#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	19:28:52 03 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	3_D2_TGACCA_L003_R1_001.fastq
SNP	1	61	NC_007779	66457	A	frequency=1
SNP	2	66	NC_007779	97880	T	frequency=1
SNP	3	84	NC_007779	167632	A	frequency=1
SNP	4	91	NC_007779	274547	G	frequency=1
DEL	5	568,582	NC_007779	274733	97240	frequency=1
SNP	6	103	NC_007779	547694	G	frequency=1
INS	7	104	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	106	NC_007779	556858	T	frequency=1
SNP	9	109	NC_007779	569996	C	frequency=1
SNP	10	128	NC_007779	749354	A	frequency=1
SNP	11	129	NC_007779	758440	A	frequency=1
SNP	12	137	NC_007779	887234	A	frequency=1
SNP	13	148	NC_007779	987574	T	frequency=1
SNP	14	181	NC_007779	1093686	C	frequency=1
SNP	15	182	NC_007779	1097580	T	frequency=2.126508e-01
SNP	16	191	NC_007779	1170573	T	frequency=1
DEL	17	570,592	NC_007779	1301041	1336	frequency=1
SNP	18	201	NC_007779	1318876	A	frequency=1
DEL	19	571,595	NC_007779	1413639	23060	frequency=1
SNP	20	221	NC_007779	1483588	A	frequency=1
DEL	21	223	NC_007779	1496775	1	frequency=1
SNP	22	235	NC_007779	1615814	A	frequency=1
DEL	23	244	NC_007779	1669599	1	frequency=1
SNP	24	262	NC_007779	1844073	A	frequency=1
SNP	25	269	NC_007779	1918872	A	frequency=1
SNP	26	272	NC_007779	1973476	A	frequency=1
SNP	27	277	NC_007779	2005401	T	frequency=1
SNP	28	284	NC_007779	2170094	A	frequency=1
DEL	29	573,602	NC_007779	2320795	1336	frequency=1
SNP	30	301	NC_007779	2406075	T	frequency=1
SNP	31	303	NC_007779	2416102	A	frequency=1
SNP	32	314	NC_007779	2538628	T	frequency=1
INS	33	607	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=6.924067e-01
SNP	34	335	NC_007779	2866111	G	frequency=1
SNP	35	349	NC_007779	3003330	A	frequency=1
SNP	36	354	NC_007779	3049815	T	frequency=1
SNP	37	384	NC_007779	3397813	G	frequency=1
DEL	38	576,615	NC_007779	3742936	1336	frequency=1
DEL	39	577,617	NC_007779	3746911	1199	frequency=1
DEL	40	423	NC_007779	3750122	1	frequency=9.616823e-01
SNP	41	424	NC_007779	3750123	T	frequency=3.169537e-02
DEL	42	578,620	NC_007779	3750591	1199	frequency=1
SNP	43	438	NC_007779	3898657	G	frequency=1
DEL	44	579,622	NC_007779	3958123	34	frequency=1
SNP	45	471	NC_007779	4090749	T	frequency=1
SNP	46	482	NC_007779	4165991	C	frequency=1
DEL	47	580,625	NC_007779	4310363	1199	frequency=1
DEL	48	541,542	NC_007779	4371271	2	frequency=1
SNP	49	556	NC_007779	4546535	A	frequency=1
RA	50	.	NC_007779	301	1	.	T	bias_e_value=4507000	bias_p_value=0.970012	fisher_strand_p_value=1	frequency=1.145077e-02	genotype_quality=1245.3	ks_quality_p_value=0.765313	log10_base_likelihood=-12.628	log10_qual_likelihood_position_model=2.94182	log10_strand_likelihood_position_model=0.380426	new_cov=1/2	polymorphism_quality=7.2	quality=7.2	quality_position_model=2.56077e-11	ref_cov=114/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/147
RA	51	.	NC_007779	302	0	T	.	bias_e_value=4562520	bias_p_value=0.981961	fisher_strand_p_value=1	frequency=1.125526e-02	genotype_quality=1038.1	ks_quality_p_value=0.816171	log10_base_likelihood=-7.26228	log10_qual_likelihood_position_model=3.20828	log10_strand_likelihood_position_model=0.378875	new_cov=1/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=1.6892e-05	ref_cov=115/148	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/150
RA	52	.	NC_007779	847	0	A	C	bias_e_value=0.0252885	bias_p_value=5.44268e-09	fisher_strand_p_value=2.34882e-10	frequency=5.326128e-02	genotype_quality=596.2	ks_quality_p_value=1	log10_base_likelihood=-9.40018	log10_qual_likelihood_position_model=13.9627	log10_strand_likelihood_position_model=9.62915	new_cov=0/10	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=141/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/22
RA	53	.	NC_007779	5595	0	G	T	bias_e_value=250.254	bias_p_value=5.38605e-05	fisher_strand_p_value=4.01156e-06	frequency=3.764439e-02	genotype_quality=1009.7	ks_quality_p_value=1	log10_base_likelihood=-6.63698	log10_qual_likelihood_position_model=14.9808	log10_strand_likelihood_position_model=5.47833	new_cov=1/22	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=153/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/167
RA	54	.	NC_007779	11143	0	G	T	bias_e_value=0.158681	bias_p_value=3.41519e-08	fisher_strand_p_value=1.60724e-09	frequency=7.834482e-02	genotype_quality=822.3	ks_quality_p_value=1	log10_base_likelihood=-17.4323	log10_qual_likelihood_position_model=20.1023	log10_strand_likelihood_position_model=8.93296	new_cov=0/28	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=127/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/131
RA	55	.	NC_007779	23556	0	A	.	bias_e_value=1302230	bias_p_value=0.280271	fisher_strand_p_value=0.255408	frequency=1.118469e-02	genotype_quality=1066.2	ks_quality_p_value=0.310458	log10_base_likelihood=-7.90047	log10_qual_likelihood_position_model=2.43019	log10_strand_likelihood_position_model=0.777596	new_cov=0/3	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.45056e-06	ref_cov=120/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/148
RA	56	.	NC_007779	29496	0	T	A	bias_e_value=1857.1	bias_p_value=0.000399691	fisher_strand_p_value=3.55448e-05	frequency=4.326725e-02	genotype_quality=755.9	ks_quality_p_value=1	log10_base_likelihood=-5.99037	log10_qual_likelihood_position_model=19.5799	log10_strand_likelihood_position_model=4.44922	new_cov=0/12	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=130/90	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=130/102
RA	57	.	NC_007779	34111	1	.	T	bias_e_value=490269	bias_p_value=0.105517	fisher_strand_p_value=0.0734333	frequency=1.634026e-02	genotype_quality=1471.0	ks_quality_p_value=0.297986	log10_base_likelihood=-22.1384	log10_qual_likelihood_position_model=4.11216	log10_strand_likelihood_position_model=1.22419	new_cov=5/0	polymorphism_quality=16.9	quality=16.9	quality_position_model=6.13658e-19	ref_cov=170/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=175/131
RA	58	.	NC_007779	36544	0	G	T	bias_e_value=122.547	bias_p_value=2.6375e-05	fisher_strand_p_value=2.27405e-06	frequency=3.629589e-02	genotype_quality=916.5	ks_quality_p_value=0.817003	log10_base_likelihood=-6.63433	log10_qual_likelihood_position_model=23.6472	log10_strand_likelihood_position_model=5.92568	new_cov=0/21	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=138/140	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/161
RA	59	.	NC_007779	39910	0	G	T	bias_e_value=62195.1	bias_p_value=0.0133858	fisher_strand_p_value=0.00206472	frequency=4.901600e-02	genotype_quality=648.2	ks_quality_p_value=0.887897	log10_base_likelihood=-7.20704	log10_qual_likelihood_position_model=14.2155	log10_strand_likelihood_position_model=2.96069	new_cov=0/18	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=66/134	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=66/154
RA	60	.	NC_007779	47305	0	G	T	bias_e_value=7.4291e-05	bias_p_value=1.59892e-11	fisher_strand_p_value=5.46929e-13	frequency=9.351397e-02	genotype_quality=932.3	ks_quality_p_value=1	log10_base_likelihood=-26.6999	log10_qual_likelihood_position_model=24.9403	log10_strand_likelihood_position_model=12.2621	new_cov=0/37	polymorphism_quality=21.5	quality=21.5	quality_position_model=Inf	ref_cov=155/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/154
RA	61	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1251.8	new_cov=165/144	quality=1251.8	ref_cov=0/0	tot_cov=165/144
RA	62	.	NC_007779	70602	0	G	T	bias_e_value=0.021821	bias_p_value=4.69639e-09	fisher_strand_p_value=2.01337e-10	frequency=7.647324e-02	genotype_quality=752.6	ks_quality_p_value=1	log10_base_likelihood=-13.128	log10_qual_likelihood_position_model=20.5975	log10_strand_likelihood_position_model=9.69608	new_cov=0/28	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=122/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/115
RA	63	.	NC_007779	72039	0	T	G	bias_e_value=0.0594432	bias_p_value=1.27936e-08	fisher_strand_p_value=5.74272e-10	frequency=5.979061e-02	genotype_quality=696.9	ks_quality_p_value=1	log10_base_likelihood=-8.06504	log10_qual_likelihood_position_model=21.8665	log10_strand_likelihood_position_model=9.24088	new_cov=21/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=64/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=85/131
RA	64	.	NC_007779	75074	0	T	G	bias_e_value=5.08732e-21	bias_p_value=1.09491e-27	fisher_strand_p_value=1.6272e-29	frequency=1.365056e-01	genotype_quality=810.1	ks_quality_p_value=1	log10_base_likelihood=-27.1175	log10_qual_likelihood_position_model=43.0037	log10_strand_likelihood_position_model=28.7886	new_cov=48/0	polymorphism_quality=21.9	quality=21.9	quality_position_model=Inf	ref_cov=35/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/171
RA	65	.	NC_007779	75079	0	C	T	bias_e_value=0.0500115	bias_p_value=1.07636e-08	fisher_strand_p_value=4.79263e-10	frequency=5.130768e-02	genotype_quality=828.3	ks_quality_p_value=1	log10_base_likelihood=-10.5378	log10_qual_likelihood_position_model=18.4465	log10_strand_likelihood_position_model=9.31943	new_cov=13/0	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=35/176	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=48/177
RA	66	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=1238.9	new_cov=148/159	quality=1238.9	ref_cov=0/0	tot_cov=148/159
RA	67	.	NC_007779	101246	0	T	G	bias_e_value=91546.8	bias_p_value=0.019703	fisher_strand_p_value=0.00408827	frequency=3.168583e-02	genotype_quality=472.9	ks_quality_p_value=0.703415	log10_base_likelihood=-8.99764	log10_qual_likelihood_position_model=5.45633	log10_strand_likelihood_position_model=2.38846	new_cov=4/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=0.00931251	ref_cov=29/93	reject=POLYMORPHISM_STRAND	tot_cov=33/93
RA	68	.	NC_007779	108790	0	C	A	bias_e_value=1800340	bias_p_value=0.387475	fisher_strand_p_value=0.590967	frequency=1.030445e-02	genotype_quality=1219.7	ks_quality_p_value=0.213593	log10_base_likelihood=-5.83095	log10_qual_likelihood_position_model=1.62623	log10_strand_likelihood_position_model=0.472955	new_cov=1/2	polymorphism_quality=0.3	quality=0.3	quality_position_model=1.47241e-05	ref_cov=158/129	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=159/131
RA	69	.	NC_007779	116855	0	G	T	bias_e_value=153.321	bias_p_value=3.29984e-05	fisher_strand_p_value=2.45797e-06	frequency=2.573776e-02	genotype_quality=978.9	ks_quality_p_value=0.962033	log10_base_likelihood=-5.91531	log10_qual_likelihood_position_model=13.6144	log10_strand_likelihood_position_model=5.60942	new_cov=0/15	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=161/110	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/125
RA	70	.	NC_007779	119384	0	T	G	bias_e_value=4.4478e-15	bias_p_value=9.57271e-22	fisher_strand_p_value=1.79347e-23	frequency=1.236763e-01	genotype_quality=806.7	ks_quality_p_value=1	log10_base_likelihood=-17.9175	log10_qual_likelihood_position_model=36.7205	log10_strand_likelihood_position_model=22.7463	new_cov=51/0	polymorphism_quality=12.6	quality=12.6	quality_position_model=Inf	ref_cov=66/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=117/162
RA	71	.	NC_007779	134366	0	G	T	bias_e_value=239.747	bias_p_value=5.15991e-05	fisher_strand_p_value=3.82991e-06	frequency=3.965282e-02	genotype_quality=1019.2	ks_quality_p_value=1	log10_base_likelihood=-12.2192	log10_qual_likelihood_position_model=16.4955	log10_strand_likelihood_position_model=5.5077	new_cov=1/22	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=154/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/170
RA	72	.	NC_007779	137009	0	G	T	bias_e_value=884.531	bias_p_value=0.000190372	fisher_strand_p_value=1.64197e-05	frequency=4.141331e-02	genotype_quality=851.2	ks_quality_p_value=0.961682	log10_base_likelihood=-6.75514	log10_qual_likelihood_position_model=20.6641	log10_strand_likelihood_position_model=4.78464	new_cov=15/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=112/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/130
RA	73	.	NC_007779	150535	0	G	A	bias_e_value=74916.2	bias_p_value=0.0161237	fisher_strand_p_value=0.0022829	frequency=3.661156e-02	genotype_quality=948.9	ks_quality_p_value=0.996799	log10_base_likelihood=-10.1334	log10_qual_likelihood_position_model=11.4372	log10_strand_likelihood_position_model=2.70232	new_cov=10/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=122/110	reject=POLYMORPHISM_STRAND	tot_cov=132/110
RA	74	.	NC_007779	150537	0	A	C	bias_e_value=232586	bias_p_value=0.050058	fisher_strand_p_value=0.00871717	frequency=1.925468e-02	genotype_quality=901.2	ks_quality_p_value=1	log10_base_likelihood=-5.83533	log10_qual_likelihood_position_model=10.285	log10_strand_likelihood_position_model=2.14482	new_cov=8/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=122/108	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=130/108
RA	75	.	NC_007779	150546	0	A	C	bias_e_value=18986	bias_p_value=0.00408623	fisher_strand_p_value=0.000471922	frequency=4.927588e-02	genotype_quality=757.2	ks_quality_p_value=1	log10_base_likelihood=-15.0976	log10_qual_likelihood_position_model=12.086	log10_strand_likelihood_position_model=3.39596	new_cov=12/0	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=97/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/95
RA	76	.	NC_007779	150548	0	A	T	bias_e_value=633279	bias_p_value=0.136297	fisher_strand_p_value=0.0303141	frequency=2.644348e-02	genotype_quality=749.4	ks_quality_p_value=1	log10_base_likelihood=-7.49376	log10_qual_likelihood_position_model=8.31847	log10_strand_likelihood_position_model=1.69718	new_cov=6/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=100/95	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=106/95
RA	77	.	NC_007779	150550	0	C	T	bias_e_value=60511.7	bias_p_value=0.0130235	fisher_strand_p_value=0.00177591	frequency=4.394722e-02	genotype_quality=771.4	ks_quality_p_value=1	log10_base_likelihood=-9.16598	log10_qual_likelihood_position_model=13.245	log10_strand_likelihood_position_model=2.87024	new_cov=10/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=96/95	reject=POLYMORPHISM_STRAND	tot_cov=106/95
RA	78	.	NC_007779	150551	0	A	T	bias_e_value=16727.6	bias_p_value=0.00360016	fisher_strand_p_value=0.00040903	frequency=5.055666e-02	genotype_quality=732.5	ks_quality_p_value=1	log10_base_likelihood=-11.4146	log10_qual_likelihood_position_model=15.0255	log10_strand_likelihood_position_model=3.49548	new_cov=12/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=93/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/95
RA	79	.	NC_007779	150552	0	G	C	bias_e_value=16727.6	bias_p_value=0.00360016	fisher_strand_p_value=0.00040903	frequency=4.452038e-02	genotype_quality=770.6	ks_quality_p_value=1	log10_base_likelihood=-9.81113	log10_qual_likelihood_position_model=14.0165	log10_strand_likelihood_position_model=3.49548	new_cov=12/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=93/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/95
RA	80	.	NC_007779	150553	0	A	T	bias_e_value=16264.8	bias_p_value=0.00350056	fisher_strand_p_value=0.000396288	frequency=4.799080e-02	genotype_quality=693.9	ks_quality_p_value=1	log10_base_likelihood=-7.71462	log10_qual_likelihood_position_model=13.7466	log10_strand_likelihood_position_model=3.52131	new_cov=12/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=92/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/95
RA	81	.	NC_007779	150558	0	T	G	bias_e_value=640668	bias_p_value=0.137887	fisher_strand_p_value=0.0307699	frequency=2.064800e-02	genotype_quality=837.7	ks_quality_p_value=1	log10_base_likelihood=-5.78388	log10_qual_likelihood_position_model=7.99413	log10_strand_likelihood_position_model=1.68073	new_cov=6/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=108/101	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=114/101
RA	82	.	NC_007779	151656	0	T	G	bias_e_value=314.694	bias_p_value=6.77296e-05	fisher_strand_p_value=5.13937e-06	frequency=2.980804e-02	genotype_quality=1067.9	ks_quality_p_value=1	log10_base_likelihood=-6.01774	log10_qual_likelihood_position_model=16.7879	log10_strand_likelihood_position_model=5.28909	new_cov=16/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=138/167	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=154/167
RA	83	.	NC_007779	158557	0	G	T	bias_e_value=15274.8	bias_p_value=0.00328749	fisher_strand_p_value=0.000369208	frequency=3.944016e-02	genotype_quality=805.4	ks_quality_p_value=1	log10_base_likelihood=-8.51962	log10_qual_likelihood_position_model=14.8384	log10_strand_likelihood_position_model=3.54125	new_cov=1/17	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=117/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/151
RA	84	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=1112.4	new_cov=136/138	quality=1112.4	ref_cov=0/0	tot_cov=137/138
RA	85	.	NC_007779	170275	0	C	A	bias_e_value=22.4105	bias_p_value=4.82328e-06	fisher_strand_p_value=3.01161e-07	frequency=4.737759e-02	genotype_quality=814.2	ks_quality_p_value=1	log10_base_likelihood=-7.93798	log10_qual_likelihood_position_model=15.1978	log10_strand_likelihood_position_model=6.5212	new_cov=19/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=99/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/131
RA	86	.	NC_007779	179257	0	A	.	bias_e_value=4075030	bias_p_value=0.877042	fisher_strand_p_value=0.619203	frequency=1.157284e-02	genotype_quality=1030.3	ks_quality_p_value=0.883482	log10_base_likelihood=-7.94264	log10_qual_likelihood_position_model=1.7835	log10_strand_likelihood_position_model=0.429446	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.21397e-07	ref_cov=130/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/128
RA	87	.	NC_007779	193489	0	G	T	bias_e_value=2850.21	bias_p_value=0.000613432	fisher_strand_p_value=5.69388e-05	frequency=4.818869e-02	genotype_quality=856.9	ks_quality_p_value=1	log10_base_likelihood=-6.68614	log10_qual_likelihood_position_model=14.0793	log10_strand_likelihood_position_model=4.33138	new_cov=16/1	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=106/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/132
RA	88	.	NC_007779	207536	0	G	T	bias_e_value=0.00329471	bias_p_value=7.09099e-10	fisher_strand_p_value=2.80301e-11	frequency=1.129160e-01	genotype_quality=664.6	ks_quality_p_value=1	log10_base_likelihood=-23.2853	log10_qual_likelihood_position_model=21.6218	log10_strand_likelihood_position_model=10.6058	new_cov=0/39	polymorphism_quality=18.0	quality=18.0	quality_position_model=Inf	ref_cov=109/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/146
RA	89	.	NC_007779	218827	1	.	A	bias_e_value=4533390	bias_p_value=0.975693	fisher_strand_p_value=1	frequency=1.094818e-02	genotype_quality=1337.9	ks_quality_p_value=0.787776	log10_base_likelihood=-12.0908	log10_qual_likelihood_position_model=3.88295	log10_strand_likelihood_position_model=0.393411	new_cov=1/2	polymorphism_quality=6.7	quality=6.7	quality_position_model=8.62751e-10	ref_cov=125/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/148
RA	90	.	NC_007779	274474	0	T	.	bias_e_value=4254430	bias_p_value=0.915653	fisher_strand_p_value=1	frequency=1.131344e-02	genotype_quality=1035.5	ks_quality_p_value=0.618479	log10_base_likelihood=-8.25662	log10_qual_likelihood_position_model=2.05432	log10_strand_likelihood_position_model=0.379499	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=9.72361e-08	ref_cov=114/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/149
RA	91	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1157.3	new_cov=128/142	quality=1157.3	ref_cov=0/0	tot_cov=128/142
RA	92	.	NC_007779	374799	0	T	G	bias_e_value=4.69759e-08	bias_p_value=1.01103e-14	fisher_strand_p_value=2.74501e-16	frequency=5.597496e-02	genotype_quality=750.9	ks_quality_p_value=1	log10_base_likelihood=-5.65525	log10_qual_likelihood_position_model=22.8514	log10_strand_likelihood_position_model=15.5615	new_cov=25/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=39/164	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=64/164
RA	93	.	NC_007779	379236	1	.	G	bias_e_value=731639	bias_p_value=0.157466	fisher_strand_p_value=0.0996841	frequency=1.666737e-02	genotype_quality=832.3	ks_quality_p_value=0.366565	log10_base_likelihood=-13.6942	log10_qual_likelihood_position_model=2.95797	log10_strand_likelihood_position_model=1.00137	new_cov=0/3	polymorphism_quality=8.3	quality=8.3	quality_position_model=9.32993e-12	ref_cov=96/81	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=96/84
