#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	20:55:42 04 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	6_D10_CAGATC_L003_R1_001.fastq
SNP	1	64	NC_007779	66457	A	frequency=1
SNP	2	68	NC_007779	97880	T	frequency=1
SNP	3	86	NC_007779	167632	A	frequency=1
SNP	4	91	NC_007779	274547	G	frequency=1
DEL	5	509,527	NC_007779	274733	97240	frequency=1
SNP	6	112	NC_007779	547694	G	frequency=1
INS	7	113	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	115	NC_007779	556858	T	frequency=1
SNP	9	117	NC_007779	569996	C	frequency=1
SNP	10	136	NC_007779	749354	A	frequency=1
SNP	11	138	NC_007779	758440	A	frequency=1
SNP	12	146	NC_007779	887234	A	frequency=1
SNP	13	153	NC_007779	987574	T	frequency=1
SNP	14	162	NC_007779	1093686	C	frequency=1
SNP	15	163	NC_007779	1097580	T	frequency=1.657109e-01
SNP	16	173	NC_007779	1170573	T	frequency=1
SNP	17	175	NC_007779	1213001	C	frequency=2.476692e-02
SNP	18	176	NC_007779	1213013	C	frequency=2.580166e-02
SNP	19	177	NC_007779	1213026	T	frequency=2.289200e-02
SNP	20	178	NC_007779	1213028	A	frequency=2.294731e-02
DEL	21	511,539	NC_007779	1301041	1336	frequency=1
SNP	22	189	NC_007779	1318876	A	frequency=1
DEL	23	512,542	NC_007779	1413639	23060	frequency=1
SNP	24	222	NC_007779	1483588	A	frequency=1
DEL	25	223	NC_007779	1496775	1	frequency=1
SNP	26	232	NC_007779	1615814	A	frequency=1
DEL	27	240	NC_007779	1669599	1	frequency=1
SNP	28	256	NC_007779	1844073	A	frequency=1
SNP	29	263	NC_007779	1918872	A	frequency=1
SNP	30	267	NC_007779	1973476	A	frequency=1
SNP	31	269	NC_007779	2005401	T	frequency=1
SNP	32	274	NC_007779	2170094	A	frequency=1
DEL	33	514,551	NC_007779	2320795	1336	frequency=1
SNP	34	296	NC_007779	2406075	T	frequency=1
SNP	35	299	NC_007779	2416102	A	frequency=1
SNP	36	307	NC_007779	2538628	T	frequency=1
INS	37	556	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=5.682425e-01
INS	38	557	NC_007779	2865278	TTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACGGCGC	frequency=2.189781e-01
SNP	39	325	NC_007779	2866111	G	frequency=1
SNP	40	334	NC_007779	3003330	A	frequency=1
SNP	41	340	NC_007779	3049815	T	frequency=1
SNP	42	373	NC_007779	3397813	G	frequency=1
DEL	43	517,566	NC_007779	3742936	1336	frequency=1
DEL	44	518,568	NC_007779	3746911	1199	frequency=1
DEL	45	414	NC_007779	3750122	1	frequency=9.573641e-01
SNP	46	415	NC_007779	3750123	T	frequency=4.310417e-02
DEL	47	519,571	NC_007779	3750591	1199	frequency=1
SNP	48	433	NC_007779	3898657	G	frequency=1
DEL	49	520,573	NC_007779	3958123	34	frequency=1
SNP	50	454	NC_007779	4090749	T	frequency=1
SNP	51	465	NC_007779	4165991	C	frequency=1
DEL	52	521,576	NC_007779	4310363	1199	frequency=1
SNP	53	482	NC_007779	4353540	C	frequency=1.054955e-02
DEL	54	483,484	NC_007779	4371271	2	frequency=1
SNP	55	495	NC_007779	4546535	A	frequency=1
RA	56	.	NC_007779	301	1	.	T	bias_e_value=3497320	bias_p_value=0.752707	fisher_strand_p_value=0.410667	frequency=2.165985e-02	genotype_quality=1282.1	ks_quality_p_value=0.938059	log10_base_likelihood=-25.6765	log10_qual_likelihood_position_model=4.61182	log10_strand_likelihood_position_model=0.697199	new_cov=1/5	polymorphism_quality=20.4	quality=20.4	quality_position_model=1.51928e-22	ref_cov=106/165	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/170
RA	57	.	NC_007779	5595	0	G	T	bias_e_value=111.2	bias_p_value=2.39328e-05	fisher_strand_p_value=1.67356e-06	frequency=4.530811e-02	genotype_quality=819.5	ks_quality_p_value=1	log10_base_likelihood=-8.66603	log10_qual_likelihood_position_model=13.0751	log10_strand_likelihood_position_model=5.80619	new_cov=0/20	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=123/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/139
RA	58	.	NC_007779	11143	0	G	T	bias_e_value=0.00140763	bias_p_value=3.02956e-10	fisher_strand_p_value=1.15709e-11	frequency=6.362200e-02	genotype_quality=982.8	ks_quality_p_value=1	log10_base_likelihood=-11.7933	log10_qual_likelihood_position_model=25.9751	log10_strand_likelihood_position_model=10.9366	new_cov=0/32	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=158/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/148
RA	59	.	NC_007779	17050	0	A	C	bias_e_value=1.50232e-08	bias_p_value=3.23334e-15	fisher_strand_p_value=8.50814e-17	frequency=1.279850e-01	genotype_quality=542.7	ks_quality_p_value=1	log10_base_likelihood=-10.4576	log10_qual_likelihood_position_model=26.5021	log10_strand_likelihood_position_model=16.0702	new_cov=0/41	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=102/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=102/92
RA	60	.	NC_007779	29486	0	C	A	bias_e_value=376.415	bias_p_value=8.10133e-05	fisher_strand_p_value=6.23915e-06	frequency=4.369831e-02	genotype_quality=827.4	ks_quality_p_value=1	log10_base_likelihood=-7.44309	log10_qual_likelihood_position_model=13.3623	log10_strand_likelihood_position_model=5.20487	new_cov=0/12	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=131/70	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/82
RA	61	.	NC_007779	29496	0	T	A	bias_e_value=369.229	bias_p_value=7.94668e-05	fisher_strand_p_value=6.11022e-06	frequency=6.047010e-02	genotype_quality=772.8	ks_quality_p_value=1	log10_base_likelihood=-9.75611	log10_qual_likelihood_position_model=25.724	log10_strand_likelihood_position_model=5.22965	new_cov=1/16	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=138/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/103
RA	62	.	NC_007779	34111	1	.	T	bias_e_value=1334210	bias_p_value=0.287152	fisher_strand_p_value=0.232155	frequency=2.307701e-02	genotype_quality=1227.2	ks_quality_p_value=0.353328	log10_base_likelihood=-27.3109	log10_qual_likelihood_position_model=3.2276	log10_strand_likelihood_position_model=0.849183	new_cov=5/1	polymorphism_quality=22.1	quality=22.1	quality_position_model=1.93622e-25	ref_cov=140/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/115
RA	63	.	NC_007779	47305	0	G	T	bias_e_value=1.52622e-05	bias_p_value=3.28478e-12	fisher_strand_p_value=1.06401e-13	frequency=9.782934e-02	genotype_quality=744.4	ks_quality_p_value=1	log10_base_likelihood=-16.2256	log10_qual_likelihood_position_model=23.5223	log10_strand_likelihood_position_model=12.9731	new_cov=0/35	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=127/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/113
RA	64	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=917.0	new_cov=122/107	quality=917.0	ref_cov=0/0	tot_cov=122/107
RA	65	.	NC_007779	70602	0	G	T	bias_e_value=2.79871e-08	bias_p_value=6.02348e-15	fisher_strand_p_value=1.61212e-16	frequency=8.900738e-02	genotype_quality=945.7	ks_quality_p_value=1	log10_base_likelihood=-19.1251	log10_qual_likelihood_position_model=33.0743	log10_strand_likelihood_position_model=15.7926	new_cov=0/40	polymorphism_quality=13.8	quality=13.8	quality_position_model=Inf	ref_cov=164/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/132
RA	66	.	NC_007779	75074	0	T	G	bias_e_value=3.7649e-19	bias_p_value=8.10295e-26	fisher_strand_p_value=1.28788e-27	frequency=1.930342e-01	genotype_quality=551.3	ks_quality_p_value=1	log10_base_likelihood=-33.5732	log10_qual_likelihood_position_model=38.3065	log10_strand_likelihood_position_model=26.8901	new_cov=50/0	polymorphism_quality=28.4	quality=28.4	quality_position_model=Inf	ref_cov=27/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=77/122
RA	67	.	NC_007779	84006	0	T	.	bias_e_value=943342	bias_p_value=0.203029	fisher_strand_p_value=0.104742	frequency=2.346516e-02	genotype_quality=849.0	ks_quality_p_value=0.487734	log10_base_likelihood=-14.8488	log10_qual_likelihood_position_model=2.15937	log10_strand_likelihood_position_model=1.04864	new_cov=3/2	polymorphism_quality=9.5	quality=9.5	quality_position_model=1.06307e-13	ref_cov=51/157	reject=INDEL_HOMOPOLYMER	tot_cov=54/159
RA	68	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=856.0	new_cov=99/113	quality=856.0	ref_cov=0/0	tot_cov=99/113
RA	69	.	NC_007779	101246	0	T	G	bias_e_value=8.45019	bias_p_value=1.81868e-06	fisher_strand_p_value=1.07202e-07	frequency=7.209349e-02	genotype_quality=440.7	ks_quality_p_value=0.994791	log10_base_likelihood=-20.739	log10_qual_likelihood_position_model=10.736	log10_strand_likelihood_position_model=6.9698	new_cov=9/0	polymorphism_quality=15.5	quality=15.5	quality_position_model=8.07441e-05	ref_cov=15/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=24/98
RA	70	.	NC_007779	107544	1	.	T	bias_e_value=2594610	bias_p_value=0.558422	fisher_strand_p_value=0.23927	frequency=9.614944e-03	genotype_quality=1008.1	ks_quality_p_value=0.93421	log10_base_likelihood=-7.73438	log10_qual_likelihood_position_model=1.80152	log10_strand_likelihood_position_model=0.621112	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=3.29241e-07	ref_cov=100/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=102/106
RA	71	.	NC_007779	119384	0	T	G	bias_e_value=1.63582e-09	bias_p_value=3.52066e-16	fisher_strand_p_value=8.74079e-18	frequency=8.514452e-02	genotype_quality=756.5	ks_quality_p_value=1	log10_base_likelihood=-10.8505	log10_qual_likelihood_position_model=31.891	log10_strand_likelihood_position_model=17.0584	new_cov=42/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=72/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/143
RA	72	.	NC_007779	134366	0	G	T	bias_e_value=1.72518	bias_p_value=3.713e-07	fisher_strand_p_value=1.98167e-08	frequency=4.512978e-02	genotype_quality=853.6	ks_quality_p_value=1	log10_base_likelihood=-8.51455	log10_qual_likelihood_position_model=16.1805	log10_strand_likelihood_position_model=7.70297	new_cov=0/21	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=143/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/118
RA	73	.	NC_007779	149550	1	.	T	bias_e_value=3203930	bias_p_value=0.689562	fisher_strand_p_value=0.502743	frequency=7.017136e-03	genotype_quality=1395.4	ks_quality_p_value=0.645189	log10_base_likelihood=-8.04848	log10_qual_likelihood_position_model=2.70404	log10_strand_likelihood_position_model=0.524707	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.06935e-06	ref_cov=154/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/129
RA	74	.	NC_007779	150535	0	G	A	bias_e_value=200513	bias_p_value=0.0431552	fisher_strand_p_value=0.00728782	frequency=2.610493e-02	genotype_quality=980.9	ks_quality_p_value=1	log10_base_likelihood=-5.91746	log10_qual_likelihood_position_model=10.8358	log10_strand_likelihood_position_model=2.31603	new_cov=8/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=119/117	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=127/118
RA	75	.	NC_007779	150546	0	A	C	bias_e_value=6270.56	bias_p_value=0.00134957	fisher_strand_p_value=0.000136379	frequency=4.704905e-02	genotype_quality=843.7	ks_quality_p_value=0.999517	log10_base_likelihood=-14.0666	log10_qual_likelihood_position_model=16.4592	log10_strand_likelihood_position_model=3.86525	new_cov=12/0	polymorphism_quality=8.7	quality=8.7	quality_position_model=Inf	ref_cov=100/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/117
RA	76	.	NC_007779	150548	0	A	T	bias_e_value=171553	bias_p_value=0.0369222	fisher_strand_p_value=0.00605104	frequency=2.778721e-02	genotype_quality=852.9	ks_quality_p_value=0.998879	log10_base_likelihood=-6.91302	log10_qual_likelihood_position_model=10.8741	log10_strand_likelihood_position_model=2.21817	new_cov=7/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=104/116	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=111/117
RA	77	.	NC_007779	150550	0	C	T	bias_e_value=167292	bias_p_value=0.0360051	fisher_strand_p_value=0.00586526	frequency=2.675819e-02	genotype_quality=911.6	ks_quality_p_value=1	log10_base_likelihood=-7.7236	log10_qual_likelihood_position_model=8.93743	log10_strand_likelihood_position_model=2.23171	new_cov=7/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=104/117	reject=POLYMORPHISM_STRAND	tot_cov=111/117
RA	78	.	NC_007779	150551	0	A	T	bias_e_value=11900	bias_p_value=0.00256116	fisher_strand_p_value=0.000278846	frequency=4.071617e-02	genotype_quality=851.0	ks_quality_p_value=1	log10_base_likelihood=-9.76239	log10_qual_likelihood_position_model=15.0536	log10_strand_likelihood_position_model=3.55464	new_cov=11/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=100/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/117
RA	79	.	NC_007779	150552	0	G	C	bias_e_value=5943.81	bias_p_value=0.00127925	fisher_strand_p_value=0.0001285	frequency=3.970146e-02	genotype_quality=888.8	ks_quality_p_value=0.999513	log10_base_likelihood=-8.98363	log10_qual_likelihood_position_model=16.5047	log10_strand_likelihood_position_model=3.8911	new_cov=12/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=99/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/117
RA	80	.	NC_007779	150553	0	A	T	bias_e_value=45710.4	bias_p_value=0.00983796	fisher_strand_p_value=0.00129224	frequency=3.165913e-02	genotype_quality=812.5	ks_quality_p_value=0.994249	log10_base_likelihood=-6.31796	log10_qual_likelihood_position_model=13.3669	log10_strand_likelihood_position_model=2.88866	new_cov=9/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=102/117	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=111/117
RA	81	.	NC_007779	150554	0	C	G	bias_e_value=44190.6	bias_p_value=0.00951085	fisher_strand_p_value=0.00123626	frequency=3.105164e-02	genotype_quality=921.0	ks_quality_p_value=0.999636	log10_base_likelihood=-6.78476	log10_qual_likelihood_position_model=11.4463	log10_strand_likelihood_position_model=2.90789	new_cov=9/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=101/117	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=110/117
RA	82	.	NC_007779	150556	0	C	T	bias_e_value=83287.2	bias_p_value=0.0179254	fisher_strand_p_value=0.00257744	frequency=2.487659e-02	genotype_quality=1010.1	ks_quality_p_value=0.998951	log10_base_likelihood=-5.79701	log10_qual_likelihood_position_model=12.3388	log10_strand_likelihood_position_model=2.58881	new_cov=8/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=113/130	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=121/130
RA	83	.	NC_007779	162886	0	C	A	bias_e_value=2.74191	bias_p_value=5.90124e-07	fisher_strand_p_value=3.2341e-08	frequency=4.851484e-02	genotype_quality=752.8	ks_quality_p_value=1	log10_base_likelihood=-7.34956	log10_qual_likelihood_position_model=17.71	log10_strand_likelihood_position_model=7.49025	new_cov=20/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=84/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/130
RA	84	.	NC_007779	164601	0	T	C	bias_e_value=913.374	bias_p_value=0.00019658	fisher_strand_p_value=1.63529e-05	frequency=8.834887e-02	genotype_quality=306.6	ks_quality_p_value=1	log10_base_likelihood=-12.6217	log10_qual_likelihood_position_model=11.2602	log10_strand_likelihood_position_model=4.78641	new_cov=10/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=27/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=37/65
RA	85	.	NC_007779	164603	0	A	C	bias_e_value=6822.58	bias_p_value=0.00146838	fisher_strand_p_value=0.000149733	frequency=5.948114e-02	genotype_quality=307.7	ks_quality_p_value=1	log10_base_likelihood=-7.60756	log10_qual_likelihood_position_model=8.52741	log10_strand_likelihood_position_model=3.82468	new_cov=8/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=28/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=36/65
RA	86	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=959.7	new_cov=108/131	quality=959.7	ref_cov=0/0	tot_cov=108/131
RA	87	.	NC_007779	175694	0	T	G	bias_e_value=3.75312e-08	bias_p_value=8.07761e-15	fisher_strand_p_value=2.17947e-16	frequency=8.101225e-02	genotype_quality=747.5	ks_quality_p_value=1	log10_base_likelihood=-9.4672	log10_qual_likelihood_position_model=25.0789	log10_strand_likelihood_position_model=15.6616	new_cov=41/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=80/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/141
RA	88	.	NC_007779	193480	0	C	G	bias_e_value=17191.8	bias_p_value=0.00370008	fisher_strand_p_value=0.000421862	frequency=3.343010e-02	genotype_quality=689.2	ks_quality_p_value=1	log10_base_likelihood=-6.73475	log10_qual_likelihood_position_model=8.52466	log10_strand_likelihood_position_model=3.37483	new_cov=8/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=65/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=73/114
RA	89	.	NC_007779	193496	0	A	T	bias_e_value=860.109	bias_p_value=0.000185116	fisher_strand_p_value=1.53157e-05	frequency=5.441380e-02	genotype_quality=673.8	ks_quality_p_value=1	log10_base_likelihood=-10.4342	log10_qual_likelihood_position_model=17.5156	log10_strand_likelihood_position_model=4.81486	new_cov=12/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=68/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/113
RA	90	.	NC_007779	207536	0	G	T	bias_e_value=1.3907	bias_p_value=2.99311e-07	fisher_strand_p_value=1.57828e-08	frequency=1.041937e-01	genotype_quality=583.4	ks_quality_p_value=1	log10_base_likelihood=-19.8853	log10_qual_likelihood_position_model=16.882	log10_strand_likelihood_position_model=7.97714	new_cov=0/32	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=93/104	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/136
RA	91	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1048.4	new_cov=128/119	quality=1048.4	ref_cov=0/1	tot_cov=128/120
RA	92	.	NC_007779	331662	0	G	A	deleted=1	frequency=1	genotype_quality=1.4	new_cov=0/1	quality=1.4	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	93	.	NC_007779	365410	0	G	T	deleted=1	frequency=1	genotype_quality=0.7	new_cov=0/1	quality=0.7	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	94	.	NC_007779	365514	0	C	T	deleted=1	frequency=1	genotype_quality=3.9	new_cov=0/1	quality=3.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	95	.	NC_007779	379236	1	.	G	bias_e_value=3890050	bias_p_value=0.83723	fisher_strand_p_value=1	frequency=1.204777e-02	genotype_quality=795.3	ks_quality_p_value=0.486775	log10_base_likelihood=-8.57513	log10_qual_likelihood_position_model=1.58389	log10_strand_likelihood_position_model=0.343051	new_cov=2/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=1.36579e-08	ref_cov=110/54	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/54
RA	96	.	NC_007779	379237	0	G	.	bias_e_value=409453	bias_p_value=0.0881239	fisher_strand_p_value=0.702669	frequency=3.803730e-02	genotype_quality=741.5	ks_quality_p_value=0.0248441	log10_base_likelihood=-23.5993	log10_qual_likelihood_position_model=3.52777	log10_strand_likelihood_position_model=0.555635	new_cov=4/3	polymorphism_quality=18.3	quality=18.3	quality_position_model=1.10233e-21	ref_cov=114/63	reject=INDEL_HOMOPOLYMER	tot_cov=118/66
RA	97	.	NC_007779	379266	0	G	C	bias_e_value=5889.42	bias_p_value=0.00126754	fisher_strand_p_value=0.000149806	frequency=5.063438e-02	genotype_quality=599.4	ks_quality_p_value=0.848645	log10_base_likelihood=-6.61157	log10_qual_likelihood_position_model=19.033	log10_strand_likelihood_position_model=3.84858	new_cov=14/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=90/86	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=104/86
RA	98	.	NC_007779	387560	0	A	C	bias_e_value=0.0019254	bias_p_value=4.14391e-10	fisher_strand_p_value=1.60264e-11	frequency=6.614685e-02	genotype_quality=701.9	ks_quality_p_value=1	log10_base_likelihood=-7.41289	log10_qual_likelihood_position_model=25.76	log10_strand_likelihood_position_model=10.8505	new_cov=0/36	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=116/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/135
RA	99	.	NC_007779	387917	0	T	G	bias_e_value=231.392	bias_p_value=4.98011e-05	fisher_strand_p_value=3.68597e-06	frequency=4.413509e-02	genotype_quality=398.9	ks_quality_p_value=1	log10_base_likelihood=-6.47661	log10_qual_likelihood_position_model=9.14963	log10_strand_likelihood_position_model=5.43933	new_cov=1/7	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=109/12	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/19
RA	100	.	NC_007779	387919	0	A	G	bias_e_value=0.0619965	bias_p_value=1.33431e-08	fisher_strand_p_value=6.00125e-10	frequency=6.339645e-02	genotype_quality=418.4	ks_quality_p_value=1	log10_base_likelihood=-8.81652	log10_qual_likelihood_position_model=11.9	log10_strand_likelihood_position_model=9.22176	new_cov=0/9	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=112/7	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=112/16
RA	101	.	NC_007779	417763	0	G	T	bias_e_value=6129.08	bias_p_value=0.00131912	fisher_strand_p_value=0.000132897	frequency=2.838230e-02	genotype_quality=660.5	ks_quality_p_value=1	log10_base_likelihood=-5.8204	log10_qual_likelihood_position_model=9.39918	log10_strand_likelihood_position_model=3.87649	new_cov=0/11	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=110/82	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/93
RA	102	.	NC_007779	440767	0	G	T	bias_e_value=0.000132567	bias_p_value=2.85315e-11	fisher_strand_p_value=9.96399e-13	frequency=1.155066e-01	genotype_quality=722.6	ks_quality_p_value=1	log10_base_likelihood=-15.586	log10_qual_likelihood_position_model=24.6001	log10_strand_likelihood_position_model=12.024	new_cov=1/39	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=127/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/127
RA	103	.	NC_007779	467487	1	.	T	bias_e_value=4645620	bias_p_value=0.999848	fisher_strand_p_value=1	frequency=1.209545e-02	genotype_quality=1195.8	ks_quality_p_value=0.982598	log10_base_likelihood=-11.7206	log10_qual_likelihood_position_model=2.62135	log10_strand_likelihood_position_model=0.364971	new_cov=1/2	polymorphism_quality=6.3	quality=6.3	quality_position_model=9.84033e-11	ref_cov=100/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=101/147
RA	104	.	NC_007779	474686	0	G	T	bias_e_value=0.171778	bias_p_value=3.69708e-08	fisher_strand_p_value=1.74675e-09	frequency=7.167959e-02	genotype_quality=707.2	ks_quality_p_value=1	log10_base_likelihood=-14.587	log10_qual_likelihood_position_model=22.0319	log10_strand_likelihood_position_model=8.75777	new_cov=0/26	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=122/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/120
RA	105	.	NC_007779	484534	0	T	C	bias_e_value=375972	bias_p_value=0.0809179	fisher_strand_p_value=0.0157882	frequency=2.576256e-02	genotype_quality=928.0	ks_quality_p_value=0.994392	log10_base_likelihood=-7.54608	log10_qual_likelihood_position_model=10.3093	log10_strand_likelihood_position_model=1.94181	new_cov=7/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=128/118	reject=POLYMORPHISM_STRAND	tot_cov=135/118
RA	106	.	NC_007779	506363	1	.	A	bias_e_value=2076080	bias_p_value=0.44682	fisher_strand_p_value=0.227058	frequency=8.928299e-03	genotype_quality=1099.6	ks_quality_p_value=0.689393	log10_base_likelihood=-8.30795	log10_qual_likelihood_position_model=1.79546	log10_strand_likelihood_position_model=0.643863	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=8.71785e-08	ref_cov=117/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/107
RA	107	.	NC_007779	513848	0	A	C	bias_e_value=4.81695e-11	bias_p_value=1.03672e-17	fisher_strand_p_value=2.36211e-19	frequency=1.305881e-01	genotype_quality=554.3	ks_quality_p_value=1	log10_base_likelihood=-12.6645	log10_qual_likelihood_position_model=27.4996	log10_strand_likelihood_position_model=18.6267	new_cov=0/38	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=113/36	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/74
RA	108	.	NC_007779	522430	1	.	T	bias_e_value=3845570	bias_p_value=0.827657	fisher_strand_p_value=0.623117	frequency=1.904774e-02	genotype_quality=1008.6	ks_quality_p_value=0.760248	log10_base_likelihood=-17.6115	log10_qual_likelihood_position_model=2.24924	log10_strand_likelihood_position_model=0.562096	new_cov=3/1	polymorphism_quality=12.3	quality=12.3	quality_position_model=6.55618e-17	ref_cov=107/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/100
RA	109	.	NC_007779	522431	0	T	.	bias_e_value=852452	bias_p_value=0.183468	fisher_strand_p_value=0.670685	frequency=2.380180e-02	genotype_quality=838.4	ks_quality_p_value=0.0665762	log10_base_likelihood=-15.3922	log10_qual_likelihood_position_model=2.56772	log10_strand_likelihood_position_model=0.524586	new_cov=2/3	polymorphism_quality=10.0	quality=10.0	quality_position_model=2.26934e-14	ref_cov=108/97	reject=INDEL_HOMOPOLYMER	tot_cov=110/100
RA	110	.	NC_007779	524490	0	T	G	bias_e_value=11.9848	bias_p_value=2.5794e-06	fisher_strand_p_value=1.54619e-07	frequency=6.607771e-02	genotype_quality=599.6	ks_quality_p_value=1	log10_base_likelihood=-9.92428	log10_qual_likelihood_position_model=16.5986	log10_strand_likelihood_position_model=6.81074	new_cov=15/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=54/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=69/114
RA	111	.	NC_007779	544570	0	A	C	bias_e_value=239136	bias_p_value=0.0514676	fisher_strand_p_value=0.00901546	frequency=2.346992e-02	genotype_quality=1021.1	ks_quality_p_value=1	log10_base_likelihood=-10.1775	log10_qual_likelihood_position_model=10.0202	log10_strand_likelihood_position_model=2.1249	new_cov=8/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=139/121	reject=POLYMORPHISM_STRAND	tot_cov=147/121
RA	112	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=985.2	new_cov=120/115	quality=985.2	ref_cov=0/0	tot_cov=120/115
RA	113	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=916.9	new_cov=99/115	quality=916.9	ref_cov=0/1	tot_cov=99/117
RA	114	.	NC_007779	556653	0	A	C	bias_e_value=2.22636e-06	bias_p_value=4.79164e-13	fisher_strand_p_value=1.45825e-14	frequency=7.712030e-02	genotype_quality=545.4	ks_quality_p_value=1	log10_base_likelihood=-5.9686	log10_qual_likelihood_position_model=21.7326	log10_strand_likelihood_position_model=13.8362	new_cov=0/25	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=114/32	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/57
RA	115	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=969.4	new_cov=119/123	quality=969.4	ref_cov=0/0	tot_cov=119/123
RA	116	.	NC_007779	562836	0	C	A	bias_e_value=116404	bias_p_value=0.0250528	fisher_strand_p_value=0.0038137	frequency=3.165245e-02	genotype_quality=704.6	ks_quality_p_value=1	log10_base_likelihood=-6.04698	log10_qual_likelihood_position_model=10.8525	log10_strand_likelihood_position_model=2.41865	new_cov=0/7	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=96/75	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=96/82
RA	117	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1183.1	new_cov=130/139	quality=1183.1	ref_cov=0/0	tot_cov=130/139
RA	118	.	NC_007779	583702	1	.	T	bias_e_value=4271910	bias_p_value=0.919415	fisher_strand_p_value=1	frequency=1.142788e-02	genotype_quality=859.0	ks_quality_p_value=0.626413	log10_base_likelihood=-7.68792	log10_qual_likelihood_position_model=2.7354	log10_strand_likelihood_position_model=0.301744	new_cov=1/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.60412e-06	ref_cov=94/79	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/80
