundant=0	total_non_overlap_reads=18
UN	661	.	NC_007779	15485	16634
UN	662	.	NC_007779	19894	20466
UN	663	.	NC_007779	223635	223642
UN	664	.	NC_007779	223840	224675
UN	665	.	NC_007779	224989	225488
UN	666	.	NC_007779	225834	225923
UN	667	.	NC_007779	226121	226203
UN	668	.	NC_007779	226399	226507
UN	669	.	NC_007779	226509	226509
UN	670	.	NC_007779	226701	226870
UN	671	.	NC_007779	227085	228591
UN	672	.	NC_007779	228787	228911
UN	673	.	NC_007779	269859	270420
UN	674	.	NC_007779	270706	270712
UN	675	.	NC_007779	273277	274275
UN	676	.	NC_007779	274733	371972
UN	677	.	NC_007779	380576	381720
UN	678	.	NC_007779	391029	392101
UN	679	.	NC_007779	525194	525848
UN	680	.	NC_007779	566089	567161
UN	681	.	NC_007779	573905	574918
UN	682	.	NC_007779	580440	580490
UN	683	.	NC_007779	607325	608476
UN	684	.	NC_007779	654214	655412
UN	685	.	NC_007779	688366	689375
UN	686	.	NC_007779	730322	730466
UN	687	.	NC_007779	730827	730860
UN	688	.	NC_007779	732510	732614
UN	689	.	NC_007779	733123	733151
UN	690	.	NC_007779	734995	735022
UN	691	.	NC_007779	1050345	1050399
UN	692	.	NC_007779	1050560	1050736
UN	693	.	NC_007779	1094763	1095829
UN	694	.	NC_007779	1105718	1106862
UN	695	.	NC_007779	1270768	1270799
UN	696	.	NC_007779	1271838	1271869
UN	697	.	NC_007779	1288372	1288460
UN	698	.	NC_007779	1301041	1302376
UN	699	.	NC_007779	1397851	1398859
UN	700	.	NC_007779	1413639	1436698
UN	701	.	NC_007779	1469720	1470864
UN	702	.	NC_007779	1471108	1472138
UN	703	.	NC_007779	1530138	1530792
UN	704	.	NC_007779	1533980	1534024
UN	705	.	NC_007779	1572478	1572486
UN	706	.	NC_007779	1572677	1572963
UN	707	.	NC_007779	1573215	1573420
UN	708	.	NC_007779	1634760	1634840
UN	709	.	NC_007779	1635028	1635244
UN	710	.	NC_007779	1635440	1635540
UN	711	.	NC_007779	1635910	1636254
UN	712	.	NC_007779	1636450	1636638
UN	713	.	NC_007779	1637648	1637699
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UN	715	.	NC_007779	1980303	1981310
UN	716	.	NC_007779	2068409	2068504
UN	717	.	NC_007779	2068701	2068747
UN	718	.	NC_007779	2068961	2069339
UN	719	.	NC_007779	2071175	2072318
UN	720	.	NC_007779	2103980	2104987
UN	721	.	NC_007779	2172403	2173467
UN	722	.	NC_007779	2176983	2178208
UN	723	.	NC_007779	2292347	2293350
UN	724	.	NC_007779	2308005	2308023
UN	725	.	NC_007779	2308231	2308249
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UN	727	.	NC_007779	2411554	2412126
UN	728	.	NC_007779	2519817	2520966
UN	729	.	NC_007779	2724814	2727806
UN	730	.	NC_007779	2728091	2728121
UN	731	.	NC_007779	2728321	2729507
UN	732	.	NC_007779	2729833	2729930
UN	733	.	NC_007779	2995113	2996257
UN	734	.	NC_007779	3128895	3147473
UN	735	.	NC_007779	3184842	3185985
UN	736	.	NC_007779	3261134	3262337
UN	737	.	NC_007779	3365505	3366515
UN	738	.	NC_007779	3423615	3424411
UN	739	.	NC_007779	3424606	3426563
UN	740	.	NC_007779	3426758	3426848
UN	741	.	NC_007779	3427045	3428592
UN	742	.	NC_007779	3459669	3460042
UN	743	.	NC_007779	3460237	3460349
UN	744	.	NC_007779	3465131	3468011
UN	745	.	NC_007779	3468301	3468330
UN	746	.	NC_007779	3468559	3470289
UN	747	.	NC_007779	3596171	3597191
UN	748	.	NC_007779	3597394	3597855
UN	749	.	NC_007779	3598088	3598748
UN	750	.	NC_007779	3598944	3599186
UN	751	.	NC_007779	3599298	3599491
UN	752	.	NC_007779	3599687	3600850
UN	753	.	NC_007779	3601045	3601421
UN	754	.	NC_007779	3689826	3689895
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UN	756	.	NC_007779	3690552	3690669
UN	757	.	NC_007779	3690874	3691015
UN	758	.	NC_007779	3691208	3692523
UN	759	.	NC_007779	3692789	3693186
UN	760	.	NC_007779	3693383	3694550
UN	761	.	NC_007779	3694743	3694931
UN	762	.	NC_007779	3742936	3744271
UN	763	.	NC_007779	3746911	3748109
UN	764	.	NC_007779	3750591	3751789
UN	765	.	NC_007779	3874863	3874904
UN	766	.	NC_007779	3875224	3876241
UN	767	.	NC_007779	3876438	3878053
UN	768	.	NC_007779	3958123	3958156
UN	769	.	NC_007779	3973174	3973377
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UN	773	.	NC_007779	4015543	4015587
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UN	776	.	NC_007779	4019430	4021046
UN	777	.	NC_007779	4056314	4056889
UN	778	.	NC_007779	4169475	4169587
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UN	780	.	NC_007779	4211520	4211763
UN	781	.	NC_007779	4211960	4213508
UN	782	.	NC_007779	4213667	4215789
UN	783	.	NC_007779	4215987	4216658
UN	784	.	NC_007779	4299523	4299550
UN	785	.	NC_007779	4299749	4299777
UN	786	.	NC_007779	4310363	4311561
UN	787	.	NC_007779	4502953	4504095
UN	788	.	NC_007779	4512231	4513265