RA	94	.	NC_007779	379237	0	G	.	bias_e_value=1020070	bias_p_value=0.219544	fisher_strand_p_value=0.721052	frequency=3.430748e-02	genotype_quality=808.7	ks_quality_p_value=0.0786912	log10_base_likelihood=-23.0365	log10_qual_likelihood_position_model=4.13382	log10_strand_likelihood_position_model=0.558886	new_cov=4/3	polymorphism_quality=17.8	quality=17.8	quality_position_model=1.68876e-20	ref_cov=97/99	reject=INDEL_HOMOPOLYMER	tot_cov=101/103
RA	95	.	NC_007779	387919	0	A	G	bias_e_value=9.03175	bias_p_value=1.94385e-06	fisher_strand_p_value=1.14458e-07	frequency=4.869127e-02	genotype_quality=433.5	ks_quality_p_value=1	log10_base_likelihood=-8.57835	log10_qual_likelihood_position_model=8.16472	log10_strand_likelihood_position_model=6.94135	new_cov=0/7	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=113/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/16
RA	96	.	NC_007779	407306	0	C	A	bias_e_value=0.683056	bias_p_value=1.4701e-07	fisher_strand_p_value=7.45709e-09	frequency=7.617569e-02	genotype_quality=739.0	ks_quality_p_value=1	log10_base_likelihood=-13.6998	log10_qual_likelihood_position_model=17.5695	log10_strand_likelihood_position_model=8.2689	new_cov=26/0	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=98/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/120
RA	97	.	NC_007779	440767	0	G	T	bias_e_value=0.00834544	bias_p_value=1.79613e-09	fisher_strand_p_value=7.38259e-11	frequency=1.027813e-01	genotype_quality=691.2	ks_quality_p_value=1	log10_base_likelihood=-19.5919	log10_qual_likelihood_position_model=21.8557	log10_strand_likelihood_position_model=10.1526	new_cov=1/34	polymorphism_quality=14.3	quality=14.3	quality_position_model=Inf	ref_cov=122/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/124
RA	98	.	NC_007779	467487	1	.	T	bias_e_value=2782150	bias_p_value=0.598783	fisher_strand_p_value=0.501338	frequency=7.194519e-03	genotype_quality=1353.3	ks_quality_p_value=0.501853	log10_base_likelihood=-7.92261	log10_qual_likelihood_position_model=1.91525	log10_strand_likelihood_position_model=0.537247	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.25525e-07	ref_cov=128/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/150
RA	99	.	NC_007779	513848	0	A	C	bias_e_value=5.40793e-16	bias_p_value=1.16391e-22	fisher_strand_p_value=2.09632e-24	frequency=1.602650e-01	genotype_quality=528.2	ks_quality_p_value=1	log10_base_likelihood=-15.9399	log10_qual_likelihood_position_model=31.6521	log10_strand_likelihood_position_model=23.6785	new_cov=0/45	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=115/28	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/73
RA	100	.	NC_007779	522430	1	.	T	bias_e_value=4213200	bias_p_value=0.90678	fisher_strand_p_value=0.654161	frequency=2.403831e-02	genotype_quality=994.1	ks_quality_p_value=0.918056	log10_base_likelihood=-23.2133	log10_qual_likelihood_position_model=2.48723	log10_strand_likelihood_position_model=0.581102	new_cov=2/3	polymorphism_quality=18.0	quality=18.0	quality_position_model=2.54972e-22	ref_cov=116/87	reject=INDEL_HOMOPOLYMER	tot_cov=118/90
RA	101	.	NC_007779	528271	1	.	T	bias_e_value=4644340	bias_p_value=0.99957	fisher_strand_p_value=1	frequency=1.069546e-02	genotype_quality=920.6	ks_quality_p_value=0.970834	log10_base_likelihood=-8.62298	log10_qual_likelihood_position_model=2.49214	log10_strand_likelihood_position_model=0.298813	new_cov=1/1	polymorphism_quality=3.2	quality=3.2	quality_position_model=9.51207e-08	ref_cov=94/91	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/92
RA	102	.	NC_007779	535125	0	T	G	bias_e_value=0.0100526	bias_p_value=2.16355e-09	fisher_strand_p_value=8.96431e-11	frequency=5.669689e-02	genotype_quality=652.5	ks_quality_p_value=1	log10_base_likelihood=-6.71899	log10_qual_likelihood_position_model=19.7689	log10_strand_likelihood_position_model=10.0475	new_cov=27/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=75/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=102/120
RA	103	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=964.4	new_cov=128/108	quality=964.4	ref_cov=0/0	tot_cov=128/108
RA	104	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=834.6	new_cov=93/103	quality=834.6	ref_cov=1/1	tot_cov=94/104
RA	105	.	NC_007779	556653	0	A	C	bias_e_value=1.88721e-07	bias_p_value=4.06172e-14	fisher_strand_p_value=1.14734e-15	frequency=6.820536e-02	genotype_quality=516.5	ks_quality_p_value=1	log10_base_likelihood=-5.92574	log10_qual_likelihood_position_model=20.7014	log10_strand_likelihood_position_model=14.9403	new_cov=0/21	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=117/18	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/39
RA	106	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=1059.6	new_cov=140/123	quality=1059.6	ref_cov=0/0	tot_cov=140/123
RA	107	.	NC_007779	562836	0	C	A	bias_e_value=237414	bias_p_value=0.051097	fisher_strand_p_value=0.0089408	frequency=3.441525e-02	genotype_quality=767.5	ks_quality_p_value=0.999557	log10_base_likelihood=-9.16168	log10_qual_likelihood_position_model=11.7761	log10_strand_likelihood_position_model=2.12024	new_cov=0/8	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=87/99	reject=POLYMORPHISM_STRAND	tot_cov=87/107
RA	108	.	NC_007779	562842	0	C	T	bias_e_value=1126600	bias_p_value=0.242471	fisher_strand_p_value=0.0653861	frequency=2.565575e-02	genotype_quality=755.0	ks_quality_p_value=0.992988	log10_base_likelihood=-7.41164	log10_qual_likelihood_position_model=6.54264	log10_strand_likelihood_position_model=1.31827	new_cov=0/5	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=86/100	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=86/105
RA	109	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1144.6	new_cov=124/138	quality=1144.6	ref_cov=0/0	tot_cov=124/138
RA	110	.	NC_007779	596918	0	G	T	bias_e_value=59.3126	bias_p_value=1.27655e-05	fisher_strand_p_value=9.2415e-07	frequency=3.898621e-02	genotype_quality=829.1	ks_quality_p_value=0.922408	log10_base_likelihood=-7.79705	log10_qual_likelihood_position_model=25.0155	log10_strand_likelihood_position_model=6.18886	new_cov=0/20	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=125/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/131
RA	111	.	NC_007779	598799	0	T	G	bias_e_value=2.08947e-15	bias_p_value=4.49703e-22	fisher_strand_p_value=8.30551e-24	frequency=2.342877e-01	genotype_quality=389.9	ks_quality_p_value=1	log10_base_likelihood=-35.5924	log10_qual_likelihood_position_model=32.7829	log10_strand_likelihood_position_model=23.0806	new_cov=42/0	polymorphism_quality=30.4	quality=30.4	quality_position_model=Inf	ref_cov=18/94	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=60/94
RA	112	.	NC_007779	606687	1	.	T	bias_e_value=2244450	bias_p_value=0.483057	fisher_strand_p_value=1	frequency=1.145077e-02	genotype_quality=1276.9	ks_quality_p_value=0.176748	log10_base_likelihood=-12.8836	log10_qual_likelihood_position_model=2.06676	log10_strand_likelihood_position_model=0.376267	new_cov=2/1	polymorphism_quality=7.5	quality=7.5	quality_position_model=1.77648e-12	ref_cov=147/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/113
RA	113	.	NC_007779	606688	0	T	.	bias_e_value=2739740	bias_p_value=0.589656	fisher_strand_p_value=0.579532	frequency=1.144314e-02	genotype_quality=1040.5	ks_quality_p_value=0.422833	log10_base_likelihood=-8.21589	log10_qual_likelihood_position_model=1.56487	log10_strand_likelihood_position_model=0.497311	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.42248e-08	ref_cov=148/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/113
RA	114	.	NC_007779	606915	0	T	G	bias_e_value=909.987	bias_p_value=0.000195851	fisher_strand_p_value=1.63542e-05	frequency=2.941418e-02	genotype_quality=512.9	ks_quality_p_value=0.995875	log10_base_likelihood=-6.07861	log10_qual_likelihood_position_model=6.26349	log10_strand_likelihood_position_model=4.78637	new_cov=4/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=6/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=10/124
RA	115	.	NC_007779	612902	0	G	.	bias_e_value=3619910	bias_p_value=0.77909	fisher_strand_p_value=0.571971	frequency=1.153088e-02	genotype_quality=1092.9	ks_quality_p_value=0.723788	log10_base_likelihood=-8.27516	log10_qual_likelihood_position_model=1.84198	log10_strand_likelihood_position_model=0.51812	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.80496e-08	ref_cov=106/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/152
RA	116	.	NC_007779	617621	0	G	T	bias_e_value=4383.84	bias_p_value=0.000943506	fisher_strand_p_value=9.16218e-05	frequency=4.712009e-02	genotype_quality=578.2	ks_quality_p_value=1	log10_base_likelihood=-5.85981	log10_qual_likelihood_position_model=10.4668	log10_strand_likelihood_position_model=4.038	new_cov=8/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=42/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=50/102
RA	117	.	NC_007779	624100	0	A	G	bias_e_value=3810020	bias_p_value=0.820006	fisher_strand_p_value=0.587028	frequency=9.990692e-03	genotype_quality=1178.4	ks_quality_p_value=0.789789	log10_base_likelihood=-5.7508	log10_qual_likelihood_position_model=2.1793	log10_strand_likelihood_position_model=0.480989	new_cov=1/2	polymorphism_quality=0.2	quality=0.2	quality_position_model=7.01755e-05	ref_cov=165/131	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=166/133
RA	118	.	NC_007779	645970	0	T	G	bias_e_value=2.31632e-18	bias_p_value=4.98526e-25	fisher_strand_p_value=8.16317e-27	frequency=1.892104e-01	genotype_quality=598.7	ks_quality_p_value=1	log10_base_likelihood=-37.8374	log10_qual_likelihood_position_model=39.0825	log10_strand_likelihood_position_model=26.0881	new_cov=44/0	polymorphism_quality=32.7	quality=32.7	quality_position_model=Inf	ref_cov=25/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=69/132
RA	119	.	NC_007779	646440	0	C	A	bias_e_value=18799	bias_p_value=0.00404598	fisher_strand_p_value=0.000466671	frequency=2.319527e-02	genotype_quality=710.4	ks_quality_p_value=1	log10_base_likelihood=-6.45695	log10_qual_likelihood_position_model=7.1023	log10_strand_likelihood_position_model=3.33921	new_cov=1/4	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=156/15	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/19
RA	120	.	NC_007779	660356	0	T	G	bias_e_value=1.9978e-11	bias_p_value=4.29973e-18	fisher_strand_p_value=9.59975e-20	frequency=1.500688e-01	genotype_quality=548.2	ks_quality_p_value=1	log10_base_likelihood=-19.9208	log10_qual_likelihood_position_model=27.4542	log10_strand_likelihood_position_model=19.0177	new_cov=44/0	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=46/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/114
RA	121	.	NC_007779	665062	0	C	A	bias_e_value=750.872	bias_p_value=0.000161605	fisher_strand_p_value=1.3694e-05	frequency=4.855204e-02	genotype_quality=789.3	ks_quality_p_value=0.964572	log10_base_likelihood=-9.17379	log10_qual_likelihood_position_model=19.6475	log10_strand_likelihood_position_model=4.86347	new_cov=0/14	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=123/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/107
RA	122	.	NC_007779	667452	0	G	T	bias_e_value=1732.97	bias_p_value=0.000372976	fisher_strand_p_value=3.30251e-05	frequency=6.551075e-02	genotype_quality=938.4	ks_quality_p_value=0.997622	log10_base_likelihood=-25.1977	log10_qual_likelihood_position_model=21.4782	log10_strand_likelihood_position_model=4.51319	new_cov=16/0	polymorphism_quality=20.0	quality=20.0	quality_position_model=Inf	ref_cov=113/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/112
RA	123	.	NC_007779	667460	0	G	T	bias_e_value=622010	bias_p_value=0.133871	fisher_strand_p_value=0.0296227	frequency=1.977539e-02	genotype_quality=1014.7	ks_quality_p_value=1	log10_base_likelihood=-5.60158	log10_qual_likelihood_position_model=10.1391	log10_strand_likelihood_position_model=1.76887	new_cov=6/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=119/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=125/119
RA	124	.	NC_007779	686495	0	A	C	bias_e_value=8.65276e-15	bias_p_value=1.86228e-21	fisher_strand_p_value=3.53393e-23	frequency=1.271958e-01	genotype_quality=604.2	ks_quality_p_value=1	log10_base_likelihood=-18.658	log10_qual_likelihood_position_model=33.5139	log10_strand_likelihood_position_model=22.4517	new_cov=0/32	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=137/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/51
RA	125	.	NC_007779	704668	0	T	G	bias_e_value=2.25381e-08	bias_p_value=4.85074e-15	fisher_strand_p_value=1.29056e-16	frequency=9.562540e-02	genotype_quality=594.2	ks_quality_p_value=1	log10_base_likelihood=-10.7432	log10_qual_likelihood_position_model=27.2399	log10_strand_likelihood_position_model=15.8892	new_cov=30/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=37/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=67/123
RA	126	.	NC_007779	706385	1	.	T	bias_e_value=241290	bias_p_value=0.0519313	fisher_strand_p_value=0.0850917	frequency=1.123619e-02	genotype_quality=1287.6	ks_quality_p_value=0.107109	log10_base_likelihood=-12.878	log10_qual_likelihood_position_model=3.54225	log10_strand_likelihood_position_model=1.07011	new_cov=3/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=2.97221e-10	ref_cov=115/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/149
RA	127	.	NC_007779	729329	0	A	.	bias_e_value=1963490	bias_p_value=0.422589	fisher_strand_p_value=0.564628	frequency=1.157475e-02	genotype_quality=1020.3	ks_quality_p_value=0.254601	log10_base_likelihood=-8.12145	log10_qual_likelihood_position_model=2.46221	log10_strand_likelihood_position_model=0.544339	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.27214e-07	ref_cov=100/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=103/156
RA	128	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=924.6	new_cov=99/127	quality=924.6	ref_cov=0/0	tot_cov=99/127
RA	129	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=1131.9	new_cov=129/147	quality=1131.9	ref_cov=0/0	tot_cov=129/147
RA	130	.	NC_007779	759019	0	C	G	bias_e_value=1.58239e-07	bias_p_value=3.40567e-14	fisher_strand_p_value=9.58114e-16	frequency=7.795048e-02	genotype_quality=668.3	ks_quality_p_value=0.998958	log10_base_likelihood=-21.052	log10_qual_likelihood_position_model=17.7619	log10_strand_likelihood_position_model=15.0186	new_cov=0/14	polymorphism_quality=15.8	quality=15.8	quality_position_model=Inf	ref_cov=150/7	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=150/21
RA	131	.	NC_007779	805128	0	A	.	bias_e_value=3581470	bias_p_value=0.770817	fisher_strand_p_value=0.573692	frequency=1.153088e-02	genotype_quality=1044.4	ks_quality_p_value=0.705472	log10_base_likelihood=-8.25661	log10_qual_likelihood_position_model=1.74542	log10_strand_likelihood_position_model=0.512944	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.40238e-08	ref_cov=107/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/151
RA	132	.	NC_007779	817515	0	G	T	bias_e_value=62.3557	bias_p_value=1.34204e-05	fisher_strand_p_value=9.00124e-07	frequency=4.799891e-02	genotype_quality=737.0	ks_quality_p_value=0.999195	log10_base_likelihood=-6.22272	log10_qual_likelihood_position_model=18.0343	log10_strand_likelihood_position_model=6.29202	new_cov=0/22	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=113/110	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/133
RA	133	.	NC_007779	825471	1	.	G	bias_e_value=1506900	bias_p_value=0.324319	fisher_strand_p_value=0.0995153	frequency=1.041603e-02	genotype_quality=1407.9	ks_quality_p_value=0.979096	log10_base_likelihood=-12.0918	log10_qual_likelihood_position_model=4.24524	log10_strand_likelihood_position_model=1.00211	new_cov=3/0	polymorphism_quality=6.7	quality=6.7	quality_position_model=8.57348e-09	ref_cov=131/154	reject=POLYMORPHISM_STRAND	tot_cov=134/154
RA	134	.	NC_007779	829585	0	G	T	bias_e_value=15.131	bias_p_value=3.25655e-06	fisher_strand_p_value=2.00954e-07	frequency=4.538631e-02	genotype_quality=766.3	ks_quality_p_value=0.986083	log10_base_likelihood=-11.1436	log10_qual_likelihood_position_model=16.0228	log10_strand_likelihood_position_model=6.6969	new_cov=12/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=51/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=63/151
RA	135	.	NC_007779	842195	0	C	A	bias_e_value=2.19466	bias_p_value=4.72343e-07	fisher_strand_p_value=2.55564e-08	frequency=4.050159e-02	genotype_quality=1075.5	ks_quality_p_value=1	log10_base_likelihood=-9.20102	log10_qual_likelihood_position_model=25.3803	log10_strand_likelihood_position_model=7.84027	new_cov=29/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=159/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=188/150
RA	136	.	NC_007779	848585	0	C	A	bias_e_value=25.9723	bias_p_value=5.58985e-06	fisher_strand_p_value=4.42072e-07	frequency=3.996849e-02	genotype_quality=891.7	ks_quality_p_value=0.797356	log10_base_likelihood=-7.49066	log10_qual_likelihood_position_model=23.8106	log10_strand_likelihood_position_model=6.37655	new_cov=22/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=132/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/136
RA	137	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=823.2	new_cov=118/99	quality=823.2	ref_cov=0/0	tot_cov=118/100
RA	138	.	NC_007779	888436	0	T	G	bias_e_value=1.32069e-05	bias_p_value=2.84243e-12	fisher_strand_p_value=9.16293e-14	frequency=5.540466e-02	genotype_quality=858.4	ks_quality_p_value=1	log10_base_likelihood=-5.56439	log10_qual_likelihood_position_model=27.1226	log10_strand_likelihood_position_model=13.038	new_cov=37/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=100/148	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/148
RA	139	.	NC_007779	893229	0	A	.	bias_e_value=3105590	bias_p_value=0.668396	fisher_strand_p_value=0.61731	frequency=1.030159e-02	genotype_quality=1112.2	ks_quality_p_value=0.495754	log10_base_likelihood=-8.05044	log10_qual_likelihood_position_model=3.08192	log10_strand_likelihood_position_model=0.432181	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.11188e-06	ref_cov=141/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/148
RA	140	.	NC_007779	904838	0	C	A	bias_e_value=2.03907e-11	bias_p_value=4.38855e-18	fisher_strand_p_value=1.16939e-19	frequency=1.278815e-01	genotype_quality=911.3	ks_quality_p_value=0.838271	log10_base_likelihood=-34.0285	log10_qual_likelihood_position_model=35.1497	log10_strand_likelihood_position_model=18.932	new_cov=46/0	polymorphism_quality=28.9	quality=28.9	quality_position_model=Inf	ref_cov=84/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/169
RA	141	.	NC_007779	915697	0	G	T	bias_e_value=92.2978	bias_p_value=1.98647e-05	fisher_strand_p_value=1.3699e-06	frequency=4.453659e-02	genotype_quality=755.2	ks_quality_p_value=1	log10_base_likelihood=-7.02219	log10_qual_likelihood_position_model=14.3472	log10_strand_likelihood_position_model=5.86331	new_cov=0/18	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=121/99	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/119
RA	142	.	NC_007779	917260	0	C	A	bias_e_value=0.0094054	bias_p_value=2.02426e-09	fisher_strand_p_value=8.36313e-11	frequency=5.809784e-02	genotype_quality=853.7	ks_quality_p_value=1	log10_base_likelihood=-10.6438	log10_qual_likelihood_position_model=20.8399	log10_strand_likelihood_position_model=10.0776	new_cov=23/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=75/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/151
RA	143	.	NC_007779	926048	1	.	T	bias_e_value=4277860	bias_p_value=0.920696	fisher_strand_p_value=1	frequency=6.993294e-03	genotype_quality=1416.6	ks_quality_p_value=0.629166	log10_base_likelihood=-8.40144	log10_qual_likelihood_position_model=1.66867	log10_strand_likelihood_position_model=0.30498	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.30505e-08	ref_cov=126/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/159
RA	144	.	NC_007779	947970	0	C	A	bias_e_value=162.577	bias_p_value=3.49904e-05	fisher_strand_p_value=2.51879e-06	frequency=3.916931e-02	genotype_quality=871.8	ks_quality_p_value=1	log10_base_likelihood=-7.56442	log10_qual_likelihood_position_model=13.5315	log10_strand_likelihood_position_model=5.59881	new_cov=17/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=111/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/136
RA	145	.	NC_007779	954820	0	A	C	bias_e_value=7.79131e-05	bias_p_value=1.67687e-11	fisher_strand_p_value=5.74563e-13	frequency=7.544422e-02	genotype_quality=703.7	ks_quality_p_value=1	log10_base_likelihood=-6.41723	log10_qual_likelihood_position_model=26.2567	log10_strand_likelihood_position_model=12.2407	new_cov=0/31	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=128/71	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/102