RA	119	.	NC_007779	589157	0	T	G	bias_e_value=4.04541e-08	bias_p_value=8.70667e-15	fisher_strand_p_value=2.3541e-16	frequency=1.093726e-01	genotype_quality=576.5	ks_quality_p_value=1	log10_base_likelihood=-10.7761	log10_qual_likelihood_position_model=34.6863	log10_strand_likelihood_position_model=15.6282	new_cov=36/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=49/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=85/114
RA	120	.	NC_007779	593216	0	T	G	bias_e_value=0.00086114	bias_p_value=1.85338e-10	fisher_strand_p_value=6.97655e-12	frequency=5.273485e-02	genotype_quality=578.7	ks_quality_p_value=0.995224	log10_base_likelihood=-5.83586	log10_qual_likelihood_position_model=18.0447	log10_strand_likelihood_position_model=11.1564	new_cov=15/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=21/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/130
RA	121	.	NC_007779	598799	0	T	G	bias_e_value=1.53507e-19	bias_p_value=3.30383e-26	fisher_strand_p_value=5.17611e-28	frequency=2.140188e-01	genotype_quality=432.5	ks_quality_p_value=1	log10_base_likelihood=-30.0008	log10_qual_likelihood_position_model=32.7236	log10_strand_likelihood_position_model=27.286	new_cov=43/0	polymorphism_quality=24.8	quality=24.8	quality_position_model=Inf	ref_cov=13/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=56/106
RA	122	.	NC_007779	606911	1	.	G	bias_e_value=164786	bias_p_value=0.0354659	fisher_strand_p_value=0.0210996	frequency=2.336407e-02	genotype_quality=1038.2	ks_quality_p_value=0.273016	log10_base_likelihood=-22.83	log10_qual_likelihood_position_model=1.90708	log10_strand_likelihood_position_model=1.67573	new_cov=5/0	polymorphism_quality=17.6	quality=17.6	quality_position_model=2.0604e-21	ref_cov=95/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=100/114
RA	123	.	NC_007779	631234	0	G	.	bias_e_value=1534890	bias_p_value=0.330344	fisher_strand_p_value=0.603487	frequency=1.199150e-02	genotype_quality=1042.0	ks_quality_p_value=0.165765	log10_base_likelihood=-8.23762	log10_qual_likelihood_position_model=3.01267	log10_strand_likelihood_position_model=0.450828	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.19301e-06	ref_cov=131/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/118
RA	124	.	NC_007779	645970	0	T	G	bias_e_value=4.69142e-12	bias_p_value=1.0097e-18	fisher_strand_p_value=2.18214e-20	frequency=1.352949e-01	genotype_quality=577.7	ks_quality_p_value=1	log10_base_likelihood=-23.2353	log10_qual_likelihood_position_model=28.301	log10_strand_likelihood_position_model=19.6611	new_cov=29/0	polymorphism_quality=18.0	quality=18.0	quality_position_model=Inf	ref_cov=20/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/127
RA	125	.	NC_007779	646440	0	C	A	bias_e_value=0.0913159	bias_p_value=1.96533e-08	fisher_strand_p_value=9.00363e-10	frequency=4.570770e-02	genotype_quality=699.1	ks_quality_p_value=1	log10_base_likelihood=-11.0283	log10_qual_likelihood_position_model=13.3377	log10_strand_likelihood_position_model=9.04558	new_cov=0/9	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=153/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/21
RA	126	.	NC_007779	657963	1	.	T	bias_e_value=4094130	bias_p_value=0.881153	fisher_strand_p_value=1	frequency=8.695602e-03	genotype_quality=1104.8	ks_quality_p_value=0.553943	log10_base_likelihood=-8.24359	log10_qual_likelihood_position_model=1.47359	log10_strand_likelihood_position_model=0.299433	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.08232e-08	ref_cov=111/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/118
RA	127	.	NC_007779	657964	0	T	.	bias_e_value=3269600	bias_p_value=0.703695	fisher_strand_p_value=1	frequency=1.679611e-02	genotype_quality=874.4	ks_quality_p_value=0.337137	log10_base_likelihood=-11.1894	log10_qual_likelihood_position_model=2.77226	log10_strand_likelihood_position_model=0.422296	new_cov=2/2	polymorphism_quality=5.8	quality=5.8	quality_position_model=5.63331e-10	ref_cov=117/117	reject=INDEL_HOMOPOLYMER	tot_cov=119/119
RA	128	.	NC_007779	660356	0	T	G	bias_e_value=6.07874e-12	bias_p_value=1.30829e-18	fisher_strand_p_value=2.8437e-20	frequency=1.579647e-01	genotype_quality=545.4	ks_quality_p_value=1	log10_base_likelihood=-17.0792	log10_qual_likelihood_position_model=31.9701	log10_strand_likelihood_position_model=19.5461	new_cov=46/0	polymorphism_quality=11.8	quality=11.8	quality_position_model=Inf	ref_cov=44/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/109
RA	129	.	NC_007779	667452	0	G	T	bias_e_value=168316	bias_p_value=0.0362255	fisher_strand_p_value=0.00590819	frequency=3.761387e-02	genotype_quality=801.8	ks_quality_p_value=1	log10_base_likelihood=-9.78412	log10_qual_likelihood_position_model=11.8637	log10_strand_likelihood_position_model=2.38037	new_cov=10/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=111/85	reject=POLYMORPHISM_STRAND	tot_cov=121/85
RA	130	.	NC_007779	685600	0	T	.	bias_e_value=2359200	bias_p_value=0.507755	fisher_strand_p_value=1	frequency=4.495621e-03	genotype_quality=2622.3	ks_quality_p_value=0.191337	log10_base_likelihood=-6.80736	log10_qual_likelihood_position_model=2.17521	log10_strand_likelihood_position_model=0.372432	new_cov=1/2	polymorphism_quality=1.3	quality=1.3	quality_position_model=4.11003e-06	ref_cov=279/383	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=281/385
RA	131	.	NC_007779	686495	0	A	C	bias_e_value=9.0505e-36	bias_p_value=1.94788e-42	fisher_strand_p_value=1.91601e-44	frequency=1.320844e-01	genotype_quality=1408.8	ks_quality_p_value=1	log10_base_likelihood=-55.1953	log10_qual_likelihood_position_model=70.8726	log10_strand_likelihood_position_model=43.7176	new_cov=0/72	polymorphism_quality=50.1	quality=50.1	quality_position_model=Inf	ref_cov=301/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=302/137
RA	132	.	NC_007779	687133	0	A	C	bias_e_value=3.08033e-06	bias_p_value=6.6296e-13	fisher_strand_p_value=2.03837e-14	frequency=2.895927e-02	genotype_quality=1946.6	ks_quality_p_value=1	log10_base_likelihood=-15.6334	log10_qual_likelihood_position_model=34.0161	log10_strand_likelihood_position_model=13.6961	new_cov=1/27	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=388/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=389/165
RA	133	.	NC_007779	704668	0	T	G	bias_e_value=7.30108e-08	bias_p_value=1.57136e-14	fisher_strand_p_value=4.31952e-16	frequency=7.764196e-02	genotype_quality=566.2	ks_quality_p_value=1	log10_base_likelihood=-7.62426	log10_qual_likelihood_position_model=23.7165	log10_strand_likelihood_position_model=15.3646	new_cov=24/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=26/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=50/127
RA	134	.	NC_007779	706385	1	.	T	bias_e_value=4567040	bias_p_value=0.982935	fisher_strand_p_value=1	frequency=1.879692e-02	genotype_quality=1260.8	ks_quality_p_value=0.821036	log10_base_likelihood=-22.1993	log10_qual_likelihood_position_model=3.40387	log10_strand_likelihood_position_model=0.464579	new_cov=2/3	polymorphism_quality=16.9	quality=16.9	quality_position_model=1.74045e-20	ref_cov=115/146	reject=INDEL_HOMOPOLYMER	tot_cov=117/149
RA	135	.	NC_007779	730377	0	C	A	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	136	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=898.7	new_cov=94/126	quality=898.7	ref_cov=0/0	tot_cov=94/126
RA	137	.	NC_007779	752693	0	A	C	bias_e_value=3.56965e-05	bias_p_value=7.68273e-12	fisher_strand_p_value=2.56151e-13	frequency=7.756281e-02	genotype_quality=819.7	ks_quality_p_value=1	log10_base_likelihood=-12.5115	log10_qual_likelihood_position_model=26.5135	log10_strand_likelihood_position_model=12.5915	new_cov=0/26	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=162/66	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/93
RA	138	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=872.2	new_cov=100/116	quality=872.2	ref_cov=0/0	tot_cov=100/116
RA	139	.	NC_007779	759019	0	C	G	bias_e_value=1.18409e-06	bias_p_value=2.54844e-13	fisher_strand_p_value=7.60501e-15	frequency=7.394171e-02	genotype_quality=619.4	ks_quality_p_value=1	log10_base_likelihood=-18.8616	log10_qual_likelihood_position_model=15.9988	log10_strand_likelihood_position_model=14.1189	new_cov=0/12	polymorphism_quality=13.6	quality=13.6	quality_position_model=Inf	ref_cov=138/4	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=138/16
RA	140	.	NC_007779	796581	0	G	T	bias_e_value=1.28989	bias_p_value=2.77614e-07	fisher_strand_p_value=1.45777e-08	frequency=6.387234e-02	genotype_quality=713.9	ks_quality_p_value=1	log10_base_likelihood=-6.49234	log10_qual_likelihood_position_model=19.2285	log10_strand_likelihood_position_model=7.83631	new_cov=0/24	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=119/94	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/118
RA	141	.	NC_007779	829585	0	G	T	bias_e_value=12215.1	bias_p_value=0.00262897	fisher_strand_p_value=0.000291451	frequency=3.963757e-02	genotype_quality=579.1	ks_quality_p_value=0.985229	log10_base_likelihood=-7.4892	log10_qual_likelihood_position_model=10.7221	log10_strand_likelihood_position_model=3.53543	new_cov=8/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=55/105	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=63/105
RA	142	.	NC_007779	835703	0	C	A	bias_e_value=140.382	bias_p_value=3.02134e-05	fisher_strand_p_value=2.15045e-06	frequency=4.710007e-02	genotype_quality=742.8	ks_quality_p_value=1	log10_base_likelihood=-7.76053	log10_qual_likelihood_position_model=17.3535	log10_strand_likelihood_position_model=5.76331	new_cov=19/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=103/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/114
RA	143	.	NC_007779	853114	0	C	G	bias_e_value=120918	bias_p_value=0.0260244	fisher_strand_p_value=0.00458431	frequency=2.161980e-02	genotype_quality=722.4	ks_quality_p_value=0.870115	log10_base_likelihood=-7.00209	log10_qual_likelihood_position_model=4.46505	log10_strand_likelihood_position_model=2.33873	new_cov=0/4	polymorphism_quality=1.5	quality=1.5	quality_position_model=0.179964	ref_cov=135/45	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=135/49
RA	144	.	NC_007779	868836	1	.	C	bias_e_value=4646330	bias_p_value=0.999999	fisher_strand_p_value=1	frequency=8.694649e-03	genotype_quality=1122.2	ks_quality_p_value=0.99878	log10_base_likelihood=-7.34313	log10_qual_likelihood_position_model=1.89549	log10_strand_likelihood_position_model=0.301244	new_cov=1/1	polymorphism_quality=1.8	quality=1.8	quality_position_model=4.88931e-07	ref_cov=122/106	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/107
RA	145	.	NC_007779	881118	0	T	.	bias_e_value=4316010	bias_p_value=0.928906	fisher_strand_p_value=1	frequency=1.016045e-02	genotype_quality=1163.0	ks_quality_p_value=0.647452	log10_base_likelihood=-7.80235	log10_qual_likelihood_position_model=2.67458	log10_strand_likelihood_position_model=0.420115	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.39932e-06	ref_cov=145/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/149
RA	146	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=757.6	new_cov=103/98	quality=757.6	ref_cov=0/0	tot_cov=103/98
RA	147	.	NC_007779	895911	0	C	A	bias_e_value=16.7236	bias_p_value=3.5993e-06	fisher_strand_p_value=2.20443e-07	frequency=4.607677e-02	genotype_quality=730.3	ks_quality_p_value=1	log10_base_likelihood=-6.55666	log10_qual_likelihood_position_model=15.147	log10_strand_likelihood_position_model=6.6567	new_cov=19/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=95/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/130
RA	148	.	NC_007779	904838	0	C	A	bias_e_value=1.49204e-06	bias_p_value=3.21122e-13	fisher_strand_p_value=1.12343e-14	frequency=8.138990e-02	genotype_quality=812.0	ks_quality_p_value=0.859112	log10_base_likelihood=-15.0303	log10_qual_likelihood_position_model=27.814	log10_strand_likelihood_position_model=13.9495	new_cov=30/0	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=67/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=97/157
RA	149	.	NC_007779	915697	0	G	T	bias_e_value=25677.8	bias_p_value=0.00552646	fisher_strand_p_value=0.000664522	frequency=3.688908e-02	genotype_quality=664.4	ks_quality_p_value=1	log10_base_likelihood=-6.49066	log10_qual_likelihood_position_model=11.6425	log10_strand_likelihood_position_model=3.44189	new_cov=1/12	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=108/78	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/90
RA	150	.	NC_007779	947970	0	C	A	bias_e_value=496.921	bias_p_value=0.000106949	fisher_strand_p_value=8.43218e-06	frequency=2.994442e-02	genotype_quality=770.1	ks_quality_p_value=1	log10_base_likelihood=-6.15293	log10_qual_likelihood_position_model=10.7866	log10_strand_likelihood_position_model=5.07406	new_cov=16/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=106/123	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/124
RA	151	.	NC_007779	954820	0	A	C	bias_e_value=0.0218874	bias_p_value=4.71068e-09	fisher_strand_p_value=2.01977e-10	frequency=7.518053e-02	genotype_quality=619.9	ks_quality_p_value=1	log10_base_likelihood=-8.42686	log10_qual_likelihood_position_model=22.412	log10_strand_likelihood_position_model=9.70995	new_cov=0/31	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=104/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=104/115
RA	152	.	NC_007779	969494	0	C	A	bias_e_value=0.104772	bias_p_value=2.25494e-08	fisher_strand_p_value=1.04129e-09	frequency=8.050728e-02	genotype_quality=662.7	ks_quality_p_value=0.998673	log10_base_likelihood=-10.1026	log10_qual_likelihood_position_model=19.2954	log10_strand_likelihood_position_model=9.00387	new_cov=29/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=88/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/107
RA	153	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=827.2	new_cov=72/130	quality=827.2	ref_cov=0/0	tot_cov=72/130
RA	154	.	NC_007779	987916	0	T	G	bias_e_value=1.91825e-06	bias_p_value=4.12853e-13	fisher_strand_p_value=1.25059e-14	frequency=9.282875e-02	genotype_quality=538.3	ks_quality_p_value=1	log10_base_likelihood=-11.9892	log10_qual_likelihood_position_model=20.175	log10_strand_likelihood_position_model=13.9029	new_cov=17/0	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=13/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=30/119
RA	155	.	NC_007779	999613	0	A	T	bias_e_value=478514	bias_p_value=0.102987	fisher_strand_p_value=0.0212228	frequency=4.321194e-02	genotype_quality=574.1	ks_quality_p_value=1	log10_base_likelihood=-7.42638	log10_qual_likelihood_position_model=10.2141	log10_strand_likelihood_position_model=1.90803	new_cov=8/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=83/64	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=91/64
RA	156	.	NC_007779	999623	0	A	T	bias_e_value=2075450	bias_p_value=0.446687	fisher_strand_p_value=0.156756	frequency=3.253460e-02	genotype_quality=553.2	ks_quality_p_value=0.998112	log10_base_likelihood=-7.7107	log10_qual_likelihood_position_model=6.21614	log10_strand_likelihood_position_model=1.07499	new_cov=5/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=0.078063	ref_cov=86/57	reject=POLYMORPHISM_STRAND	tot_cov=91/57
RA	157	.	NC_007779	1006080	0	C	A	bias_e_value=0.497026	bias_p_value=1.06972e-07	fisher_strand_p_value=5.33554e-09	frequency=5.420065e-02	genotype_quality=850.1	ks_quality_p_value=1	log10_base_likelihood=-6.49092	log10_qual_likelihood_position_model=19.1147	log10_strand_likelihood_position_model=8.27282	new_cov=24/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=105/142	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/142
RA	158	.	NC_007779	1019391	0	A	.	bias_e_value=1184400	bias_p_value=0.254911	fisher_strand_p_value=0.12953	frequency=1.525688e-02	genotype_quality=1031.7	ks_quality_p_value=0.536828	log10_base_likelihood=-10.938	log10_qual_likelihood_position_model=4.34649	log10_strand_likelihood_position_model=1.04801	new_cov=4/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=1.89281e-07	ref_cov=140/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/118
RA	159	.	NC_007779	1020666	1	.	A	bias_e_value=3954900	bias_p_value=0.851188	fisher_strand_p_value=0.506831	frequency=7.299423e-03	genotype_quality=1361.2	ks_quality_p_value=0.999785	log10_base_likelihood=-7.93732	log10_qual_likelihood_position_model=2.8247	log10_strand_likelihood_position_model=0.496061	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.74152e-06	ref_cov=119/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/155
RA	160	.	NC_007779	1037529	0	T	G	bias_e_value=4460.9	bias_p_value=0.000960091	fisher_strand_p_value=9.3832e-05	frequency=3.100777e-02	genotype_quality=492.9	ks_quality_p_value=0.995474	log10_base_likelihood=-6.93104	log10_qual_likelihood_position_model=5.42602	log10_strand_likelihood_position_model=4.02765	new_cov=4/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=10/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=14/114
RA	161	.	NC_007779	1058914	0	A	C	bias_e_value=5.83395	bias_p_value=1.2556e-06	fisher_strand_p_value=7.20371e-08	frequency=5.096483e-02	genotype_quality=599.8	ks_quality_p_value=0.999018	log10_base_likelihood=-7.0458	log10_qual_likelihood_position_model=17.1659	log10_strand_likelihood_position_model=7.14244	new_cov=0/14	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=117/45	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/59
RA	162	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1206.9	new_cov=113/166	quality=1206.9	ref_cov=0/0	tot_cov=113/166
RA	163	.	NC_007779	1097580	0	C	T	bias_e_value=1458230	bias_p_value=0.313844	fisher_strand_p_value=0.417738	frequency=1.657109e-01	genotype_quality=733.0	ks_quality_p_value=0.222582	log10_base_likelihood=-126.173	log10_qual_likelihood_position_model=15.1036	log10_strand_likelihood_position_model=1.04252	new_cov=22/24	polymorphism_quality=121.3	quality=121.3	quality_position_model=1.44415e-112	ref_cov=95/136	tot_cov=117/161
RA	164	.	NC_007779	1097583	1	.	A	bias_e_value=4528370	bias_p_value=0.974612	fisher_strand_p_value=1	frequency=7.692337e-03	genotype_quality=935.0	ks_quality_p_value=0.783295	log10_base_likelihood=-8.07911	log10_qual_likelihood_position_model=1.58177	log10_strand_likelihood_position_model=0.307763	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.06081e-08	ref_cov=111/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/148
RA	165	.	NC_007779	1115091	0	C	A	bias_e_value=27.8027	bias_p_value=5.98379e-06	fisher_strand_p_value=3.79067e-07	frequency=7.187080e-02	genotype_quality=715.8	ks_quality_p_value=1	log10_base_likelihood=-13.7436	log10_qual_likelihood_position_model=17.3228	log10_strand_likelihood_position_model=6.42128	new_cov=0/16	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=119/70	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/86
RA	166	.	NC_007779	1116582	0	G	C	bias_e_value=2.86256e-12	bias_p_value=6.16089e-19	fisher_strand_p_value=1.32082e-20	frequency=1.461391e-01	genotype_quality=400.4	ks_quality_p_value=0.997185	log10_base_likelihood=-35.3221	log10_qual_likelihood_position_model=16.6239	log10_strand_likelihood_position_model=19.8792	new_cov=0/19	polymorphism_quality=30.2	quality=30.2	quality_position_model=Inf	ref_cov=105/2	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=106/21
RA	167	.	NC_007779	1122800	1	.	A	bias_e_value=4630400	bias_p_value=0.996572	fisher_strand_p_value=1	frequency=8.546829e-03	genotype_quality=1143.7	ks_quality_p_value=0.918351	log10_base_likelihood=-8.15095	log10_qual_likelihood_position_model=1.01526	log10_strand_likelihood_position_model=0.308437	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=8.93027e-09	ref_cov=133/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/100
RA	168	.	NC_007779	1148417	0	C	A	bias_e_value=199.568	bias_p_value=4.29516e-05	fisher_strand_p_value=3.7616e-06	frequency=4.397011e-02	genotype_quality=862.9	ks_quality_p_value=0.83525	log10_base_likelihood=-6.63065	log10_qual_likelihood_position_model=24.7744	log10_strand_likelihood_position_model=5.72318	new_cov=22/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=135/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/120
RA	169	.	NC_007779	1153441	1	.	G	bias_e_value=1695940	bias_p_value=0.365007	fisher_strand_p_value=0.115624	frequency=8.028030e-03	genotype_quality=1220.1	ks_quality_p_value=0.99974	log10_base_likelihood=-6.59167	log10_qual_likelihood_position_model=2.75723	log10_strand_likelihood_position_model=0.936953	new_cov=2/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=0.00011264	ref_cov=83/164	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=85/164
RA	170	.	NC_007779	1155150	0	T	G	bias_e_value=9529.36	bias_p_value=0.00205094	fisher_strand_p_value=0.000217547	frequency=3.903198e-02	genotype_quality=473.2	ks_quality_p_value=0.999344	log10_base_likelihood=-9.59828	log10_qual_likelihood_position_model=6.08676	log10_strand_likelihood_position_model=3.66245	new_cov=5/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=20/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=25/101
RA	171	.	NC_007779	1156695	0	A	.	bias_e_value=4612890	bias_p_value=0.992802	fisher_strand_p_value=1	frequency=1.264954e-02	genotype_quality=951.9	ks_quality_p_value=0.882437	log10_base_likelihood=-8.12848	log10_qual_likelihood_position_model=1.90346	log10_strand_likelihood_position_model=0.418693	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.01129e-07	ref_cov=116/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/120
RA	172	.	NC_007779	1158848	0	T	G	bias_e_value=2.8175e-07	bias_p_value=6.06392e-14	fisher_strand_p_value=1.7331e-15	frequency=1.135602e-01	genotype_quality=626.3	ks_quality_p_value=1	log10_base_likelihood=-15.5768	log10_qual_likelihood_position_model=25.2444	log10_strand_likelihood_position_model=14.7612	new_cov=36/0	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=57/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/118
RA	173	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1195.0	new_cov=193/101	quality=1195.0	ref_cov=0/0	tot_cov=193/101
RA	174	.	NC_007779	1177683	0	A	G	bias_e_value=4.56854	bias_p_value=9.83258e-07	fisher_strand_p_value=5.55315e-08	frequency=7.387114e-02	genotype_quality=549.8	ks_quality_p_value=1	log10_base_likelihood=-10.9168	log10_qual_likelihood_position_model=14.6599	log10_strand_likelihood_position_model=7.25546	new_cov=15/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=46/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/110
RA	175	.	NC_007779	1213001	0	T	C	bias_e_value=4197510	bias_p_value=0.903403	fisher_strand_p_value=1	frequency=2.476692e-02	genotype_quality=1103.3	ks_quality_p_value=0.594006	log10_base_likelihood=-16.4745	log10_qual_likelihood_position_model=4.32395	log10_strand_likelihood_position_model=0.528399	new_cov=4/3	polymorphism_quality=11.1	quality=11.1	quality_position_model=1.11056e-13	ref_cov=162/113	tot_cov=166/116
RA	176	.	NC_007779	1213013	0	T	C	bias_e_value=3644820	bias_p_value=0.784452	fisher_strand_p_value=1	frequency=2.580166e-02	genotype_quality=1052.1	ks_quality_p_value=0.420117	log10_base_likelihood=-17.5782	log10_qual_likelihood_position_model=3.25035	log10_strand_likelihood_position_model=0.527158	new_cov=4/3	polymorphism_quality=12.3	quality=12.3	quality_position_model=6.77448e-16	ref_cov=154/110	tot_cov=158/113
RA	177	.	NC_007779	1213026	0	C	T	bias_e_value=4614500	bias_p_value=0.993149	fisher_strand_p_value=1	frequency=2.289200e-02	genotype_quality=1076.8	ks_quality_p_value=0.885251	log10_base_likelihood=-11.7942	log10_qual_likelihood_position_model=3.34632	log10_strand_likelihood_position_model=0.510893	new_cov=4/2	polymorphism_quality=6.4	quality=6.4	quality_position_model=6.45844e-10	ref_cov=150/105	tot_cov=154/107
RA	178	.	NC_007779	1213028	0	G	A	bias_e_value=4641460	bias_p_value=0.998951	fisher_strand_p_value=1	frequency=2.294731e-02	genotype_quality=1078.2	ks_quality_p_value=0.954548	log10_base_likelihood=-11.4809	log10_qual_likelihood_position_model=3.76484	log10_strand_likelihood_position_model=0.515609	new_cov=4/2	polymorphism_quality=6.1	quality=6.1	quality_position_model=3.68754e-09	ref_cov=148/106	tot_cov=152/109
RA	179	.	NC_007779	1219648	0	G	T	bias_e_value=6830.48	bias_p_value=0.00147008	fisher_strand_p_value=0.000149926	frequency=2.750683e-02	genotype_quality=924.2	ks_quality_p_value=1	log10_base_likelihood=-7.30365	log10_qual_likelihood_position_model=10.5492	log10_strand_likelihood_position_model=3.82412	new_cov=0/12	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=138/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/133
RA	180	.	NC_007779	1224173	0	G	A	bias_e_value=1963.85	bias_p_value=0.000422667	fisher_strand_p_value=3.78165e-05	frequency=5.188894e-02	genotype_quality=745.0	ks_quality_p_value=0.999415	log10_base_likelihood=-9.16813	log10_qual_likelihood_position_model=16.4712	log10_strand_likelihood_position_model=4.72335	new_cov=0/15	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=117/102	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/117
RA	181	.	NC_007779	1225577	1	.	G	bias_e_value=2122030	bias_p_value=0.45671	fisher_strand_p_value=0.165831	frequency=9.614944e-03	genotype_quality=1027.2	ks_quality_p_value=0.976385	log10_base_likelihood=-8.1667	log10_qual_likelihood_position_model=1.36173	log10_strand_likelihood_position_model=0.780335	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=6.0125e-08	ref_cov=83/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=85/123
RA	182	.	NC_007779	1245628	0	C	A	bias_e_value=5715.95	bias_p_value=0.00123021	fisher_strand_p_value=0.000125369	frequency=2.585030e-02	genotype_quality=967.1	ks_quality_p_value=0.980925	log10_base_likelihood=-6.01807	log10_qual_likelihood_position_model=19.008	log10_strand_likelihood_position_model=3.96034	new_cov=14/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=132/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/128
RA	183	.	NC_007779	1262472	0	A	C	bias_e_value=0.0445991	bias_p_value=9.59877e-09	fisher_strand_p_value=4.25126e-10	frequency=6.475449e-02	genotype_quality=654.2	ks_quality_p_value=1	log10_base_likelihood=-8.0024	log10_qual_likelihood_position_model=19.1991	log10_strand_likelihood_position_model=9.37148	new_cov=0/27	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=112/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/107
RA	184	.	NC_007779	1273399	0	T	G	bias_e_value=5.85308e-24	bias_p_value=1.25972e-30	fisher_strand_p_value=1.69882e-32	frequency=1.482339e-01	genotype_quality=750.1	ks_quality_p_value=1	log10_base_likelihood=-31.7991	log10_qual_likelihood_position_model=40.9807	log10_strand_likelihood_position_model=31.7699	new_cov=46/0	polymorphism_quality=26.6	quality=26.6	quality_position_model=Inf	ref_cov=22/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=68/168
RA	185	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=40.6	new_cov=6/7	quality=40.6	ref_cov=0/0	tot_cov=6/7
RA	186	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=7.2	new_cov=2/2	quality=7.2	ref_cov=0/0	reject=EVALUE	tot_cov=2/2
RA	187	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=34.6	new_cov=10/6	quality=34.6	ref_cov=0/0	tot_cov=10/6
RA	188	.	NC_007779	1289242	1	.	G	bias_e_value=1952320	bias_p_value=0.420185	fisher_strand_p_value=0.239471	frequency=9.433746e-03	genotype_quality=1049.6	ks_quality_p_value=0.59514	log10_base_likelihood=-8.30614	log10_qual_likelihood_position_model=0.980372	log10_strand_likelihood_position_model=0.620748	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.19346e-08	ref_cov=102/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/108
RA	189	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1017.1	new_cov=113/141	quality=1017.1	ref_cov=0/0	tot_cov=113/141
RA	190	.	NC_007779	1325276	0	G	T	bias_e_value=342.367	bias_p_value=7.36855e-05	fisher_strand_p_value=5.76825e-06	frequency=3.635788e-02	genotype_quality=812.7	ks_quality_p_value=0.976083	log10_base_likelihood=-5.76527	log10_qual_likelihood_position_model=14.0624	log10_strand_likelihood_position_model=5.23896	new_cov=0/13	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=139/84	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/97
RA	191	.	NC_007779	1330179	0	T	G	bias_e_value=0.00143835	bias_p_value=3.09568e-10	fisher_strand_p_value=1.18336e-11	frequency=9.248829e-02	genotype_quality=610.7	ks_quality_p_value=1	log10_base_likelihood=-15.3632	log10_qual_likelihood_position_model=26.5894	log10_strand_likelihood_position_model=10.9269	new_cov=31/0	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=67/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/103
RA	192	.	NC_007779	1347809	1	.	A	bias_e_value=4645470	bias_p_value=0.999815	fisher_strand_p_value=1	frequency=8.657455e-03	genotype_quality=1141.1	ks_quality_p_value=0.980829	log10_base_likelihood=-7.89479	log10_qual_likelihood_position_model=2.74307	log10_strand_likelihood_position_model=0.299806	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=9.89915e-07	ref_cov=110/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/120
RA	193	.	NC_007779	1352913	1	.	T	bias_e_value=4477.19	bias_p_value=0.000963596	fisher_strand_p_value=0.000167976	frequency=5.128241e-02	genotype_quality=674.2	ks_quality_p_value=0.558325	log10_base_likelihood=-39.1974	log10_qual_likelihood_position_model=4.27304	log10_strand_likelihood_position_model=3.77475	new_cov=8/0	polymorphism_quality=34.1	quality=34.1	quality_position_model=2.03605e-33	ref_cov=47/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=55/101
RA	194	.	NC_007779	1371749	1	.	T	bias_e_value=4310840	bias_p_value=0.927794	fisher_strand_p_value=1	frequency=2.489662e-02	genotype_quality=1122.7	ks_quality_p_value=0.644906	log10_base_likelihood=-26.9269	log10_qual_likelihood_position_model=5.78707	log10_strand_likelihood_position_model=0.516424	new_cov=3/3	polymorphism_quality=21.7	quality=21.7	quality_position_model=8.3764e-23	ref_cov=104/131	reject=INDEL_HOMOPOLYMER	tot_cov=107/134
RA	195	.	NC_007779	1371749	2	.	T	bias_e_value=2772090	bias_p_value=0.596619	fisher_strand_p_value=0.504219	frequency=8.298874e-03	genotype_quality=1168.0	ks_quality_p_value=0.495881	log10_base_likelihood=-8.31819	log10_qual_likelihood_position_model=1.36083	log10_strand_likelihood_position_model=0.511272	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.20698e-08	ref_cov=107/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/134
RA	196	.	NC_007779	1385794	1	.	T	bias_e_value=3612350	bias_p_value=0.777462	fisher_strand_p_value=0.497738	frequency=9.008408e-03	genotype_quality=1090.5	ks_quality_p_value=0.828037	log10_base_likelihood=-8.29452	log10_qual_likelihood_position_model=1.56689	log10_strand_likelihood_position_model=0.60403	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=4.75088e-08	ref_cov=109/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/111
RA	197	.	NC_007779	1405508	0	G	T	bias_e_value=135.588	bias_p_value=2.91818e-05	fisher_strand_p_value=2.30771e-06	frequency=5.029583e-02	genotype_quality=454.8	ks_quality_p_value=0.897646	log10_base_likelihood=-11.9359	log10_qual_likelihood_position_model=8.23931	log10_strand_likelihood_position_model=5.63682	new_cov=6/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=10/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/103
RA	198	.	NC_007779	1409137	0	G	T	bias_e_value=7.37167e-11	bias_p_value=1.58656e-17	fisher_strand_p_value=3.65111e-19	frequency=1.641073e-01	genotype_quality=688.8	ks_quality_p_value=1	log10_base_likelihood=-35.348	log10_qual_likelihood_position_model=25.8957	log10_strand_likelihood_position_model=18.5207	new_cov=0/53	polymorphism_quality=30.2	quality=30.2	quality_position_model=Inf	ref_cov=129/79	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/132
RA	199	.	NC_007779	1413639	0	T	A	deleted=1	frequency=1	genotype_quality=2.3	new_cov=0/1	quality=2.3	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	200	.	NC_007779	1413640	0	G	C	deleted=1	frequency=1	genotype_quality=2.3	new_cov=0/1	quality=2.3	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	201	.	NC_007779	1413647	0	G	C	deleted=1	frequency=1	genotype_quality=2.3	new_cov=0/1	quality=2.3	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	202	.	NC_007779	1433588	0	G	A	deleted=1	frequency=1	genotype_quality=3.0	new_cov=0/1	quality=3.0	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	203	.	NC_007779	1433591	0	A	G	deleted=1	frequency=1	genotype_quality=3.2	new_cov=0/1	quality=3.2	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	204	.	NC_007779	1433594	0	C	T	deleted=1	frequency=1	genotype_quality=3.6	new_cov=0/1	quality=3.6	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	205	.	NC_007779	1433598	0	A	C	deleted=1	frequency=1	genotype_quality=4.1	new_cov=0/1	quality=4.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	206	.	NC_007779	1433600	0	C	T	deleted=1	frequency=1	genotype_quality=3.6	new_cov=0/1	quality=3.6	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	207	.	NC_007779	1433612	0	T	A	deleted=1	frequency=1	genotype_quality=3.8	new_cov=0/1	quality=3.8	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	208	.	NC_007779	1433621	0	G	A	deleted=1	frequency=1	genotype_quality=3.8	new_cov=0/1	quality=3.8	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	209	.	NC_007779	1433624	0	T	C	deleted=1	frequency=1	genotype_quality=3.3	new_cov=0/1	quality=3.3	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	210	.	NC_007779	1433630	0	C	G	deleted=1	frequency=1	genotype_quality=4.1	new_cov=0/1	quality=4.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	211	.	NC_007779	1433636	0	T	C	deleted=1	frequency=1	genotype_quality=4.5	new_cov=0/1	quality=4.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	212	.	NC_007779	1433642	0	T	C	deleted=1	frequency=1	genotype_quality=3.8	new_cov=0/1	quality=3.8	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	213	.	NC_007779	1433648	0	G	T	deleted=1	frequency=1	genotype_quality=4.1	new_cov=0/1	quality=4.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	214	.	NC_007779	1433651	0	C	T	deleted=1	frequency=1	genotype_quality=3.9	new_cov=0/1	quality=3.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	215	.	NC_007779	1433672	0	C	T	deleted=1	frequency=1	genotype_quality=3.8	new_cov=0/1	quality=3.8	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	216	.	NC_007779	1433675	0	C	A	deleted=1	frequency=1	genotype_quality=3.6	new_cov=0/1	quality=3.6	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	217	.	NC_007779	1438937	0	T	.	bias_e_value=1535910	bias_p_value=0.330564	fisher_strand_p_value=0.130001	frequency=2.070904e-02	genotype_quality=747.9	ks_quality_p_value=0.770249	log10_base_likelihood=-10.9714	log10_qual_likelihood_position_model=3.81555	log10_strand_likelihood_position_model=1.03573	new_cov=4/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=4.79043e-08	ref_cov=103/86	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/86
RA	218	.	NC_007779	1449735	1	.	G	bias_e_value=2745490	bias_p_value=0.590893	fisher_strand_p_value=0.246809	frequency=8.510590e-03	genotype_quality=1166.0	ks_quality_p_value=0.996427	log10_base_likelihood=-8.0403	log10_qual_likelihood_position_model=2.33888	log10_strand_likelihood_position_model=0.60764	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.54551e-07	ref_cov=115/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/118
RA	219	.	NC_007779	1457034	0	T	A	bias_e_value=349123	bias_p_value=0.0751396	fisher_strand_p_value=0.0144371	frequency=3.823376e-02	genotype_quality=645.9	ks_quality_p_value=0.992138	log10_base_likelihood=-6.92278	log10_qual_likelihood_position_model=11.1144	log10_strand_likelihood_position_model=2.01916	new_cov=7/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=83/82	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=90/82
RA	220	.	NC_007779	1461304	0	G	T	bias_e_value=1118.82	bias_p_value=0.000240796	fisher_strand_p_value=2.04071e-05	frequency=3.590107e-02	genotype_quality=762.1	ks_quality_p_value=1	log10_base_likelihood=-8.1763	log10_qual_likelihood_position_model=11.9076	log10_strand_likelihood_position_model=4.69022	new_cov=0/13	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=119/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/98
RA	221	.	NC_007779	1476017	0	T	.	bias_e_value=2493780	bias_p_value=0.536719	fisher_strand_p_value=0.360246	frequency=1.842213e-02	genotype_quality=795.9	ks_quality_p_value=0.581128	log10_base_likelihood=-11.2123	log10_qual_likelihood_position_model=2.47868	log10_strand_likelihood_position_model=0.622854	new_cov=3/1	polymorphism_quality=5.8	quality=5.8	quality_position_model=4.28419e-10	ref_cov=103/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/111
RA	222	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=663.1	new_cov=117/52	quality=663.1	ref_cov=0/0	tot_cov=117/52
RA	223	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1140.9	new_cov=103/127	quality=1140.9	ref_cov=0/0	tot_cov=103/127
RA	224	.	NC_007779	1502096	0	T	.	bias_e_value=3910850	bias_p_value=0.841707	fisher_strand_p_value=0.605071	frequency=1.498413e-02	genotype_quality=784.5	ks_quality_p_value=0.814861	log10_base_likelihood=-7.8756	log10_qual_likelihood_position_model=2.95108	log10_strand_likelihood_position_model=0.447386	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.43499e-06	ref_cov=104/93	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/95
RA	225	.	NC_007779	1515709	0	A	G	bias_e_value=0.0266786	bias_p_value=5.74187e-09	fisher_strand_p_value=2.48394e-10	frequency=1.371269e-01	genotype_quality=545.6	ks_quality_p_value=1	log10_base_likelihood=-21.3745	log10_qual_likelihood_position_model=34.9876	log10_strand_likelihood_position_model=9.9146	new_cov=33/1	polymorphism_quality=16.1	quality=16.1	quality_position_model=Inf	ref_cov=73/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/106
RA	226	.	NC_007779	1515714	0	A	T	bias_e_value=13640.2	bias_p_value=0.00293569	fisher_strand_p_value=0.000325048	frequency=4.488182e-02	genotype_quality=642.7	ks_quality_p_value=1	log10_base_likelihood=-6.15107	log10_qual_likelihood_position_model=13.195	log10_strand_likelihood_position_model=3.48805	new_cov=11/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=88/101	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=99/101
RA	227	.	NC_007779	1527474	0	G	A	bias_e_value=7.99099	bias_p_value=1.71985e-06	fisher_strand_p_value=1.00499e-07	frequency=7.753277e-02	genotype_quality=800.0	ks_quality_p_value=1	log10_base_likelihood=-16.4231	log10_qual_likelihood_position_model=24.111	log10_strand_likelihood_position_model=7.0095	new_cov=1/20	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=139/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/100
RA	228	.	NC_007779	1527479	0	C	A	bias_e_value=463.105	bias_p_value=9.96712e-05	fisher_strand_p_value=7.91552e-06	frequency=4.151535e-02	genotype_quality=844.3	ks_quality_p_value=0.986828	log10_base_likelihood=-7.65326	log10_qual_likelihood_position_model=18.2304	log10_strand_likelihood_position_model=5.10152	new_cov=0/13	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=132/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=132/96
RA	229	.	NC_007779	1537499	0	A	G	bias_e_value=0.000589244	bias_p_value=1.26819e-10	fisher_strand_p_value=4.68187e-12	frequency=9.644985e-02	genotype_quality=674.5	ks_quality_p_value=1	log10_base_likelihood=-9.9984	log10_qual_likelihood_position_model=23.0709	log10_strand_likelihood_position_model=11.3296	new_cov=30/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=76/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/126
RA	230	.	NC_007779	1562518	0	A	C	bias_e_value=0.0143457	bias_p_value=3.08753e-09	fisher_strand_p_value=1.29924e-10	frequency=1.062512e-01	genotype_quality=403.2	ks_quality_p_value=1	log10_base_likelihood=-10.4578	log10_qual_likelihood_position_model=17.0447	log10_strand_likelihood_position_model=9.88631	new_cov=0/28	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=80/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/78
RA	231	.	NC_007779	1595962	1	.	C	bias_e_value=4430250	bias_p_value=0.953495	fisher_strand_p_value=1	frequency=8.810043e-03	genotype_quality=1092.1	ks_quality_p_value=0.710956	log10_base_likelihood=-8.54321	log10_qual_likelihood_position_model=2.07465	log10_strand_likelihood_position_model=0.300539	new_cov=1/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=4.27441e-08	ref_cov=119/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/107
RA	232	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=891.8	new_cov=108/128	quality=891.8	ref_cov=0/0	tot_cov=108/128
RA	233	.	NC_007779	1628027	0	G	T	bias_e_value=1.05658	bias_p_value=2.27401e-07	fisher_strand_p_value=1.42364e-08	frequency=1.983151e-01	genotype_quality=335.3	ks_quality_p_value=0.829594	log10_base_likelihood=-46.0081	log10_qual_likelihood_position_model=21.0994	log10_strand_likelihood_position_model=7.87033	new_cov=28/0	polymorphism_quality=40.9	quality=40.9	quality_position_model=3.53682e-19	ref_cov=50/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=78/58
RA	234	.	NC_007779	1641155	0	T	.	bias_e_value=4456710	bias_p_value=0.959189	fisher_strand_p_value=1	frequency=1.368999e-02	genotype_quality=861.5	ks_quality_p_value=0.728259	log10_base_likelihood=-8.29488	log10_qual_likelihood_position_model=1.52684	log10_strand_likelihood_position_model=0.37478	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.50212e-08	ref_cov=93/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=94/125
RA	235	.	NC_007779	1651009	0	T	G	bias_e_value=4.60828e-11	bias_p_value=9.9181e-18	fisher_strand_p_value=2.25746e-19	frequency=1.536288e-01	genotype_quality=534.6	ks_quality_p_value=1	log10_base_likelihood=-26.6058	log10_qual_likelihood_position_model=29.4199	log10_strand_likelihood_position_model=18.6464	new_cov=33/0	polymorphism_quality=21.4	quality=21.4	quality_position_model=Inf	ref_cov=27/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=60/114
RA	236	.	NC_007779	1664999	0	G	A	bias_e_value=362040	bias_p_value=0.0779196	fisher_strand_p_value=0.0149819	frequency=3.144836e-02	genotype_quality=734.0	ks_quality_p_value=1	log10_base_likelihood=-7.53629	log10_qual_likelihood_position_model=7.70115	log10_strand_likelihood_position_model=1.98228	new_cov=7/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=95/91	reject=POLYMORPHISM_STRAND	tot_cov=102/91
RA	237	.	NC_007779	1665001	0	A	C	bias_e_value=208157	bias_p_value=0.0448002	fisher_strand_p_value=0.00762682	frequency=3.236771e-02	genotype_quality=720.0	ks_quality_p_value=0.999579	log10_base_likelihood=-11.2368	log10_qual_likelihood_position_model=9.41219	log10_strand_likelihood_position_model=2.24401	new_cov=8/0	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=98/93	reject=POLYMORPHISM_STRAND	tot_cov=106/93
RA	238	.	NC_007779	1665005	0	G	T	bias_e_value=189286	bias_p_value=0.0407389	fisher_strand_p_value=0.00680024	frequency=3.690434e-02	genotype_quality=753.1	ks_quality_p_value=1	log10_base_likelihood=-9.59429	log10_qual_likelihood_position_model=9.01511	log10_strand_likelihood_position_model=2.3998	new_cov=8/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=90/94	reject=POLYMORPHISM_STRAND	tot_cov=98/94
RA	239	.	NC_007779	1665006	0	C	A	bias_e_value=105118	bias_p_value=0.0226239	fisher_strand_p_value=0.00338381	frequency=3.230095e-02	genotype_quality=747.4	ks_quality_p_value=0.999504	log10_base_likelihood=-8.60523	log10_qual_likelihood_position_model=9.64449	log10_strand_likelihood_position_model=2.64938	new_cov=9/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=92/94	reject=POLYMORPHISM_STRAND	tot_cov=101/94
RA	240	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=1052.3	new_cov=107/104	quality=1052.3	ref_cov=0/0	tot_cov=107/104
RA	241	.	NC_007779	1669786	0	G	A	bias_e_value=348917	bias_p_value=0.0750951	fisher_strand_p_value=0.0143132	frequency=1.884270e-02	genotype_quality=948.3	ks_quality_p_value=1	log10_base_likelihood=-5.60443	log10_qual_likelihood_position_model=6.64339	log10_strand_likelihood_position_model=1.84426	new_cov=0/6	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=123/116	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=123/122
RA	242	.	NC_007779	1677110	0	G	T	bias_e_value=0.574883	bias_p_value=1.23728e-07	fisher_strand_p_value=8.91182e-09	frequency=7.302999e-02	genotype_quality=684.0	ks_quality_p_value=0.697821	log10_base_likelihood=-11.5896	log10_qual_likelihood_position_model=28.8664	log10_strand_likelihood_position_model=8.15787	new_cov=0/28	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=110/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/130
RA	243	.	NC_007779	1681402	0	T	G	bias_e_value=4.1461e-08	bias_p_value=8.92338e-15	fisher_strand_p_value=2.41434e-16	frequency=8.658981e-02	genotype_quality=779.1	ks_quality_p_value=1	log10_base_likelihood=-12.9037	log10_qual_likelihood_position_model=30.3717	log10_strand_likelihood_position_model=15.6172	new_cov=32/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=57/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/151
RA	244	.	NC_007779	1686426	0	A	C	bias_e_value=0.00144266	bias_p_value=3.10495e-10	fisher_strand_p_value=1.18705e-11	frequency=7.138538e-02	genotype_quality=615.8	ks_quality_p_value=1	log10_base_likelihood=-8.6268	log10_qual_likelihood_position_model=33.0641	log10_strand_likelihood_position_model=10.9255	new_cov=0/29	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=111/66	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/95
RA	245	.	NC_007779	1705204	0	A	C	bias_e_value=1844.28	bias_p_value=0.000396931	fisher_strand_p_value=3.52755e-05	frequency=6.339788e-02	genotype_quality=662.5	ks_quality_p_value=1	log10_base_likelihood=-11.783	log10_qual_likelihood_position_model=20.436	log10_strand_likelihood_position_model=4.47149	new_cov=16/0	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=88/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/88
RA	246	.	NC_007779	1705210	0	G	T	bias_e_value=52140.8	bias_p_value=0.0112219	fisher_strand_p_value=0.00149515	frequency=5.366325e-02	genotype_quality=665.4	ks_quality_p_value=1	log10_base_likelihood=-13.9404	log10_qual_likelihood_position_model=12.6614	log10_strand_likelihood_position_model=3.10123	new_cov=10/0	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=79/88	reject=POLYMORPHISM_STRAND	tot_cov=89/88
RA	247	.	NC_007779	1705224	0	G	T	bias_e_value=65815	bias_p_value=0.0141649	fisher_strand_p_value=0.00195755	frequency=4.473209e-02	genotype_quality=716.9	ks_quality_p_value=1	log10_base_likelihood=-8.73414	log10_qual_likelihood_position_model=12.2321	log10_strand_likelihood_position_model=2.78778	new_cov=10/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=89/85	reject=POLYMORPHISM_STRAND	tot_cov=99/85
RA	248	.	NC_007779	1716031	1	.	T	bias_e_value=3711540	bias_p_value=0.79881	fisher_strand_p_value=0.612295	frequency=1.470566e-02	genotype_quality=971.6	ks_quality_p_value=0.71381	log10_base_likelihood=-13.0198	log10_qual_likelihood_position_model=1.84622	log10_strand_likelihood_position_model=0.437306	new_cov=1/2	polymorphism_quality=7.6	quality=7.6	quality_position_model=8.87192e-13	ref_cov=104/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/99
RA	249	.	NC_007779	1716032	0	T	.	bias_e_value=3342930	bias_p_value=0.719478	fisher_strand_p_value=0.610622	frequency=1.462555e-02	genotype_quality=822.4	ks_quality_p_value=0.576377	log10_base_likelihood=-8.3961	log10_qual_likelihood_position_model=1.31385	log10_strand_likelihood_position_model=0.439592	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.38382e-08	ref_cov=105/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/99
RA	250	.	NC_007779	1728625	0	A	.	bias_e_value=604528	bias_p_value=0.130109	fisher_strand_p_value=0.246914	frequency=1.248932e-02	genotype_quality=951.9	ks_quality_p_value=0.115664	log10_base_likelihood=-7.92575	log10_qual_likelihood_position_model=2.52198	log10_strand_likelihood_position_model=0.897673	new_cov=0/3	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.27113e-06	ref_cov=119/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/121
RA	251	.	NC_007779	1744363	0	C	A	bias_e_value=212.809	bias_p_value=4.58016e-05	fisher_strand_p_value=3.36742e-06	frequency=5.318832e-02	genotype_quality=733.0	ks_quality_p_value=1	log10_base_likelihood=-6.10482	log10_qual_likelihood_position_model=20.0536	log10_strand_likelihood_position_model=5.50177	new_cov=21/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=110/100	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/100
RA	252	.	NC_007779	1759412	0	T	.	bias_e_value=4640070	bias_p_value=0.998653	fisher_strand_p_value=1	frequency=1.469517e-02	genotype_quality=801.3	ks_quality_p_value=0.948547	log10_base_likelihood=-8.22087	log10_qual_likelihood_position_model=2.19768	log10_strand_likelihood_position_model=0.375718	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.47695e-07	ref_cov=87/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=88/116
RA	253	.	NC_007779	1763744	0	C	A	bias_e_value=1.56767e-08	bias_p_value=3.37399e-15	fisher_strand_p_value=8.88848e-17	frequency=1.091776e-01	genotype_quality=752.9	ks_quality_p_value=1	log10_base_likelihood=-22.1954	log10_qual_likelihood_position_model=24.199	log10_strand_likelihood_position_model=16.0512	new_cov=39/0	polymorphism_quality=16.9	quality=16.9	quality_position_model=Inf	ref_cov=74/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/147
RA	254	.	NC_007779	1820099	0	A	C	bias_e_value=1.95672e-06	bias_p_value=4.21132e-13	fisher_strand_p_value=1.27646e-14	frequency=1.041574e-01	genotype_quality=675.2	ks_quality_p_value=1	log10_base_likelihood=-13.8722	log10_qual_likelihood_position_model=27.6704	log10_strand_likelihood_position_model=13.894	new_cov=0/27	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=137/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/74
RA	255	.	NC_007779	1840899	0	G	T	bias_e_value=212.078	bias_p_value=4.56441e-05	fisher_strand_p_value=3.35493e-06	frequency=4.853535e-02	genotype_quality=663.9	ks_quality_p_value=1	log10_base_likelihood=-7.30798	log10_qual_likelihood_position_model=15.5266	log10_strand_likelihood_position_model=5.47432	new_cov=0/17	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=102/84	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/101
RA	256	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=878.1	new_cov=113/106	quality=878.1	ref_cov=0/0	tot_cov=113/107
RA	257	.	NC_007779	1852047	0	G	T	bias_e_value=1515.55	bias_p_value=0.000326181	fisher_strand_p_value=2.84438e-05	frequency=2.444172e-02	genotype_quality=851.6	ks_quality_p_value=1	log10_base_likelihood=-6.27761	log10_qual_likelihood_position_model=10.4149	log10_strand_likelihood_position_model=4.54601	new_cov=0/12	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=144/97	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/109
RA	258	.	NC_007779	1879381	0	C	A	bias_e_value=59.8497	bias_p_value=1.28811e-05	fisher_strand_p_value=8.60718e-07	frequency=4.392910e-02	genotype_quality=940.0	ks_quality_p_value=1	log10_base_likelihood=-9.81147	log10_qual_likelihood_position_model=16.3138	log10_strand_likelihood_position_model=6.06514	new_cov=0/12	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=155/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/76
RA	259	.	NC_007779	1879404	0	A	C	bias_e_value=7.26923e-17	bias_p_value=1.56451e-23	fisher_strand_p_value=2.71782e-25	frequency=1.085076e-01	genotype_quality=780.7	ks_quality_p_value=1	log10_base_likelihood=-21.214	log10_qual_likelihood_position_model=37.3934	log10_strand_likelihood_position_model=24.5658	new_cov=0/37	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=168/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/66
RA	260	.	NC_007779	1896056	0	A	.	bias_e_value=4646190	bias_p_value=0.999969	fisher_strand_p_value=1	frequency=1.350307e-02	genotype_quality=897.4	ks_quality_p_value=0.992133	log10_base_likelihood=-8.0499	log10_qual_likelihood_position_model=2.45581	log10_strand_likelihood_position_model=0.384147	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.19979e-07	ref_cov=98/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/123
RA	261	.	NC_007779	1906475	1	.	C	bias_e_value=1277450	bias_p_value=0.274937	fisher_strand_p_value=0.198669	frequency=9.216309e-03	genotype_quality=1045.2	ks_quality_p_value=0.388588	log10_base_likelihood=-8.51782	log10_qual_likelihood_position_model=1.37425	log10_strand_likelihood_position_model=0.701871	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.23011e-08	ref_cov=95/120	reject=POLYMORPHISM_STRAND	tot_cov=97/120
RA	262	.	NC_007779	1906477	1	.	G	bias_e_value=18431.2	bias_p_value=0.00396682	fisher_strand_p_value=0.000469362	frequency=4.102421e-02	genotype_quality=876.3	ks_quality_p_value=0.972309	log10_base_likelihood=-33.0311	log10_qual_likelihood_position_model=9.53898	log10_strand_likelihood_position_model=3.32849	new_cov=8/0	polymorphism_quality=27.9	quality=27.9	quality_position_model=2.44134e-22	ref_cov=69/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=77/118
RA	263	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=925.7	new_cov=107/134	quality=925.7	ref_cov=0/0	tot_cov=107/134
RA	264	.	NC_007779	1920746	0	G	T	bias_e_value=0.00030903	bias_p_value=6.65105e-11	fisher_strand_p_value=2.39616e-12	frequency=8.015537e-02	genotype_quality=757.3	ks_quality_p_value=1	log10_base_likelihood=-10.2829	log10_qual_likelihood_position_model=22.3196	log10_strand_likelihood_position_model=11.6205	new_cov=0/31	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=128/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/112
RA	265	.	NC_007779	1956118	0	C	A	bias_e_value=0.5139	bias_p_value=1.10603e-07	fisher_strand_p_value=5.54791e-09	frequency=6.666517e-02	genotype_quality=590.8	ks_quality_p_value=0.996117	log10_base_likelihood=-18.7153	log10_qual_likelihood_position_model=12.5092	log10_strand_likelihood_position_model=8.25587	new_cov=0/11	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=124/21	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/32