RA	146	.	NC_007779	969494	0	C	A	bias_e_value=0.0513799	bias_p_value=1.10582e-08	fisher_strand_p_value=4.92997e-10	frequency=7.963133e-02	genotype_quality=792.2	ks_quality_p_value=1	log10_base_likelihood=-17.6293	log10_qual_likelihood_position_model=19.7693	log10_strand_likelihood_position_model=9.3478	new_cov=30/0	polymorphism_quality=12.3	quality=12.3	quality_position_model=Inf	ref_cov=106/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/127
RA	147	.	NC_007779	987422	1	.	T	bias_e_value=4622290	bias_p_value=0.994826	fisher_strand_p_value=1	frequency=8.733749e-03	genotype_quality=1114.7	ks_quality_p_value=0.900017	log10_base_likelihood=-8.28676	log10_qual_likelihood_position_model=2.07432	log10_strand_likelihood_position_model=0.302797	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.90625e-08	ref_cov=124/103	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/104
RA	148	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=1006.7	new_cov=85/161	quality=1006.7	ref_cov=0/0	tot_cov=85/161
RA	149	.	NC_007779	987916	0	T	G	bias_e_value=1.38408e-08	bias_p_value=2.97886e-15	fisher_strand_p_value=7.82117e-17	frequency=8.003330e-02	genotype_quality=682.6	ks_quality_p_value=1	log10_base_likelihood=-14.0082	log10_qual_likelihood_position_model=22.46	log10_strand_likelihood_position_model=16.1067	new_cov=19/0	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=16/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/153
RA	150	.	NC_007779	999606	0	A	T	bias_e_value=952594	bias_p_value=0.205021	fisher_strand_p_value=0.0517574	frequency=4.038239e-02	genotype_quality=631.4	ks_quality_p_value=1	log10_base_likelihood=-10.2006	log10_qual_likelihood_position_model=7.15108	log10_strand_likelihood_position_model=1.57082	new_cov=8/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=0.00395549	ref_cov=104/62	reject=POLYMORPHISM_STRAND	tot_cov=112/62
RA	151	.	NC_007779	999607	0	A	C	bias_e_value=136071	bias_p_value=0.0292857	fisher_strand_p_value=0.00458697	frequency=4.758120e-02	genotype_quality=604.6	ks_quality_p_value=1	log10_base_likelihood=-9.56016	log10_qual_likelihood_position_model=10.9716	log10_strand_likelihood_position_model=2.41083	new_cov=12/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=99/62	reject=POLYMORPHISM_STRAND	tot_cov=112/62
RA	152	.	NC_007779	999613	0	A	T	bias_e_value=114408	bias_p_value=0.0246233	fisher_strand_p_value=0.00373671	frequency=6.519032e-02	genotype_quality=626.2	ks_quality_p_value=1	log10_base_likelihood=-16.5913	log10_qual_likelihood_position_model=13.7814	log10_strand_likelihood_position_model=2.6125	new_cov=12/0	polymorphism_quality=11.3	quality=11.3	quality_position_model=0.180711	ref_cov=95/66	reject=POLYMORPHISM_STRAND	tot_cov=108/67
RA	153	.	NC_007779	1005043	1	.	G	bias_e_value=1339840	bias_p_value=0.288365	fisher_strand_p_value=0.0838787	frequency=1.200008e-02	genotype_quality=1231.1	ks_quality_p_value=0.983713	log10_base_likelihood=-12.4131	log10_qual_likelihood_position_model=2.19613	log10_strand_likelihood_position_model=1.07635	new_cov=3/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=3.77765e-11	ref_cov=107/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/140
RA	154	.	NC_007779	1005102	1	.	T	bias_e_value=1705570	bias_p_value=0.36708	fisher_strand_p_value=0.232165	frequency=9.661674e-03	genotype_quality=1016.5	ks_quality_p_value=0.502039	log10_base_likelihood=-8.06504	log10_qual_likelihood_position_model=2.59641	log10_strand_likelihood_position_model=0.634202	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.03232e-06	ref_cov=98/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=100/107
RA	155	.	NC_007779	1006080	0	C	A	bias_e_value=0.0215847	bias_p_value=4.64554e-09	fisher_strand_p_value=1.9906e-10	frequency=6.642866e-02	genotype_quality=953.6	ks_quality_p_value=1	log10_base_likelihood=-13.7787	log10_qual_likelihood_position_model=20.6066	log10_strand_likelihood_position_model=9.85291	new_cov=31/0	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=129/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/156
RA	156	.	NC_007779	1035834	0	C	A	bias_e_value=293.931	bias_p_value=6.32609e-05	fisher_strand_p_value=4.77353e-06	frequency=3.978539e-02	genotype_quality=969.6	ks_quality_p_value=1	log10_base_likelihood=-9.06344	log10_qual_likelihood_position_model=14.9591	log10_strand_likelihood_position_model=5.48866	new_cov=18/0	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=137/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/149
RA	157	.	NC_007779	1050680	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	158	.	NC_007779	1050681	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	159	.	NC_007779	1050682	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	160	.	NC_007779	1050684	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	161	.	NC_007779	1050685	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	162	.	NC_007779	1050687	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	163	.	NC_007779	1050688	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	164	.	NC_007779	1050689	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	165	.	NC_007779	1050690	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	166	.	NC_007779	1050691	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	167	.	NC_007779	1050693	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	168	.	NC_007779	1050694	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	169	.	NC_007779	1050695	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	170	.	NC_007779	1050696	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	171	.	NC_007779	1050697	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	172	.	NC_007779	1050698	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	173	.	NC_007779	1050699	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	174	.	NC_007779	1050700	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	175	.	NC_007779	1050701	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	176	.	NC_007779	1050702	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	177	.	NC_007779	1050703	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	178	.	NC_007779	1050704	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	179	.	NC_007779	1058914	0	A	C	bias_e_value=0.0201415	bias_p_value=4.33492e-09	fisher_strand_p_value=1.85176e-10	frequency=4.645443e-02	genotype_quality=663.5	ks_quality_p_value=1	log10_base_likelihood=-7.35445	log10_qual_likelihood_position_model=21.1496	log10_strand_likelihood_position_model=9.73241	new_cov=0/17	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=136/41	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/58
RA	180	.	NC_007779	1092328	0	C	A	bias_e_value=173710	bias_p_value=0.0373865	fisher_strand_p_value=0.00613527	frequency=2.864838e-02	genotype_quality=978.9	ks_quality_p_value=1	log10_base_likelihood=-8.59955	log10_qual_likelihood_position_model=11.1166	log10_strand_likelihood_position_model=2.36696	new_cov=11/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=134/129	reject=POLYMORPHISM_STRAND	tot_cov=145/130
RA	181	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1276.6	new_cov=137/155	quality=1276.6	ref_cov=0/0	tot_cov=137/155
RA	182	.	NC_007779	1097580	0	C	T	bias_e_value=3141140	bias_p_value=0.676047	fisher_strand_p_value=0.489694	frequency=2.126508e-01	genotype_quality=760.5	ks_quality_p_value=0.638263	log10_base_likelihood=-189.785	log10_qual_likelihood_position_model=16.128	log10_strand_likelihood_position_model=1.08297	new_cov=27/40	polymorphism_quality=185.0	quality=185.0	quality_position_model=3.27395e-175	ref_cov=113/135	tot_cov=140/175
RA	183	.	NC_007779	1097634	0	G	.	bias_e_value=3721290	bias_p_value=0.800909	fisher_strand_p_value=1	frequency=1.453876e-02	genotype_quality=862.8	ks_quality_p_value=0.439608	log10_base_likelihood=-11.5677	log10_qual_likelihood_position_model=2.5305	log10_strand_likelihood_position_model=0.433983	new_cov=2/2	polymorphism_quality=6.2	quality=6.2	quality_position_model=1.34034e-10	ref_cov=120/151	reject=INDEL_HOMOPOLYMER	tot_cov=122/153
RA	184	.	NC_007779	1097764	1	.	A	bias_e_value=4278770	bias_p_value=0.920892	fisher_strand_p_value=1	frequency=3.526688e-03	genotype_quality=2325.8	ks_quality_p_value=0.629588	log10_base_likelihood=-7.13217	log10_qual_likelihood_position_model=1.83135	log10_strand_likelihood_position_model=0.310135	new_cov=1/1	polymorphism_quality=1.6	quality=1.6	quality_position_model=7.09838e-07	ref_cov=240/325	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=241/326
RA	185	.	NC_007779	1105181	1	.	T	bias_e_value=2985270	bias_p_value=0.6425	fisher_strand_p_value=1	frequency=8.584023e-03	genotype_quality=1148.9	ks_quality_p_value=0.2848	log10_base_likelihood=-8.44758	log10_qual_likelihood_position_model=1.73897	log10_strand_likelihood_position_model=0.300131	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.41326e-08	ref_cov=110/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/122
RA	186	.	NC_007779	1116582	0	G	C	bias_e_value=5.90748e-12	bias_p_value=1.27143e-18	fisher_strand_p_value=2.76183e-20	frequency=1.264281e-01	genotype_quality=489.9	ks_quality_p_value=1	log10_base_likelihood=-32.6259	log10_qual_likelihood_position_model=18.3053	log10_strand_likelihood_position_model=19.5588	new_cov=0/19	polymorphism_quality=27.4	quality=27.4	quality_position_model=Inf	ref_cov=123/4	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/23
RA	187	.	NC_007779	1120197	0	C	A	bias_e_value=1.13369	bias_p_value=2.43997e-07	fisher_strand_p_value=1.27339e-08	frequency=6.000185e-02	genotype_quality=688.6	ks_quality_p_value=0.999024	log10_base_likelihood=-7.57743	log10_qual_likelihood_position_model=17.6298	log10_strand_likelihood_position_model=7.89504	new_cov=24/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=92/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/118
RA	188	.	NC_007779	1148417	0	C	A	bias_e_value=358.567	bias_p_value=7.71721e-05	fisher_strand_p_value=6.57141e-06	frequency=3.664112e-02	genotype_quality=876.9	ks_quality_p_value=0.900771	log10_base_likelihood=-6.72356	log10_qual_likelihood_position_model=19.2828	log10_strand_likelihood_position_model=5.23024	new_cov=18/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=124/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/127
RA	189	.	NC_007779	1151485	0	C	A	bias_e_value=4.11766	bias_p_value=8.86217e-07	fisher_strand_p_value=4.97416e-08	frequency=7.369041e-02	genotype_quality=808.9	ks_quality_p_value=1	log10_base_likelihood=-15.4146	log10_qual_likelihood_position_model=16.3213	log10_strand_likelihood_position_model=7.4124	new_cov=26/0	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=114/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/118
RA	190	.	NC_007779	1158848	0	T	G	bias_e_value=1.22786e-08	bias_p_value=2.64265e-15	fisher_strand_p_value=6.9161e-17	frequency=7.376671e-02	genotype_quality=822.1	ks_quality_p_value=1	log10_base_likelihood=-11.4304	log10_qual_likelihood_position_model=28.0945	log10_strand_likelihood_position_model=16.1601	new_cov=39/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=78/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/155
RA	191	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1061.2	new_cov=154/106	quality=1061.2	ref_cov=0/0	tot_cov=154/106
RA	192	.	NC_007779	1176573	0	A	G	bias_e_value=30271.8	bias_p_value=0.00651521	fisher_strand_p_value=0.000801471	frequency=3.097725e-02	genotype_quality=873.8	ks_quality_p_value=1	log10_base_likelihood=-8.65136	log10_qual_likelihood_position_model=12.6503	log10_strand_likelihood_position_model=3.09611	new_cov=0/9	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=128/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/111
RA	193	.	NC_007779	1176575	0	G	T	bias_e_value=124239	bias_p_value=0.0267392	fisher_strand_p_value=0.00412851	frequency=2.380848e-02	genotype_quality=936.2	ks_quality_p_value=0.99761	log10_base_likelihood=-5.56737	log10_qual_likelihood_position_model=10.6834	log10_strand_likelihood_position_model=2.38421	new_cov=0/7	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=125/101	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=125/108
RA	194	.	NC_007779	1224173	0	G	A	bias_e_value=63.495	bias_p_value=1.36656e-05	fisher_strand_p_value=9.17025e-07	frequency=4.774189e-02	genotype_quality=829.0	ks_quality_p_value=1	log10_base_likelihood=-5.59399	log10_qual_likelihood_position_model=18.2226	log10_strand_likelihood_position_model=6.03762	new_cov=0/17	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=139/101	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/118
RA	195	.	NC_007779	1262472	0	A	C	bias_e_value=9.12336e-06	bias_p_value=1.96356e-12	fisher_strand_p_value=6.25275e-14	frequency=7.576990e-02	genotype_quality=759.9	ks_quality_p_value=1	log10_base_likelihood=-8.97228	log10_qual_likelihood_position_model=32.1345	log10_strand_likelihood_position_model=13.2039	new_cov=0/38	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=132/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/128
RA	196	.	NC_007779	1273395	1	.	G	bias_e_value=1657190	bias_p_value=0.356665	fisher_strand_p_value=0.117279	frequency=7.812500e-03	genotype_quality=1273.4	ks_quality_p_value=0.952916	log10_base_likelihood=-8.15943	log10_qual_likelihood_position_model=1.55328	log10_strand_likelihood_position_model=0.930778	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.38187e-07	ref_cov=86/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=88/168
RA	197	.	NC_007779	1273399	0	T	G	bias_e_value=4.46545e-22	bias_p_value=9.6107e-29	fisher_strand_p_value=1.37774e-30	frequency=1.413918e-01	genotype_quality=774.0	ks_quality_p_value=1	log10_base_likelihood=-26.6249	log10_qual_likelihood_position_model=39.2623	log10_strand_likelihood_position_model=29.8608	new_cov=44/0	polymorphism_quality=21.4	quality=21.4	quality_position_model=Inf	ref_cov=25/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=70/171
RA	198	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=129.0	new_cov=18/21	quality=129.0	ref_cov=0/0	tot_cov=18/21
RA	199	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=45.9	new_cov=9/9	quality=45.9	ref_cov=0/0	tot_cov=9/9
RA	200	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=26.6	new_cov=6/5	quality=26.6	ref_cov=0/0	tot_cov=6/5
RA	201	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1061.7	new_cov=130/134	quality=1061.7	ref_cov=0/0	tot_cov=130/135
RA	202	.	NC_007779	1325276	0	G	T	bias_e_value=1178.36	bias_p_value=0.000253611	fisher_strand_p_value=2.23702e-05	frequency=3.263092e-02	genotype_quality=848.0	ks_quality_p_value=0.965431	log10_base_likelihood=-7.62044	log10_qual_likelihood_position_model=15.1621	log10_strand_likelihood_position_model=4.65033	new_cov=0/14	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=136/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/126
RA	203	.	NC_007779	1330179	0	T	G	bias_e_value=13.2255	bias_p_value=2.84643e-06	fisher_strand_p_value=1.71705e-07	frequency=4.686356e-02	genotype_quality=781.6	ks_quality_p_value=1	log10_base_likelihood=-7.28009	log10_qual_likelihood_position_model=18.9287	log10_strand_likelihood_position_model=7.0259	new_cov=22/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=102/123	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/123
RA	204	.	NC_007779	1352913	1	.	T	bias_e_value=121540	bias_p_value=0.0261583	fisher_strand_p_value=0.0263607	frequency=2.366924e-02	genotype_quality=786.9	ks_quality_p_value=0.152239	log10_base_likelihood=-18.7676	log10_qual_likelihood_position_model=2.2645	log10_strand_likelihood_position_model=1.57904	new_cov=4/0	polymorphism_quality=13.5	quality=13.5	quality_position_model=4.90905e-17	ref_cov=65/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=69/100
RA	205	.	NC_007779	1352917	1	.	C	bias_e_value=1208390	bias_p_value=0.260074	fisher_strand_p_value=0.0780882	frequency=1.995754e-02	genotype_quality=699.1	ks_quality_p_value=0.915404	log10_base_likelihood=-9.81229	log10_qual_likelihood_position_model=3.04242	log10_strand_likelihood_position_model=1.10741	new_cov=2/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=1.4251e-07	ref_cov=40/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=43/107
RA	206	.	NC_007779	1352922	0	T	C	bias_e_value=1.32335	bias_p_value=2.84816e-07	fisher_strand_p_value=1.5333e-08	frequency=6.132650e-02	genotype_quality=478.8	ks_quality_p_value=0.97679	log10_base_likelihood=-11.8291	log10_qual_likelihood_position_model=12.4714	log10_strand_likelihood_position_model=7.81437	new_cov=9/0	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=14/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=23/121
RA	207	.	NC_007779	1352924	0	A	C	bias_e_value=0.359497	bias_p_value=7.73723e-08	fisher_strand_p_value=3.79468e-09	frequency=7.011271e-02	genotype_quality=488.4	ks_quality_p_value=1	log10_base_likelihood=-13.5495	log10_qual_likelihood_position_model=15.2097	log10_strand_likelihood_position_model=8.42492	new_cov=11/1	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=14/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=25/123
RA	208	.	NC_007779	1360909	0	G	T	bias_e_value=6854.98	bias_p_value=0.00147535	fisher_strand_p_value=0.000150525	frequency=3.169727e-02	genotype_quality=861.2	ks_quality_p_value=1	log10_base_likelihood=-5.64716	log10_qual_likelihood_position_model=11.2139	log10_strand_likelihood_position_model=3.82239	new_cov=0/12	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=126/110	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/122
RA	209	.	NC_007779	1363985	0	G	.	bias_e_value=502801	bias_p_value=0.108215	fisher_strand_p_value=0.237341	frequency=7.838249e-03	genotype_quality=1096.3	ks_quality_p_value=0.0951828	log10_base_likelihood=-5.62092	log10_qual_likelihood_position_model=1.25895	log10_strand_likelihood_position_model=0.624627	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=1.45264e-05	ref_cov=122/130	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/131
RA	210	.	NC_007779	1371749	1	.	T	bias_e_value=36702.1	bias_p_value=0.00789915	fisher_strand_p_value=0.0567609	frequency=1.454544e-02	genotype_quality=1318.7	ks_quality_p_value=0.0175958	log10_base_likelihood=-17.3033	log10_qual_likelihood_position_model=3.57704	log10_strand_likelihood_position_model=1.24595	new_cov=4/0	polymorphism_quality=12.0	quality=12.0	quality_position_model=1.48739e-14	ref_cov=131/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/140
RA	211	.	NC_007779	1378219	0	A	C	bias_e_value=6.14417e-08	bias_p_value=1.32237e-14	fisher_strand_p_value=3.61742e-16	frequency=1.115298e-01	genotype_quality=695.5	ks_quality_p_value=1	log10_base_likelihood=-14.2221	log10_qual_likelihood_position_model=47.3931	log10_strand_likelihood_position_model=15.5842	new_cov=0/45	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=118/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/120
RA	212	.	NC_007779	1404189	0	C	A	bias_e_value=4.26865	bias_p_value=9.18713e-07	fisher_strand_p_value=5.16762e-08	frequency=5.110312e-02	genotype_quality=742.9	ks_quality_p_value=1	log10_base_likelihood=-5.57138	log10_qual_likelihood_position_model=16.0653	log10_strand_likelihood_position_model=7.28671	new_cov=19/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=84/133	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/134
RA	213	.	NC_007779	1405508	0	G	T	bias_e_value=2.5818	bias_p_value=5.55664e-07	fisher_strand_p_value=3.03466e-08	frequency=1.196246e-01	genotype_quality=481.1	ks_quality_p_value=1	log10_base_likelihood=-31.3876	log10_qual_likelihood_position_model=17.71	log10_strand_likelihood_position_model=7.53507	new_cov=16/3	polymorphism_quality=26.2	quality=26.2	quality_position_model=4.54205e-08	ref_cov=23/102	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=39/105
RA	214	.	NC_007779	1409137	0	G	T	bias_e_value=1.43257e-12	bias_p_value=3.08323e-19	fisher_strand_p_value=6.49325e-21	frequency=2.790947e-01	genotype_quality=433.6	ks_quality_p_value=1	log10_base_likelihood=-74.7146	log10_qual_likelihood_position_model=27.029	log10_strand_likelihood_position_model=20.2411	new_cov=0/63	polymorphism_quality=69.7	quality=69.7	quality_position_model=1.09897e-29	ref_cov=91/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/117
RA	215	.	NC_007779	1412694	0	C	A	bias_e_value=12.882	bias_p_value=2.7725e-06	fisher_strand_p_value=1.66963e-07	frequency=7.583904e-02	genotype_quality=652.8	ks_quality_p_value=1	log10_base_likelihood=-11.8022	log10_qual_likelihood_position_model=13.0102	log10_strand_likelihood_position_model=6.79146	new_cov=23/0	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=90/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/99