RA	266	.	NC_007779	1971508	0	A	C	bias_e_value=0.00145229	bias_p_value=3.12567e-10	fisher_strand_p_value=1.19528e-11	frequency=8.014870e-02	genotype_quality=493.6	ks_quality_p_value=1	log10_base_likelihood=-13.181	log10_qual_likelihood_position_model=16.2583	log10_strand_likelihood_position_model=10.9225	new_cov=0/13	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=116/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/26
RA	267	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=806.9	new_cov=108/98	quality=806.9	ref_cov=0/0	tot_cov=108/98
RA	268	.	NC_007779	2004055	0	A	C	bias_e_value=1.92077e-17	bias_p_value=4.13395e-24	fisher_strand_p_value=7.01632e-26	frequency=2.379293e-01	genotype_quality=556.6	ks_quality_p_value=1	log10_base_likelihood=-60.8586	log10_qual_likelihood_position_model=41.7195	log10_strand_likelihood_position_model=25.1539	new_cov=0/64	polymorphism_quality=55.8	quality=55.8	quality_position_model=Inf	ref_cov=117/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/115
RA	269	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=947.2	new_cov=110/122	quality=947.2	ref_cov=0/0	tot_cov=110/122
RA	270	.	NC_007779	2036123	1	.	T	bias_e_value=3560940	bias_p_value=0.766398	fisher_strand_p_value=0.534869	frequency=1.117325e-02	genotype_quality=875.5	ks_quality_p_value=0.747604	log10_base_likelihood=-8.36454	log10_qual_likelihood_position_model=1.38073	log10_strand_likelihood_position_model=0.39329	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.56615e-08	ref_cov=112/65	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/65
RA	271	.	NC_007779	2065611	0	C	A	bias_e_value=32.9576	bias_p_value=7.09326e-06	fisher_strand_p_value=4.54583e-07	frequency=5.016947e-02	genotype_quality=723.6	ks_quality_p_value=1	log10_base_likelihood=-7.94556	log10_qual_likelihood_position_model=17.6518	log10_strand_likelihood_position_model=6.45839	new_cov=23/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=106/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/107
RA	272	.	NC_007779	2098223	0	T	G	bias_e_value=0.231493	bias_p_value=4.98227e-08	fisher_strand_p_value=2.38932e-09	frequency=4.648924e-02	genotype_quality=656.1	ks_quality_p_value=1	log10_base_likelihood=-6.4088	log10_qual_likelihood_position_model=16.3905	log10_strand_likelihood_position_model=8.62173	new_cov=20/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=64/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=84/126
RA	273	.	NC_007779	2107011	0	A	.	bias_e_value=1492470	bias_p_value=0.321214	fisher_strand_p_value=0.250047	frequency=1.189518e-02	genotype_quality=1009.3	ks_quality_p_value=0.384348	log10_base_likelihood=-8.04929	log10_qual_likelihood_position_model=2.0635	log10_strand_likelihood_position_model=0.827484	new_cov=3/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.75195e-07	ref_cov=131/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/118
RA	274	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1032.6	new_cov=117/136	quality=1032.6	ref_cov=0/0	tot_cov=117/136
RA	275	.	NC_007779	2199432	0	G	C	bias_e_value=59.8041	bias_p_value=1.28713e-05	fisher_strand_p_value=8.7436e-07	frequency=4.518604e-02	genotype_quality=569.1	ks_quality_p_value=0.983594	log10_base_likelihood=-8.47442	log10_qual_likelihood_position_model=8.49351	log10_strand_likelihood_position_model=6.05831	new_cov=0/7	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=126/16	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/23
RA	276	.	NC_007779	2213136	0	G	T	bias_e_value=0.00410107	bias_p_value=8.82647e-10	fisher_strand_p_value=3.52076e-11	frequency=8.838320e-02	genotype_quality=584.1	ks_quality_p_value=1	log10_base_likelihood=-18.4394	log10_qual_likelihood_position_model=17.3874	log10_strand_likelihood_position_model=10.4534	new_cov=16/0	polymorphism_quality=13.1	quality=13.1	quality_position_model=Inf	ref_cov=27/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=43/123
RA	277	.	NC_007779	2229341	0	G	T	bias_e_value=2477.64	bias_p_value=0.000533246	fisher_strand_p_value=4.8797e-05	frequency=7.132292e-02	genotype_quality=610.8	ks_quality_p_value=1	log10_base_likelihood=-11.3295	log10_qual_likelihood_position_model=15.2605	log10_strand_likelihood_position_model=4.38545	new_cov=0/20	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=79/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/131
RA	278	.	NC_007779	2232587	0	G	A	bias_e_value=208682	bias_p_value=0.0449132	fisher_strand_p_value=0.0076468	frequency=2.252483e-02	genotype_quality=651.9	ks_quality_p_value=1	log10_base_likelihood=-7.38946	log10_qual_likelihood_position_model=5.36878	log10_strand_likelihood_position_model=2.11652	new_cov=5/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=77/132	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=82/132
RA	279	.	NC_007779	2249963	0	T	G	bias_e_value=0.00045071	bias_p_value=9.70034e-11	fisher_strand_p_value=3.54473e-12	frequency=8.965540e-02	genotype_quality=620.4	ks_quality_p_value=1	log10_base_likelihood=-7.33399	log10_qual_likelihood_position_model=31.5791	log10_strand_likelihood_position_model=11.4504	new_cov=30/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=64/111	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=94/111
RA	280	.	NC_007779	2254201	0	G	T	bias_e_value=2.02912	bias_p_value=4.36714e-07	fisher_strand_p_value=2.35232e-08	frequency=6.947517e-02	genotype_quality=736.8	ks_quality_p_value=1	log10_base_likelihood=-15.6703	log10_qual_likelihood_position_model=14.6635	log10_strand_likelihood_position_model=7.6285	new_cov=0/23	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=120/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/116
RA	281	.	NC_007779	2262756	0	A	C	bias_e_value=4073870	bias_p_value=0.876793	fisher_strand_p_value=0.61074	frequency=1.289463e-02	genotype_quality=926.7	ks_quality_p_value=0.895049	log10_base_likelihood=-6.89064	log10_qual_likelihood_position_model=2.90956	log10_strand_likelihood_position_model=0.439984	new_cov=1/2	polymorphism_quality=1.4	quality=1.4	quality_position_model=2.33892e-05	ref_cov=119/110	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=120/112
RA	282	.	NC_007779	2264335	0	A	C	bias_e_value=0.0409554	bias_p_value=8.81456e-09	fisher_strand_p_value=3.88858e-10	frequency=3.145504e-02	genotype_quality=763.0	ks_quality_p_value=1	log10_base_likelihood=-6.0389	log10_qual_likelihood_position_model=19.7781	log10_strand_likelihood_position_model=9.41021	new_cov=0/20	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=147/65	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/85
RA	283	.	NC_007779	2266892	0	G	T	bias_e_value=1208.57	bias_p_value=0.000260112	fisher_strand_p_value=2.22028e-05	frequency=2.824402e-02	genotype_quality=952.2	ks_quality_p_value=1	log10_base_likelihood=-5.89631	log10_qual_likelihood_position_model=12.9278	log10_strand_likelihood_position_model=4.78186	new_cov=0/16	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=138/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/147
RA	284	.	NC_007779	2271208	0	A	C	bias_e_value=12366	bias_p_value=0.00266146	fisher_strand_p_value=0.000291134	frequency=3.235531e-02	genotype_quality=873.5	ks_quality_p_value=1	log10_base_likelihood=-5.68491	log10_qual_likelihood_position_model=18.8377	log10_strand_likelihood_position_model=3.57692	new_cov=0/13	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=114/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/135
RA	285	.	NC_007779	2278635	0	C	A	bias_e_value=3.03468	bias_p_value=6.53134e-07	fisher_strand_p_value=3.60459e-08	frequency=6.179237e-02	genotype_quality=688.6	ks_quality_p_value=0.998892	log10_base_likelihood=-7.29747	log10_qual_likelihood_position_model=17.6306	log10_strand_likelihood_position_model=7.66592	new_cov=26/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=97/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/107
RA	286	.	NC_007779	2307309	0	T	C	bias_e_value=3.71599	bias_p_value=7.99769e-07	fisher_strand_p_value=4.46172e-08	frequency=6.096840e-02	genotype_quality=602.7	ks_quality_p_value=1	log10_base_likelihood=-6.55443	log10_qual_likelihood_position_model=17.6036	log10_strand_likelihood_position_model=7.3505	new_cov=0/15	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=125/52	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/67
RA	287	.	NC_007779	2307320	1	.	A	bias_e_value=1860870	bias_p_value=0.400503	fisher_strand_p_value=0.213154	frequency=7.843018e-03	genotype_quality=1263.9	ks_quality_p_value=0.622074	log10_base_likelihood=-8.3735	log10_qual_likelihood_position_model=1.36422	log10_strand_likelihood_position_model=0.671306	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.85344e-08	ref_cov=116/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/137
RA	288	.	NC_007779	2331120	0	T	G	bias_e_value=8.63267e-12	bias_p_value=1.85795e-18	fisher_strand_p_value=4.07017e-20	frequency=1.354046e-01	genotype_quality=667.7	ks_quality_p_value=1	log10_base_likelihood=-23.301	log10_qual_likelihood_position_model=31.4539	log10_strand_likelihood_position_model=19.3904	new_cov=45/0	polymorphism_quality=18.0	quality=18.0	quality_position_model=Inf	ref_cov=58/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/136
RA	289	.	NC_007779	2332580	0	A	C	bias_e_value=8.68961e-12	bias_p_value=1.87021e-18	fisher_strand_p_value=4.09762e-20	frequency=1.108603e-01	genotype_quality=614.9	ks_quality_p_value=1	log10_base_likelihood=-7.75714	log10_qual_likelihood_position_model=29.4227	log10_strand_likelihood_position_model=19.3875	new_cov=0/47	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=121/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/103
RA	290	.	NC_007779	2342393	0	A	C	bias_e_value=0.000487371	bias_p_value=1.04894e-10	fisher_strand_p_value=3.84446e-12	frequency=6.743574e-02	genotype_quality=697.5	ks_quality_p_value=1	log10_base_likelihood=-6.44227	log10_qual_likelihood_position_model=22.9116	log10_strand_likelihood_position_model=11.4152	new_cov=0/23	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=140/54	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/78
RA	291	.	NC_007779	2348480	0	G	T	bias_e_value=1.5725	bias_p_value=3.38439e-07	fisher_strand_p_value=1.7969e-08	frequency=5.614710e-02	genotype_quality=825.5	ks_quality_p_value=1	log10_base_likelihood=-6.48474	log10_qual_likelihood_position_model=23.7899	log10_strand_likelihood_position_model=7.74548	new_cov=0/20	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=127/78	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/98
RA	292	.	NC_007779	2353815	0	A	C	bias_e_value=9.29751e-05	bias_p_value=2.00104e-11	fisher_strand_p_value=6.89964e-13	frequency=6.939268e-02	genotype_quality=545.6	ks_quality_p_value=1	log10_base_likelihood=-7.14384	log10_qual_likelihood_position_model=19.2554	log10_strand_likelihood_position_model=12.1612	new_cov=0/19	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=116/25	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/44
RA	293	.	NC_007779	2354291	0	A	C	bias_e_value=0.208609	bias_p_value=4.48977e-08	fisher_strand_p_value=2.1419e-09	frequency=5.523634e-02	genotype_quality=871.8	ks_quality_p_value=1	log10_base_likelihood=-7.51649	log10_qual_likelihood_position_model=25.2161	log10_strand_likelihood_position_model=8.6692	new_cov=0/23	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=153/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=153/122
RA	294	.	NC_007779	2379467	0	C	T	bias_e_value=3569680	bias_p_value=0.76828	fisher_strand_p_value=1	frequency=1.820850e-02	genotype_quality=642.5	ks_quality_p_value=0.40193	log10_base_likelihood=-5.6792	log10_qual_likelihood_position_model=3.30209	log10_strand_likelihood_position_model=0.375896	new_cov=2/1	polymorphism_quality=0.1	quality=0.1	quality_position_model=0.00104321	ref_cov=91/70	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=93/71
RA	295	.	NC_007779	2387486	1	.	A	bias_e_value=1984870	bias_p_value=0.427191	fisher_strand_p_value=0.274153	frequency=1.136303e-02	genotype_quality=1297.9	ks_quality_p_value=0.533052	log10_base_likelihood=-12.434	log10_qual_likelihood_position_model=2.5923	log10_strand_likelihood_position_model=0.680505	new_cov=0/3	polymorphism_quality=7.0	quality=7.0	quality_position_model=3.59899e-11	ref_cov=107/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/157
RA	296	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=943.6	new_cov=137/100	quality=943.6	ref_cov=0/0	tot_cov=137/100
RA	297	.	NC_007779	2410316	0	A	C	bias_e_value=0.00218379	bias_p_value=4.70003e-10	fisher_strand_p_value=1.82697e-11	frequency=5.628014e-02	genotype_quality=667.2	ks_quality_p_value=1	log10_base_likelihood=-7.71184	log10_qual_likelihood_position_model=25.8521	log10_strand_likelihood_position_model=10.7383	new_cov=0/24	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=128/59	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/83
RA	298	.	NC_007779	2412225	1	.	A	bias_e_value=2675110	bias_p_value=0.575746	fisher_strand_p_value=0.241467	frequency=7.633209e-03	genotype_quality=1289.9	ks_quality_p_value=0.974437	log10_base_likelihood=-8.1073	log10_qual_likelihood_position_model=2.25745	log10_strand_likelihood_position_model=0.617142	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.97721e-07	ref_cov=133/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/129
RA	299	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=904.2	new_cov=107/123	quality=904.2	ref_cov=0/0	tot_cov=107/123
RA	300	.	NC_007779	2417605	0	C	A	bias_e_value=0.000366689	bias_p_value=7.892e-11	fisher_strand_p_value=4.94565e-12	frequency=1.167459e-01	genotype_quality=723.4	ks_quality_p_value=0.578595	log10_base_likelihood=-18.6843	log10_qual_likelihood_position_model=37.8552	log10_strand_likelihood_position_model=11.3665	new_cov=41/0	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=103/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/110
RA	301	.	NC_007779	2418805	1	.	A	bias_e_value=3038790	bias_p_value=0.65402	fisher_strand_p_value=0.503352	frequency=7.936478e-03	genotype_quality=1244.5	ks_quality_p_value=0.584267	log10_base_likelihood=-8.51866	log10_qual_likelihood_position_model=1.88304	log10_strand_likelihood_position_model=0.51818	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=4.82103e-08	ref_cov=137/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/113
RA	302	.	NC_007779	2465370	0	C	A	bias_e_value=10297.3	bias_p_value=0.00221622	fisher_strand_p_value=0.000237255	frequency=3.557014e-02	genotype_quality=542.4	ks_quality_p_value=0.99937	log10_base_likelihood=-5.85123	log10_qual_likelihood_position_model=8.18499	log10_strand_likelihood_position_model=3.62479	new_cov=0/6	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=104/31	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/38
RA	303	.	NC_007779	2468327	0	C	.	bias_e_value=516965	bias_p_value=0.111263	fisher_strand_p_value=0.0250678	frequency=4.999065e-02	genotype_quality=879.4	ks_quality_p_value=0.93342	log10_base_likelihood=-36.4577	log10_qual_likelihood_position_model=5.04261	log10_strand_likelihood_position_model=1.89223	new_cov=1/10	polymorphism_quality=31.3	quality=31.3	quality_position_model=8.85175e-32	ref_cov=96/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=97/123
RA	304	.	NC_007779	2475171	1	.	T	bias_e_value=3494740	bias_p_value=0.75215	fisher_strand_p_value=0.515008	frequency=1.142883e-02	genotype_quality=859.1	ks_quality_p_value=0.746875	log10_base_likelihood=-8.32912	log10_qual_likelihood_position_model=1.38737	log10_strand_likelihood_position_model=0.453717	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.99771e-08	ref_cov=102/71	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/71
RA	305	.	NC_007779	2476279	0	C	G	bias_e_value=3426100	bias_p_value=0.737377	fisher_strand_p_value=0.369606	frequency=2.288914e-02	genotype_quality=762.2	ks_quality_p_value=0.999716	log10_base_likelihood=-7.11927	log10_qual_likelihood_position_model=6.46418	log10_strand_likelihood_position_model=0.769977	new_cov=1/4	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=91/94	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=92/98
RA	306	.	NC_007779	2517218	0	A	C	bias_e_value=1.0384e-09	bias_p_value=2.23489e-16	fisher_strand_p_value=5.48514e-18	frequency=7.975817e-02	genotype_quality=583.9	ks_quality_p_value=1	log10_base_likelihood=-8.74054	log10_qual_likelihood_position_model=29.9549	log10_strand_likelihood_position_model=17.2608	new_cov=0/25	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=133/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/47
RA	307	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=1001.5	new_cov=113/138	quality=1001.5	ref_cov=0/0	tot_cov=113/138
RA	308	.	NC_007779	2556426	0	G	T	bias_e_value=0.397695	bias_p_value=8.55933e-08	fisher_strand_p_value=1.52829e-08	frequency=8.557796e-02	genotype_quality=679.7	ks_quality_p_value=0.276116	log10_base_likelihood=-16.4888	log10_qual_likelihood_position_model=28.487	log10_strand_likelihood_position_model=7.90084	new_cov=0/31	polymorphism_quality=11.2	quality=11.2	quality_position_model=Inf	ref_cov=105/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/147
RA	309	.	NC_007779	2579404	0	G	T	bias_e_value=1247.93	bias_p_value=0.000268584	fisher_strand_p_value=2.29947e-05	frequency=3.045750e-02	genotype_quality=812.7	ks_quality_p_value=1	log10_base_likelihood=-7.87152	log10_qual_likelihood_position_model=12.4288	log10_strand_likelihood_position_model=4.63837	new_cov=0/13	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=126/92	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/105
RA	310	.	NC_007779	2581900	0	G	T	bias_e_value=0.171564	bias_p_value=3.69247e-08	fisher_strand_p_value=1.74446e-09	frequency=5.729103e-02	genotype_quality=869.7	ks_quality_p_value=1	log10_base_likelihood=-9.92577	log10_qual_likelihood_position_model=20.0983	log10_strand_likelihood_position_model=8.75834	new_cov=0/25	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=141/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/126
RA	311	.	NC_007779	2584429	0	T	.	bias_e_value=3431240	bias_p_value=0.738484	fisher_strand_p_value=0.61877	frequency=1.243973e-02	genotype_quality=936.1	ks_quality_p_value=0.598954	log10_base_likelihood=-8.22074	log10_qual_likelihood_position_model=2.06006	log10_strand_likelihood_position_model=0.429716	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.2103e-07	ref_cov=121/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/119
RA	312	.	NC_007779	2601998	0	A	C	bias_e_value=3.98594e-08	bias_p_value=8.57867e-15	fisher_strand_p_value=2.31853e-16	frequency=9.519243e-02	genotype_quality=544.4	ks_quality_p_value=1	log10_base_likelihood=-19.3029	log10_qual_likelihood_position_model=21.1404	log10_strand_likelihood_position_model=15.6348	new_cov=0/18	polymorphism_quality=14.0	quality=14.0	quality_position_model=Inf	ref_cov=126/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/29
RA	313	.	NC_007779	2623159	0	T	G	bias_e_value=9.51409e-14	bias_p_value=2.04766e-20	fisher_strand_p_value=4.07477e-22	frequency=1.592970e-01	genotype_quality=599.7	ks_quality_p_value=1	log10_base_likelihood=-23.9256	log10_qual_likelihood_position_model=30.594	log10_strand_likelihood_position_model=21.3899	new_cov=46/0	polymorphism_quality=18.7	quality=18.7	quality_position_model=Inf	ref_cov=43/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/124
RA	314	.	NC_007779	2648595	0	A	C	bias_e_value=1.89861e-05	bias_p_value=4.08626e-12	fisher_strand_p_value=1.33338e-13	frequency=6.814003e-02	genotype_quality=555.7	ks_quality_p_value=1	log10_base_likelihood=-7.66114	log10_qual_likelihood_position_model=19.1946	log10_strand_likelihood_position_model=12.875	new_cov=0/16	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=129/16	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/32
RA	315	.	NC_007779	2652909	0	T	.	bias_e_value=4646320	bias_p_value=0.999998	fisher_strand_p_value=1	frequency=1.553822e-02	genotype_quality=1023.3	ks_quality_p_value=0.99778	log10_base_likelihood=-10.3887	log10_qual_likelihood_position_model=3.49164	log10_strand_likelihood_position_model=0.426408	new_cov=2/2	polymorphism_quality=5.0	quality=5.0	quality_position_model=2.08188e-08	ref_cov=135/118	reject=INDEL_HOMOPOLYMER	tot_cov=137/120
RA	316	.	NC_007779	2676695	0	T	G	bias_e_value=0.00749581	bias_p_value=1.61327e-09	fisher_strand_p_value=6.60062e-11	frequency=6.670380e-02	genotype_quality=544.7	ks_quality_p_value=1	log10_base_likelihood=-5.69672	log10_qual_likelihood_position_model=29.4242	log10_strand_likelihood_position_model=10.1804	new_cov=25/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=50/97	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=75/97
RA	317	.	NC_007779	2746690	1	.	A	bias_e_value=4604230	bias_p_value=0.990938	fisher_strand_p_value=1	frequency=9.346008e-03	genotype_quality=1056.1	ks_quality_p_value=0.86843	log10_base_likelihood=-8.47106	log10_qual_likelihood_position_model=0.735964	log10_strand_likelihood_position_model=0.306495	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.14866e-09	ref_cov=92/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=93/121
RA	318	.	NC_007779	2791171	0	G	T	bias_e_value=8.06862	bias_p_value=1.73656e-06	fisher_strand_p_value=1.01536e-07	frequency=4.816389e-02	genotype_quality=818.0	ks_quality_p_value=1	log10_base_likelihood=-6.88904	log10_qual_likelihood_position_model=18.3816	log10_strand_likelihood_position_model=6.99338	new_cov=0/21	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=130/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/123
RA	319	.	NC_007779	2815240	1	.	A	bias_e_value=3805560	bias_p_value=0.819046	fisher_strand_p_value=0.50511	frequency=8.968353e-03	genotype_quality=1090.1	ks_quality_p_value=0.915406	log10_base_likelihood=-8.27056	log10_qual_likelihood_position_model=1.32322	log10_strand_likelihood_position_model=0.504326	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.22317e-08	ref_cov=98/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=98/125
RA	320	.	NC_007779	2816615	0	G	C	bias_e_value=0.0510694	bias_p_value=1.09913e-08	fisher_strand_p_value=6.24844e-10	frequency=8.557367e-02	genotype_quality=665.0	ks_quality_p_value=0.784001	log10_base_likelihood=-16.8627	log10_qual_likelihood_position_model=24.4971	log10_strand_likelihood_position_model=9.20423	new_cov=22/0	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=66/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=88/125
RA	321	.	NC_007779	2817030	0	G	C	bias_e_value=7.16809e-10	bias_p_value=1.54274e-16	fisher_strand_p_value=6.57037e-18	frequency=1.629653e-01	genotype_quality=606.2	ks_quality_p_value=0.570958	log10_base_likelihood=-46.0596	log10_qual_likelihood_position_model=34.8365	log10_strand_likelihood_position_model=17.1824	new_cov=39/0	polymorphism_quality=41.0	quality=41.0	quality_position_model=Inf	ref_cov=54/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=93/128
RA	322	.	NC_007779	2825118	1	.	A	bias_e_value=4583980	bias_p_value=0.986579	fisher_strand_p_value=1	frequency=1.345253e-02	genotype_quality=1070.7	ks_quality_p_value=0.840704	log10_base_likelihood=-12.6858	log10_qual_likelihood_position_model=1.95641	log10_strand_likelihood_position_model=0.388462	new_cov=2/1	polymorphism_quality=7.3	quality=7.3	quality_position_model=2.24496e-12	ref_cov=120/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/101
RA	323	.	NC_007779	2833989	0	A	C	bias_e_value=3.54529e-09	bias_p_value=7.6303e-16	fisher_strand_p_value=1.93245e-17	frequency=9.919548e-02	genotype_quality=647.3	ks_quality_p_value=1	log10_base_likelihood=-11.2978	log10_qual_likelihood_position_model=25.6818	log10_strand_likelihood_position_model=16.7139	new_cov=0/32	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=134/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/74
RA	324	.	NC_007779	2847445	0	G	T	bias_e_value=0.0957935	bias_p_value=2.0617e-08	fisher_strand_p_value=9.46688e-10	frequency=7.111931e-02	genotype_quality=769.5	ks_quality_p_value=1	log10_base_likelihood=-8.81981	log10_qual_likelihood_position_model=19.1616	log10_strand_likelihood_position_model=9.02379	new_cov=0/27	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=127/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/123
RA	325	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1174.9	new_cov=126/148	quality=1174.9	ref_cov=0/0	tot_cov=126/148
RA	326	.	NC_007779	2868094	0	C	A	bias_e_value=0.000751044	bias_p_value=1.61642e-10	fisher_strand_p_value=6.03429e-12	frequency=1.199136e-01	genotype_quality=689.7	ks_quality_p_value=0.99821	log10_base_likelihood=-18.7289	log10_qual_likelihood_position_model=23.3765	log10_strand_likelihood_position_model=11.2685	new_cov=37/0	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=91/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/111
RA	327	.	NC_007779	2895131	0	A	C	bias_e_value=6.85501e-09	bias_p_value=1.47536e-15	fisher_strand_p_value=3.80164e-17	frequency=1.724162e-01	genotype_quality=461.5	ks_quality_p_value=1	log10_base_likelihood=-23.5091	log10_qual_likelihood_position_model=33.8219	log10_strand_likelihood_position_model=16.42	new_cov=0/36	polymorphism_quality=18.3	quality=18.3	quality_position_model=Inf	ref_cov=93/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/69
RA	328	.	NC_007779	2898954	0	A	.	bias_e_value=4618060	bias_p_value=0.993915	fisher_strand_p_value=1	frequency=1.144218e-02	genotype_quality=1058.0	ks_quality_p_value=0.89173	log10_base_likelihood=-8.07915	log10_qual_likelihood_position_model=1.32131	log10_strand_likelihood_position_model=0.424308	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.88378e-08	ref_cov=130/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/131
RA	329	.	NC_007779	2899216	0	T	.	bias_e_value=4563130	bias_p_value=0.982093	fisher_strand_p_value=1	frequency=1.185036e-02	genotype_quality=994.5	ks_quality_p_value=0.816823	log10_base_likelihood=-8.37635	log10_qual_likelihood_position_model=2.47747	log10_strand_likelihood_position_model=0.424242	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.23101e-07	ref_cov=124/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/127
RA	330	.	NC_007779	2926157	0	T	G	bias_e_value=9.78134e-08	bias_p_value=2.10517e-14	fisher_strand_p_value=5.83515e-16	frequency=5.536604e-02	genotype_quality=641.4	ks_quality_p_value=1	log10_base_likelihood=-6.63438	log10_qual_likelihood_position_model=22.1256	log10_strand_likelihood_position_model=15.2339	new_cov=19/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=18/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/146
RA	331	.	NC_007779	2939008	0	A	C	bias_e_value=321.927	bias_p_value=6.92863e-05	fisher_strand_p_value=5.26733e-06	frequency=4.869366e-02	genotype_quality=705.4	ks_quality_p_value=1	log10_base_likelihood=-6.16149	log10_qual_likelihood_position_model=16.9209	log10_strand_likelihood_position_model=5.27841	new_cov=0/16	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=113/91	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/107
RA	332	.	NC_007779	2983097	0	A	C	bias_e_value=5.01207e-06	bias_p_value=1.07872e-12	fisher_strand_p_value=3.3687e-14	frequency=8.838892e-02	genotype_quality=558.5	ks_quality_p_value=1	log10_base_likelihood=-6.58902	log10_qual_likelihood_position_model=37.3958	log10_strand_likelihood_position_model=13.4725	new_cov=0/37	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=101/59	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=101/96
RA	333	.	NC_007779	2987535	0	A	C	bias_e_value=4.1864e-07	bias_p_value=9.01013e-14	fisher_strand_p_value=2.6055e-15	frequency=1.035323e-01	genotype_quality=824.4	ks_quality_p_value=1	log10_base_likelihood=-18.9895	log10_qual_likelihood_position_model=40.4396	log10_strand_likelihood_position_model=14.5841	new_cov=0/42	polymorphism_quality=13.7	quality=13.7	quality_position_model=Inf	ref_cov=144/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/139
RA	334	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=969.7	new_cov=114/126	quality=969.7	ref_cov=0/0	tot_cov=114/126
RA	335	.	NC_007779	3019578	0	T	.	bias_e_value=1903480	bias_p_value=0.409675	fisher_strand_p_value=0.280536	frequency=1.126766e-02	genotype_quality=1025.4	ks_quality_p_value=0.488978	log10_base_likelihood=-7.77271	log10_qual_likelihood_position_model=2.94307	log10_strand_likelihood_position_model=0.657388	new_cov=0/3	polymorphism_quality=2.3	quality=2.3	quality_position_model=5.07507e-06	ref_cov=105/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/161
RA	336	.	NC_007779	3034413	0	A	C	bias_e_value=1.05803e-13	bias_p_value=2.27714e-20	fisher_strand_p_value=4.54122e-22	frequency=1.415987e-01	genotype_quality=566.3	ks_quality_p_value=1	log10_base_likelihood=-15.6551	log10_qual_likelihood_position_model=30.9024	log10_strand_likelihood_position_model=21.3428	new_cov=0/41	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=121/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/75
RA	337	.	NC_007779	3035390	0	T	C	bias_e_value=1.47467e-06	bias_p_value=3.17385e-13	fisher_strand_p_value=9.53573e-15	frequency=1.322231e-01	genotype_quality=476.7	ks_quality_p_value=1	log10_base_likelihood=-26.7037	log10_qual_likelihood_position_model=21.9949	log10_strand_likelihood_position_model=14.0206	new_cov=0/28	polymorphism_quality=21.5	quality=21.5	quality_position_model=Inf	ref_cov=123/43	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/71
RA	338	.	NC_007779	3044712	0	T	C	bias_e_value=1398.64	bias_p_value=0.00030102	fisher_strand_p_value=2.60699e-05	frequency=3.761005e-02	genotype_quality=380.1	ks_quality_p_value=0.999237	log10_base_likelihood=-5.89908	log10_qual_likelihood_position_model=5.5429	log10_strand_likelihood_position_model=4.58386	new_cov=5/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=11/101	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/101
RA	339	.	NC_007779	3044714	0	A	C	bias_e_value=6132.5	bias_p_value=0.00131986	fisher_strand_p_value=0.000132979	frequency=5.097628e-02	genotype_quality=362.7	ks_quality_p_value=1	log10_base_likelihood=-6.95777	log10_qual_likelihood_position_model=8.58305	log10_strand_likelihood_position_model=3.89152	new_cov=6/2	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=13/104	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=19/107
RA	340	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=971.4	new_cov=114/129	quality=971.4	ref_cov=0/0	tot_cov=114/129
RA	341	.	NC_007779	3084663	0	C	A	bias_e_value=0.0719792	bias_p_value=1.54916e-08	fisher_strand_p_value=7.01692e-10	frequency=4.898310e-02	genotype_quality=953.2	ks_quality_p_value=1	log10_base_likelihood=-8.02652	log10_qual_likelihood_position_model=24.7807	log10_strand_likelihood_position_model=9.15385	new_cov=27/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=114/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/151
RA	342	.	NC_007779	3088549	0	G	T	bias_e_value=13.4988	bias_p_value=2.90525e-06	fisher_strand_p_value=1.75483e-07	frequency=8.266783e-02	genotype_quality=674.1	ks_quality_p_value=1	log10_base_likelihood=-10.918	log10_qual_likelihood_position_model=20.2473	log10_strand_likelihood_position_model=6.91145	new_cov=0/29	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=94/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/143
RA	343	.	NC_007779	3145269	0	C	A	deleted=1	frequency=1	genotype_quality=0.7	new_cov=1/0	quality=0.7	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	344	.	NC_007779	3145272	0	T	C	deleted=1	frequency=1	genotype_quality=0.7	new_cov=1/0	quality=0.7	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	345	.	NC_007779	3152854	1	.	A	bias_e_value=3661710	bias_p_value=0.788086	fisher_strand_p_value=0.60707	frequency=1.234531e-02	genotype_quality=1182.0	ks_quality_p_value=0.698984	log10_base_likelihood=-12.8822	log10_qual_likelihood_position_model=1.60546	log10_strand_likelihood_position_model=0.445358	new_cov=1/2	polymorphism_quality=7.5	quality=7.5	quality_position_model=7.09697e-13	ref_cov=126/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/116
RA	346	.	NC_007779	3162929	0	G	C	bias_e_value=5453.99	bias_p_value=0.00117383	fisher_strand_p_value=0.000124334	frequency=3.520966e-02	genotype_quality=715.1	ks_quality_p_value=0.938868	log10_base_likelihood=-5.80969	log10_qual_likelihood_position_model=14.5074	log10_strand_likelihood_position_model=3.90541	new_cov=11/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=85/115	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=96/115
RA	347	.	NC_007779	3186085	0	T	.	bias_e_value=4499750	bias_p_value=0.968453	fisher_strand_p_value=1	frequency=9.924889e-03	genotype_quality=1186.5	ks_quality_p_value=0.759566	log10_base_likelihood=-7.87217	log10_qual_likelihood_position_model=2.32389	log10_strand_likelihood_position_model=0.398408	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.84889e-07	ref_cov=159/140	reject=POLYMORPHISM_STRAND	tot_cov=161/141
RA	348	.	NC_007779	3193538	1	.	A	bias_e_value=2117210	bias_p_value=0.455672	fisher_strand_p_value=0.164199	frequency=6.943703e-03	genotype_quality=1422.7	ks_quality_p_value=0.982622	log10_base_likelihood=-7.78919	log10_qual_likelihood_position_model=1.9982	log10_strand_likelihood_position_model=0.784631	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=6.83667e-07	ref_cov=115/171	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/171
RA	349	.	NC_007779	3212355	0	G	C	bias_e_value=1280.89	bias_p_value=0.000275678	fisher_strand_p_value=2.44954e-05	frequency=4.499626e-02	genotype_quality=721.3	ks_quality_p_value=0.965892	log10_base_likelihood=-9.6168	log10_qual_likelihood_position_model=12.5428	log10_strand_likelihood_position_model=4.61092	new_cov=11/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=71/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=82/125
RA	350	.	NC_007779	3216602	0	C	A	bias_e_value=195820	bias_p_value=0.0421451	fisher_strand_p_value=0.12256	frequency=1.619053e-02	genotype_quality=998.7	ks_quality_p_value=0.0577936	log10_base_likelihood=-7.40298	log10_qual_likelihood_position_model=4.37516	log10_strand_likelihood_position_model=1.16568	new_cov=0/4	polymorphism_quality=1.9	quality=1.9	quality_position_model=0.00148225	ref_cov=120/123	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=120/128
RA	351	.	NC_007779	3216614	0	C	T	bias_e_value=323220	bias_p_value=0.0695646	fisher_strand_p_value=0.122575	frequency=1.597786e-02	genotype_quality=1020.8	ks_quality_p_value=0.106261	log10_base_likelihood=-7.49705	log10_qual_likelihood_position_model=2.94768	log10_strand_likelihood_position_model=1.16599	new_cov=0/4	polymorphism_quality=2.0	quality=2.0	quality_position_model=3.4329e-05	ref_cov=121/124	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=121/128
RA	352	.	NC_007779	3216644	0	A	G	bias_e_value=1065930	bias_p_value=0.229414	fisher_strand_p_value=0.122418	frequency=1.456451e-02	genotype_quality=1051.1	ks_quality_p_value=0.491895	log10_base_likelihood=-8.4867	log10_qual_likelihood_position_model=2.73292	log10_strand_likelihood_position_model=1.1883	new_cov=0/4	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.96896e-06	ref_cov=135/135	reject=POLYMORPHISM_STRAND	tot_cov=135/139
RA	353	.	NC_007779	3216647	0	C	A	bias_e_value=1735710	bias_p_value=0.373566	fisher_strand_p_value=0.122516	frequency=1.439381e-02	genotype_quality=1146.4	ks_quality_p_value=0.976136	log10_base_likelihood=-6.35236	log10_qual_likelihood_position_model=3.42369	log10_strand_likelihood_position_model=1.18207	new_cov=0/4	polymorphism_quality=0.8	quality=0.8	quality_position_model=0.00198797	ref_cov=135/136	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=136/140
RA	354	.	NC_007779	3231302	0	C	G	bias_e_value=31.1798	bias_p_value=6.71064e-06	fisher_strand_p_value=4.28435e-07	frequency=5.921459e-02	genotype_quality=749.0	ks_quality_p_value=1	log10_base_likelihood=-12.2064	log10_qual_likelihood_position_model=14.1829	log10_strand_likelihood_position_model=6.36811	new_cov=0/14	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=132/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/78
RA	355	.	NC_007779	3238315	1	.	T	bias_e_value=3845820	bias_p_value=0.82771	fisher_strand_p_value=0.498581	frequency=1.599979e-02	genotype_quality=557.5	ks_quality_p_value=0.950286	log10_base_likelihood=-8.26001	log10_qual_likelihood_position_model=2.08312	log10_strand_likelihood_position_model=0.544713	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.53184e-07	ref_cov=65/58	reject=POLYMORPHISM_STRAND	tot_cov=67/58
RA	356	.	NC_007779	3238317	1	.	C	bias_e_value=3323690	bias_p_value=0.715335	fisher_strand_p_value=0.495868	frequency=1.639366e-02	genotype_quality=528.9	ks_quality_p_value=0.701806	log10_base_likelihood=-8.59249	log10_qual_likelihood_position_model=2.13572	log10_strand_likelihood_position_model=0.605664	new_cov=2/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=9.08944e-08	ref_cov=59/61	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=61/61
RA	357	.	NC_007779	3238322	0	T	C	bias_e_value=34174.8	bias_p_value=0.00735522	fisher_strand_p_value=0.000920482	frequency=5.419588e-02	genotype_quality=359.7	ks_quality_p_value=1	log10_base_likelihood=-6.21042	log10_qual_likelihood_position_model=9.58218	log10_strand_likelihood_position_model=3.03598	new_cov=8/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=45/69	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=53/69
RA	358	.	NC_007779	3239641	0	T	G	bias_e_value=48.0678	bias_p_value=1.03453e-05	fisher_strand_p_value=6.806e-07	frequency=4.818821e-02	genotype_quality=570.4	ks_quality_p_value=1	log10_base_likelihood=-5.60814	log10_qual_likelihood_position_model=13.8406	log10_strand_likelihood_position_model=6.16711	new_cov=18/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=74/100	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/100
RA	359	.	NC_007779	3243783	1	.	T	bias_e_value=576334	bias_p_value=0.124041	fisher_strand_p_value=1	frequency=8.889198e-03	genotype_quality=1068.3	ks_quality_p_value=0.0268669	log10_base_likelihood=-8.22789	log10_qual_likelihood_position_model=2.8451	log10_strand_likelihood_position_model=0.311001	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.84521e-07	ref_cov=93/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=94/131
RA	360	.	NC_007779	3256890	1	.	A	bias_e_value=2085220	bias_p_value=0.448789	fisher_strand_p_value=0.217775	frequency=7.604599e-03	genotype_quality=1293.7	ks_quality_p_value=0.723665	log10_base_likelihood=-8.2509	log10_qual_likelihood_position_model=1.20157	log10_strand_likelihood_position_model=0.661992	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.53759e-08	ref_cov=140/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/123
RA	361	.	NC_007779	3274975	0	G	T	bias_e_value=1.3074	bias_p_value=2.81383e-07	fisher_strand_p_value=1.53644e-08	frequency=3.241539e-02	genotype_quality=900.8	ks_quality_p_value=0.962398	log10_base_likelihood=-6.58292	log10_qual_likelihood_position_model=17.1504	log10_strand_likelihood_position_model=7.81348	new_cov=0/13	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=176/52	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=176/66
RA	362	.	NC_007779	3279132	0	A	.	bias_e_value=2190210	bias_p_value=0.471385	fisher_strand_p_value=1	frequency=1.148605e-02	genotype_quality=1040.3	ks_quality_p_value=0.170086	log10_base_likelihood=-8.18049	log10_qual_likelihood_position_model=1.84788	log10_strand_likelihood_position_model=0.409983	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=7.6655e-08	ref_cov=133/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/126
RA	363	.	NC_007779	3280326	0	A	C	bias_e_value=7.69274e-20	bias_p_value=1.65566e-26	fisher_strand_p_value=2.56571e-28	frequency=1.506863e-01	genotype_quality=671.9	ks_quality_p_value=1	log10_base_likelihood=-21.6535	log10_qual_likelihood_position_model=37.8415	log10_strand_likelihood_position_model=27.5908	new_cov=0/49	polymorphism_quality=16.4	quality=16.4	quality_position_model=Inf	ref_cov=148/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=148/83
RA	364	.	NC_007779	3287872	1	.	G	bias_e_value=3729940	bias_p_value=0.80277	fisher_strand_p_value=0.502744	frequency=9.661674e-03	genotype_quality=1009.9	ks_quality_p_value=0.878935	log10_base_likelihood=-8.4651	log10_qual_likelihood_position_model=2.59641	log10_strand_likelihood_position_model=0.519854	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.01312e-07	ref_cov=112/93	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/93
RA	365	.	NC_007779	3295537	0	G	C	bias_e_value=4616.38	bias_p_value=0.000993553	fisher_strand_p_value=9.70212e-05	frequency=3.998756e-02	genotype_quality=661.0	ks_quality_p_value=1	log10_base_likelihood=-6.92224	log10_qual_likelihood_position_model=10.3194	log10_strand_likelihood_position_model=4.01313	new_cov=10/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=65/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=75/107
RA	366	.	NC_007779	3300073	0	T	G	bias_e_value=0.00534151	bias_p_value=1.14962e-09	fisher_strand_p_value=4.6366e-11	frequency=1.135650e-01	genotype_quality=511.2	ks_quality_p_value=1	log10_base_likelihood=-11.6976	log10_qual_likelihood_position_model=31.6494	log10_strand_likelihood_position_model=10.6159	new_cov=35/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=68/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/86
RA	367	.	NC_007779	3347716	1	.	G	bias_e_value=2465560	bias_p_value=0.530647	fisher_strand_p_value=0.244805	frequency=8.333206e-03	genotype_quality=1188.3	ks_quality_p_value=0.839398	log10_base_likelihood=-8.16171	log10_qual_likelihood_position_model=0.826338	log10_strand_likelihood_position_model=0.61118	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.14038e-08	ref_cov=117/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/121
RA	368	.	NC_007779	3357279	0	C	A	bias_e_value=29.0586	bias_p_value=6.25409e-06	fisher_strand_p_value=4.45979e-07	frequency=4.998636e-02	genotype_quality=665.6	ks_quality_p_value=0.891023	log10_base_likelihood=-7.07348	log10_qual_likelihood_position_model=17.3564	log10_strand_likelihood_position_model=6.35069	new_cov=16/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=72/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=88/120
RA	369	.	NC_007779	3385701	0	T	.	bias_e_value=4630220	bias_p_value=0.996531	fisher_strand_p_value=1	frequency=1.044178e-02	genotype_quality=1106.3	ks_quality_p_value=0.917874	log10_base_likelihood=-7.62731	log10_qual_likelihood_position_model=2.84602	log10_strand_likelihood_position_model=0.392284	new_cov=1/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=3.01018e-06	ref_cov=130/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/156
RA	370	.	NC_007779	3389914	0	A	C	bias_e_value=8.01401e-06	bias_p_value=1.7248e-12	fisher_strand_p_value=5.46913e-14	frequency=8.913946e-02	genotype_quality=687.3	ks_quality_p_value=1	log10_base_likelihood=-9.79774	log10_qual_likelihood_position_model=29.926	log10_strand_likelihood_position_model=13.3158	new_cov=0/40	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=117/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/122
RA	371	.	NC_007779	3392267	0	C	A	bias_e_value=0.166226	bias_p_value=3.57758e-08	fisher_strand_p_value=1.68754e-09	frequency=4.534054e-02	genotype_quality=912.4	ks_quality_p_value=1	log10_base_likelihood=-8.34522	log10_qual_likelihood_position_model=18.2827	log10_strand_likelihood_position_model=8.78164	new_cov=22/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=79/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/166
RA	372	.	NC_007779	3397405	0	A	C	bias_e_value=3.653e-07	bias_p_value=7.86212e-14	fisher_strand_p_value=2.26434e-15	frequency=6.951714e-02	genotype_quality=613.2	ks_quality_p_value=1	log10_base_likelihood=-6.15572	log10_qual_likelihood_position_model=21.9812	log10_strand_likelihood_position_model=14.6451	new_cov=0/29	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=128/44	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/75
RA	373	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1157.7	new_cov=149/122	quality=1157.7	ref_cov=0/0	tot_cov=149/122
RA	374	.	NC_007779	3404070	0	T	G	bias_e_value=0.000961503	bias_p_value=2.06938e-10	fisher_strand_p_value=7.78586e-12	frequency=9.291553e-02	genotype_quality=596.8	ks_quality_p_value=1	log10_base_likelihood=-13.3538	log10_qual_likelihood_position_model=21.9207	log10_strand_likelihood_position_model=11.1087	new_cov=32/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=70/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=102/105
RA	375	.	NC_007779	3407691	0	T	G	bias_e_value=0.138259	bias_p_value=2.97567e-08	fisher_strand_p_value=1.39094e-09	frequency=4.052448e-02	genotype_quality=773.7	ks_quality_p_value=1	log10_base_likelihood=-5.59179	log10_qual_likelihood_position_model=25.4982	log10_strand_likelihood_position_model=8.85669	new_cov=19/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=63/140	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/140
RA	376	.	NC_007779	3407746	0	C	A	bias_e_value=133.555	bias_p_value=2.87441e-05	fisher_strand_p_value=2.03808e-06	frequency=4.556656e-02	genotype_quality=817.3	ks_quality_p_value=1	log10_base_likelihood=-8.24547	log10_qual_likelihood_position_model=19.6996	log10_strand_likelihood_position_model=5.7056	new_cov=18/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=91/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/138
RA	377	.	NC_007779	3412753	0	C	T	bias_e_value=4.23474	bias_p_value=9.11416e-07	fisher_strand_p_value=5.12414e-08	frequency=5.341768e-02	genotype_quality=767.5	ks_quality_p_value=1	log10_base_likelihood=-7.80604	log10_qual_likelihood_position_model=19.1398	log10_strand_likelihood_position_model=7.29038	new_cov=0/16	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=136/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/81
RA	378	.	NC_007779	3421203	0	T	C	bias_e_value=0.000826344	bias_p_value=1.77849e-10	fisher_strand_p_value=6.652e-12	frequency=7.407713e-02	genotype_quality=648.8	ks_quality_p_value=1	log10_base_likelihood=-6.31939	log10_qual_likelihood_position_model=19.6953	log10_strand_likelihood_position_model=11.177	new_cov=0/23	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=131/52	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/75
RA	379	.	NC_007779	3431259	0	T	G	bias_e_value=1056880	bias_p_value=0.227465	fisher_strand_p_value=0.0596399	frequency=1.914120e-02	genotype_quality=820.0	ks_quality_p_value=0.998064	log10_base_likelihood=-5.82756	log10_qual_likelihood_position_model=7.37556	log10_strand_likelihood_position_model=1.52549	new_cov=0/5	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=109/104	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=109/109
RA	380	.	NC_007779	3439587	0	A	C	bias_e_value=359922	bias_p_value=0.0774636	fisher_strand_p_value=0.0151093	frequency=3.900719e-02	genotype_quality=775.3	ks_quality_p_value=0.984393	log10_base_likelihood=-10.9716	log10_qual_likelihood_position_model=10.696	log10_strand_likelihood_position_model=1.99547	new_cov=10/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=130/79	reject=POLYMORPHISM_STRAND	tot_cov=140/79
RA	381	.	NC_007779	3439592	0	G	.	bias_e_value=521715	bias_p_value=0.112285	fisher_strand_p_value=0.0238148	frequency=3.692436e-02	genotype_quality=772.2	ks_quality_p_value=0.993983	log10_base_likelihood=-18.1369	log10_qual_likelihood_position_model=10.9594	log10_strand_likelihood_position_model=1.75838	new_cov=8/0	polymorphism_quality=12.8	quality=12.8	quality_position_model=2.54724e-07	ref_cov=120/82	reject=POLYMORPHISM_STRAND	tot_cov=134/82
RA	382	.	NC_007779	3439597	1	.	G	bias_e_value=3047490	bias_p_value=0.655892	fisher_strand_p_value=0.295674	frequency=1.568604e-02	genotype_quality=904.3	ks_quality_p_value=0.999833	log10_base_likelihood=-7.63548	log10_qual_likelihood_position_model=4.0167	log10_strand_likelihood_position_model=0.609639	new_cov=3/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=8.56509e-05	ref_cov=117/71	reject=POLYMORPHISM_STRAND	tot_cov=120/71
RA	383	.	NC_007779	3439598	1	.	T	bias_e_value=2105410	bias_p_value=0.453134	fisher_strand_p_value=0.160371	frequency=2.645493e-02	genotype_quality=878.5	ks_quality_p_value=0.997415	log10_base_likelihood=-21.4622	log10_qual_likelihood_position_model=5.90853	log10_strand_likelihood_position_model=0.999892	new_cov=5/0	polymorphism_quality=16.2	quality=16.2	quality_position_model=1.16568e-16	ref_cov=115/69	reject=POLYMORPHISM_STRAND	tot_cov=120/69
RA	384	.	NC_007779	3439601	0	G	T	bias_e_value=9316.73	bias_p_value=0.00200518	fisher_strand_p_value=0.000211987	frequency=8.438635e-02	genotype_quality=711.2	ks_quality_p_value=1	log10_base_likelihood=-18.5564	log10_qual_likelihood_position_model=21.5782	log10_strand_likelihood_position_model=3.73167	new_cov=18/0	polymorphism_quality=13.3	quality=13.3	quality_position_model=Inf	ref_cov=110/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/73
RA	385	.	NC_007779	3439605	0	T	C	bias_e_value=141176	bias_p_value=0.0303845	fisher_strand_p_value=0.00479187	frequency=4.514313e-02	genotype_quality=704.2	ks_quality_p_value=1	log10_base_likelihood=-7.76586	log10_qual_likelihood_position_model=17.914	log10_strand_likelihood_position_model=2.56541	new_cov=13/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=120/73	reject=POLYMORPHISM_STRAND	tot_cov=133/73
RA	386	.	NC_007779	3439607	0	G	T	bias_e_value=9354.59	bias_p_value=0.00201333	fisher_strand_p_value=0.00021295	frequency=7.879829e-02	genotype_quality=757.3	ks_quality_p_value=1	log10_base_likelihood=-17.2448	log10_qual_likelihood_position_model=20.1047	log10_strand_likelihood_position_model=3.82472	new_cov=19/0	polymorphism_quality=11.9	quality=11.9	quality_position_model=Inf	ref_cov=114/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/73
RA	387	.	NC_007779	3475527	0	T	G	bias_e_value=0.000928444	bias_p_value=1.99823e-10	fisher_strand_p_value=7.50789e-12	frequency=1.062684e-01	genotype_quality=621.6	ks_quality_p_value=1	log10_base_likelihood=-16.913	log10_qual_likelihood_position_model=23.895	log10_strand_likelihood_position_model=11.2572	new_cov=36/0	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=80/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/103
RA	388	.	NC_007779	3475533	0	C	T	bias_e_value=1.53351	bias_p_value=3.30048e-07	fisher_strand_p_value=1.74989e-08	frequency=1.016245e-01	genotype_quality=690.4	ks_quality_p_value=1	log10_base_likelihood=-19.8507	log10_qual_likelihood_position_model=32.9641	log10_strand_likelihood_position_model=7.7694	new_cov=26/0	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=97/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/109
RA	389	.	NC_007779	3478395	1	.	T	bias_e_value=3379930	bias_p_value=0.727441	fisher_strand_p_value=1	frequency=7.462502e-03	genotype_quality=1283.7	ks_quality_p_value=0.359654	log10_base_likelihood=-8.07688	log10_qual_likelihood_position_model=1.83929	log10_strand_likelihood_position_model=0.300957	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=7.41399e-08	ref_cov=125/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/142
RA	390	.	NC_007779	3478396	0	T	.	bias_e_value=2491380	bias_p_value=0.536204	fisher_strand_p_value=0.250501	frequency=1.093960e-02	genotype_quality=1082.8	ks_quality_p_value=0.834405	log10_base_likelihood=-8.00474	log10_qual_likelihood_position_model=1.54763	log10_strand_likelihood_position_model=0.824399	new_cov=0/3	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.52987e-07	ref_cov=128/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/146
RA	391	.	NC_007779	3499066	0	A	C	bias_e_value=0.314868	bias_p_value=6.77671e-08	fisher_strand_p_value=3.30104e-09	frequency=6.069565e-02	genotype_quality=657.2	ks_quality_p_value=1	log10_base_likelihood=-9.07148	log10_qual_likelihood_position_model=18.2667	log10_strand_likelihood_position_model=8.48135	new_cov=0/16	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=132/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/63
RA	392	.	NC_007779	3519465	1	.	A	bias_e_value=2704010	bias_p_value=0.581967	fisher_strand_p_value=0.241595	frequency=7.518768e-03	genotype_quality=1319.5	ks_quality_p_value=0.991831	log10_base_likelihood=-8.05968	log10_qual_likelihood_position_model=2.2439	log10_strand_likelihood_position_model=0.616913	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.31252e-07	ref_cov=135/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/131
RA	393	.	NC_007779	3520391	0	C	G	bias_e_value=0.000633353	bias_p_value=1.36312e-10	fisher_strand_p_value=5.0463e-12	frequency=5.850935e-02	genotype_quality=595.0	ks_quality_p_value=1	log10_base_likelihood=-11.2528	log10_qual_likelihood_position_model=12.2389	log10_strand_likelihood_position_model=11.297	new_cov=11/0	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=9/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=20/142
RA	394	.	NC_007779	3523734	0	G	T	bias_e_value=1.8102	bias_p_value=3.89597e-07	fisher_strand_p_value=2.08498e-08	frequency=5.016184e-02	genotype_quality=845.4	ks_quality_p_value=1	log10_base_likelihood=-9.89238	log10_qual_likelihood_position_model=20.1462	log10_strand_likelihood_position_model=7.70223	new_cov=0/28	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=123/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/154
RA	395	.	NC_007779	3523811	1	.	T	bias_e_value=4263380	bias_p_value=0.91758	fisher_strand_p_value=1	frequency=7.662773e-03	genotype_quality=1290.9	ks_quality_p_value=0.622516	log10_base_likelihood=-8.17995	log10_qual_likelihood_position_model=1.16193	log10_strand_likelihood_position_model=0.301209	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.16051e-08	ref_cov=121/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/139
RA	396	.	NC_007779	3526752	1	.	T	bias_e_value=2625370	bias_p_value=0.565041	fisher_strand_p_value=0.235915	frequency=8.771896e-03	genotype_quality=1124.6	ks_quality_p_value=0.966346	log10_base_likelihood=-8.00904	log10_qual_likelihood_position_model=2.59339	log10_strand_likelihood_position_model=0.627245	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.1528e-06	ref_cov=117/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/111