RA	216	.	NC_007779	1413849	0	C	T	deleted=1	frequency=1	genotype_quality=2.7	new_cov=1/0	quality=2.7	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	217	.	NC_007779	1434298	0	C	A	deleted=1	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	218	.	NC_007779	1434304	0	T	A	deleted=1	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	219	.	NC_007779	1434312	0	C	A	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	220	.	NC_007779	1437447	0	G	C	bias_e_value=5.10094e-06	bias_p_value=1.09784e-12	fisher_strand_p_value=3.43038e-14	frequency=7.352686e-02	genotype_quality=756.9	ks_quality_p_value=1	log10_base_likelihood=-8.45947	log10_qual_likelihood_position_model=21.6479	log10_strand_likelihood_position_model=13.4647	new_cov=0/24	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=161/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/73
RA	221	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=793.8	new_cov=158/41	quality=793.8	ref_cov=0/0	tot_cov=158/41
RA	222	.	NC_007779	1493621	0	T	C	bias_e_value=2628.38	bias_p_value=0.000565689	fisher_strand_p_value=5.20758e-05	frequency=3.362751e-02	genotype_quality=825.6	ks_quality_p_value=1	log10_base_likelihood=-6.9877	log10_qual_likelihood_position_model=11.3809	log10_strand_likelihood_position_model=4.28336	new_cov=0/10	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=147/82	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/92
RA	223	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1231.0	new_cov=119/134	quality=1231.0	ref_cov=1/0	tot_cov=120/134
RA	224	.	NC_007779	1504851	0	C	A	bias_e_value=105504	bias_p_value=0.0227069	fisher_strand_p_value=0.00339673	frequency=3.955460e-02	genotype_quality=586.2	ks_quality_p_value=1	log10_base_likelihood=-6.70187	log10_qual_likelihood_position_model=14.5599	log10_strand_likelihood_position_model=2.74176	new_cov=16/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=126/65	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=142/65
RA	225	.	NC_007779	1507752	0	A	C	bias_e_value=2.08858	bias_p_value=4.49512e-07	fisher_strand_p_value=2.42524e-08	frequency=6.914520e-02	genotype_quality=666.7	ks_quality_p_value=1	log10_base_likelihood=-8.98469	log10_qual_likelihood_position_model=19.8448	log10_strand_likelihood_position_model=7.62588	new_cov=1/22	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=120/69	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/91
RA	226	.	NC_007779	1515709	0	A	G	bias_e_value=1.41112e-07	bias_p_value=3.03707e-14	fisher_strand_p_value=8.50709e-16	frequency=1.525650e-01	genotype_quality=598.3	ks_quality_p_value=1	log10_base_likelihood=-24.8991	log10_qual_likelihood_position_model=43.0031	log10_strand_likelihood_position_model=15.0702	new_cov=41/0	polymorphism_quality=19.7	quality=19.7	quality_position_model=Inf	ref_cov=71/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/121
RA	227	.	NC_007779	1515714	0	A	T	bias_e_value=128.301	bias_p_value=2.76134e-05	fisher_strand_p_value=1.95193e-06	frequency=5.978966e-02	genotype_quality=732.6	ks_quality_p_value=1	log10_base_likelihood=-9.48941	log10_qual_likelihood_position_model=15.6031	log10_strand_likelihood_position_model=5.70954	new_cov=17/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=94/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/120
RA	228	.	NC_007779	1527474	0	G	A	bias_e_value=22.8403	bias_p_value=4.91578e-06	fisher_strand_p_value=3.07325e-07	frequency=1.002579e-01	genotype_quality=671.3	ks_quality_p_value=1	log10_base_likelihood=-20.4861	log10_qual_likelihood_position_model=25.3202	log10_strand_likelihood_position_model=6.79594	new_cov=0/25	polymorphism_quality=15.2	quality=15.2	quality_position_model=Inf	ref_cov=98/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/125
RA	229	.	NC_007779	1527479	0	C	A	bias_e_value=12841.7	bias_p_value=0.00276384	fisher_strand_p_value=0.000331188	frequency=4.681683e-02	genotype_quality=771.3	ks_quality_p_value=0.917126	log10_base_likelihood=-8.22056	log10_qual_likelihood_position_model=19.4997	log10_strand_likelihood_position_model=3.77044	new_cov=0/14	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=100/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=100/123
RA	230	.	NC_007779	1533124	0	C	A	bias_e_value=2080770	bias_p_value=0.447832	fisher_strand_p_value=0.157078	frequency=2.781391e-02	genotype_quality=643.3	ks_quality_p_value=1	log10_base_likelihood=-6.33448	log10_qual_likelihood_position_model=7.52891	log10_strand_likelihood_position_model=1.06696	new_cov=0/5	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=59/90	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=59/95
RA	231	.	NC_007779	1533140	0	C	A	bias_e_value=1178400	bias_p_value=0.25362	fisher_strand_p_value=0.0701584	frequency=3.229523e-02	genotype_quality=635.7	ks_quality_p_value=0.984227	log10_base_likelihood=-8.91325	log10_qual_likelihood_position_model=6.41249	log10_strand_likelihood_position_model=1.248	new_cov=0/5	polymorphism_quality=3.5	quality=3.5	quality_position_model=0.00714149	ref_cov=66/82	reject=POLYMORPHISM_STRAND	tot_cov=66/87
RA	232	.	NC_007779	1533144	0	T	G	bias_e_value=1894010	bias_p_value=0.407635	fisher_strand_p_value=0.136151	frequency=2.772713e-02	genotype_quality=526.6	ks_quality_p_value=1	log10_base_likelihood=-6.61772	log10_qual_likelihood_position_model=5.12632	log10_strand_likelihood_position_model=0.977204	new_cov=0/4	polymorphism_quality=1.1	quality=1.1	quality_position_model=0.0574209	ref_cov=57/73	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=57/77
RA	233	.	NC_007779	1537499	0	A	G	bias_e_value=0.0340853	bias_p_value=7.33596e-09	fisher_strand_p_value=3.2091e-10	frequency=8.225441e-02	genotype_quality=686.2	ks_quality_p_value=1	log10_base_likelihood=-8.93291	log10_qual_likelihood_position_model=21.6778	log10_strand_likelihood_position_model=9.49362	new_cov=26/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=81/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/124
RA	234	.	NC_007779	1552377	0	A	C	bias_e_value=4.05367e-09	bias_p_value=8.72446e-16	fisher_strand_p_value=2.21728e-17	frequency=9.585619e-02	genotype_quality=716.8	ks_quality_p_value=1	log10_base_likelihood=-10.5882	log10_qual_likelihood_position_model=32.9251	log10_strand_likelihood_position_model=16.6542	new_cov=0/38	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=135/59	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/97
RA	235	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=911.1	new_cov=118/121	quality=911.1	ref_cov=2/0	tot_cov=120/121
RA	236	.	NC_007779	1626063	1	.	T	bias_e_value=678034	bias_p_value=0.145929	fisher_strand_p_value=0.498963	frequency=8.367538e-03	genotype_quality=1174.8	ks_quality_p_value=0.0663474	log10_base_likelihood=-8.05326	log10_qual_likelihood_position_model=2.26925	log10_strand_likelihood_position_model=0.564643	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.10619e-07	ref_cov=123/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/114
RA	237	.	NC_007779	1626064	0	T	.	bias_e_value=631448	bias_p_value=0.135903	fisher_strand_p_value=0.216398	frequency=2.499104e-02	genotype_quality=931.3	ks_quality_p_value=0.139564	log10_base_likelihood=-18.1516	log10_qual_likelihood_position_model=4.50946	log10_strand_likelihood_position_model=0.951891	new_cov=5/1	polymorphism_quality=12.8	quality=12.8	quality_position_model=9.09871e-15	ref_cov=121/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/114
RA	238	.	NC_007779	1628027	0	G	T	bias_e_value=10.1085	bias_p_value=2.17558e-06	fisher_strand_p_value=1.40147e-07	frequency=1.751604e-01	genotype_quality=300.5	ks_quality_p_value=0.920547	log10_base_likelihood=-30.9717	log10_qual_likelihood_position_model=17.3574	log10_strand_likelihood_position_model=6.91869	new_cov=21/0	polymorphism_quality=25.8	quality=25.8	quality_position_model=1.22037e-08	ref_cov=38/55	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=59/55
RA	239	.	NC_007779	1647535	0	C	A	bias_e_value=3.25214	bias_p_value=6.99938e-07	fisher_strand_p_value=3.87427e-08	frequency=4.576683e-02	genotype_quality=863.9	ks_quality_p_value=1	log10_base_likelihood=-9.83904	log10_qual_likelihood_position_model=14.3454	log10_strand_likelihood_position_model=7.41181	new_cov=18/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=90/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/157
RA	240	.	NC_007779	1651004	1	.	G	bias_e_value=2736710	bias_p_value=0.589005	fisher_strand_p_value=0.248117	frequency=1.456356e-02	genotype_quality=1011.1	ks_quality_p_value=0.985755	log10_base_likelihood=-13.7937	log10_qual_likelihood_position_model=1.89608	log10_strand_likelihood_position_model=0.847138	new_cov=3/0	polymorphism_quality=8.4	quality=8.4	quality_position_model=4.24398e-13	ref_cov=105/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/98
RA	241	.	NC_007779	1651009	0	T	G	bias_e_value=2.83098e-14	bias_p_value=6.09293e-21	fisher_strand_p_value=1.18336e-22	frequency=1.928558e-01	genotype_quality=470.1	ks_quality_p_value=1	log10_base_likelihood=-25.1134	log10_qual_likelihood_position_model=30.5233	log10_strand_likelihood_position_model=21.9269	new_cov=38/0	polymorphism_quality=19.9	quality=19.9	quality_position_model=Inf	ref_cov=20/104	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=58/104
RA	242	.	NC_007779	1660545	0	G	T	bias_e_value=185.879	bias_p_value=4.00056e-05	fisher_strand_p_value=2.91006e-06	frequency=4.457283e-02	genotype_quality=692.1	ks_quality_p_value=1	log10_base_likelihood=-6.73748	log10_qual_likelihood_position_model=13.6845	log10_strand_likelihood_position_model=5.57057	new_cov=0/19	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=102/96	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/115
RA	243	.	NC_007779	1660637	0	G	T	bias_e_value=2.55158	bias_p_value=5.49161e-07	fisher_strand_p_value=2.99711e-08	frequency=6.712627e-02	genotype_quality=652.6	ks_quality_p_value=1	log10_base_likelihood=-7.32295	log10_qual_likelihood_position_model=17.2674	log10_strand_likelihood_position_model=7.54772	new_cov=0/27	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=99/96	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/124
RA	244	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=1041.0	new_cov=101/107	quality=1041.0	ref_cov=0/0	tot_cov=101/107
RA	245	.	NC_007779	1681402	0	T	G	bias_e_value=0.432632	bias_p_value=9.31127e-08	fisher_strand_p_value=4.61071e-09	frequency=4.488087e-02	genotype_quality=729.1	ks_quality_p_value=1	log10_base_likelihood=-5.69021	log10_qual_likelihood_position_model=21.2091	log10_strand_likelihood_position_model=8.33623	new_cov=19/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=67/134	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=87/134
RA	246	.	NC_007779	1703335	0	G	C	bias_e_value=1047.57	bias_p_value=0.000225462	fisher_strand_p_value=1.89919e-05	frequency=3.705597e-02	genotype_quality=567.9	ks_quality_p_value=1	log10_base_likelihood=-9.81931	log10_qual_likelihood_position_model=8.12935	log10_strand_likelihood_position_model=4.72143	new_cov=6/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=20/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=26/120
RA	247	.	NC_007779	1705204	0	A	C	bias_e_value=975.408	bias_p_value=0.000209931	fisher_strand_p_value=1.75683e-05	frequency=4.807043e-02	genotype_quality=775.4	ks_quality_p_value=1	log10_base_likelihood=-8.30271	log10_qual_likelihood_position_model=23.0052	log10_strand_likelihood_position_model=4.93946	new_cov=16/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=94/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/106
RA	248	.	NC_007779	1705210	0	G	T	bias_e_value=6583.87	bias_p_value=0.001417	fisher_strand_p_value=0.000143912	frequency=5.417395e-02	genotype_quality=774.3	ks_quality_p_value=1	log10_base_likelihood=-15.2954	log10_qual_likelihood_position_model=16.14	log10_strand_likelihood_position_model=3.8419	new_cov=12/0	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=89/104	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/104
RA	249	.	NC_007779	1705224	0	G	T	bias_e_value=14732.3	bias_p_value=0.00317075	fisher_strand_p_value=0.000354673	frequency=4.901600e-02	genotype_quality=828.3	ks_quality_p_value=0.999445	log10_base_likelihood=-13.018	log10_qual_likelihood_position_model=14.7626	log10_strand_likelihood_position_model=3.70283	new_cov=12/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=96/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/106
RA	250	.	NC_007779	1713510	0	A	C	bias_e_value=0.172755	bias_p_value=3.71809e-08	fisher_strand_p_value=1.75717e-09	frequency=5.948210e-02	genotype_quality=758.2	ks_quality_p_value=1	log10_base_likelihood=-8.05673	log10_qual_likelihood_position_model=27.3387	log10_strand_likelihood_position_model=8.75519	new_cov=0/25	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=126/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/116
RA	251	.	NC_007779	1716031	1	.	T	bias_e_value=320411	bias_p_value=0.0689599	fisher_strand_p_value=0.625286	frequency=1.694965e-02	genotype_quality=1115.1	ks_quality_p_value=0.0206078	log10_base_likelihood=-17.7299	log10_qual_likelihood_position_model=2.77159	log10_strand_likelihood_position_model=0.546397	new_cov=3/1	polymorphism_quality=12.4	quality=12.4	quality_position_model=1.62374e-16	ref_cov=123/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/110
RA	252	.	NC_007779	1716032	0	T	.	bias_e_value=4500370	bias_p_value=0.968587	fisher_strand_p_value=1	frequency=1.249218e-02	genotype_quality=967.4	ks_quality_p_value=0.760053	log10_base_likelihood=-8.2511	log10_qual_likelihood_position_model=1.76237	log10_strand_likelihood_position_model=0.400812	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.17178e-08	ref_cov=125/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/113
RA	253	.	NC_007779	1746048	0	C	A	bias_e_value=1.3688	bias_p_value=2.94599e-07	fisher_strand_p_value=1.55854e-08	frequency=6.584930e-02	genotype_quality=716.4	ks_quality_p_value=0.995844	log10_base_likelihood=-10.6448	log10_qual_likelihood_position_model=18.4322	log10_strand_likelihood_position_model=7.94731	new_cov=25/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=93/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/114
RA	254	.	NC_007779	1763744	0	C	A	bias_e_value=2.96706e-07	bias_p_value=6.3858e-14	fisher_strand_p_value=1.82788e-15	frequency=1.198587e-01	genotype_quality=713.1	ks_quality_p_value=1	log10_base_likelihood=-26.1198	log10_qual_likelihood_position_model=23.3714	log10_strand_likelihood_position_model=14.7381	new_cov=41/0	polymorphism_quality=20.9	quality=20.9	quality_position_model=Inf	ref_cov=84/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/134
RA	255	.	NC_007779	1772183	1	.	T	bias_e_value=4174090	bias_p_value=0.898363	fisher_strand_p_value=1	frequency=7.604599e-03	genotype_quality=1282.7	ks_quality_p_value=0.584476	log10_base_likelihood=-8.11839	log10_qual_likelihood_position_model=1.56828	log10_strand_likelihood_position_model=0.326748	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.74721e-08	ref_cov=98/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/164
RA	256	.	NC_007779	1777105	0	C	A	bias_e_value=9.4193	bias_p_value=2.02725e-06	fisher_strand_p_value=1.19684e-07	frequency=4.150105e-02	genotype_quality=893.2	ks_quality_p_value=1	log10_base_likelihood=-6.62425	log10_qual_likelihood_position_model=14.2728	log10_strand_likelihood_position_model=6.92196	new_cov=17/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=89/152	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/152
RA	257	.	NC_007779	1784132	0	G	T	bias_e_value=4143.12	bias_p_value=0.000891696	fisher_strand_p_value=8.61162e-05	frequency=3.994179e-02	genotype_quality=808.6	ks_quality_p_value=0.999439	log10_base_likelihood=-7.80204	log10_qual_likelihood_position_model=18.3979	log10_strand_likelihood_position_model=4.22217	new_cov=0/16	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=109/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/138
RA	258	.	NC_007779	1820099	0	A	C	bias_e_value=1.85078	bias_p_value=3.9833e-07	fisher_strand_p_value=2.13439e-08	frequency=6.694126e-02	genotype_quality=740.8	ks_quality_p_value=1	log10_base_likelihood=-11.1634	log10_qual_likelihood_position_model=20.2309	log10_strand_likelihood_position_model=7.67073	new_cov=0/20	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=128/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/100
RA	259	.	NC_007779	1823573	1	.	A	bias_e_value=962209	bias_p_value=0.20709	fisher_strand_p_value=0.108102	frequency=1.176453e-02	genotype_quality=1237.3	ks_quality_p_value=0.485264	log10_base_likelihood=-13.1571	log10_qual_likelihood_position_model=1.53828	log10_strand_likelihood_position_model=0.966168	new_cov=0/3	polymorphism_quality=7.8	quality=7.8	quality_position_model=1.07965e-12	ref_cov=133/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/122
RA	260	.	NC_007779	1832491	0	G	T	bias_e_value=245.325	bias_p_value=5.27997e-05	fisher_strand_p_value=3.92626e-06	frequency=5.685425e-02	genotype_quality=662.4	ks_quality_p_value=1	log10_base_likelihood=-10.2757	log10_qual_likelihood_position_model=15.2953	log10_strand_likelihood_position_model=5.55216	new_cov=0/20	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=96/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=96/117
RA	261	.	NC_007779	1843974	1	.	T	bias_e_value=2662980	bias_p_value=0.573136	fisher_strand_p_value=0.237102	frequency=9.478569e-03	genotype_quality=1038.4	ks_quality_p_value=0.984788	log10_base_likelihood=-8.3747	log10_qual_likelihood_position_model=1.8014	log10_strand_likelihood_position_model=0.625064	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=7.21206e-08	ref_cov=101/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=103/108
RA	262	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=1009.8	new_cov=136/113	quality=1009.8	ref_cov=0/0	tot_cov=136/113
RA	263	.	NC_007779	1846634	0	A	.	bias_e_value=2275320	bias_p_value=0.489702	fisher_strand_p_value=1	frequency=1.094151e-02	genotype_quality=1107.3	ks_quality_p_value=0.180606	log10_base_likelihood=-8.24871	log10_qual_likelihood_position_model=1.71525	log10_strand_likelihood_position_model=0.392091	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=4.55418e-08	ref_cov=146/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/126
RA	264	.	NC_007779	1861399	0	A	C	bias_e_value=1.23437e-11	bias_p_value=2.65665e-18	fisher_strand_p_value=5.86684e-20	frequency=9.511614e-02	genotype_quality=646.7	ks_quality_p_value=1	log10_base_likelihood=-13.3705	log10_qual_likelihood_position_model=33.3365	log10_strand_likelihood_position_model=19.2316	new_cov=0/33	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=138/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/66
RA	265	.	NC_007779	1879404	0	A	C	bias_e_value=1.01852e-08	bias_p_value=2.1921e-15	fisher_strand_p_value=5.7083e-17	frequency=5.032253e-02	genotype_quality=659.3	ks_quality_p_value=1	log10_base_likelihood=-5.77715	log10_qual_likelihood_position_model=23.3544	log10_strand_likelihood_position_model=16.2435	new_cov=0/20	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=147/17	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/38
RA	266	.	NC_007779	1896056	0	A	.	bias_e_value=267485	bias_p_value=0.0575691	fisher_strand_p_value=0.156706	frequency=1.605701e-02	genotype_quality=1009.5	ks_quality_p_value=0.065924	log10_base_likelihood=-11.5695	log10_qual_likelihood_position_model=2.11232	log10_strand_likelihood_position_model=0.865368	new_cov=3/1	polymorphism_quality=6.2	quality=6.2	quality_position_model=1.37686e-10	ref_cov=92/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/154
RA	267	.	NC_007779	1906477	1	.	G	bias_e_value=941466	bias_p_value=0.202626	fisher_strand_p_value=0.0518084	frequency=1.309967e-02	genotype_quality=1099.0	ks_quality_p_value=0.983444	log10_base_likelihood=-10.8991	log10_qual_likelihood_position_model=4.13728	log10_strand_likelihood_position_model=1.2856	new_cov=3/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=2.22262e-07	ref_cov=83/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=86/143
RA	268	.	NC_007779	1906488	0	G	T	bias_e_value=4198.39	bias_p_value=0.000903591	fisher_strand_p_value=8.73398e-05	frequency=3.596973e-02	genotype_quality=825.2	ks_quality_p_value=1	log10_base_likelihood=-5.74096	log10_qual_likelihood_position_model=13.3303	log10_strand_likelihood_position_model=4.07664	new_cov=11/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=72/142	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=83/143
RA	269	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=1072.3	new_cov=146/128	quality=1072.3	ref_cov=0/0	tot_cov=146/128
RA	270	.	NC_007779	1938748	1	.	A	bias_e_value=1994090	bias_p_value=0.429175	fisher_strand_p_value=0.498188	frequency=7.692337e-03	genotype_quality=1270.0	ks_quality_p_value=0.295413	log10_base_likelihood=-8.17018	log10_qual_likelihood_position_model=2.52724	log10_strand_likelihood_position_model=0.590428	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=6.12138e-07	ref_cov=130/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/128
RA	271	.	NC_007779	1971508	0	A	C	bias_e_value=4.8615e-06	bias_p_value=1.04631e-12	fisher_strand_p_value=3.2643e-14	frequency=8.459568e-02	genotype_quality=583.7	ks_quality_p_value=1	log10_base_likelihood=-17.3682	log10_qual_likelihood_position_model=19.3621	log10_strand_likelihood_position_model=13.4862	new_cov=0/16	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=137/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/31
RA	272	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=849.8	new_cov=117/100	quality=849.8	ref_cov=0/0	tot_cov=117/100
RA	273	.	NC_007779	1978921	1	.	A	bias_e_value=1358840	bias_p_value=0.292455	fisher_strand_p_value=0.120978	frequency=1.079082e-02	genotype_quality=1341.0	ks_quality_p_value=0.695653	log10_base_likelihood=-12.7433	log10_qual_likelihood_position_model=1.68099	log10_strand_likelihood_position_model=0.917295	new_cov=0/3	polymorphism_quality=7.4	quality=7.4	quality_position_model=3.55727e-12	ref_cov=140/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/138
RA	274	.	NC_007779	1993894	0	A	C	bias_e_value=67.7139	bias_p_value=1.45736e-05	fisher_strand_p_value=9.82504e-07	frequency=4.192734e-02	genotype_quality=893.3	ks_quality_p_value=1	log10_base_likelihood=-9.44846	log10_qual_likelihood_position_model=23.7407	log10_strand_likelihood_position_model=6.14678	new_cov=0/20	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=130/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=130/136
RA	275	.	NC_007779	2004055	0	A	C	bias_e_value=8.35291e-20	bias_p_value=1.79774e-26	fisher_strand_p_value=2.78951e-28	frequency=2.120643e-01	genotype_quality=625.4	ks_quality_p_value=1	log10_base_likelihood=-52.0236	log10_qual_likelihood_position_model=40.4789	log10_strand_likelihood_position_model=27.5545	new_cov=0/65	polymorphism_quality=46.9	quality=46.9	quality_position_model=Inf	ref_cov=134/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/117
RA	276	.	NC_007779	2004055	1	.	C	bias_e_value=1574520	bias_p_value=0.338875	fisher_strand_p_value=0.209031	frequency=8.330345e-03	genotype_quality=1105.6	ks_quality_p_value=0.496446	log10_base_likelihood=-6.77494	log10_qual_likelihood_position_model=2.98046	log10_strand_likelihood_position_model=0.67979	new_cov=0/2	polymorphism_quality=1.3	quality=1.3	quality_position_model=6.61435e-05	ref_cov=130/108	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/110
RA	277	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=945.7	new_cov=124/108	quality=945.7	ref_cov=0/0	tot_cov=125/108
RA	278	.	NC_007779	2014008	0	T	.	bias_e_value=839647	bias_p_value=0.180712	fisher_strand_p_value=0.106732	frequency=1.275730e-02	genotype_quality=945.9	ks_quality_p_value=0.410075	log10_base_likelihood=-8.26913	log10_qual_likelihood_position_model=1.85156	log10_strand_likelihood_position_model=0.971706	new_cov=3/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.3897e-07	ref_cov=109/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/123
RA	279	.	NC_007779	2032185	0	G	C	bias_e_value=19.1225	bias_p_value=4.11562e-06	fisher_strand_p_value=2.66639e-07	frequency=4.923105e-02	genotype_quality=552.3	ks_quality_p_value=0.953684	log10_base_likelihood=-11.4065	log10_qual_likelihood_position_model=10.6743	log10_strand_likelihood_position_model=6.57408	new_cov=7/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=12/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=19/122
RA	280	.	NC_007779	2060392	0	T	G	bias_e_value=4.40804e-05	bias_p_value=9.48714e-12	fisher_strand_p_value=3.18631e-13	frequency=5.395222e-02	genotype_quality=878.8	ks_quality_p_value=1	log10_base_likelihood=-7.89533	log10_qual_likelihood_position_model=43.0186	log10_strand_likelihood_position_model=12.4967	new_cov=37/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=110/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/151
RA	281	.	NC_007779	2095582	0	G	T	bias_e_value=3.6741	bias_p_value=7.90753e-07	fisher_strand_p_value=4.41174e-08	frequency=4.937887e-02	genotype_quality=828.0	ks_quality_p_value=0.999256	log10_base_likelihood=-8.68618	log10_qual_likelihood_position_model=16.7123	log10_strand_likelihood_position_model=7.37205	new_cov=0/25	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=128/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/144
RA	282	.	NC_007779	2098223	0	T	G	bias_e_value=0.0360161	bias_p_value=7.75152e-09	fisher_strand_p_value=3.39946e-10	frequency=5.697060e-02	genotype_quality=695.5	ks_quality_p_value=1	log10_base_likelihood=-6.58651	log10_qual_likelihood_position_model=23.398	log10_strand_likelihood_position_model=9.47705	new_cov=26/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=69/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=95/130
RA	283	.	NC_007779	2107010	1	.	A	bias_e_value=4207100	bias_p_value=0.905467	fisher_strand_p_value=1	frequency=7.721901e-03	genotype_quality=1265.4	ks_quality_p_value=0.597994	log10_base_likelihood=-8.18459	log10_qual_likelihood_position_model=1.72524	log10_strand_likelihood_position_model=0.301693	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.38108e-08	ref_cov=138/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/120
RA	284	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1229.1	new_cov=115/185	quality=1229.1	ref_cov=0/0	tot_cov=115/185
RA	285	.	NC_007779	2174678	0	C	G	bias_e_value=0.00338582	bias_p_value=7.28707e-10	fisher_strand_p_value=2.88376e-11	frequency=7.747078e-02	genotype_quality=768.8	ks_quality_p_value=1	log10_base_likelihood=-15.6963	log10_qual_likelihood_position_model=21.1699	log10_strand_likelihood_position_model=10.54	new_cov=0/20	polymorphism_quality=10.4	quality=10.4	quality_position_model=Inf	ref_cov=147/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/72
RA	286	.	NC_007779	2200802	0	A	.	bias_e_value=3638800	bias_p_value=0.783156	fisher_strand_p_value=1	frequency=1.135635e-02	genotype_quality=1069.8	ks_quality_p_value=0.418626	log10_base_likelihood=-8.27695	log10_qual_likelihood_position_model=2.38289	log10_strand_likelihood_position_model=0.424321	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.25729e-07	ref_cov=131/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/132
RA	287	.	NC_007779	2211749	0	G	C	bias_e_value=117.295	bias_p_value=2.52447e-05	fisher_strand_p_value=1.77358e-06	frequency=4.826498e-02	genotype_quality=659.2	ks_quality_p_value=0.999339	log10_base_likelihood=-13.1991	log10_qual_likelihood_position_model=10.2679	log10_strand_likelihood_position_model=5.75115	new_cov=10/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=41/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=51/128
RA	288	.	NC_007779	2213136	0	G	T	bias_e_value=1.40607e-06	bias_p_value=3.0262e-13	fisher_strand_p_value=1.09886e-14	frequency=1.305718e-01	genotype_quality=595.9	ks_quality_p_value=0.826193	log10_base_likelihood=-51.5634	log10_qual_likelihood_position_model=24.426	log10_strand_likelihood_position_model=13.9591	new_cov=26/0	polymorphism_quality=46.5	quality=46.5	quality_position_model=2.90377e-15	ref_cov=40/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=66/129
RA	289	.	NC_007779	2226744	0	T	G	bias_e_value=7.49488	bias_p_value=1.61307e-06	fisher_strand_p_value=9.38861e-08	frequency=7.436466e-02	genotype_quality=763.0	ks_quality_p_value=1	log10_base_likelihood=-13.4843	log10_qual_likelihood_position_model=22.3102	log10_strand_likelihood_position_model=7.23074	new_cov=25/0	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=112/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/118
RA	290	.	NC_007779	2232587	0	G	A	bias_e_value=398226	bias_p_value=0.0857077	fisher_strand_p_value=0.0169014	frequency=2.446175e-02	genotype_quality=589.2	ks_quality_p_value=0.997718	log10_base_likelihood=-7.0363	log10_qual_likelihood_position_model=7.38161	log10_strand_likelihood_position_model=1.77208	new_cov=5/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=85/111	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=90/111
RA	291	.	NC_007779	2249963	0	T	G	bias_e_value=7.74769e-05	bias_p_value=1.66749e-11	fisher_strand_p_value=5.71233e-13	frequency=7.692575e-02	genotype_quality=748.7	ks_quality_p_value=1	log10_base_likelihood=-9.17913	log10_qual_likelihood_position_model=33.4296	log10_strand_likelihood_position_model=12.2432	new_cov=31/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=77/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=109/137
RA	292	.	NC_007779	2254201	0	G	T	bias_e_value=0.000121845	bias_p_value=2.6224e-11	fisher_strand_p_value=9.13027e-13	frequency=9.370613e-02	genotype_quality=767.4	ks_quality_p_value=1	log10_base_likelihood=-12.6017	log10_qual_likelihood_position_model=26.3656	log10_strand_likelihood_position_model=12.1109	new_cov=0/37	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=124/92	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/129
RA	293	.	NC_007779	2278635	0	C	A	bias_e_value=24.9779	bias_p_value=5.37583e-06	fisher_strand_p_value=3.38257e-07	frequency=2.911854e-02	genotype_quality=918.7	ks_quality_p_value=0.999551	log10_base_likelihood=-6.17844	log10_qual_likelihood_position_model=16.2374	log10_strand_likelihood_position_model=6.47075	new_cov=16/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=97/162	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/162
RA	294	.	NC_007779	2331120	0	T	G	bias_e_value=5.89701e-16	bias_p_value=1.26918e-22	fisher_strand_p_value=2.28954e-24	frequency=1.820450e-01	genotype_quality=679.3	ks_quality_p_value=1	log10_base_likelihood=-33.6359	log10_qual_likelihood_position_model=38.9054	log10_strand_likelihood_position_model=23.6481	new_cov=66/0	polymorphism_quality=28.5	quality=28.5	quality_position_model=Inf	ref_cov=72/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/132
RA	295	.	NC_007779	2332580	0	A	C	bias_e_value=6.36287e-12	bias_p_value=1.36944e-18	fisher_strand_p_value=2.97964e-20	frequency=8.539486e-02	genotype_quality=760.8	ks_quality_p_value=1	log10_base_likelihood=-14.1756	log10_qual_likelihood_position_model=29.9715	log10_strand_likelihood_position_model=19.5258	new_cov=0/37	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=161/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/87
RA	296	.	NC_007779	2334630	0	C	A	bias_e_value=2.73331	bias_p_value=5.88272e-07	fisher_strand_p_value=3.22336e-08	frequency=4.547882e-02	genotype_quality=817.7	ks_quality_p_value=1	log10_base_likelihood=-7.0706	log10_qual_likelihood_position_model=18.4875	log10_strand_likelihood_position_model=7.49169	new_cov=22/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=103/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/136
RA	297	.	NC_007779	2342393	0	A	C	bias_e_value=5.48491e-05	bias_p_value=1.18048e-11	fisher_strand_p_value=3.99505e-13	frequency=5.107880e-02	genotype_quality=897.8	ks_quality_p_value=1	log10_base_likelihood=-5.65743	log10_qual_likelihood_position_model=24.0788	log10_strand_likelihood_position_model=12.3985	new_cov=0/26	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=178/76	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=178/102
RA	298	.	NC_007779	2353815	0	A	C	bias_e_value=0.00190662	bias_p_value=4.1035e-10	fisher_strand_p_value=1.58639e-11	frequency=5.485010e-02	genotype_quality=663.7	ks_quality_p_value=1	log10_base_likelihood=-6.29772	log10_qual_likelihood_position_model=21.0018	log10_strand_likelihood_position_model=10.7996	new_cov=0/20	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=131/43	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/63
RA	299	.	NC_007779	2354291	0	A	C	bias_e_value=0.00111976	bias_p_value=2.40998e-10	fisher_strand_p_value=9.12167e-12	frequency=6.956148e-02	genotype_quality=887.1	ks_quality_p_value=1	log10_base_likelihood=-11.1886	log10_qual_likelihood_position_model=24.9615	log10_strand_likelihood_position_model=11.0399	new_cov=0/27	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=162/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=162/117
RA	300	.	NC_007779	2373239	0	A	C	bias_e_value=2.35001e-07	bias_p_value=5.05777e-14	fisher_strand_p_value=1.43786e-15	frequency=7.257509e-02	genotype_quality=643.6	ks_quality_p_value=1	log10_base_likelihood=-5.69108	log10_qual_likelihood_position_model=31.1809	log10_strand_likelihood_position_model=14.8423	new_cov=0/31	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=125/47	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/80
RA	301	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=1070.1	new_cov=140/126	quality=1070.1	ref_cov=0/0	tot_cov=140/126
RA	302	.	NC_007779	2410316	0	A	C	bias_e_value=1.1784e-08	bias_p_value=2.5362e-15	fisher_strand_p_value=6.6302e-17	frequency=1.254754e-01	genotype_quality=692.9	ks_quality_p_value=1	log10_base_likelihood=-30.3891	log10_qual_likelihood_position_model=30.9186	log10_strand_likelihood_position_model=16.1785	new_cov=0/42	polymorphism_quality=25.2	quality=25.2	quality_position_model=Inf	ref_cov=129/70	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/112
RA	303	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=1041.0	new_cov=111/151	quality=1041.0	ref_cov=0/0	tot_cov=111/151
RA	304	.	NC_007779	2417605	0	C	A	bias_e_value=0.00462936	bias_p_value=9.96348e-10	fisher_strand_p_value=6.52714e-11	frequency=1.209121e-01	genotype_quality=681.6	ks_quality_p_value=0.61197	log10_base_likelihood=-21.6594	log10_qual_likelihood_position_model=32.7064	log10_strand_likelihood_position_model=10.2436	new_cov=41/0	polymorphism_quality=16.4	quality=16.4	quality_position_model=Inf	ref_cov=111/102	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/102
RA	305	.	NC_007779	2418805	1	.	A	bias_e_value=1953320	bias_p_value=0.4204	fisher_strand_p_value=1	frequency=7.434845e-03	genotype_quality=1333.3	ks_quality_p_value=0.142629	log10_base_likelihood=-8.24283	log10_qual_likelihood_position_model=1.03559	log10_strand_likelihood_position_model=0.299563	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.37972e-09	ref_cov=131/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/137
RA	306	.	NC_007779	2465370	0	C	A	bias_e_value=0.241889	bias_p_value=5.20602e-08	fisher_strand_p_value=2.60938e-09	frequency=7.654428e-02	genotype_quality=576.0	ks_quality_p_value=0.95891	log10_base_likelihood=-22.9579	log10_qual_likelihood_position_model=14.524	log10_strand_likelihood_position_model=8.58346	new_cov=0/13	polymorphism_quality=17.7	quality=17.7	quality_position_model=Inf	ref_cov=117/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/39
RA	307	.	NC_007779	2468327	0	C	.	bias_e_value=4643400	bias_p_value=0.999369	fisher_strand_p_value=1	frequency=2.117634e-02	genotype_quality=967.4	ks_quality_p_value=0.964686	log10_base_likelihood=-14.5854	log10_qual_likelihood_position_model=3.41814	log10_strand_likelihood_position_model=0.469747	new_cov=2/3	polymorphism_quality=9.2	quality=9.2	quality_position_model=9.71717e-13	ref_cov=105/126	reject=INDEL_HOMOPOLYMER	tot_cov=107/129
RA	308	.	NC_007779	2475172	0	T	.	bias_e_value=3684830	bias_p_value=0.793062	fisher_strand_p_value=1	frequency=2.701950e-02	genotype_quality=741.9	ks_quality_p_value=0.430183	log10_base_likelihood=-15.523	log10_qual_likelihood_position_model=2.09823	log10_strand_likelihood_position_model=0.460414	new_cov=3/2	polymorphism_quality=10.2	quality=10.2	quality_position_model=4.79044e-15	ref_cov=102/78	reject=INDEL_HOMOPOLYMER	tot_cov=105/80
RA	309	.	NC_007779	2476279	0	C	G	bias_e_value=258061	bias_p_value=0.0555408	fisher_strand_p_value=0.0098892	frequency=2.959061e-02	genotype_quality=901.8	ks_quality_p_value=1	log10_base_likelihood=-8.98006	log10_qual_likelihood_position_model=10.553	log10_strand_likelihood_position_model=2.0613	new_cov=0/8	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=100/119	reject=POLYMORPHISM_STRAND	tot_cov=100/127
RA	310	.	NC_007779	2476287	0	T	G	bias_e_value=386862	bias_p_value=0.0832618	fisher_strand_p_value=0.0162663	frequency=2.300644e-02	genotype_quality=844.7	ks_quality_p_value=1	log10_base_likelihood=-6.58581	log10_qual_likelihood_position_model=10.0573	log10_strand_likelihood_position_model=1.90613	new_cov=0/7	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=102/113	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=102/120
RA	311	.	NC_007779	2476289	0	A	T	bias_e_value=364531	bias_p_value=0.0784556	fisher_strand_p_value=0.0151096	frequency=2.838039e-02	genotype_quality=827.9	ks_quality_p_value=1	log10_base_likelihood=-6.88346	log10_qual_likelihood_position_model=10.2994	log10_strand_likelihood_position_model=1.98176	new_cov=0/7	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=102/107	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=102/114
RA	312	.	NC_007779	2488915	1	.	A	bias_e_value=4591960	bias_p_value=0.988299	fisher_strand_p_value=1	frequency=8.510590e-03	genotype_quality=1160.2	ks_quality_p_value=0.850974	log10_base_likelihood=-8.50546	log10_qual_likelihood_position_model=1.71253	log10_strand_likelihood_position_model=0.300509	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.97697e-08	ref_cov=123/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/111
RA	313	.	NC_007779	2517218	0	A	C	bias_e_value=4.08604e-11	bias_p_value=8.79412e-18	fisher_strand_p_value=1.99604e-19	frequency=9.917974e-02	genotype_quality=539.5	ks_quality_p_value=1	log10_base_likelihood=-8.45159	log10_qual_likelihood_position_model=35.9783	log10_strand_likelihood_position_model=18.6998	new_cov=0/34	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=115/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/63
RA	314	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=956.4	new_cov=116/122	quality=956.4	ref_cov=0/0	tot_cov=116/122
RA	315	.	NC_007779	2556426	0	G	T	bias_e_value=3.15545	bias_p_value=6.79127e-07	fisher_strand_p_value=4.65097e-08	frequency=5.859661e-02	genotype_quality=678.1	ks_quality_p_value=0.806808	log10_base_likelihood=-9.83649	log10_qual_likelihood_position_model=19.275	log10_strand_likelihood_position_model=7.33246	new_cov=0/20	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=117/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/98
RA	316	.	NC_007779	2579404	0	G	T	bias_e_value=94.7537	bias_p_value=2.03932e-05	fisher_strand_p_value=1.4091e-06	frequency=4.318810e-02	genotype_quality=860.5	ks_quality_p_value=1	log10_base_likelihood=-6.61669	log10_qual_likelihood_position_model=14.7673	log10_strand_likelihood_position_model=5.85106	new_cov=0/17	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=134/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/119
RA	317	.	NC_007779	2581900	0	G	T	bias_e_value=0.0101076	bias_p_value=2.17538e-09	fisher_strand_p_value=9.01546e-11	frequency=7.107639e-02	genotype_quality=850.1	ks_quality_p_value=1	log10_base_likelihood=-12.0162	log10_qual_likelihood_position_model=22.6304	log10_strand_likelihood_position_model=10.045	new_cov=0/29	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=141/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/131
RA	318	.	NC_007779	2601998	0	A	C	bias_e_value=5.73263e-11	bias_p_value=1.2338e-17	fisher_strand_p_value=2.82259e-19	frequency=1.072421e-01	genotype_quality=545.6	ks_quality_p_value=1	log10_base_likelihood=-28.6582	log10_qual_likelihood_position_model=20.7585	log10_strand_likelihood_position_model=18.5494	new_cov=0/20	polymorphism_quality=23.5	quality=23.5	quality_position_model=Inf	ref_cov=130/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/28
RA	319	.	NC_007779	2616347	0	A	C	bias_e_value=1.61854e-06	bias_p_value=3.48348e-13	fisher_strand_p_value=1.04963e-14	frequency=6.716251e-02	genotype_quality=754.7	ks_quality_p_value=1	log10_base_likelihood=-15.6218	log10_qual_likelihood_position_model=22.2106	log10_strand_likelihood_position_model=13.979	new_cov=0/24	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=158/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/68
RA	320	.	NC_007779	2618856	1	.	A	bias_e_value=2346230	bias_p_value=0.504964	fisher_strand_p_value=1	frequency=1.195145e-02	genotype_quality=1220.0	ks_quality_p_value=0.189654	log10_base_likelihood=-12.3236	log10_qual_likelihood_position_model=3.31529	log10_strand_likelihood_position_model=0.375644	new_cov=1/2	polymorphism_quality=6.9	quality=6.9	quality_position_model=1.25041e-10	ref_cov=107/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/143