RA	397	.	NC_007779	3530293	1	.	A	bias_e_value=4630270	bias_p_value=0.996543	fisher_strand_p_value=1	frequency=7.873535e-03	genotype_quality=1243.5	ks_quality_p_value=0.918006	log10_base_likelihood=-7.44886	log10_qual_likelihood_position_model=2.72877	log10_strand_likelihood_position_model=0.311357	new_cov=1/1	polymorphism_quality=1.9	quality=1.9	quality_position_model=2.87063e-06	ref_cov=147/105	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/106
RA	398	.	NC_007779	3543547	0	A	C	bias_e_value=4.10637e-11	bias_p_value=8.83788e-18	fisher_strand_p_value=2.0062e-19	frequency=1.802516e-01	genotype_quality=653.5	ks_quality_p_value=1	log10_base_likelihood=-33.3368	log10_qual_likelihood_position_model=51.7692	log10_strand_likelihood_position_model=18.8392	new_cov=0/61	polymorphism_quality=28.2	quality=28.2	quality_position_model=Inf	ref_cov=116/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/145
RA	399	.	NC_007779	3550877	0	C	A	bias_e_value=0.00200038	bias_p_value=4.30529e-10	fisher_strand_p_value=1.66762e-11	frequency=6.144428e-02	genotype_quality=950.5	ks_quality_p_value=1	log10_base_likelihood=-9.67181	log10_qual_likelihood_position_model=23.6815	log10_strand_likelihood_position_model=10.7779	new_cov=32/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=112/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/150
RA	400	.	NC_007779	3560478	0	G	T	bias_e_value=2622.45	bias_p_value=0.000564413	fisher_strand_p_value=5.19464e-05	frequency=2.587414e-02	genotype_quality=896.4	ks_quality_p_value=1	log10_base_likelihood=-5.66625	log10_qual_likelihood_position_model=14.019	log10_strand_likelihood_position_model=4.36369	new_cov=0/15	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=122/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/136
RA	401	.	NC_007779	3576400	1	.	A	bias_e_value=2832460	bias_p_value=0.609611	fisher_strand_p_value=0.260595	frequency=1.111031e-02	genotype_quality=1311.1	ks_quality_p_value=0.99593	log10_base_likelihood=-11.4784	log10_qual_likelihood_position_model=3.81562	log10_strand_likelihood_position_model=0.743739	new_cov=0/3	polymorphism_quality=6.1	quality=6.1	quality_position_model=7.18354e-09	ref_cov=117/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/153
RA	402	.	NC_007779	3580297	0	G	T	bias_e_value=2.87715	bias_p_value=6.1923e-07	fisher_strand_p_value=3.40502e-08	frequency=3.713322e-02	genotype_quality=966.3	ks_quality_p_value=0.999438	log10_base_likelihood=-5.61827	log10_qual_likelihood_position_model=18.3542	log10_strand_likelihood_position_model=7.46788	new_cov=0/22	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=152/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/139
RA	403	.	NC_007779	3653996	1	.	G	bias_e_value=3580920	bias_p_value=0.770699	fisher_strand_p_value=0.511065	frequency=8.298874e-03	genotype_quality=1167.4	ks_quality_p_value=0.791666	log10_base_likelihood=-8.07602	log10_qual_likelihood_position_model=1.94268	log10_strand_likelihood_position_model=0.473085	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.43262e-07	ref_cov=138/101	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/101
RA	404	.	NC_007779	3654011	0	A	C	bias_e_value=59.9311	bias_p_value=1.28986e-05	fisher_strand_p_value=8.61972e-07	frequency=3.650951e-02	genotype_quality=908.0	ks_quality_p_value=1	log10_base_likelihood=-5.6883	log10_qual_likelihood_position_model=19.5828	log10_strand_likelihood_position_model=6.06451	new_cov=0/16	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=151/100	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/116
RA	405	.	NC_007779	3686204	1	.	A	bias_e_value=2248370	bias_p_value=0.483901	fisher_strand_p_value=1	frequency=1.171875e-02	genotype_quality=1237.0	ks_quality_p_value=0.177235	log10_base_likelihood=-12.7787	log10_qual_likelihood_position_model=2.2301	log10_strand_likelihood_position_model=0.37149	new_cov=2/1	polymorphism_quality=7.4	quality=7.4	quality_position_model=3.29886e-12	ref_cov=146/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/108
RA	406	.	NC_007779	3688858	0	A	C	bias_e_value=4.54523e-09	bias_p_value=9.7824e-16	fisher_strand_p_value=2.49359e-17	frequency=1.079679e-01	genotype_quality=621.0	ks_quality_p_value=1	log10_base_likelihood=-11.6385	log10_qual_likelihood_position_model=31.0031	log10_strand_likelihood_position_model=16.6032	new_cov=0/37	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=121/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/86
RA	407	.	NC_007779	3689613	1	.	A	bias_e_value=3912330	bias_p_value=0.842025	fisher_strand_p_value=0.498258	frequency=8.130074e-03	genotype_quality=1214.7	ks_quality_p_value=0.99045	log10_base_likelihood=-7.60804	log10_qual_likelihood_position_model=2.44565	log10_strand_likelihood_position_model=0.582821	new_cov=0/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.90341e-06	ref_cov=120/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/126
RA	408	.	NC_007779	3721173	0	T	.	bias_e_value=3684770	bias_p_value=0.793049	fisher_strand_p_value=0.684358	frequency=2.180862e-02	genotype_quality=1038.0	ks_quality_p_value=0.628571	log10_base_likelihood=-17.608	log10_qual_likelihood_position_model=3.8189	log10_strand_likelihood_position_model=0.612876	new_cov=2/4	polymorphism_quality=12.3	quality=12.3	quality_position_model=2.91808e-15	ref_cov=133/136	reject=INDEL_HOMOPOLYMER	tot_cov=135/140
RA	409	.	NC_007779	3729313	0	G	T	bias_e_value=0.26245	bias_p_value=5.64854e-08	fisher_strand_p_value=3.26063e-09	frequency=6.205034e-02	genotype_quality=800.7	ks_quality_p_value=0.836059	log10_base_likelihood=-10.3127	log10_qual_likelihood_position_model=26.5012	log10_strand_likelihood_position_model=8.73972	new_cov=0/27	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=128/102	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/129
RA	410	.	NC_007779	3731041	1	.	T	bias_e_value=3835600	bias_p_value=0.82551	fisher_strand_p_value=0.621761	frequency=1.739120e-02	genotype_quality=1096.2	ks_quality_p_value=0.757303	log10_base_likelihood=-17.4244	log10_qual_likelihood_position_model=4.05968	log10_strand_likelihood_position_model=0.594498	new_cov=3/1	polymorphism_quality=12.1	quality=12.1	quality_position_model=7.54543e-15	ref_cov=113/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/114
RA	411	.	NC_007779	3732310	0	G	T	bias_e_value=3.45645e-07	bias_p_value=7.43909e-14	fisher_strand_p_value=2.139e-15	frequency=1.353703e-01	genotype_quality=724.5	ks_quality_p_value=1	log10_base_likelihood=-35.4193	log10_qual_likelihood_position_model=22.7039	log10_strand_likelihood_position_model=14.7216	new_cov=0/44	polymorphism_quality=30.3	quality=30.3	quality_position_model=Inf	ref_cov=127/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/134
RA	412	.	NC_007779	3734126	0	G	T	bias_e_value=89.2047	bias_p_value=1.91989e-05	fisher_strand_p_value=1.32066e-06	frequency=3.964996e-02	genotype_quality=959.4	ks_quality_p_value=1	log10_base_likelihood=-11.3419	log10_qual_likelihood_position_model=17.5709	log10_strand_likelihood_position_model=5.87921	new_cov=0/17	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=152/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/133
RA	413	.	NC_007779	3741461	0	A	T	bias_e_value=29841	bias_p_value=0.00642249	fisher_strand_p_value=0.00078848	frequency=3.233051e-02	genotype_quality=813.1	ks_quality_p_value=1	log10_base_likelihood=-5.80788	log10_qual_likelihood_position_model=14.2184	log10_strand_likelihood_position_model=3.10321	new_cov=9/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=99/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=108/126
RA	414	.	NC_007779	3750122	0	C	.	bias_e_value=53254.4	bias_p_value=0.0114616	fisher_strand_p_value=0.36777	frequency=9.573641e-01	genotype_quality=1176.3	ks_quality_p_value=0.00416583	log10_base_likelihood=-53.4451	log10_qual_likelihood_position_model=7.68814	log10_strand_likelihood_position_model=0.824126	new_cov=128/119	polymorphism_quality=48.4	quality=48.4	quality_position_model=2.7984e-47	ref_cov=4/7	tot_cov=132/126
RA	415	.	NC_007779	3750123	0	C	T	bias_e_value=2057810	bias_p_value=0.442889	fisher_strand_p_value=0.36762	frequency=4.310417e-02	genotype_quality=973.9	ks_quality_p_value=0.420054	log10_base_likelihood=-24.4968	log10_qual_likelihood_position_model=9.71568	log10_strand_likelihood_position_model=0.824393	new_cov=4/7	polymorphism_quality=19.3	quality=19.3	quality_position_model=4.70404e-16	ref_cov=127/118	tot_cov=132/126
RA	416	.	NC_007779	3761469	0	A	C	bias_e_value=0.105243	bias_p_value=2.26507e-08	fisher_strand_p_value=1.0448e-09	frequency=7.934380e-02	genotype_quality=462.5	ks_quality_p_value=1	log10_base_likelihood=-10.5694	log10_qual_likelihood_position_model=16.3841	log10_strand_likelihood_position_model=8.98581	new_cov=1/14	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=106/18	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/32
RA	417	.	NC_007779	3763528	0	A	C	bias_e_value=3213.75	bias_p_value=0.000691675	fisher_strand_p_value=6.55885e-05	frequency=2.608204e-02	genotype_quality=569.0	ks_quality_p_value=0.99103	log10_base_likelihood=-6.46405	log10_qual_likelihood_position_model=6.11418	log10_strand_likelihood_position_model=4.18317	new_cov=0/4	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=136/11	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=136/15
RA	418	.	NC_007779	3788380	0	G	T	bias_e_value=0.00285084	bias_p_value=6.13568e-10	fisher_strand_p_value=2.41103e-11	frequency=1.464934e-01	genotype_quality=561.5	ks_quality_p_value=1	log10_base_likelihood=-25.7807	log10_qual_likelihood_position_model=20.0893	log10_strand_likelihood_position_model=10.6696	new_cov=0/38	polymorphism_quality=20.5	quality=20.5	quality_position_model=Inf	ref_cov=85/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/114
RA	419	.	NC_007779	3812429	0	G	T	bias_e_value=1179.58	bias_p_value=0.000253873	fisher_strand_p_value=2.16212e-05	frequency=2.822781e-02	genotype_quality=882.2	ks_quality_p_value=1	log10_base_likelihood=-6.26178	log10_qual_likelihood_position_model=12.6475	log10_strand_likelihood_position_model=4.66512	new_cov=0/14	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=132/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/121
RA	420	.	NC_007779	3813810	0	T	G	bias_e_value=2.49878e-09	bias_p_value=5.37796e-16	fisher_strand_p_value=1.34975e-17	frequency=9.662962e-02	genotype_quality=589.2	ks_quality_p_value=1	log10_base_likelihood=-10.1131	log10_qual_likelihood_position_model=27.8331	log10_strand_likelihood_position_model=16.8697	new_cov=33/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=38/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=71/121
RA	421	.	NC_007779	3835358	1	.	A	bias_e_value=1806640	bias_p_value=0.388831	fisher_strand_p_value=0.157809	frequency=1.092815e-02	genotype_quality=904.5	ks_quality_p_value=0.804024	log10_base_likelihood=-8.08015	log10_qual_likelihood_position_model=2.5313	log10_strand_likelihood_position_model=0.801867	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.27327e-06	ref_cov=71/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=73/110
RA	422	.	NC_007779	3840318	1	.	A	bias_e_value=652380	bias_p_value=0.140408	fisher_strand_p_value=0.230151	frequency=8.510590e-03	genotype_quality=1163.6	ks_quality_p_value=0.136851	log10_base_likelihood=-8.23114	log10_qual_likelihood_position_model=1.05634	log10_strand_likelihood_position_model=0.637987	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.77915e-08	ref_cov=122/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/113
RA	423	.	NC_007779	3841756	0	A	.	bias_e_value=745359	bias_p_value=0.160419	fisher_strand_p_value=0.420349	frequency=2.630711e-02	genotype_quality=917.2	ks_quality_p_value=0.08906	log10_base_likelihood=-18.1812	log10_qual_likelihood_position_model=2.17623	log10_strand_likelihood_position_model=0.697202	new_cov=2/4	polymorphism_quality=12.9	quality=12.9	quality_position_model=2.0041e-17	ref_cov=120/102	reject=INDEL_HOMOPOLYMER	tot_cov=122/106
RA	424	.	NC_007779	3845596	0	G	T	bias_e_value=0.424315	bias_p_value=9.13226e-08	fisher_strand_p_value=4.5175e-09	frequency=8.085394e-02	genotype_quality=731.9	ks_quality_p_value=1	log10_base_likelihood=-18.3082	log10_qual_likelihood_position_model=16.6666	log10_strand_likelihood_position_model=8.43369	new_cov=0/29	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=114/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/135
RA	425	.	NC_007779	3846240	0	G	C	bias_e_value=357.302	bias_p_value=7.68997e-05	fisher_strand_p_value=5.94226e-06	frequency=5.184364e-02	genotype_quality=552.0	ks_quality_p_value=0.992334	log10_base_likelihood=-6.41519	log10_qual_likelihood_position_model=11.1132	log10_strand_likelihood_position_model=5.22605	new_cov=0/11	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=107/48	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=107/59
RA	426	.	NC_007779	3859254	1	.	T	bias_e_value=860564	bias_p_value=0.185214	fisher_strand_p_value=0.0556951	frequency=1.500034e-02	genotype_quality=966.0	ks_quality_p_value=0.81182	log10_base_likelihood=-13.4701	log10_qual_likelihood_position_model=1.16268	log10_strand_likelihood_position_model=1.25418	new_cov=3/0	polymorphism_quality=8.1	quality=8.1	quality_position_model=4.21664e-13	ref_cov=74/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=77/123
RA	427	.	NC_007779	3859263	0	T	C	bias_e_value=2.85852	bias_p_value=6.1522e-07	fisher_strand_p_value=3.3798e-08	frequency=5.863428e-02	genotype_quality=575.5	ks_quality_p_value=1	log10_base_likelihood=-10.8342	log10_qual_likelihood_position_model=15.8186	log10_strand_likelihood_position_model=7.47111	new_cov=13/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=40/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=53/129
RA	428	.	NC_007779	3859270	0	G	C	bias_e_value=56.3281	bias_p_value=1.21231e-05	fisher_strand_p_value=8.0657e-07	frequency=5.340195e-02	genotype_quality=673.9	ks_quality_p_value=1	log10_base_likelihood=-15.5813	log10_qual_likelihood_position_model=10.8151	log10_strand_likelihood_position_model=6.09336	new_cov=10/0	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=37/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=47/130
RA	429	.	NC_007779	3873374	1	.	T	bias_e_value=1424500	bias_p_value=0.306586	fisher_strand_p_value=0.621842	frequency=1.666641e-02	genotype_quality=1163.3	ks_quality_p_value=0.144645	log10_base_likelihood=-17.2357	log10_qual_likelihood_position_model=2.8638	log10_strand_likelihood_position_model=0.602083	new_cov=1/3	polymorphism_quality=11.9	quality=11.9	quality_position_model=7.28149e-16	ref_cov=119/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/120
RA	430	.	NC_007779	3873375	0	T	.	bias_e_value=3700680	bias_p_value=0.796474	fisher_strand_p_value=0.622021	frequency=1.631546e-02	genotype_quality=971.5	ks_quality_p_value=0.698128	log10_base_likelihood=-11.0004	log10_qual_likelihood_position_model=3.05883	log10_strand_likelihood_position_model=0.591446	new_cov=1/3	polymorphism_quality=5.6	quality=5.6	quality_position_model=2.5872e-09	ref_cov=120/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=121/124
RA	431	.	NC_007779	3891907	0	T	.	bias_e_value=2678580	bias_p_value=0.576493	fisher_strand_p_value=0.331013	frequency=1.792717e-02	genotype_quality=871.9	ks_quality_p_value=0.712391	log10_base_likelihood=-11.3247	log10_qual_likelihood_position_model=2.61848	log10_strand_likelihood_position_model=0.693096	new_cov=3/1	polymorphism_quality=5.9	quality=5.9	quality_position_model=5.39529e-10	ref_cov=98/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=101/122
RA	432	.	NC_007779	3893880	0	G	T	bias_e_value=0.630222	bias_p_value=1.35639e-07	fisher_strand_p_value=6.85705e-09	frequency=6.188250e-02	genotype_quality=727.4	ks_quality_p_value=0.999091	log10_base_likelihood=-8.98589	log10_qual_likelihood_position_model=18.9771	log10_strand_likelihood_position_model=8.16386	new_cov=0/24	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=125/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/118
RA	433	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1114.2	new_cov=112/152	quality=1114.2	ref_cov=0/0	tot_cov=112/152
RA	434	.	NC_007779	3900680	0	T	G	bias_e_value=3.9654e-13	bias_p_value=8.53447e-20	fisher_strand_p_value=1.74904e-21	frequency=9.658766e-02	genotype_quality=707.6	ks_quality_p_value=1	log10_base_likelihood=-23.6602	log10_qual_likelihood_position_model=30.2932	log10_strand_likelihood_position_model=20.7572	new_cov=25/0	polymorphism_quality=18.4	quality=18.4	quality_position_model=Inf	ref_cov=16/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=41/161
RA	435	.	NC_007779	3910746	0	C	A	bias_e_value=0.018061	bias_p_value=3.88715e-09	fisher_strand_p_value=1.65245e-10	frequency=7.409334e-02	genotype_quality=859.6	ks_quality_p_value=1	log10_base_likelihood=-13.1042	log10_qual_likelihood_position_model=28.6781	log10_strand_likelihood_position_model=9.80976	new_cov=36/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=131/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/130
RA	436	.	NC_007779	3930443	0	T	G	bias_e_value=1.34657e-09	bias_p_value=2.89814e-16	fisher_strand_p_value=7.15979e-18	frequency=7.137156e-02	genotype_quality=695.2	ks_quality_p_value=1	log10_base_likelihood=-6.53125	log10_qual_likelihood_position_model=30.7787	log10_strand_likelihood_position_model=17.1451	new_cov=32/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=44/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=76/145
RA	437	.	NC_007779	3946445	1	.	T	bias_e_value=2391760	bias_p_value=0.514762	fisher_strand_p_value=0.196093	frequency=8.297920e-03	genotype_quality=1185.0	ks_quality_p_value=0.997503	log10_base_likelihood=-7.35456	log10_qual_likelihood_position_model=3.6161	log10_strand_likelihood_position_model=0.707539	new_cov=0/2	polymorphism_quality=1.9	quality=1.9	quality_position_model=8.11988e-05	ref_cov=134/105	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=134/107
RA	438	.	NC_007779	3952095	1	.	G	bias_e_value=10514	bias_p_value=0.00226285	fisher_strand_p_value=0.000285609	frequency=3.703690e-02	genotype_quality=873.2	ks_quality_p_value=0.849761	log10_base_likelihood=-32.5092	log10_qual_likelihood_position_model=3.78344	log10_strand_likelihood_position_model=3.54423	new_cov=7/0	polymorphism_quality=27.3	quality=27.3	quality_position_model=2.10071e-27	ref_cov=54/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=61/128
RA	439	.	NC_007779	3986830	0	T	.	bias_e_value=2266470	bias_p_value=0.487799	fisher_strand_p_value=0.574019	frequency=1.432610e-02	genotype_quality=840.8	ks_quality_p_value=0.312701	log10_base_likelihood=-7.58269	log10_qual_likelihood_position_model=2.82269	log10_strand_likelihood_position_model=0.510271	new_cov=1/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=4.21022e-06	ref_cov=120/86	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=121/88
RA	440	.	NC_007779	4016769	1	.	C	bias_e_value=1893940	bias_p_value=0.407621	fisher_strand_p_value=0.136176	frequency=7.627487e-03	genotype_quality=1297.6	ks_quality_p_value=0.999765	log10_base_likelihood=-6.11351	log10_qual_likelihood_position_model=4.53391	log10_strand_likelihood_position_model=0.865899	new_cov=2/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=0.0314437	ref_cov=95/165	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=97/165
RA	441	.	NC_007779	4023068	0	T	G	bias_e_value=1334.09	bias_p_value=0.000287129	fisher_strand_p_value=2.47371e-05	frequency=3.726006e-02	genotype_quality=461.4	ks_quality_p_value=1	log10_base_likelihood=-5.7739	log10_qual_likelihood_position_model=8.74452	log10_strand_likelihood_position_model=4.60665	new_cov=9/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=36/92	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=45/92
RA	442	.	NC_007779	4029633	0	T	G	bias_e_value=1.51588e-13	bias_p_value=3.26252e-20	fisher_strand_p_value=6.55431e-22	frequency=1.460152e-01	genotype_quality=557.6	ks_quality_p_value=1	log10_base_likelihood=-24.88	log10_qual_likelihood_position_model=33.0907	log10_strand_likelihood_position_model=21.1835	new_cov=32/0	polymorphism_quality=19.6	quality=19.6	quality_position_model=Inf	ref_cov=19/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=51/122
RA	443	.	NC_007779	4031691	1	.	T	bias_e_value=1376060	bias_p_value=0.296161	fisher_strand_p_value=0.0982921	frequency=1.315784e-02	genotype_quality=736.5	ks_quality_p_value=0.871496	log10_base_likelihood=-8.60531	log10_qual_likelihood_position_model=1.43242	log10_strand_likelihood_position_model=1.00748	new_cov=2/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=4.30109e-08	ref_cov=46/104	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=48/104
RA	444	.	NC_007779	4036507	0	G	T	bias_e_value=6.04671	bias_p_value=1.3014e-06	fisher_strand_p_value=9.05619e-08	frequency=4.635906e-02	genotype_quality=827.4	ks_quality_p_value=0.825445	log10_base_likelihood=-5.85019	log10_qual_likelihood_position_model=22.874	log10_strand_likelihood_position_model=7.24135	new_cov=0/23	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=136/116	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/140
RA	445	.	NC_007779	4043703	0	C	A	bias_e_value=83.3061	bias_p_value=1.79294e-05	fisher_strand_p_value=1.22713e-06	frequency=3.478813e-02	genotype_quality=786.1	ks_quality_p_value=1	log10_base_likelihood=-7.20205	log10_qual_likelihood_position_model=10.019	log10_strand_likelihood_position_model=5.91111	new_cov=17/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=102/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/136
RA	446	.	NC_007779	4052978	0	G	T	bias_e_value=0.000494445	bias_p_value=1.06416e-10	fisher_strand_p_value=3.9024e-12	frequency=6.242132e-02	genotype_quality=788.3	ks_quality_p_value=1	log10_base_likelihood=-6.60984	log10_qual_likelihood_position_model=20.9532	log10_strand_likelihood_position_model=11.4087	new_cov=0/30	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=140/85	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/115
RA	447	.	NC_007779	4055100	0	G	T	bias_e_value=58.5503	bias_p_value=1.26014e-05	fisher_strand_p_value=8.72386e-07	frequency=5.540609e-02	genotype_quality=692.0	ks_quality_p_value=0.963689	log10_base_likelihood=-8.49826	log10_qual_likelihood_position_model=20.2769	log10_strand_likelihood_position_model=6.05929	new_cov=15/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=71/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/121
RA	448	.	NC_007779	4055329	0	T	G	bias_e_value=5.83513e-16	bias_p_value=1.25586e-22	fisher_strand_p_value=2.26508e-24	frequency=1.225638e-01	genotype_quality=691.7	ks_quality_p_value=1	log10_base_likelihood=-20.0456	log10_qual_likelihood_position_model=30.6759	log10_strand_likelihood_position_model=23.6449	new_cov=37/0	polymorphism_quality=14.8	quality=14.8	quality_position_model=Inf	ref_cov=29/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=67/156
RA	449	.	NC_007779	4059484	1	.	T	bias_e_value=560128	bias_p_value=0.120553	fisher_strand_p_value=1	frequency=1.224518e-02	genotype_quality=1178.1	ks_quality_p_value=0.0259073	log10_base_likelihood=-12.7396	log10_qual_likelihood_position_model=2.37516	log10_strand_likelihood_position_model=0.415528	new_cov=2/1	polymorphism_quality=7.4	quality=7.4	quality_position_model=5.6401e-12	ref_cov=123/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/120
RA	450	.	NC_007779	4059485	0	T	.	bias_e_value=1247170	bias_p_value=0.268421	fisher_strand_p_value=0.24726	frequency=1.213741e-02	genotype_quality=986.5	ks_quality_p_value=0.302	log10_base_likelihood=-8.16372	log10_qual_likelihood_position_model=2.26868	log10_strand_likelihood_position_model=0.882096	new_cov=3/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=6.72971e-07	ref_cov=123/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/121
RA	451	.	NC_007779	4062114	0	T	G	bias_e_value=1.1202e-15	bias_p_value=2.41094e-22	fisher_strand_p_value=4.40112e-24	frequency=1.160312e-01	genotype_quality=595.0	ks_quality_p_value=1	log10_base_likelihood=-10.658	log10_qual_likelihood_position_model=36.2789	log10_strand_likelihood_position_model=23.3564	new_cov=36/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=22/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=60/134
RA	452	.	NC_007779	4064463	0	G	T	bias_e_value=5.06275	bias_p_value=1.08962e-06	fisher_strand_p_value=6.19194e-08	frequency=5.799866e-02	genotype_quality=688.4	ks_quality_p_value=1	log10_base_likelihood=-6.12233	log10_qual_likelihood_position_model=15.7083	log10_strand_likelihood_position_model=7.20817	new_cov=0/22	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=114/90	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/112
RA	453	.	NC_007779	4087369	0	T	.	bias_e_value=487139	bias_p_value=0.104844	fisher_strand_p_value=0.250199	frequency=1.407433e-02	genotype_quality=852.3	ks_quality_p_value=0.0867549	log10_base_likelihood=-8.17651	log10_qual_likelihood_position_model=1.88112	log10_strand_likelihood_position_model=0.819797	new_cov=3/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.22592e-07	ref_cov=111/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/99
RA	454	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1071.1	new_cov=137/135	quality=1071.1	ref_cov=0/0	tot_cov=137/135
RA	455	.	NC_007779	4098730	0	G	T	bias_e_value=7.00632e-08	bias_p_value=1.50793e-14	fisher_strand_p_value=4.14031e-16	frequency=1.296477e-01	genotype_quality=678.6	ks_quality_p_value=1	log10_base_likelihood=-21.4438	log10_qual_likelihood_position_model=25.0119	log10_strand_likelihood_position_model=15.383	new_cov=0/42	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=129/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/120
RA	456	.	NC_007779	4114782	0	G	T	bias_e_value=4309.3	bias_p_value=0.000927462	fisher_strand_p_value=8.98979e-05	frequency=2.913475e-02	genotype_quality=897.9	ks_quality_p_value=1	log10_base_likelihood=-5.81671	log10_qual_likelihood_position_model=15.2588	log10_strand_likelihood_position_model=4.2078	new_cov=0/16	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=121/137	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/153
RA	457	.	NC_007779	4115400	1	.	C	bias_e_value=461507	bias_p_value=0.0993272	fisher_strand_p_value=0.0202783	frequency=1.593590e-02	genotype_quality=883.7	ks_quality_p_value=1	log10_base_likelihood=-7.31161	log10_qual_likelihood_position_model=3.25921	log10_strand_likelihood_position_model=1.69297	new_cov=0/3	polymorphism_quality=1.8	quality=1.8	quality_position_model=0.000425678	ref_cov=136/49	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/52
RA	458	.	NC_007779	4124974	0	G	T	bias_e_value=3.62089e-07	bias_p_value=7.79302e-14	fisher_strand_p_value=2.24385e-15	frequency=1.043935e-01	genotype_quality=780.2	ks_quality_p_value=1	log10_base_likelihood=-19.8021	log10_qual_likelihood_position_model=21.9134	log10_strand_likelihood_position_model=14.649	new_cov=0/39	polymorphism_quality=14.5	quality=14.5	quality_position_model=Inf	ref_cov=139/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/121