RA	321	.	NC_007779	2623159	0	T	G	bias_e_value=9.83256e-15	bias_p_value=2.1162e-21	fisher_strand_p_value=4.02574e-23	frequency=1.776509e-01	genotype_quality=649.9	ks_quality_p_value=1	log10_base_likelihood=-31.5976	log10_qual_likelihood_position_model=39.1739	log10_strand_likelihood_position_model=22.3952	new_cov=58/0	polymorphism_quality=26.4	quality=26.4	quality_position_model=Inf	ref_cov=60/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/125
RA	322	.	NC_007779	2648595	0	A	C	bias_e_value=5.85939e-05	bias_p_value=1.26108e-11	fisher_strand_p_value=4.27772e-13	frequency=6.780338e-02	genotype_quality=602.0	ks_quality_p_value=1	log10_base_likelihood=-9.18777	log10_qual_likelihood_position_model=19.3701	log10_strand_likelihood_position_model=12.3688	new_cov=0/14	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=140/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/28
RA	323	.	NC_007779	2754327	0	A	.	bias_e_value=2154300	bias_p_value=0.463656	fisher_strand_p_value=0.270183	frequency=1.114368e-02	genotype_quality=1093.5	ks_quality_p_value=0.61349	log10_base_likelihood=-7.96865	log10_qual_likelihood_position_model=3.67888	log10_strand_likelihood_position_model=0.696717	new_cov=0/3	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.06157e-05	ref_cov=111/155	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/158
RA	324	.	NC_007779	2756310	1	.	T	bias_e_value=4496420	bias_p_value=0.967735	fisher_strand_p_value=1	frequency=8.474350e-03	genotype_quality=1163.1	ks_quality_p_value=0.756972	log10_base_likelihood=-8.20785	log10_qual_likelihood_position_model=1.74052	log10_strand_likelihood_position_model=0.303701	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.31928e-08	ref_cov=105/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/130
RA	325	.	NC_007779	2772065	0	T	.	bias_e_value=1312950	bias_p_value=0.282578	fisher_strand_p_value=0.592565	frequency=1.228809e-02	genotype_quality=987.0	ks_quality_p_value=0.135354	log10_base_likelihood=-8.37144	log10_qual_likelihood_position_model=1.86094	log10_strand_likelihood_position_model=0.469123	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=5.77758e-08	ref_cov=109/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/133
RA	326	.	NC_007779	2797644	0	C	A	bias_e_value=1388.15	bias_p_value=0.000298762	fisher_strand_p_value=2.58465e-05	frequency=4.135990e-02	genotype_quality=856.2	ks_quality_p_value=0.9996	log10_base_likelihood=-8.34147	log10_qual_likelihood_position_model=10.5591	log10_strand_likelihood_position_model=4.5876	new_cov=0/11	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=145/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/95
RA	327	.	NC_007779	2816615	0	G	C	bias_e_value=0.227969	bias_p_value=4.90644e-08	fisher_strand_p_value=2.95826e-09	frequency=8.175182e-02	genotype_quality=634.9	ks_quality_p_value=0.79477	log10_base_likelihood=-21.2079	log10_qual_likelihood_position_model=19.6745	log10_strand_likelihood_position_model=8.52896	new_cov=18/0	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=54/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=72/125
RA	328	.	NC_007779	2816615	1	.	C	bias_e_value=1180990	bias_p_value=0.254176	fisher_strand_p_value=0.124236	frequency=1.041698e-02	genotype_quality=833.0	ks_quality_p_value=0.557485	log10_base_likelihood=-8.42057	log10_qual_likelihood_position_model=2.96227	log10_strand_likelihood_position_model=0.905751	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.03116e-06	ref_cov=66/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=68/124
RA	329	.	NC_007779	2817030	0	G	C	bias_e_value=2.36014e-09	bias_p_value=5.07957e-16	fisher_strand_p_value=2.57317e-17	frequency=1.634383e-01	genotype_quality=560.7	ks_quality_p_value=0.494717	log10_base_likelihood=-41.5468	log10_qual_likelihood_position_model=35.3383	log10_strand_likelihood_position_model=16.5895	new_cov=37/0	polymorphism_quality=36.4	quality=36.4	quality_position_model=Inf	ref_cov=48/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=85/119
RA	330	.	NC_007779	2833875	0	A	C	bias_e_value=0.135443	bias_p_value=2.91505e-08	fisher_strand_p_value=1.36122e-09	frequency=5.663490e-02	genotype_quality=733.5	ks_quality_p_value=1	log10_base_likelihood=-6.62282	log10_qual_likelihood_position_model=21.5986	log10_strand_likelihood_position_model=8.86607	new_cov=0/25	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=122/84	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/109
RA	331	.	NC_007779	2833989	0	A	C	bias_e_value=3.19261e-07	bias_p_value=6.87125e-14	fisher_strand_p_value=1.97109e-15	frequency=8.339119e-02	genotype_quality=683.3	ks_quality_p_value=1	log10_base_likelihood=-10.6005	log10_qual_likelihood_position_model=25.5642	log10_strand_likelihood_position_model=14.7053	new_cov=0/22	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=146/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/51
RA	332	.	NC_007779	2839296	0	A	G	bias_e_value=0.00677056	bias_p_value=1.45718e-09	fisher_strand_p_value=5.93622e-11	frequency=6.093359e-02	genotype_quality=645.0	ks_quality_p_value=1	log10_base_likelihood=-8.06304	log10_qual_likelihood_position_model=16.0364	log10_strand_likelihood_position_model=10.2265	new_cov=16/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=35/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=51/145
RA	333	.	NC_007779	2847445	0	G	T	bias_e_value=0.0393547	bias_p_value=8.47006e-09	fisher_strand_p_value=3.72974e-10	frequency=9.873962e-02	genotype_quality=706.3	ks_quality_p_value=1	log10_base_likelihood=-19.3516	log10_qual_likelihood_position_model=20.364	log10_strand_likelihood_position_model=9.51504	new_cov=0/32	polymorphism_quality=14.1	quality=14.1	quality_position_model=Inf	ref_cov=113/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/132
RA	334	.	NC_007779	2862783	1	.	T	bias_e_value=3931850	bias_p_value=0.846226	fisher_strand_p_value=0.503352	frequency=7.936478e-03	genotype_quality=1244.9	ks_quality_p_value=0.992347	log10_base_likelihood=-7.45464	log10_qual_likelihood_position_model=3.72189	log10_strand_likelihood_position_model=0.51818	new_cov=0/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=5.1817e-05	ref_cov=113/137	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=113/139
RA	335	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1269.3	new_cov=139/153	quality=1269.3	ref_cov=0/0	tot_cov=139/153
RA	336	.	NC_007779	2868094	0	C	A	bias_e_value=3.06066	bias_p_value=6.58726e-07	fisher_strand_p_value=3.63324e-08	frequency=6.723690e-02	genotype_quality=784.3	ks_quality_p_value=1	log10_base_likelihood=-9.90816	log10_qual_likelihood_position_model=17.3148	log10_strand_likelihood_position_model=7.62282	new_cov=24/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=101/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/122
RA	337	.	NC_007779	2895131	0	A	C	bias_e_value=7.51348e-13	bias_p_value=1.61708e-19	fisher_strand_p_value=3.35893e-21	frequency=1.112332e-01	genotype_quality=716.6	ks_quality_p_value=1	log10_base_likelihood=-14.2834	log10_qual_likelihood_position_model=41.916	log10_strand_likelihood_position_model=20.4738	new_cov=0/40	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=142/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/84
RA	338	.	NC_007779	2898837	0	G	T	bias_e_value=65.4512	bias_p_value=1.40866e-05	fisher_strand_p_value=9.47345e-07	frequency=3.680992e-02	genotype_quality=960.1	ks_quality_p_value=1	log10_base_likelihood=-6.60024	log10_qual_likelihood_position_model=14.4639	log10_strand_likelihood_position_model=6.02349	new_cov=0/18	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=149/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/137
RA	339	.	NC_007779	2898954	0	A	.	bias_e_value=3772690	bias_p_value=0.811972	fisher_strand_p_value=0.708726	frequency=2.681255e-02	genotype_quality=1043.6	ks_quality_p_value=0.639635	log10_base_likelihood=-21.7079	log10_qual_likelihood_position_model=3.09189	log10_strand_likelihood_position_model=0.593691	new_cov=3/4	polymorphism_quality=16.4	quality=16.4	quality_position_model=3.57101e-20	ref_cov=136/118	reject=INDEL_HOMOPOLYMER	tot_cov=139/122
RA	340	.	NC_007779	2915479	0	C	G	bias_e_value=496.757	bias_p_value=0.000106914	fisher_strand_p_value=8.52262e-06	frequency=3.249836e-02	genotype_quality=825.8	ks_quality_p_value=0.989034	log10_base_likelihood=-5.6854	log10_qual_likelihood_position_model=13.9856	log10_strand_likelihood_position_model=5.06943	new_cov=0/10	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=147/61	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/71
RA	341	.	NC_007779	2926157	0	T	G	bias_e_value=2.05796e-13	bias_p_value=4.42921e-20	fisher_strand_p_value=8.95428e-22	frequency=1.293759e-01	genotype_quality=564.6	ks_quality_p_value=1	log10_base_likelihood=-14.7486	log10_qual_likelihood_position_model=32.1273	log10_strand_likelihood_position_model=21.048	new_cov=35/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=24/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=59/121
RA	342	.	NC_007779	2953753	0	C	.	bias_e_value=3951680	bias_p_value=0.850495	fisher_strand_p_value=0.601721	frequency=1.152992e-02	genotype_quality=1050.3	ks_quality_p_value=0.840431	log10_base_likelihood=-8.1409	log10_qual_likelihood_position_model=1.3901	log10_strand_likelihood_position_model=0.453747	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=3.14494e-08	ref_cov=137/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/122
RA	343	.	NC_007779	2969054	0	T	.	bias_e_value=4178160	bias_p_value=0.899238	fisher_strand_p_value=0.601888	frequency=1.139164e-02	genotype_quality=1040.7	ks_quality_p_value=0.973784	log10_base_likelihood=-7.5193	log10_qual_likelihood_position_model=3.11004	log10_strand_likelihood_position_model=0.453514	new_cov=1/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=8.56098e-06	ref_cov=138/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/124
RA	344	.	NC_007779	2983097	0	A	C	bias_e_value=4.58621e-09	bias_p_value=9.87061e-16	fisher_strand_p_value=2.51666e-17	frequency=1.438799e-01	genotype_quality=550.0	ks_quality_p_value=1	log10_base_likelihood=-13.9754	log10_qual_likelihood_position_model=42.9833	log10_strand_likelihood_position_model=16.5992	new_cov=0/45	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=105/57	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/102
RA	345	.	NC_007779	2987535	0	A	C	bias_e_value=1.68936e-05	bias_p_value=3.6359e-12	fisher_strand_p_value=1.18177e-13	frequency=9.092951e-02	genotype_quality=788.4	ks_quality_p_value=1	log10_base_likelihood=-15.4993	log10_qual_likelihood_position_model=36.9745	log10_strand_likelihood_position_model=12.9275	new_cov=0/38	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=134/94	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/132
RA	346	.	NC_007779	2994409	1	.	T	bias_e_value=4288830	bias_p_value=0.923057	fisher_strand_p_value=1	frequency=7.999420e-03	genotype_quality=1240.1	ks_quality_p_value=0.634305	log10_base_likelihood=-8.05789	log10_qual_likelihood_position_model=1.52183	log10_strand_likelihood_position_model=0.317018	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.78597e-08	ref_cov=149/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/100
RA	347	.	NC_007779	2994410	0	T	.	bias_e_value=124269	bias_p_value=0.0267455	fisher_strand_p_value=0.0632328	frequency=1.185131e-02	genotype_quality=1026.7	ks_quality_p_value=0.0651528	log10_base_likelihood=-8.47481	log10_qual_likelihood_position_model=1.45764	log10_strand_likelihood_position_model=1.19906	new_cov=0/3	polymorphism_quality=3.0	quality=3.0	quality_position_model=9.83278e-08	ref_cov=151/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/102
RA	348	.	NC_007779	2994663	1	.	T	bias_e_value=4488280	bias_p_value=0.965982	fisher_strand_p_value=1	frequency=8.808136e-03	genotype_quality=1128.9	ks_quality_p_value=0.750769	log10_base_likelihood=-6.9992	log10_qual_likelihood_position_model=2.68483	log10_strand_likelihood_position_model=0.299188	new_cov=1/1	polymorphism_quality=1.5	quality=1.5	quality_position_model=7.41539e-06	ref_cov=111/114	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/115
RA	349	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=990.4	new_cov=118/125	quality=990.4	ref_cov=0/1	tot_cov=118/126
RA	350	.	NC_007779	3029385	0	C	A	bias_e_value=13.9231	bias_p_value=2.99658e-06	fisher_strand_p_value=1.94082e-07	frequency=4.345608e-02	genotype_quality=728.3	ks_quality_p_value=0.934452	log10_base_likelihood=-11.2031	log10_qual_likelihood_position_model=12.5803	log10_strand_likelihood_position_model=6.71201	new_cov=0/10	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=149/35	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=149/45
RA	351	.	NC_007779	3034413	0	A	C	bias_e_value=7.7635e-19	bias_p_value=1.67089e-25	fisher_strand_p_value=2.68712e-27	frequency=1.743879e-01	genotype_quality=574.7	ks_quality_p_value=1	log10_base_likelihood=-25.8751	log10_qual_likelihood_position_model=35.7378	log10_strand_likelihood_position_model=26.5707	new_cov=0/47	polymorphism_quality=20.6	quality=20.6	quality_position_model=Inf	ref_cov=130/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/75
RA	352	.	NC_007779	3035390	0	T	C	bias_e_value=4.19346e-08	bias_p_value=9.02532e-15	fisher_strand_p_value=2.44269e-16	frequency=1.583405e-01	genotype_quality=406.1	ks_quality_p_value=1	log10_base_likelihood=-32.1311	log10_qual_likelihood_position_model=23.806	log10_strand_likelihood_position_model=15.6121	new_cov=0/28	polymorphism_quality=26.9	quality=26.9	quality_position_model=Inf	ref_cov=111/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/58
RA	353	.	NC_007779	3044685	1	.	T	bias_e_value=2732660	bias_p_value=0.588132	fisher_strand_p_value=0.525972	frequency=1.169586e-02	genotype_quality=793.1	ks_quality_p_value=0.463835	log10_base_likelihood=-8.08954	log10_qual_likelihood_position_model=2.86139	log10_strand_likelihood_position_model=0.41695	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.09145e-06	ref_cov=65/104	reject=POLYMORPHISM_STRAND	tot_cov=65/106
RA	354	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=873.7	new_cov=100/117	quality=873.7	ref_cov=0/0	tot_cov=101/117
RA	355	.	NC_007779	3051976	0	G	T	bias_e_value=54.9609	bias_p_value=1.18289e-05	fisher_strand_p_value=7.85618e-07	frequency=5.707216e-02	genotype_quality=793.2	ks_quality_p_value=1	log10_base_likelihood=-11.1547	log10_qual_likelihood_position_model=18.7354	log10_strand_likelihood_position_model=6.36702	new_cov=0/20	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=116/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/118
RA	356	.	NC_007779	3059421	0	T	.	bias_e_value=4489720	bias_p_value=0.966293	fisher_strand_p_value=1	frequency=1.127052e-02	genotype_quality=1054.2	ks_quality_p_value=0.751857	log10_base_likelihood=-8.23935	log10_qual_likelihood_position_model=1.48967	log10_strand_likelihood_position_model=0.411761	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.85386e-08	ref_cov=128/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/137
RA	357	.	NC_007779	3074129	0	G	T	bias_e_value=0.383645	bias_p_value=8.25695e-08	fisher_strand_p_value=4.0632e-09	frequency=5.434990e-02	genotype_quality=883.0	ks_quality_p_value=1	log10_base_likelihood=-12.1678	log10_qual_likelihood_position_model=18.5837	log10_strand_likelihood_position_model=8.39113	new_cov=0/24	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=140/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/125
RA	358	.	NC_007779	3082394	1	.	A	bias_e_value=3870920	bias_p_value=0.833114	fisher_strand_p_value=1	frequency=8.230209e-03	genotype_quality=1153.2	ks_quality_p_value=0.481103	log10_base_likelihood=-7.62836	log10_qual_likelihood_position_model=2.51415	log10_strand_likelihood_position_model=0.303147	new_cov=1/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.09182e-06	ref_cov=109/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/133
RA	359	.	NC_007779	3084663	0	C	A	bias_e_value=8.72129	bias_p_value=1.87703e-06	fisher_strand_p_value=1.10282e-07	frequency=2.869701e-02	genotype_quality=1016.6	ks_quality_p_value=1	log10_base_likelihood=-5.73432	log10_qual_likelihood_position_model=15.2178	log10_strand_likelihood_position_model=6.95749	new_cov=20/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=120/160	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/160
RA	360	.	NC_007779	3088549	0	G	T	bias_e_value=3.92834	bias_p_value=8.45472e-07	fisher_strand_p_value=4.73222e-08	frequency=7.167959e-02	genotype_quality=731.4	ks_quality_p_value=1	log10_base_likelihood=-7.57768	log10_qual_likelihood_position_model=20.4136	log10_strand_likelihood_position_model=7.44227	new_cov=0/31	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=103/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/155
RA	361	.	NC_007779	3152854	1	.	A	bias_e_value=1405320	bias_p_value=0.302459	fisher_strand_p_value=0.498128	frequency=7.575989e-03	genotype_quality=1301.6	ks_quality_p_value=0.177143	log10_base_likelihood=-8.40037	log10_qual_likelihood_position_model=1.58774	log10_strand_likelihood_position_model=0.597134	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.81797e-08	ref_cov=131/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/131
RA	362	.	NC_007779	3152855	0	A	.	bias_e_value=3784640	bias_p_value=0.814544	fisher_strand_p_value=0.684028	frequency=2.221489e-02	genotype_quality=1064.6	ks_quality_p_value=0.667505	log10_base_likelihood=-18.2582	log10_qual_likelihood_position_model=3.46544	log10_strand_likelihood_position_model=0.622013	new_cov=4/2	polymorphism_quality=13.0	quality=13.0	quality_position_model=2.8526e-16	ref_cov=132/132	reject=INDEL_HOMOPOLYMER	tot_cov=136/134
RA	363	.	NC_007779	3160153	0	G	C	bias_e_value=22.7971	bias_p_value=4.90647e-06	fisher_strand_p_value=3.06705e-07	frequency=3.664970e-02	genotype_quality=626.3	ks_quality_p_value=1	log10_base_likelihood=-8.48803	log10_qual_likelihood_position_model=9.96696	log10_strand_likelihood_position_model=6.51328	new_cov=7/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=15/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=24/142
RA	364	.	NC_007779	3188902	1	.	A	bias_e_value=1329330	bias_p_value=0.286102	fisher_strand_p_value=0.499735	frequency=7.662773e-03	genotype_quality=1288.8	ks_quality_p_value=0.163302	log10_base_likelihood=-8.4702	log10_qual_likelihood_position_model=1.8351	log10_strand_likelihood_position_model=0.555014	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=5.26915e-08	ref_cov=136/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/123
RA	365	.	NC_007779	3195962	0	G	T	bias_e_value=217.644	bias_p_value=4.68421e-05	fisher_strand_p_value=3.45008e-06	frequency=6.041956e-02	genotype_quality=698.0	ks_quality_p_value=1	log10_base_likelihood=-9.03939	log10_qual_likelihood_position_model=17.3986	log10_strand_likelihood_position_model=5.64983	new_cov=0/25	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=94/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/150
RA	366	.	NC_007779	3212355	0	G	C	bias_e_value=0.0681376	bias_p_value=1.46648e-08	fisher_strand_p_value=6.92709e-10	frequency=8.892488e-02	genotype_quality=642.5	ks_quality_p_value=0.956416	log10_base_likelihood=-17.4017	log10_qual_likelihood_position_model=21.0744	log10_strand_likelihood_position_model=9.15945	new_cov=21/0	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=57/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=78/117
RA	367	.	NC_007779	3223274	0	G	T	bias_e_value=188.497	bias_p_value=4.0569e-05	fisher_strand_p_value=2.95429e-06	frequency=6.490183e-02	genotype_quality=604.2	ks_quality_p_value=1	log10_base_likelihood=-8.79744	log10_qual_likelihood_position_model=13.1292	log10_strand_likelihood_position_model=5.55581	new_cov=0/19	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=92/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/105
RA	368	.	NC_007779	3231302	0	C	G	bias_e_value=61.983	bias_p_value=1.33402e-05	fisher_strand_p_value=9.08671e-07	frequency=5.014610e-02	genotype_quality=717.1	ks_quality_p_value=0.983456	log10_base_likelihood=-7.83268	log10_qual_likelihood_position_model=14.3633	log10_strand_likelihood_position_model=6.04159	new_cov=0/13	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=130/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/74
RA	369	.	NC_007779	3231439	1	.	A	bias_e_value=4618380	bias_p_value=0.993985	fisher_strand_p_value=1	frequency=8.298874e-03	genotype_quality=1187.8	ks_quality_p_value=0.89234	log10_base_likelihood=-8.17415	log10_qual_likelihood_position_model=3.20593	log10_strand_likelihood_position_model=0.30049	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.5401e-06	ref_cov=126/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/114