RA	459	.	NC_007779	4126059	0	T	C	bias_e_value=588999	bias_p_value=0.126766	fisher_strand_p_value=0.273133	frequency=1.242638e-02	genotype_quality=938.5	ks_quality_p_value=0.101136	log10_base_likelihood=-6.88642	log10_qual_likelihood_position_model=2.08809	log10_strand_likelihood_position_model=0.683783	new_cov=3/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=5.83328e-06	ref_cov=140/98	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=143/98
RA	460	.	NC_007779	4128670	0	T	.	bias_e_value=2612470	bias_p_value=0.562265	fisher_strand_p_value=0.372867	frequency=1.983070e-02	genotype_quality=968.2	ks_quality_p_value=0.60639	log10_base_likelihood=-14.3082	log10_qual_likelihood_position_model=3.67802	log10_strand_likelihood_position_model=0.749136	new_cov=1/4	polymorphism_quality=8.9	quality=8.9	quality_position_model=6.61594e-12	ref_cov=119/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/132
RA	461	.	NC_007779	4135553	0	T	G	bias_e_value=66.6289	bias_p_value=1.43401e-05	fisher_strand_p_value=9.65632e-07	frequency=3.925323e-02	genotype_quality=494.1	ks_quality_p_value=1	log10_base_likelihood=-8.1819	log10_qual_likelihood_position_model=11.5269	log10_strand_likelihood_position_model=6.02455	new_cov=2/8	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=143/14	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/22
RA	462	.	NC_007779	4135555	0	A	G	bias_e_value=14.6748	bias_p_value=3.15835e-06	fisher_strand_p_value=1.91801e-07	frequency=3.768635e-02	genotype_quality=554.9	ks_quality_p_value=1	log10_base_likelihood=-7.32529	log10_qual_likelihood_position_model=9.17199	log10_strand_likelihood_position_model=6.71715	new_cov=0/7	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=145/14	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/21
RA	463	.	NC_007779	4135559	1	.	A	bias_e_value=384205	bias_p_value=0.0826901	fisher_strand_p_value=0.0161277	frequency=1.298332e-02	genotype_quality=728.7	ks_quality_p_value=1	log10_base_likelihood=-6.13732	log10_qual_likelihood_position_model=3.29303	log10_strand_likelihood_position_model=1.79243	new_cov=0/2	polymorphism_quality=0.6	quality=0.6	quality_position_model=0.0122187	ref_cov=134/18	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=134/20
RA	464	.	NC_007779	4157323	0	C	A	bias_e_value=0.380418	bias_p_value=8.18749e-08	fisher_strand_p_value=4.53774e-09	frequency=5.945158e-02	genotype_quality=746.2	ks_quality_p_value=0.887503	log10_base_likelihood=-7.93512	log10_qual_likelihood_position_model=27.0853	log10_strand_likelihood_position_model=8.34316	new_cov=25/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=92/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/122
RA	465	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=945.3	new_cov=125/98	quality=945.3	ref_cov=0/0	tot_cov=125/99
RA	466	.	NC_007779	4174730	0	T	.	bias_e_value=4325360	bias_p_value=0.930919	fisher_strand_p_value=0.652122	frequency=2.249908e-02	genotype_quality=865.9	ks_quality_p_value=1	log10_base_likelihood=-13.6308	log10_qual_likelihood_position_model=5.02197	log10_strand_likelihood_position_model=0.548347	new_cov=1/4	polymorphism_quality=8.3	quality=8.3	quality_position_model=4.82436e-10	ref_cov=83/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=84/138
RA	467	.	NC_007779	4197139	0	T	G	bias_e_value=2.14677e-10	bias_p_value=4.62035e-17	fisher_strand_p_value=1.09074e-18	frequency=1.157198e-01	genotype_quality=521.4	ks_quality_p_value=1	log10_base_likelihood=-17.4543	log10_qual_likelihood_position_model=22.7238	log10_strand_likelihood_position_model=17.9623	new_cov=21/0	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=10/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=31/123
RA	468	.	NC_007779	4207565	0	C	A	bias_e_value=0.934469	bias_p_value=2.0112e-07	fisher_strand_p_value=1.03757e-08	frequency=7.409382e-02	genotype_quality=691.4	ks_quality_p_value=1	log10_base_likelihood=-12.1195	log10_qual_likelihood_position_model=21.1724	log10_strand_likelihood_position_model=8.03968	new_cov=28/0	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=98/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/105
RA	469	.	NC_007779	4213830	0	C	G	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	470	.	NC_007779	4218761	0	C	G	bias_e_value=191089	bias_p_value=0.0411268	fisher_strand_p_value=0.00687806	frequency=2.796555e-02	genotype_quality=780.0	ks_quality_p_value=1	log10_base_likelihood=-6.63704	log10_qual_likelihood_position_model=8.80846	log10_strand_likelihood_position_model=2.38239	new_cov=0/8	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=97/94	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=98/102
RA	471	.	NC_007779	4224249	0	T	.	bias_e_value=1298720	bias_p_value=0.279515	fisher_strand_p_value=0.622041	frequency=1.561642e-02	genotype_quality=1017.4	ks_quality_p_value=0.126994	log10_base_likelihood=-11.2974	log10_qual_likelihood_position_model=2.41735	log10_strand_likelihood_position_model=0.60208	new_cov=1/3	polymorphism_quality=5.9	quality=5.9	quality_position_model=2.88697e-10	ref_cov=127/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/128
RA	472	.	NC_007779	4226513	0	C	A	bias_e_value=1.20277	bias_p_value=2.58864e-07	fisher_strand_p_value=1.35406e-08	frequency=5.739069e-02	genotype_quality=826.4	ks_quality_p_value=1	log10_base_likelihood=-8.92444	log10_qual_likelihood_position_model=18.4919	log10_strand_likelihood_position_model=7.86836	new_cov=24/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=104/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/131
RA	473	.	NC_007779	4227183	0	T	G	bias_e_value=3.27195e-05	bias_p_value=7.04201e-12	fisher_strand_p_value=2.34085e-13	frequency=6.500006e-02	genotype_quality=820.7	ks_quality_p_value=1	log10_base_likelihood=-8.5809	log10_qual_likelihood_position_model=27.8119	log10_strand_likelihood_position_model=12.6306	new_cov=32/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=84/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/148
RA	474	.	NC_007779	4254547	1	.	A	bias_e_value=2160580	bias_p_value=0.465007	fisher_strand_p_value=1	frequency=8.333206e-03	genotype_quality=1191.0	ks_quality_p_value=0.166507	log10_base_likelihood=-8.28148	log10_qual_likelihood_position_model=0.957892	log10_strand_likelihood_position_model=0.321779	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.90379e-09	ref_cov=146/92	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/93
RA	475	.	NC_007779	4289840	0	G	T	bias_e_value=0.333402	bias_p_value=7.17559e-08	fisher_strand_p_value=3.5056e-09	frequency=5.113983e-02	genotype_quality=665.7	ks_quality_p_value=1	log10_base_likelihood=-5.86496	log10_qual_likelihood_position_model=14.9545	log10_strand_likelihood_position_model=8.45524	new_cov=0/24	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=124/87	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/112
RA	476	.	NC_007779	4312373	1	.	T	bias_e_value=3336530	bias_p_value=0.718101	fisher_strand_p_value=0.498755	frequency=9.090424e-03	genotype_quality=1075.2	ks_quality_p_value=0.703015	log10_base_likelihood=-8.58221	log10_qual_likelihood_position_model=1.42759	log10_strand_likelihood_position_model=0.565264	new_cov=0/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=1.5705e-08	ref_cov=105/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/115
RA	477	.	NC_007779	4318992	0	T	G	bias_e_value=1277.55	bias_p_value=0.000274958	fisher_strand_p_value=2.35922e-05	frequency=3.881931e-02	genotype_quality=527.1	ks_quality_p_value=1	log10_base_likelihood=-7.49822	log10_qual_likelihood_position_model=12.9019	log10_strand_likelihood_position_model=4.64579	new_cov=4/7	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=140/12	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/19
RA	478	.	NC_007779	4318994	0	A	G	bias_e_value=38.8106	bias_p_value=8.35296e-06	fisher_strand_p_value=5.41375e-07	frequency=3.221989e-02	genotype_quality=565.2	ks_quality_p_value=1	log10_base_likelihood=-7.19552	log10_qual_likelihood_position_model=7.11258	log10_strand_likelihood_position_model=6.2665	new_cov=0/6	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=145/11	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/17
RA	479	.	NC_007779	4337469	0	A	C	bias_e_value=1.63092e-10	bias_p_value=3.51011e-17	fisher_strand_p_value=8.23176e-19	frequency=1.718097e-01	genotype_quality=474.6	ks_quality_p_value=1	log10_base_likelihood=-19.8781	log10_qual_likelihood_position_model=27.3034	log10_strand_likelihood_position_model=18.0845	new_cov=0/39	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=98/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/73
RA	480	.	NC_007779	4338829	0	T	.	bias_e_value=2972370	bias_p_value=0.639724	fisher_strand_p_value=1	frequency=1.213741e-02	genotype_quality=957.9	ks_quality_p_value=0.282597	log10_base_likelihood=-8.217	log10_qual_likelihood_position_model=2.01807	log10_strand_likelihood_position_model=0.422445	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.08584e-07	ref_cov=122/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/124
RA	481	.	NC_007779	4348529	0	T	G	bias_e_value=0.000175311	bias_p_value=3.7731e-11	fisher_strand_p_value=1.33114e-12	frequency=6.800318e-02	genotype_quality=695.6	ks_quality_p_value=1	log10_base_likelihood=-9.82052	log10_qual_likelihood_position_model=27.8149	log10_strand_likelihood_position_model=11.8758	new_cov=25/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=56/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=81/136
RA	482	.	NC_007779	4353540	0	T	C	bias_e_value=4646330	bias_p_value=0.999999	fisher_strand_p_value=1	frequency=1.054955e-02	genotype_quality=2202.2	ks_quality_p_value=0.998598	log10_base_likelihood=-10.0049	log10_qual_likelihood_position_model=5.25447	log10_strand_likelihood_position_model=0.520183	new_cov=3/3	polymorphism_quality=4.6	quality=4.6	quality_position_model=4.41266e-06	ref_cov=244/308	tot_cov=247/311
RA	483	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=875.3	new_cov=98/77	quality=875.3	ref_cov=1/0	tot_cov=99/77
RA	484	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=874.6	new_cov=98/77	quality=874.6	ref_cov=0/0	tot_cov=99/77
RA	485	.	NC_007779	4414724	1	.	T	bias_e_value=4646190	bias_p_value=0.999968	fisher_strand_p_value=1	frequency=1.357460e-02	genotype_quality=1077.5	ks_quality_p_value=0.992061	log10_base_likelihood=-12.4647	log10_qual_likelihood_position_model=3.45392	log10_strand_likelihood_position_model=0.351701	new_cov=1/2	polymorphism_quality=7.1	quality=7.1	quality_position_model=1.17492e-10	ref_cov=79/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=80/141
RA	486	.	NC_007779	4429120	0	G	T	bias_e_value=1.81177e-06	bias_p_value=3.89935e-13	fisher_strand_p_value=1.9485e-14	frequency=9.298134e-02	genotype_quality=838.3	ks_quality_p_value=0.605114	log10_base_likelihood=-20.7377	log10_qual_likelihood_position_model=38.6704	log10_strand_likelihood_position_model=13.7103	new_cov=0/38	polymorphism_quality=15.5	quality=15.5	quality_position_model=Inf	ref_cov=146/94	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/133
RA	487	.	NC_007779	4455463	0	T	G	bias_e_value=32.0789	bias_p_value=6.90415e-06	fisher_strand_p_value=4.41646e-07	frequency=5.159903e-02	genotype_quality=668.5	ks_quality_p_value=1	log10_base_likelihood=-7.71651	log10_qual_likelihood_position_model=20.5321	log10_strand_likelihood_position_model=6.36642	new_cov=16/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=57/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/125
RA	488	.	NC_007779	4479134	0	G	T	bias_e_value=0.605056	bias_p_value=1.30222e-07	fisher_strand_p_value=6.56302e-09	frequency=7.241106e-02	genotype_quality=653.2	ks_quality_p_value=1	log10_base_likelihood=-9.76847	log10_qual_likelihood_position_model=21.6261	log10_strand_likelihood_position_model=8.39761	new_cov=0/30	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=105/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/131
RA	489	.	NC_007779	4484848	0	T	.	bias_e_value=2991330	bias_p_value=0.643805	fisher_strand_p_value=1	frequency=1.002598e-02	genotype_quality=1188.8	ks_quality_p_value=0.285841	log10_base_likelihood=-7.95247	log10_qual_likelihood_position_model=2.01238	log10_strand_likelihood_position_model=0.394511	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.88343e-07	ref_cov=136/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/161
RA	490	.	NC_007779	4508940	1	.	T	bias_e_value=728697	bias_p_value=0.156833	fisher_strand_p_value=0.134199	frequency=7.905006e-03	genotype_quality=1241.1	ks_quality_p_value=0.270863	log10_base_likelihood=-8.02654	log10_qual_likelihood_position_model=1.68067	log10_strand_likelihood_position_model=0.87225	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.23645e-07	ref_cov=160/91	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/93
RA	491	.	NC_007779	4515952	0	G	T	bias_e_value=0.216198	bias_p_value=4.65309e-08	fisher_strand_p_value=2.2238e-09	frequency=5.577564e-02	genotype_quality=750.2	ks_quality_p_value=1	log10_base_likelihood=-7.49815	log10_qual_likelihood_position_model=27.5697	log10_strand_likelihood_position_model=8.6529	new_cov=0/26	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=128/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/126
RA	492	.	NC_007779	4540870	0	T	G	bias_e_value=4.66963e-17	bias_p_value=1.00501e-23	fisher_strand_p_value=1.73233e-25	frequency=9.229803e-02	genotype_quality=743.0	ks_quality_p_value=1	log10_base_likelihood=-9.76185	log10_qual_likelihood_position_model=34.8386	log10_strand_likelihood_position_model=24.7614	new_cov=41/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=34/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=75/161
RA	493	.	NC_007779	4540877	0	A	T	bias_e_value=0.000190576	bias_p_value=4.10165e-11	fisher_strand_p_value=1.45148e-12	frequency=8.178520e-02	genotype_quality=733.7	ks_quality_p_value=1	log10_base_likelihood=-13.3677	log10_qual_likelihood_position_model=17.6463	log10_strand_likelihood_position_model=11.8382	new_cov=21/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=48/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=69/156
RA	494	.	NC_007779	4545657	1	.	A	bias_e_value=1468970	bias_p_value=0.316158	fisher_strand_p_value=1	frequency=8.368492e-03	genotype_quality=1180.6	ks_quality_p_value=0.0939571	log10_base_likelihood=-8.28512	log10_qual_likelihood_position_model=1.26642	log10_strand_likelihood_position_model=0.300496	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.15671e-08	ref_cov=125/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/113
RA	495	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=799.6	new_cov=107/88	quality=799.6	ref_cov=0/0	tot_cov=108/88
RA	496	.	NC_007779	4549850	0	T	.	bias_e_value=3415540	bias_p_value=0.735106	fisher_strand_p_value=1	frequency=1.281071e-02	genotype_quality=894.5	ks_quality_p_value=0.367227	log10_base_likelihood=-8.13713	log10_qual_likelihood_position_model=2.10276	log10_strand_likelihood_position_model=0.38595	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.4736e-07	ref_cov=127/104	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/105
RA	497	.	NC_007779	4554525	1	.	T	bias_e_value=285258	bias_p_value=0.0613943	fisher_strand_p_value=0.0560208	frequency=1.522827e-02	genotype_quality=926.0	ks_quality_p_value=0.199471	log10_base_likelihood=-12.4395	log10_qual_likelihood_position_model=4.05721	log10_strand_likelihood_position_model=1.25165	new_cov=3/0	polymorphism_quality=7.1	quality=7.1	quality_position_model=4.35068e-09	ref_cov=73/121	reject=POLYMORPHISM_STRAND	tot_cov=76/121
RA	498	.	NC_007779	4554532	0	T	C	bias_e_value=233.918	bias_p_value=5.03447e-05	fisher_strand_p_value=3.72945e-06	frequency=4.938984e-02	genotype_quality=533.5	ks_quality_p_value=1	log10_base_likelihood=-9.14324	log10_qual_likelihood_position_model=11.206	log10_strand_likelihood_position_model=5.42836	new_cov=10/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=42/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=52/118
RA	499	.	NC_007779	4557828	0	A	.	bias_e_value=4621060	bias_p_value=0.994561	fisher_strand_p_value=1	frequency=1.326466e-02	genotype_quality=876.6	ks_quality_p_value=0.897531	log10_base_likelihood=-8.09518	log10_qual_likelihood_position_model=2.23997	log10_strand_likelihood_position_model=0.380698	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.23167e-07	ref_cov=124/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/99
RA	500	.	NC_007779	4561440	1	.	T	bias_e_value=3348880	bias_p_value=0.720758	fisher_strand_p_value=0.570031	frequency=1.357460e-02	genotype_quality=1070.5	ks_quality_p_value=0.619573	log10_base_likelihood=-13.1891	log10_qual_likelihood_position_model=2.05598	log10_strand_likelihood_position_model=0.522911	new_cov=1/2	polymorphism_quality=7.8	quality=7.8	quality_position_model=1.19278e-12	ref_cov=129/89	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/91
RA	501	.	NC_007779	4578176	0	A	G	bias_e_value=0.00843654	bias_p_value=1.81574e-09	fisher_strand_p_value=7.46667e-11	frequency=6.549788e-02	genotype_quality=621.4	ks_quality_p_value=1	log10_base_likelihood=-6.92654	log10_qual_likelihood_position_model=16.276	log10_strand_likelihood_position_model=10.1269	new_cov=16/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=34/139	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=50/139
RA	502	.	NC_007779	4599760	0	C	A	bias_e_value=1.25123e-05	bias_p_value=2.69295e-12	fisher_strand_p_value=8.66545e-14	frequency=7.381201e-02	genotype_quality=875.2	ks_quality_p_value=1	log10_base_likelihood=-11.645	log10_qual_likelihood_position_model=23.8759	log10_strand_likelihood_position_model=13.0622	new_cov=31/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=81/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/158
RA	503	.	NC_007779	4610781	0	A	C	bias_e_value=0.000962288	bias_p_value=2.07107e-10	fisher_strand_p_value=7.79246e-12	frequency=8.211565e-02	genotype_quality=690.3	ks_quality_p_value=1	log10_base_likelihood=-17.7353	log10_qual_likelihood_position_model=24.0331	log10_strand_likelihood_position_model=11.1083	new_cov=0/25	polymorphism_quality=12.4	quality=12.4	quality_position_model=Inf	ref_cov=131/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/86
RA	504	.	NC_007779	4613456	0	C	A	bias_e_value=7486.38	bias_p_value=0.00161124	fisher_strand_p_value=0.000166053	frequency=3.200531e-02	genotype_quality=722.3	ks_quality_p_value=1	log10_base_likelihood=-5.68721	log10_qual_likelihood_position_model=11.5375	log10_strand_likelihood_position_model=4.0354	new_cov=15/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=118/108	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/108
RA	505	.	NC_007779	4635770	0	G	T	bias_e_value=65.928	bias_p_value=1.41892e-05	fisher_strand_p_value=9.54745e-07	frequency=5.763721e-02	genotype_quality=741.1	ks_quality_p_value=1	log10_base_likelihood=-11.1414	log10_qual_likelihood_position_model=11.2357	log10_strand_likelihood_position_model=6.15338	new_cov=0/20	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=124/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/132
RA	506	.	NC_007779	4636470	0	C	G	bias_e_value=1.54763e-05	bias_p_value=3.33087e-12	fisher_strand_p_value=1.08144e-13	frequency=1.148257e-01	genotype_quality=560.8	ks_quality_p_value=0.998161	log10_base_likelihood=-17.9768	log10_qual_likelihood_position_model=18.5514	log10_strand_likelihood_position_model=12.966	new_cov=22/0	polymorphism_quality=12.7	quality=12.7	quality_position_model=Inf	ref_cov=29/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=51/115
RA	507	.	NC_007779	4642414	1	.	A	bias_e_value=230316	bias_p_value=0.0495694	fisher_strand_p_value=0.248157	frequency=1.282024e-02	genotype_quality=1127.1	ks_quality_p_value=0.0347131	log10_base_likelihood=-12.6693	log10_qual_likelihood_position_model=2.69818	log10_strand_likelihood_position_model=0.853733	new_cov=0/3	polymorphism_quality=7.3	quality=7.3	quality_position_model=3.9902e-11	ref_cov=112/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/122
RA	508	.	NC_007779	4644244	1	.	T	bias_e_value=4196410	bias_p_value=0.903166	fisher_strand_p_value=0.602216	frequency=1.127720e-02	genotype_quality=1280.3	ks_quality_p_value=0.98561	log10_base_likelihood=-11.5551	log10_qual_likelihood_position_model=2.67204	log10_strand_likelihood_position_model=0.453059	new_cov=1/2	polymorphism_quality=6.2	quality=6.2	quality_position_model=2.01669e-10	ref_cov=140/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/125
MC	509	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=230	right_inside_cov=0	right_outside_cov=228
MC	510	.	NC_007779	1288302	1288518	73	59	left_inside_cov=173	left_outside_cov=176	right_inside_cov=173	right_outside_cov=174
MC	511	.	NC_007779	1301041	1302376	1326	0	left_inside_cov=0	left_outside_cov=277	right_inside_cov=0	right_outside_cov=279
MC	512	.	NC_007779	1413639	1436698	0	0	left_inside_cov=1	left_outside_cov=303	right_inside_cov=1	right_outside_cov=301
MC	513	.	NC_007779	2176983	2178208	1194	0	left_inside_cov=0	left_outside_cov=283	right_inside_cov=0	right_outside_cov=198
MC	514	.	NC_007779	2320795	2322130	1327	0	left_inside_cov=0	left_outside_cov=261	right_inside_cov=0	right_outside_cov=262
MC	515	.	NC_007779	3128824	3147473	1178	0	left_inside_cov=173	left_outside_cov=178	right_inside_cov=0	right_outside_cov=259
MC	516	.	NC_007779	3261134	3262337	1194	0	left_inside_cov=0	left_outside_cov=238	right_inside_cov=0	right_outside_cov=237
MC	517	.	NC_007779	3742936	3744271	1325	0	left_inside_cov=0	left_outside_cov=304	right_inside_cov=2	right_outside_cov=305
MC	518	.	NC_007779	3746911	3748109	1194	0	left_inside_cov=1	left_outside_cov=273	right_inside_cov=1	right_outside_cov=272
MC	519	.	NC_007779	3750591	3751789	1198	0	left_inside_cov=0	left_outside_cov=357	right_inside_cov=0	right_outside_cov=357
MC	520	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=273	right_inside_cov=0	right_outside_cov=273
MC	521	.	NC_007779	4310363	4311561	1194	0	left_inside_cov=0	left_outside_cov=293	right_inside_cov=0	right_outside_cov=293
JC	522	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=109	coverage_plus=142	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=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=252	pos_hash_score=134	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=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=251
JC	523	.	NC_007779	15391	1	NC_007779	458023	-1	0	alignment_overlap=4	coverage_minus=3	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=3.010609e-02	junction_possible_overlap_registers=86	key=NC_007779__15387__1__NC_007779__458023__-1__4____101__101__1__0	max_left=62	max_left_minus=62	max_left_plus=53	max_min_left=44	max_min_left_minus=44	max_min_left_plus=28	max_min_right=44	max_min_right_minus=35	max_min_right_plus=44	max_pos_hash_score=172	max_right=85	max_right_minus=85	max_right_plus=69	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.03	new_junction_frequency=3.010609e-02	new_junction_read_count=7	pos_hash_score=5	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.00	side_2_overlap=4	side_2_possible_overlap_registers=90	side_2_read_count=236	side_2_redundant=0	total_non_overlap_reads=5
JC	524	.	NC_007779	273179	1	NC_007779	657877	1	0	alignment_overlap=0	coverage_minus=54	coverage_plus=65	flanking_left=101	flanking_right=101	frequency=4.332130e-01	junction_possible_overlap_registers=90	key=NC_007779__273179__1__NC_007779__657877__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=43	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=0.51	new_junction_frequency=4.332130e-01	new_junction_read_count=120	pos_hash_score=80	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=0.67	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=157	side_2_redundant=0	total_non_overlap_reads=119
JC	525	.	NC_007779	274373	-1	NC_007779	657880	-1	0	alignment_overlap=0	coverage_minus=59	coverage_plus=49	flanking_left=101	flanking_right=101	frequency=3.985507e-01	junction_possible_overlap_registers=90	key=NC_007779__274373__-1__NC_007779__657880__-1__0____101__101__1__0	max_left=83	max_left_minus=83	max_left_plus=83	max_min_left=50	max_min_left_minus=50	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=47	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=0.47	new_junction_frequency=3.985507e-01	new_junction_read_count=110	pos_hash_score=77	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=0.70	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=166	side_2_redundant=0	total_non_overlap_reads=108
JC	526	.	NC_007779	274373	-1	NC_007779	679371	1	0	alignment_overlap=0	coverage_minus=200	coverage_plus=196	flanking_left=101	flanking_right=101	frequency=6.312500e-01	junction_possible_overlap_registers=90	key=NC_007779__274373__-1__NC_007779__679371__1__0____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.72	new_junction_frequency=6.312500e-01	new_junction_read_count=404	pos_hash_score=154	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=236	side_2_redundant=0	total_non_overlap_reads=396
JC	527	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=10	coverage_minus=89	coverage_plus=91	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371963__1__10____101__101__0__0	max_left=85	max_left_minus=85	max_left_plus=85	max_min_left=44	max_min_left_minus=44	max_min_left_plus=44	max_min_right=45	max_min_right_minus=45	max_min_right_plus=44	max_pos_hash_score=160	max_right=85	max_right_minus=85	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=1.000000e+00	new_junction_read_count=180	pos_hash_score=103	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=180
JC	528	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=100	coverage_plus=57	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=61	max_min_left=33	max_min_left_minus=33	max_min_left_plus=32	max_min_right=34	max_min_right_minus=34	max_min_right_plus=32	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=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=159	pos_hash_score=81	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=157	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	529	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=124	coverage_plus=77	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=88	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=47	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=NA	new_junction_read_count=202	pos_hash_score=117	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=201
JC	530	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=103	coverage_plus=113	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=48	max_min_left_minus=47	max_min_left_plus=48	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=0.95	new_junction_frequency=NA	new_junction_read_count=219	pos_hash_score=115	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=216