RA	370	.	NC_007779	3231832	1	.	G	bias_e_value=504014	bias_p_value=0.108476	fisher_strand_p_value=0.0242556	frequency=1.923084e-02	genotype_quality=1008.8	ks_quality_p_value=0.934203	log10_base_likelihood=-18.1449	log10_qual_likelihood_position_model=3.27392	log10_strand_likelihood_position_model=1.61519	new_cov=4/0	polymorphism_quality=12.8	quality=12.8	quality_position_model=2.42251e-15	ref_cov=79/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=83/125
RA	371	.	NC_007779	3238322	0	T	C	bias_e_value=31309.2	bias_p_value=0.00673847	fisher_strand_p_value=0.000835216	frequency=4.364014e-02	genotype_quality=493.9	ks_quality_p_value=0.997195	log10_base_likelihood=-5.83174	log10_qual_likelihood_position_model=9.6199	log10_strand_likelihood_position_model=3.0782	new_cov=8/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=58/89	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=66/89
RA	372	.	NC_007779	3243783	1	.	T	bias_e_value=1867250	bias_p_value=0.401877	fisher_strand_p_value=0.506627	frequency=8.849144e-03	genotype_quality=1071.9	ks_quality_p_value=0.26307	log10_base_likelihood=-8.44828	log10_qual_likelihood_position_model=1.89472	log10_strand_likelihood_position_model=0.495277	new_cov=0/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=5.5497e-08	ref_cov=98/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=98/128
RA	373	.	NC_007779	3259711	0	A	C	bias_e_value=3.41289e-05	bias_p_value=7.34534e-12	fisher_strand_p_value=2.44523e-13	frequency=1.191306e-01	genotype_quality=614.6	ks_quality_p_value=1	log10_base_likelihood=-13.1349	log10_qual_likelihood_position_model=31.319	log10_strand_likelihood_position_model=12.6227	new_cov=2/36	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=118/56	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=120/92
RA	374	.	NC_007779	3272305	0	C	A	bias_e_value=34.0281	bias_p_value=7.32365e-06	fisher_strand_p_value=4.70377e-07	frequency=4.824162e-02	genotype_quality=899.6	ks_quality_p_value=1	log10_base_likelihood=-11.1073	log10_qual_likelihood_position_model=15.9912	log10_strand_likelihood_position_model=6.46606	new_cov=21/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=121/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/136
RA	375	.	NC_007779	3280326	0	A	C	bias_e_value=1.97771e-16	bias_p_value=4.25649e-23	fisher_strand_p_value=7.52748e-25	frequency=1.311197e-01	genotype_quality=741.1	ks_quality_p_value=1	log10_base_likelihood=-21.9386	log10_qual_likelihood_position_model=34.67	log10_strand_likelihood_position_model=24.1234	new_cov=0/52	polymorphism_quality=16.7	quality=16.7	quality_position_model=Inf	ref_cov=154/56	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=154/108
RA	376	.	NC_007779	3285688	1	.	G	bias_e_value=1961060	bias_p_value=0.422067	fisher_strand_p_value=0.208026	frequency=8.546829e-03	genotype_quality=1159.3	ks_quality_p_value=0.68975	log10_base_likelihood=-8.38682	log10_qual_likelihood_position_model=0.959871	log10_strand_likelihood_position_model=0.681882	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.08527e-08	ref_cov=105/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/127
RA	377	.	NC_007779	3300073	0	T	G	bias_e_value=0.000212217	bias_p_value=4.56741e-11	fisher_strand_p_value=1.6227e-12	frequency=1.155572e-01	genotype_quality=577.5	ks_quality_p_value=1	log10_base_likelihood=-17.0114	log10_qual_likelihood_position_model=33.4471	log10_strand_likelihood_position_model=11.8114	new_cov=36/0	polymorphism_quality=11.7	quality=11.7	quality_position_model=Inf	ref_cov=71/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/100
RA	378	.	NC_007779	3333612	0	T	G	bias_e_value=0.0222849	bias_p_value=4.79623e-09	fisher_strand_p_value=2.05811e-10	frequency=4.376602e-02	genotype_quality=634.8	ks_quality_p_value=1	log10_base_likelihood=-10.7898	log10_qual_likelihood_position_model=12.7713	log10_strand_likelihood_position_model=9.68653	new_cov=9/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=9/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=18/150
RA	379	.	NC_007779	3357279	0	C	A	bias_e_value=2.54429	bias_p_value=5.4759e-07	fisher_strand_p_value=3.69284e-08	frequency=5.224895e-02	genotype_quality=671.6	ks_quality_p_value=0.809144	log10_base_likelihood=-5.69535	log10_qual_likelihood_position_model=20.5669	log10_strand_likelihood_position_model=7.43264	new_cov=21/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=83/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/118
RA	380	.	NC_007779	3362866	1	.	A	bias_e_value=4586750	bias_p_value=0.987177	fisher_strand_p_value=1	frequency=7.194519e-03	genotype_quality=1375.0	ks_quality_p_value=0.84419	log10_base_likelihood=-8.37871	log10_qual_likelihood_position_model=1.28122	log10_strand_likelihood_position_model=0.300906	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=9.60419e-09	ref_cov=130/146	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/147
RA	381	.	NC_007779	3385700	1	.	T	bias_e_value=4477260	bias_p_value=0.963612	fisher_strand_p_value=1	frequency=6.968498e-03	genotype_quality=1389.7	ks_quality_p_value=0.742655	log10_base_likelihood=-8.06733	log10_qual_likelihood_position_model=1.10644	log10_strand_likelihood_position_model=0.299941	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.32505e-08	ref_cov=138/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/148
RA	382	.	NC_007779	3389914	0	A	C	bias_e_value=9.01178e-05	bias_p_value=1.93955e-11	fisher_strand_p_value=6.68015e-13	frequency=5.584764e-02	genotype_quality=779.4	ks_quality_p_value=1	log10_base_likelihood=-5.89896	log10_qual_likelihood_position_model=26.7321	log10_strand_likelihood_position_model=12.1752	new_cov=0/32	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=140/84	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/117
RA	383	.	NC_007779	3392918	0	C	A	bias_e_value=4432.91	bias_p_value=0.000954067	fisher_strand_p_value=9.31024e-05	frequency=2.669430e-02	genotype_quality=888.5	ks_quality_p_value=0.996305	log10_base_likelihood=-6.85407	log10_qual_likelihood_position_model=11.5893	log10_strand_likelihood_position_model=4.18178	new_cov=14/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=124/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/130
RA	384	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1133.4	new_cov=133/131	quality=1133.4	ref_cov=0/0	tot_cov=133/132
RA	385	.	NC_007779	3404070	0	T	G	bias_e_value=2.65595e-05	bias_p_value=5.71623e-12	fisher_strand_p_value=1.88662e-13	frequency=7.839108e-02	genotype_quality=659.6	ks_quality_p_value=1	log10_base_likelihood=-9.31909	log10_qual_likelihood_position_model=27.5429	log10_strand_likelihood_position_model=12.7243	new_cov=32/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=65/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=97/121
RA	386	.	NC_007779	3412772	0	A	C	bias_e_value=2.4427e-08	bias_p_value=5.25726e-15	fisher_strand_p_value=1.4018e-16	frequency=5.808449e-02	genotype_quality=681.8	ks_quality_p_value=1	log10_base_likelihood=-6.81122	log10_qual_likelihood_position_model=24.3302	log10_strand_likelihood_position_model=15.8533	new_cov=0/23	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=149/27	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/50
RA	387	.	NC_007779	3421217	0	C	G	bias_e_value=1723.53	bias_p_value=0.000370944	fisher_strand_p_value=3.35027e-05	frequency=2.660751e-02	genotype_quality=939.1	ks_quality_p_value=0.977524	log10_base_likelihood=-7.23157	log10_qual_likelihood_position_model=11.5125	log10_strand_likelihood_position_model=4.47492	new_cov=0/10	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=172/90	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=172/100
RA	388	.	NC_007779	3439587	0	A	C	bias_e_value=2120.02	bias_p_value=0.000456278	fisher_strand_p_value=4.11088e-05	frequency=3.699780e-02	genotype_quality=924.2	ks_quality_p_value=1	log10_base_likelihood=-7.58537	log10_qual_likelihood_position_model=19.7809	log10_strand_likelihood_position_model=4.57171	new_cov=15/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=114/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/124
RA	389	.	NC_007779	3439592	0	G	.	bias_e_value=1061960	bias_p_value=0.228558	fisher_strand_p_value=0.0599229	frequency=2.041340e-02	genotype_quality=938.5	ks_quality_p_value=0.999826	log10_base_likelihood=-11.339	log10_qual_likelihood_position_model=7.04224	log10_strand_likelihood_position_model=1.52344	new_cov=5/0	polymorphism_quality=5.9	quality=5.9	quality_position_model=0.000152863	ref_cov=116/121	reject=POLYMORPHISM_STRAND	tot_cov=123/121
RA	390	.	NC_007779	3439598	1	.	T	bias_e_value=1779200	bias_p_value=0.382927	fisher_strand_p_value=0.125056	frequency=1.809883e-02	genotype_quality=1047.1	ks_quality_p_value=0.991859	log10_base_likelihood=-15.404	log10_qual_likelihood_position_model=5.93629	log10_strand_likelihood_position_model=1.10049	new_cov=4/0	polymorphism_quality=10.1	quality=10.1	quality_position_model=2.33868e-10	ref_cov=114/103	reject=POLYMORPHISM_STRAND	tot_cov=118/103
RA	391	.	NC_007779	3439601	0	G	T	bias_e_value=7364.91	bias_p_value=0.0015851	fisher_strand_p_value=0.000163052	frequency=5.340385e-02	genotype_quality=872.8	ks_quality_p_value=1	log10_base_likelihood=-11.7938	log10_qual_likelihood_position_model=16.3435	log10_strand_likelihood_position_model=3.81267	new_cov=14/0	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=113/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/105
RA	392	.	NC_007779	3439607	0	G	T	bias_e_value=546922	bias_p_value=0.117711	fisher_strand_p_value=0.0251325	frequency=3.131104e-02	genotype_quality=886.5	ks_quality_p_value=1	log10_base_likelihood=-5.75462	log10_qual_likelihood_position_model=12.2331	log10_strand_likelihood_position_model=1.90499	new_cov=10/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=117/100	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=127/101
RA	393	.	NC_007779	3440270	0	C	A	bias_e_value=0.367589	bias_p_value=7.91137e-08	fisher_strand_p_value=3.88455e-09	frequency=5.576420e-02	genotype_quality=875.5	ks_quality_p_value=1	log10_base_likelihood=-11.9529	log10_qual_likelihood_position_model=18.1729	log10_strand_likelihood_position_model=8.62997	new_cov=27/0	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=116/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/141
RA	394	.	NC_007779	3475527	0	T	G	bias_e_value=6.70831e-07	bias_p_value=1.44379e-13	fisher_strand_p_value=4.23454e-15	frequency=8.032036e-02	genotype_quality=883.7	ks_quality_p_value=1	log10_base_likelihood=-14.1304	log10_qual_likelihood_position_model=30.481	log10_strand_likelihood_position_model=14.3732	new_cov=36/0	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=89/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/161
RA	395	.	NC_007779	3475533	0	C	T	bias_e_value=0.00373294	bias_p_value=8.03417e-10	fisher_strand_p_value=3.19225e-11	frequency=8.430386e-02	genotype_quality=926.0	ks_quality_p_value=1	log10_base_likelihood=-21.699	log10_qual_likelihood_position_model=34.8534	log10_strand_likelihood_position_model=10.4959	new_cov=28/0	polymorphism_quality=16.4	quality=16.4	quality_position_model=Inf	ref_cov=107/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=135/166
RA	396	.	NC_007779	3499066	0	A	C	bias_e_value=0.00922713	bias_p_value=1.98589e-09	fisher_strand_p_value=8.19786e-11	frequency=6.820345e-02	genotype_quality=743.2	ks_quality_p_value=1	log10_base_likelihood=-10.417	log10_qual_likelihood_position_model=22.9641	log10_strand_likelihood_position_model=10.0863	new_cov=0/18	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=148/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/65
RA	397	.	NC_007779	3523734	0	G	T	bias_e_value=0.00175508	bias_p_value=3.77735e-10	fisher_strand_p_value=1.45545e-11	frequency=7.194233e-02	genotype_quality=950.9	ks_quality_p_value=1	log10_base_likelihood=-16.212	log10_qual_likelihood_position_model=29.5513	log10_strand_likelihood_position_model=10.837	new_cov=0/33	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=152/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/153
RA	398	.	NC_007779	3543547	0	A	C	bias_e_value=4.25494e-15	bias_p_value=9.15763e-22	fisher_strand_p_value=1.71425e-23	frequency=1.481991e-01	genotype_quality=777.6	ks_quality_p_value=1	log10_base_likelihood=-23.0532	log10_qual_likelihood_position_model=54.1986	log10_strand_likelihood_position_model=22.7659	new_cov=0/59	polymorphism_quality=17.8	quality=17.8	quality_position_model=Inf	ref_cov=146/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/135
RA	399	.	NC_007779	3550877	0	C	A	bias_e_value=10.4601	bias_p_value=2.25126e-06	fisher_strand_p_value=1.33789e-07	frequency=3.854656e-02	genotype_quality=986.0	ks_quality_p_value=1	log10_base_likelihood=-8.3202	log10_qual_likelihood_position_model=15.3177	log10_strand_likelihood_position_model=6.87358	new_cov=20/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=119/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/156
RA	400	.	NC_007779	3560478	0	G	T	bias_e_value=1546.98	bias_p_value=0.000332946	fisher_strand_p_value=2.90907e-05	frequency=3.121185e-02	genotype_quality=1073.6	ks_quality_p_value=1	log10_base_likelihood=-7.66424	log10_qual_likelihood_position_model=15.0372	log10_strand_likelihood_position_model=4.60233	new_cov=0/18	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=139/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/182
RA	401	.	NC_007779	3561761	0	T	.	bias_e_value=4621220	bias_p_value=0.994596	fisher_strand_p_value=1	frequency=9.957314e-03	genotype_quality=1193.8	ks_quality_p_value=0.897857	log10_base_likelihood=-7.82043	log10_qual_likelihood_position_model=2.12688	log10_strand_likelihood_position_model=0.391464	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=3.36932e-07	ref_cov=161/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=164/137
RA	402	.	NC_007779	3566055	0	C	A	bias_e_value=104576	bias_p_value=0.0225073	fisher_strand_p_value=0.00343725	frequency=2.340889e-02	genotype_quality=1074.7	ks_quality_p_value=0.978001	log10_base_likelihood=-5.93852	log10_qual_likelihood_position_model=11.2292	log10_strand_likelihood_position_model=2.75113	new_cov=9/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=136/144	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=145/145
RA	403	.	NC_007779	3576400	1	.	A	bias_e_value=4245610	bias_p_value=0.913755	fisher_strand_p_value=0.626401	frequency=1.142788e-02	genotype_quality=1690.2	ks_quality_p_value=0.981089	log10_base_likelihood=-16.5188	log10_qual_likelihood_position_model=3.04201	log10_strand_likelihood_position_model=0.546028	new_cov=1/3	polymorphism_quality=11.2	quality=11.2	quality_position_model=5.18228e-15	ref_cov=162/184	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=163/187
RA	404	.	NC_007779	3576401	0	A	.	bias_e_value=826527	bias_p_value=0.177888	fisher_strand_p_value=0.0456751	frequency=1.132298e-02	genotype_quality=1431.6	ks_quality_p_value=0.938554	log10_base_likelihood=-10.888	log10_qual_likelihood_position_model=3.67839	log10_strand_likelihood_position_model=1.34032	new_cov=4/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=8.70404e-08	ref_cov=160/189	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=164/189
RA	405	.	NC_007779	3580297	0	G	T	bias_e_value=9.35682	bias_p_value=2.01381e-06	fisher_strand_p_value=1.1884e-07	frequency=3.993702e-02	genotype_quality=1088.4	ks_quality_p_value=1	log10_base_likelihood=-9.17375	log10_qual_likelihood_position_model=16.2036	log10_strand_likelihood_position_model=7.05601	new_cov=0/23	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=162/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/170
RA	406	.	NC_007779	3586831	1	.	T	bias_e_value=4186160	bias_p_value=0.90096	fisher_strand_p_value=1	frequency=8.955002e-03	genotype_quality=1657.1	ks_quality_p_value=0.58935	log10_base_likelihood=-12.4338	log10_qual_likelihood_position_model=2.28399	log10_strand_likelihood_position_model=0.42081	new_cov=1/2	polymorphism_quality=7.0	quality=7.0	quality_position_model=9.45938e-12	ref_cov=165/167	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/169
RA	407	.	NC_007779	3609441	0	T	G	bias_e_value=2.35745e-09	bias_p_value=5.07378e-16	fisher_strand_p_value=1.27151e-17	frequency=6.162691e-02	genotype_quality=805.3	ks_quality_p_value=1	log10_base_likelihood=-8.93548	log10_qual_likelihood_position_model=30.1227	log10_strand_likelihood_position_model=16.8957	new_cov=32/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=53/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/163
RA	408	.	NC_007779	3653996	1	.	G	bias_e_value=1871030	bias_p_value=0.402691	fisher_strand_p_value=0.5531	frequency=1.239681e-02	genotype_quality=1173.7	ks_quality_p_value=0.241697	log10_base_likelihood=-12.9766	log10_qual_likelihood_position_model=2.74217	log10_strand_likelihood_position_model=0.55009	new_cov=3/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=1.0507e-11	ref_cov=156/83	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/83
RA	409	.	NC_007779	3686204	1	.	A	bias_e_value=4500590	bias_p_value=0.968634	fisher_strand_p_value=1	frequency=1.034451e-02	genotype_quality=1413.7	ks_quality_p_value=0.760226	log10_base_likelihood=-13.0075	log10_qual_likelihood_position_model=2.76821	log10_strand_likelihood_position_model=0.371181	new_cov=2/1	polymorphism_quality=7.6	quality=7.6	quality_position_model=6.82022e-12	ref_cov=166/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=168/122
RA	410	.	NC_007779	3686205	0	A	.	bias_e_value=3814540	bias_p_value=0.820979	fisher_strand_p_value=0.644818	frequency=1.355076e-02	genotype_quality=1176.8	ks_quality_p_value=0.720973	log10_base_likelihood=-11.1579	log10_qual_likelihood_position_model=2.30837	log10_strand_likelihood_position_model=0.475429	new_cov=3/1	polymorphism_quality=5.7	quality=5.7	quality_position_model=2.30103e-10	ref_cov=170/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=173/122
RA	411	.	NC_007779	3688850	0	A	C	bias_e_value=4.63977e-05	bias_p_value=9.98587e-12	fisher_strand_p_value=3.35979e-13	frequency=1.000328e-01	genotype_quality=630.5	ks_quality_p_value=1	log10_base_likelihood=-6.3802	log10_qual_likelihood_position_model=24.402	log10_strand_likelihood_position_model=12.4737	new_cov=0/29	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=119/56	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/85
RA	412	.	NC_007779	3688858	0	A	C	bias_e_value=8.83033e-16	bias_p_value=1.9005e-22	fisher_strand_p_value=3.45403e-24	frequency=1.803832e-01	genotype_quality=591.0	ks_quality_p_value=1	log10_base_likelihood=-27.9831	log10_qual_likelihood_position_model=38.6621	log10_strand_likelihood_position_model=23.4617	new_cov=0/51	polymorphism_quality=22.8	quality=22.8	quality_position_model=Inf	ref_cov=122/41	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/92
RA	413	.	NC_007779	3689827	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	414	.	NC_007779	3689828	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	415	.	NC_007779	3728146	1	.	T	bias_e_value=1602830	bias_p_value=0.344966	fisher_strand_p_value=0.10691	frequency=1.265812e-02	genotype_quality=766.9	ks_quality_p_value=0.995951	log10_base_likelihood=-8.40567	log10_qual_likelihood_position_model=1.81477	log10_strand_likelihood_position_model=0.970983	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.57731e-07	ref_cov=50/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=52/106
RA	416	.	NC_007779	3728155	0	T	C	bias_e_value=0.00915668	bias_p_value=1.97073e-09	fisher_strand_p_value=8.21464e-11	frequency=6.362200e-02	genotype_quality=449.7	ks_quality_p_value=0.990012	log10_base_likelihood=-9.79404	log10_qual_likelihood_position_model=11.7442	log10_strand_likelihood_position_model=10.0854	new_cov=10/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=8/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=18/121
RA	417	.	NC_007779	3728157	0	A	C	bias_e_value=2676.51	bias_p_value=0.000576048	fisher_strand_p_value=5.31271e-05	frequency=7.593870e-02	genotype_quality=403.7	ks_quality_p_value=1	log10_base_likelihood=-10.2737	log10_qual_likelihood_position_model=16.0124	log10_strand_likelihood_position_model=4.30293	new_cov=8/6	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=11/113	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=19/120
RA	418	.	NC_007779	3729313	0	G	T	bias_e_value=0.0669396	bias_p_value=1.4407e-08	fisher_strand_p_value=9.17742e-10	frequency=4.366875e-02	genotype_quality=1110.9	ks_quality_p_value=0.708613	log10_base_likelihood=-6.96301	log10_qual_likelihood_position_model=30.0457	log10_strand_likelihood_position_model=9.03728	new_cov=0/26	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=183/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=183/162