JC	531	.	NC_007779	458011	1	NC_007779	607234	1	0	alignment_overlap=3	coverage_minus=3	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=2.180867e-02	junction_possible_overlap_registers=87	key=NC_007779__458011__1__NC_007779__607231__1__3____101__101__0__1	max_left=78	max_left_minus=78	max_left_plus=24	max_min_left=38	max_min_left_minus=38	max_min_left_plus=24	max_min_right=20	max_min_right_minus=20	max_min_right_plus=0	max_pos_hash_score=174	max_right=78	max_right_minus=60	max_right_plus=78	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=2.180867e-02	new_junction_read_count=5	pos_hash_score=4	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.99	side_1_overlap=3	side_1_possible_overlap_registers=90	side_1_read_count=232	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=5
JC	532	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=105	coverage_plus=110	flanking_left=101	flanking_right=101	frequency=9.530813e-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=88	max_left_plus=92	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=174	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=9.530813e-01	new_junction_read_count=216	pos_hash_score=122	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.05	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=215
JC	533	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=129	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=47	max_min_left_plus=47	max_min_right=47	max_min_right_minus=46	max_min_right_plus=47	max_pos_hash_score=170	max_right=90	max_right_minus=90	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=240	pos_hash_score=128	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=239
JC	534	.	NC_007779	679374	-1	NC_007779	688273	1	0	alignment_overlap=0	coverage_minus=8	coverage_plus=4	flanking_left=101	flanking_right=101	frequency=4.705882e-02	junction_possible_overlap_registers=90	key=NC_007779__679374__-1__NC_007779__688273__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=75	max_min_left=34	max_min_left_minus=14	max_min_left_plus=34	max_min_right=45	max_min_right_minus=43	max_min_right_plus=45	max_pos_hash_score=180	max_right=95	max_right_minus=93	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.05	new_junction_frequency=4.705882e-02	new_junction_read_count=12	pos_hash_score=12	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.03	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=243	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=12
JC	535	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=23	coverage_plus=27	flanking_left=101	flanking_right=101	frequency=2.890359e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=79	max_left_minus=79	max_left_plus=78	max_min_left=42	max_min_left_minus=40	max_min_left_plus=42	max_min_right=39	max_min_right_minus=39	max_min_right_plus=37	max_pos_hash_score=148	max_right=78	max_right_minus=76	max_right_plus=78	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.26	new_junction_frequency=2.890359e-01	new_junction_read_count=50	pos_hash_score=41	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.65	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=152	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.62	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=121	side_2_redundant=0	total_non_overlap_reads=50
JC	536	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=27	coverage_plus=19	flanking_left=101	flanking_right=101	frequency=2.728711e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=76	max_left_minus=74	max_left_plus=76	max_min_left=41	max_min_left_minus=40	max_min_left_plus=41	max_min_right=41	max_min_right_minus=41	max_min_right_plus=40	max_pos_hash_score=148	max_right=73	max_right_minus=73	max_right_plus=71	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.24	new_junction_frequency=2.728711e-01	new_junction_read_count=46	pos_hash_score=39	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.64	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=151	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.62	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=121	side_2_redundant=0	total_non_overlap_reads=46
JC	537	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=99	coverage_plus=117	flanking_left=101	flanking_right=101	frequency=9.778672e-01	junction_possible_overlap_registers=88	key=NC_007779__1221489__1__NC_007779__1301039__1__2____101__101__0__1	max_left=91	max_left_minus=91	max_left_plus=89	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=86	max_right_minus=86	max_right_plus=83	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.94	new_junction_frequency=9.778672e-01	new_junction_read_count=216	pos_hash_score=112	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=5	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=216
JC	538	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=87	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=48	max_pos_hash_score=180	max_right=88	max_right_minus=88	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=210	pos_hash_score=115	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=209
JC	539	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=115	coverage_plus=120	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=83	key=NC_007779__1301040__-1__NC_007779__1302370__1__7____101__101__0__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=46	max_min_left_minus=46	max_min_left_plus=43	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=166	max_right=88	max_right_minus=88	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.09	new_junction_frequency=1.000000e+00	new_junction_read_count=237	pos_hash_score=125	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=235
JC	540	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=104	coverage_plus=110	flanking_left=101	flanking_right=101	frequency=9.183673e-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=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=9.183673e-01	new_junction_read_count=215	pos_hash_score=127	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.08	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=20	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=214
JC	541	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=111	coverage_plus=98	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=87	max_left_minus=85	max_left_plus=87	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=210	pos_hash_score=119	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=209
JC	542	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=85	coverage_plus=103	flanking_left=101	flanking_right=101	frequency=9.981322e-01	junction_possible_overlap_registers=64	key=NC_007779__1413638__-1__NC_007779__1436673__1__26____101__101__0__0	max_left=69	max_left_minus=67	max_left_plus=69	max_min_left=37	max_min_left_minus=36	max_min_left_plus=37	max_min_right=37	max_min_right_minus=37	max_min_right_plus=37	max_pos_hash_score=128	max_right=70	max_right_minus=70	max_right_plus=69	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.13	new_junction_frequency=9.981322e-01	new_junction_read_count=190	pos_hash_score=96	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=26	side_1_possible_overlap_registers=90	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=64	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=188
JC	543	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=113	coverage_plus=93	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1672780__-1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=86	max_right_minus=86	max_right_plus=85	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=109	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=206
JC	544	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=134	coverage_plus=110	flanking_left=101	flanking_right=101	frequency=9.494163e-01	junction_possible_overlap_registers=90	key=NC_007779__1907280__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=9.494163e-01	new_junction_read_count=244	pos_hash_score=128	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.06	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=13	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=244
JC	545	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=98	coverage_plus=120	flanking_left=101	flanking_right=101	frequency=9.437229e-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=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=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=9.437229e-01	new_junction_read_count=218	pos_hash_score=119	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.06	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=13	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=218
JC	546	.	NC_007779	1909344	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=11	coverage_plus=18	flanking_left=101	flanking_right=101	frequency=1.150794e-01	junction_possible_overlap_registers=90	key=NC_007779__1909344__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=94	max_left_minus=86	max_left_plus=94	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=48	max_pos_hash_score=180	max_right=88	max_right_minus=88	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.12	new_junction_frequency=1.150794e-01	new_junction_read_count=29	pos_hash_score=28	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.95	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=223	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=29
JC	547	.	NC_007779	1909352	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=21	coverage_plus=24	flanking_left=101	flanking_right=101	frequency=1.642336e-01	junction_possible_overlap_registers=90	key=NC_007779__1909352__-1__NC_007779__2411458__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=93	max_min_left=50	max_min_left_minus=47	max_min_left_plus=50	max_min_right=49	max_min_right_minus=41	max_min_right_plus=49	max_pos_hash_score=180	max_right=88	max_right_minus=88	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.19	new_junction_frequency=1.642336e-01	new_junction_read_count=45	pos_hash_score=41	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.97	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=229	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=45
JC	548	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=117	coverage_plus=37	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1980091__1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=40	max_min_right=50	max_min_right_minus=50	max_min_right_plus=46	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.66	new_junction_frequency=1.000000e+00	new_junction_read_count=155	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=154
JC	549	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=115	coverage_plus=105	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__1980095__-1__NC_007779__2176983__1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=46	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=178	max_right=92	max_right_minus=91	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=223	pos_hash_score=117	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=220
JC	550	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=91	coverage_plus=86	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=49	max_min_left_minus=49	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=87	max_right_minus=85	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.76	new_junction_frequency=1.000000e+00	new_junction_read_count=180	pos_hash_score=102	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=177
JC	551	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=101	coverage_plus=114	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=87	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=47	max_min_right_minus=45	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=217	pos_hash_score=115	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=215
JC	552	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=78	coverage_plus=138	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=85	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=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=216	pos_hash_score=117	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=216
JC	553	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=134	coverage_plus=163	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=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=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.27	new_junction_frequency=1.000000e+00	new_junction_read_count=299	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=297
JC	554	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=115	coverage_plus=137	flanking_left=101	flanking_right=101	frequency=9.545455e-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=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=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.07	new_junction_frequency=9.545455e-01	new_junction_read_count=252	pos_hash_score=136	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.05	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=12	side_2_redundant=0	total_non_overlap_reads=252
JC	555	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=90	coverage_plus=96	flanking_left=101	flanking_right=101	frequency=9.790576e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=49	max_min_left_minus=49	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.79	new_junction_frequency=9.790576e-01	new_junction_read_count=187	pos_hash_score=108	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=186
JC	556	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=73	coverage_plus=102	flanking_left=101	flanking_right=101	frequency=5.682425e-01	junction_possible_overlap_registers=86	key=NC_007779__2865229__1__NC_007779__2865278__-1__4____101__101__0__0	max_left=90	max_left_minus=90	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=45	max_min_right=47	max_min_right_minus=46	max_min_right_plus=47	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.89	new_junction_frequency=5.682425e-01	new_junction_read_count=201	pos_hash_score=105	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.72	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=170	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.64	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=143	side_2_redundant=0	total_non_overlap_reads=175
JC	557	.	NC_007779	2865229	1	NC_007779	2865278	-1	-42	alignment_overlap=-42	coverage_minus=11	coverage_plus=13	flanking_left=101	flanking_right=101	frequency=2.189781e-01	junction_possible_overlap_registers=48	key=NC_007779__2865229__1__NC_007779__2865278__-1__-42__CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA__101__101__0__0	max_left=41	max_left_minus=39	max_left_plus=41	max_min_left=27	max_min_left_minus=27	max_min_left_plus=26	max_min_right=29	max_min_right_minus=28	max_min_right_plus=29	max_pos_hash_score=96	max_right=43	max_right_minus=43	max_right_plus=41	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.19	new_junction_frequency=2.189781e-01	new_junction_read_count=24	pos_hash_score=18	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.72	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=170	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.64	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=151	side_2_redundant=0	total_non_overlap_reads=24	unique_read_sequence=CGTTTGCGCGAAATCCTGCAAACGCAGGGGCTGAATATCGAA
JC	558	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=107	coverage_plus=128	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3147474__1__NC_007779__3262328__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=93	max_right_minus=85	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=235	pos_hash_score=120	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=235
JC	559	.	NC_007779	3184754	1	NC_007779	3186086	-1	0	alignment_overlap=3	coverage_minus=1	coverage_plus=3	flanking_left=101	flanking_right=101	frequency=2.574792e-02	junction_possible_overlap_registers=87	key=NC_007779__3184751__1__NC_007779__3186086__-1__3____101__101__1__0	max_left=72	max_left_minus=23	max_left_plus=72	max_min_left=23	max_min_left_minus=23	max_min_left_plus=15	max_min_right=39	max_min_right_minus=0	max_min_right_plus=39	max_pos_hash_score=174	max_right=83	max_right_minus=75	max_right_plus=83	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.03	new_junction_frequency=2.574792e-02	new_junction_read_count=7	pos_hash_score=4	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.16	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=274	side_2_redundant=0	total_non_overlap_reads=4
JC	560	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=131	coverage_plus=127	flanking_left=101	flanking_right=101	frequency=9.811959e-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=49	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=9.811959e-01	new_junction_read_count=258	pos_hash_score=140	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=5	side_2_redundant=0	total_non_overlap_reads=258
JC	561	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=120	coverage_plus=89	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=88	max_left_minus=88	max_left_plus=88	max_min_left=47	max_min_left_minus=47	max_min_left_plus=46	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=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=210	pos_hash_score=112	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=209	unique_read_sequence=CTTTGC
JC	562	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=102	coverage_plus=142	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=245	pos_hash_score=129	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=244
JC	563	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=112	coverage_plus=111	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=84	max_left_minus=83	max_left_plus=84	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=223	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=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=223
JC	564	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=146	coverage_plus=127	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=275	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=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=273
JC	565	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=83	coverage_plus=140	flanking_left=101	flanking_right=101	frequency=9.870996e-01	junction_possible_overlap_registers=89	key=NC_007779__3512759__-1__NC_007779__3744263__-1__1____101__101__0__1	max_left=94	max_left_minus=93	max_left_plus=94	max_min_left=49	max_min_left_minus=47	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=0.97	new_junction_frequency=9.870996e-01	new_junction_read_count=227	pos_hash_score=117	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=3	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=223
JC	566	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=125	coverage_plus=125	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=82	key=NC_007779__3742935__-1__NC_007779__3744264__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=86	max_min_left=46	max_min_left_minus=46	max_min_left_plus=45	max_min_right=46	max_min_right_minus=46	max_min_right_plus=45	max_pos_hash_score=164	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=250	pos_hash_score=130	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=82	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=250
JC	567	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=172	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=9.966997e-01	junction_possible_overlap_registers=90	key=NC_007779__3744263__-1__NC_007779__3903274__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.28	new_junction_frequency=9.966997e-01	new_junction_read_count=302	pos_hash_score=140	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=1	side_2_redundant=0	total_non_overlap_reads=301
JC	568	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=108	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=9.978621e-01	junction_possible_overlap_registers=86	key=NC_007779__3746910__-1__NC_007779__3748106__1__4____101__101__0__0	max_left=91	max_left_minus=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=46	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=90	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=9.978621e-01	new_junction_read_count=223	pos_hash_score=123	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=223
JC	569	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=121	coverage_plus=118	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3746911__1__NC_007779__3748646__-1__0____101__101__1__0	max_left=92	max_left_minus=90	max_left_plus=92	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=276	pos_hash_score=123	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=239
JC	570	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=126	coverage_plus=120	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=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=247	pos_hash_score=137	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=246
JC	571	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=165	coverage_plus=143	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3750590__-1__NC_007779__3751786__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=46	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=1.37	new_junction_frequency=1.000000e+00	new_junction_read_count=308	pos_hash_score=145	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=308
JC	572	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=138	coverage_plus=116	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3903279__-1__NC_007779__4504191__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=92	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=255	pos_hash_score=131	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=254
JC	573	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=127	coverage_plus=115	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=91	max_min_left=49	max_min_left_minus=49	max_min_left_plus=46	max_min_right=49	max_min_right_minus=48	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.06	new_junction_frequency=1.000000e+00	new_junction_read_count=243	pos_hash_score=126	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=242
JC	574	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=115	coverage_plus=136	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=252	pos_hash_score=136	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=251
JC	575	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=142	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3988379__-1__NC_007779__4009199__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=275	pos_hash_score=145	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=274
JC	576	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=132	coverage_plus=125	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=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=47	max_min_right_minus=47	max_min_right_plus=46	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.15	new_junction_frequency=1.000000e+00	new_junction_read_count=258	pos_hash_score=124	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=257
JC	577	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=103	coverage_plus=115	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=92	max_left_plus=94	max_min_left=50	max_min_left_minus=50	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=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.94	new_junction_frequency=1.000000e+00	new_junction_read_count=222	pos_hash_score=123	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=218
JC	578	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=110	coverage_plus=163	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=92	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.35	new_junction_frequency=1.000000e+00	new_junction_read_count=318	pos_hash_score=142	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=273
JC	579	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=135	coverage_plus=178	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4355060__1__NC_007779__4502861__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=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=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.33	new_junction_frequency=1.000000e+00	new_junction_read_count=314	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=313
JC	580	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=114	coverage_plus=111	flanking_left=101	flanking_right=101	frequency=9.913835e-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=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=9.913835e-01	new_junction_read_count=225	pos_hash_score=126	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=2	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=225
JC	581	.	NC_007779	4547362	1	NC_007779	4547676	1	0	alignment_overlap=9	coverage_minus=17	coverage_plus=7	flanking_left=101	flanking_right=101	frequency=1.202405e-01	junction_possible_overlap_registers=81	key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0	max_left=81	max_left_minus=74	max_left_plus=81	max_min_left=45	max_min_left_minus=45	max_min_left_plus=33	max_min_right=45	max_min_right_minus=45	max_min_right_plus=25	max_pos_hash_score=162	max_right=84	max_right_minus=84	max_right_plus=76	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.11	new_junction_frequency=1.202405e-01	new_junction_read_count=24	pos_hash_score=22	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.76	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=178	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.90	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=191	side_2_redundant=0	total_non_overlap_reads=24
JC	582	.	NC_007779	4547370	-1	NC_007779	4547666	-1	0	alignment_overlap=9	coverage_minus=18	coverage_plus=8	flanking_left=101	flanking_right=101	frequency=1.275448e-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=66	max_min_left=36	max_min_left_minus=36	max_min_left_plus=36	max_min_right=46	max_min_right_minus=46	max_min_right_plus=45	max_pos_hash_score=162	max_right=85	max_right_minus=85	max_right_plus=73	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.12	new_junction_frequency=1.275448e-01	new_junction_read_count=26	pos_hash_score=23	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.78	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=183	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.90	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=191	side_2_redundant=0	total_non_overlap_reads=26
UN	583	.	NC_007779	15485	16634
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UN	689	.	NC_007779	3874863	3874904
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UN	708	.	NC_007779	4299523	4299551
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UN	710	.	NC_007779	4310363	4311561
UN	711	.	NC_007779	4502953	4504095
UN	712	.	NC_007779	4512236	4513265