RA	419	.	NC_007779	3731041	1	.	T	bias_e_value=2954660	bias_p_value=0.635913	fisher_strand_p_value=0.371403	frequency=1.879501e-02	genotype_quality=1272.5	ks_quality_p_value=0.752803	log10_base_likelihood=-20.5048	log10_qual_likelihood_position_model=4.50563	log10_strand_likelihood_position_model=0.770731	new_cov=1/4	polymorphism_quality=15.2	quality=15.2	quality_position_model=2.41183e-17	ref_cov=128/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/137
RA	420	.	NC_007779	3732310	0	G	T	bias_e_value=4.48806e-08	bias_p_value=9.65937e-15	fisher_strand_p_value=2.62224e-16	frequency=1.008959e-01	genotype_quality=903.9	ks_quality_p_value=0.998858	log10_base_likelihood=-23.7762	log10_qual_likelihood_position_model=26.785	log10_strand_likelihood_position_model=15.5813	new_cov=0/42	polymorphism_quality=18.5	quality=18.5	quality_position_model=Inf	ref_cov=156/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/137
RA	421	.	NC_007779	3734364	1	.	A	bias_e_value=459167	bias_p_value=0.0988235	fisher_strand_p_value=0.251566	frequency=1.075268e-02	genotype_quality=1372.6	ks_quality_p_value=0.0800948	log10_base_likelihood=-12.5334	log10_qual_likelihood_position_model=3.6297	log10_strand_likelihood_position_model=0.81259	new_cov=0/3	polymorphism_quality=7.1	quality=7.1	quality_position_model=4.4877e-10	ref_cov=129/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/150
RA	422	.	NC_007779	3734365	0	A	.	bias_e_value=2139070	bias_p_value=0.460378	fisher_strand_p_value=0.33652	frequency=1.412773e-02	genotype_quality=1137.1	ks_quality_p_value=0.48715	log10_base_likelihood=-11.4986	log10_qual_likelihood_position_model=3.19863	log10_strand_likelihood_position_model=0.679405	new_cov=3/1	polymorphism_quality=6.1	quality=6.1	quality_position_model=1.36441e-09	ref_cov=127/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/153
RA	423	.	NC_007779	3750122	0	C	.	bias_e_value=803818	bias_p_value=0.173001	fisher_strand_p_value=1	frequency=9.616823e-01	genotype_quality=1330.5	ks_quality_p_value=0.0413257	log10_base_likelihood=-49.5248	log10_qual_likelihood_position_model=5.88354	log10_strand_likelihood_position_model=0.577959	new_cov=124/152	polymorphism_quality=44.4	quality=44.4	quality_position_model=2.11632e-45	ref_cov=4/5	tot_cov=129/158
RA	424	.	NC_007779	3750123	0	C	T	bias_e_value=4444780	bias_p_value=0.956621	fisher_strand_p_value=1	frequency=3.169537e-02	genotype_quality=1119.9	ks_quality_p_value=0.720298	log10_base_likelihood=-18.5919	log10_qual_likelihood_position_model=7.55699	log10_strand_likelihood_position_model=0.578166	new_cov=4/5	polymorphism_quality=13.3	quality=13.3	quality_position_model=1.71028e-12	ref_cov=125/152	tot_cov=129/158
RA	425	.	NC_007779	3763528	0	A	C	bias_e_value=0.12025	bias_p_value=2.58807e-08	fisher_strand_p_value=1.20154e-09	frequency=4.809523e-02	genotype_quality=504.8	ks_quality_p_value=1	log10_base_likelihood=-8.70125	log10_qual_likelihood_position_model=10.8415	log10_strand_likelihood_position_model=8.92026	new_cov=0/8	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=123/6	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/14
RA	426	.	NC_007779	3788380	0	G	T	bias_e_value=7.63341	bias_p_value=1.64289e-06	fisher_strand_p_value=9.57298e-08	frequency=5.931616e-02	genotype_quality=922.2	ks_quality_p_value=1	log10_base_likelihood=-10.93	log10_qual_likelihood_position_model=18.2703	log10_strand_likelihood_position_model=7.28812	new_cov=0/27	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=129/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/164
RA	427	.	NC_007779	3813810	0	T	G	bias_e_value=4.05819e-06	bias_p_value=8.73419e-13	fisher_strand_p_value=2.70915e-14	frequency=8.699656e-02	genotype_quality=606.1	ks_quality_p_value=1	log10_base_likelihood=-6.12361	log10_qual_likelihood_position_model=24.0089	log10_strand_likelihood_position_model=13.5672	new_cov=35/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=62/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=97/114
RA	428	.	NC_007779	3824606	1	.	T	bias_e_value=792630	bias_p_value=0.170593	fisher_strand_p_value=1	frequency=1.476002e-02	genotype_quality=1288.0	ks_quality_p_value=0.0405722	log10_base_likelihood=-17.2048	log10_qual_likelihood_position_model=3.46418	log10_strand_likelihood_position_model=0.429072	new_cov=2/2	polymorphism_quality=11.9	quality=11.9	quality_position_model=2.12628e-15	ref_cov=122/145	reject=INDEL_HOMOPOLYMER	tot_cov=124/147
RA	429	.	NC_007779	3828029	0	G	T	bias_e_value=476.718	bias_p_value=0.000102601	fisher_strand_p_value=9.10446e-06	frequency=5.242872e-02	genotype_quality=941.7	ks_quality_p_value=0.885359	log10_base_likelihood=-16.73	log10_qual_likelihood_position_model=21.7013	log10_strand_likelihood_position_model=5.28861	new_cov=17/0	polymorphism_quality=11.4	quality=11.4	quality_position_model=Inf	ref_cov=122/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/137
RA	430	.	NC_007779	3845596	0	G	T	bias_e_value=0.00527549	bias_p_value=1.13541e-09	fisher_strand_p_value=4.57689e-11	frequency=5.110550e-02	genotype_quality=940.6	ks_quality_p_value=1	log10_base_likelihood=-6.40205	log10_qual_likelihood_position_model=24.1443	log10_strand_likelihood_position_model=10.3394	new_cov=0/31	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=152/116	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/149
RA	431	.	NC_007779	3859254	1	.	T	bias_e_value=758464	bias_p_value=0.163239	fisher_strand_p_value=0.0414047	frequency=1.415062e-02	genotype_quality=1025.7	ks_quality_p_value=0.924965	log10_base_likelihood=-13.145	log10_qual_likelihood_position_model=1.74992	log10_strand_likelihood_position_model=1.38295	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=4.86135e-12	ref_cov=71/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=74/138
RA	432	.	NC_007779	3859263	0	T	C	bias_e_value=0.00871339	bias_p_value=1.87533e-09	fisher_strand_p_value=7.72238e-11	frequency=6.244087e-02	genotype_quality=562.0	ks_quality_p_value=1	log10_base_likelihood=-10.648	log10_qual_likelihood_position_model=15.9603	log10_strand_likelihood_position_model=10.1122	new_cov=14/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=26/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=40/142
RA	433	.	NC_007779	3859270	0	G	C	bias_e_value=215.968	bias_p_value=4.64815e-05	fisher_strand_p_value=3.42141e-06	frequency=3.804970e-02	genotype_quality=715.4	ks_quality_p_value=1	log10_base_likelihood=-10.7189	log10_qual_likelihood_position_model=9.75618	log10_strand_likelihood_position_model=5.46579	new_cov=8/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=33/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=41/143
RA	434	.	NC_007779	3873375	0	T	.	bias_e_value=771867	bias_p_value=0.166124	fisher_strand_p_value=0.595518	frequency=1.208782e-02	genotype_quality=991.8	ks_quality_p_value=0.0658002	log10_base_likelihood=-8.11108	log10_qual_likelihood_position_model=1.82204	log10_strand_likelihood_position_model=0.463874	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.66893e-08	ref_cov=112/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/134
RA	435	.	NC_007779	3891907	0	T	.	bias_e_value=3606040	bias_p_value=0.776106	fisher_strand_p_value=0.636447	frequency=1.686859e-02	genotype_quality=927.8	ks_quality_p_value=0.645172	log10_base_likelihood=-11.3494	log10_qual_likelihood_position_model=2.24769	log10_strand_likelihood_position_model=0.495994	new_cov=3/1	polymorphism_quality=5.9	quality=5.9	quality_position_model=1.33246e-10	ref_cov=132/101	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/102
RA	436	.	NC_007779	3893880	0	G	T	bias_e_value=356.555	bias_p_value=7.6739e-05	fisher_strand_p_value=5.88337e-06	frequency=3.941917e-02	genotype_quality=839.9	ks_quality_p_value=1	log10_base_likelihood=-9.87582	log10_qual_likelihood_position_model=14.8789	log10_strand_likelihood_position_model=5.23037	new_cov=0/15	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=144/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/124
RA	437	.	NC_007779	3895373	0	T	G	bias_e_value=0.0591296	bias_p_value=1.27261e-08	fisher_strand_p_value=5.711e-10	frequency=6.231737e-02	genotype_quality=588.0	ks_quality_p_value=1	log10_base_likelihood=-7.4543	log10_qual_likelihood_position_model=23.7213	log10_strand_likelihood_position_model=9.24329	new_cov=21/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=60/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=82/124
RA	438	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1199.3	new_cov=157/124	quality=1199.3	ref_cov=0/0	tot_cov=157/124
RA	439	.	NC_007779	3900676	1	.	G	bias_e_value=2108490	bias_p_value=0.453796	fisher_strand_p_value=0.197319	frequency=8.402824e-03	genotype_quality=1182.2	ks_quality_p_value=0.812481	log10_base_likelihood=-8.43191	log10_qual_likelihood_position_model=1.35968	log10_strand_likelihood_position_model=0.70483	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.66075e-08	ref_cov=104/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/132
RA	440	.	NC_007779	3900680	0	T	G	bias_e_value=1.18853e-14	bias_p_value=2.55799e-21	fisher_strand_p_value=4.88414e-23	frequency=1.251502e-01	genotype_quality=581.0	ks_quality_p_value=1	log10_base_likelihood=-26.2843	log10_qual_likelihood_position_model=28.129	log10_strand_likelihood_position_model=22.3112	new_cov=24/0	polymorphism_quality=21.1	quality=21.1	quality_position_model=Inf	ref_cov=7/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=31/135
RA	441	.	NC_007779	3901914	0	A	G	bias_e_value=958180	bias_p_value=0.206223	fisher_strand_p_value=0.256482	frequency=1.061821e-02	genotype_quality=1104.4	ks_quality_p_value=0.203382	log10_base_likelihood=-5.68461	log10_qual_likelihood_position_model=2.96365	log10_strand_likelihood_position_model=0.770492	new_cov=3/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=0.00118558	ref_cov=153/125	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=156/125
RA	442	.	NC_007779	3910746	0	C	A	bias_e_value=0.000421759	bias_p_value=9.07724e-11	fisher_strand_p_value=3.3087e-12	frequency=6.640768e-02	genotype_quality=933.6	ks_quality_p_value=1	log10_base_likelihood=-14.4071	log10_qual_likelihood_position_model=23.945	log10_strand_likelihood_position_model=11.4803	new_cov=33/0	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=113/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/160
RA	443	.	NC_007779	3912296	1	.	G	bias_e_value=3388160	bias_p_value=0.729212	fisher_strand_p_value=1	frequency=8.810997e-03	genotype_quality=1089.0	ks_quality_p_value=0.36139	log10_base_likelihood=-8.6086	log10_qual_likelihood_position_model=1.75493	log10_strand_likelihood_position_model=0.323457	new_cov=1/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=1.80726e-08	ref_cov=139/86	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/87
RA	444	.	NC_007779	3912297	0	G	.	bias_e_value=4140950	bias_p_value=0.89123	fisher_strand_p_value=1	frequency=1.281261e-02	genotype_quality=968.0	ks_quality_p_value=0.571465	log10_base_likelihood=-8.39903	log10_qual_likelihood_position_model=2.14044	log10_strand_likelihood_position_model=0.361108	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=8.13866e-08	ref_cov=139/92	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/93
RA	445	.	NC_007779	3921345	0	T	.	bias_e_value=596582	bias_p_value=0.128398	fisher_strand_p_value=0.116131	frequency=1.033783e-02	genotype_quality=1165.4	ks_quality_p_value=0.241789	log10_base_likelihood=-8.23531	log10_qual_likelihood_position_model=1.55147	log10_strand_likelihood_position_model=0.935053	new_cov=0/3	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.15997e-07	ref_cov=148/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/142
RA	446	.	NC_007779	3930443	0	T	G	bias_e_value=1.68178e-11	bias_p_value=3.61959e-18	fisher_strand_p_value=8.04959e-20	frequency=1.169548e-01	genotype_quality=636.2	ks_quality_p_value=1	log10_base_likelihood=-16.0765	log10_qual_likelihood_position_model=31.63	log10_strand_likelihood_position_model=19.0942	new_cov=38/0	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=41/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/129
RA	447	.	NC_007779	3933153	0	G	T	bias_e_value=1013.21	bias_p_value=0.000218067	fisher_strand_p_value=1.83243e-05	frequency=3.750038e-02	genotype_quality=781.3	ks_quality_p_value=0.999373	log10_base_likelihood=-6.36074	log10_qual_likelihood_position_model=14.3179	log10_strand_likelihood_position_model=4.9292	new_cov=0/16	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=115/103	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/119
RA	448	.	NC_007779	3952095	1	.	G	bias_e_value=900491	bias_p_value=0.193807	fisher_strand_p_value=0.0480769	frequency=1.428509e-02	genotype_quality=1026.3	ks_quality_p_value=0.998759	log10_base_likelihood=-12.1804	log10_qual_likelihood_position_model=2.3707	log10_strand_likelihood_position_model=1.31806	new_cov=3/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=1.74381e-10	ref_cov=74/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=77/133
RA	449	.	NC_007779	3981333	0	A	.	bias_e_value=473184	bias_p_value=0.10184	fisher_strand_p_value=0.0921025	frequency=1.204109e-02	genotype_quality=1004.8	ks_quality_p_value=0.227199	log10_base_likelihood=-8.35047	log10_qual_likelihood_position_model=2.62358	log10_strand_likelihood_position_model=1.03573	new_cov=3/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.45587e-06	ref_cov=110/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/136
RA	450	.	NC_007779	3982533	1	.	A	bias_e_value=4638360	bias_p_value=0.998284	fisher_strand_p_value=1	frequency=7.379532e-03	genotype_quality=1354.2	ks_quality_p_value=0.941996	log10_base_likelihood=-8.20003	log10_qual_likelihood_position_model=1.17663	log10_strand_likelihood_position_model=0.299714	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.14174e-08	ref_cov=131/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/139
RA	451	.	NC_007779	3986829	1	.	T	bias_e_value=2665630	bias_p_value=0.573706	fisher_strand_p_value=1	frequency=8.888245e-03	genotype_quality=1114.0	ks_quality_p_value=0.233888	log10_base_likelihood=-8.06918	log10_qual_likelihood_position_model=1.48759	log10_strand_likelihood_position_model=0.307419	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.32077e-08	ref_cov=127/96	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/97
RA	452	.	NC_007779	3986830	0	T	.	bias_e_value=540307	bias_p_value=0.116287	fisher_strand_p_value=0.0705842	frequency=2.192211e-02	genotype_quality=915.3	ks_quality_p_value=0.3506	log10_base_likelihood=-15.1909	log10_qual_likelihood_position_model=2.69322	log10_strand_likelihood_position_model=1.25162	new_cov=5/0	polymorphism_quality=9.8	quality=9.8	quality_position_model=2.68239e-13	ref_cov=124/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/99
RA	453	.	NC_007779	4015577	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	454	.	NC_007779	4015578	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	455	.	NC_007779	4015579	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	456	.	NC_007779	4015580	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	457	.	NC_007779	4015581	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	458	.	NC_007779	4015584	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	459	.	NC_007779	4015585	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	460	.	NC_007779	4015586	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	461	.	NC_007779	4015587	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	462	.	NC_007779	4023068	0	T	G	bias_e_value=0.00716397	bias_p_value=1.54186e-09	fisher_strand_p_value=6.29625e-11	frequency=7.719707e-02	genotype_quality=533.0	ks_quality_p_value=1	log10_base_likelihood=-12.3198	log10_qual_likelihood_position_model=16.1863	log10_strand_likelihood_position_model=10.2009	new_cov=15/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=23/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=38/116
RA	463	.	NC_007779	4029633	0	T	G	bias_e_value=2.91939e-08	bias_p_value=6.2832e-15	fisher_strand_p_value=1.68358e-16	frequency=1.249270e-01	genotype_quality=564.3	ks_quality_p_value=1	log10_base_likelihood=-20.6353	log10_qual_likelihood_position_model=28.0791	log10_strand_likelihood_position_model=15.7738	new_cov=29/0	polymorphism_quality=15.4	quality=15.4	quality_position_model=Inf	ref_cov=32/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/115
RA	464	.	NC_007779	4031691	1	.	T	bias_e_value=24646.3	bias_p_value=0.00530447	fisher_strand_p_value=0.00190047	frequency=2.824879e-02	genotype_quality=817.9	ks_quality_p_value=0.333747	log10_base_likelihood=-23.2376	log10_qual_likelihood_position_model=3.76326	log10_strand_likelihood_position_model=2.72114	new_cov=5/0	polymorphism_quality=18.0	quality=18.0	quality_position_model=6.87694e-19	ref_cov=47/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=52/125
RA	465	.	NC_007779	4043703	0	C	A	bias_e_value=2.11053	bias_p_value=4.54235e-07	fisher_strand_p_value=2.45219e-08	frequency=4.169369e-02	genotype_quality=858.2	ks_quality_p_value=1	log10_base_likelihood=-10.0255	log10_qual_likelihood_position_model=14.3404	log10_strand_likelihood_position_model=7.61045	new_cov=21/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=102/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/148
RA	466	.	NC_007779	4055100	0	G	T	bias_e_value=117.203	bias_p_value=2.52249e-05	fisher_strand_p_value=1.79515e-06	frequency=4.246712e-02	genotype_quality=803.1	ks_quality_p_value=0.986495	log10_base_likelihood=-6.71276	log10_qual_likelihood_position_model=20.714	log10_strand_likelihood_position_model=5.7459	new_cov=14/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=81/139	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/140
RA	467	.	NC_007779	4055329	0	T	G	bias_e_value=1.28049e-08	bias_p_value=2.75592e-15	fisher_strand_p_value=7.2207e-17	frequency=8.835411e-02	genotype_quality=600.3	ks_quality_p_value=1	log10_base_likelihood=-14.286	log10_qual_likelihood_position_model=21.3208	log10_strand_likelihood_position_model=16.1414	new_cov=24/0	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=25/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/136
RA	468	.	NC_007779	4062114	0	T	G	bias_e_value=4.53445e-08	bias_p_value=9.7592e-15	fisher_strand_p_value=2.64707e-16	frequency=8.919573e-02	genotype_quality=661.4	ks_quality_p_value=1	log10_base_likelihood=-14.1174	log10_qual_likelihood_position_model=25.985	log10_strand_likelihood_position_model=15.5772	new_cov=26/0	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=35/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/142
RA	469	.	NC_007779	4064463	0	G	T	bias_e_value=0.471798	bias_p_value=1.01542e-07	fisher_strand_p_value=5.05092e-09	frequency=8.522701e-02	genotype_quality=664.1	ks_quality_p_value=1	log10_base_likelihood=-11.6025	log10_qual_likelihood_position_model=17.8706	log10_strand_likelihood_position_model=8.32289	new_cov=0/27	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=106/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/116
RA	470	.	NC_007779	4084209	0	A	G	bias_e_value=2.66076	bias_p_value=5.72658e-07	fisher_strand_p_value=3.13292e-08	frequency=5.029249e-02	genotype_quality=793.1	ks_quality_p_value=1	log10_base_likelihood=-6.00104	log10_qual_likelihood_position_model=15.0182	log10_strand_likelihood_position_model=7.50405	new_cov=19/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=88/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=107/145
RA	471	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1109.0	new_cov=132/146	quality=1109.0	ref_cov=0/0	tot_cov=132/146
RA	472	.	NC_007779	4098730	0	G	T	bias_e_value=0.305417	bias_p_value=6.5733e-08	fisher_strand_p_value=3.19696e-09	frequency=5.976009e-02	genotype_quality=758.4	ks_quality_p_value=1	log10_base_likelihood=-12.199	log10_qual_likelihood_position_model=15.9228	log10_strand_likelihood_position_model=8.49526	new_cov=0/23	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=135/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/114
RA	473	.	NC_007779	4115400	1	.	C	bias_e_value=791546	bias_p_value=0.170359	fisher_strand_p_value=0.0404994	frequency=1.506424e-02	genotype_quality=934.1	ks_quality_p_value=1	log10_base_likelihood=-9.5895	log10_qual_likelihood_position_model=4.52077	log10_strand_likelihood_position_model=1.39255	new_cov=0/3	polymorphism_quality=4.1	quality=4.1	quality_position_model=1.68489e-05	ref_cov=130/66	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/69
RA	474	.	NC_007779	4124974	0	G	T	bias_e_value=5.95847e-05	bias_p_value=1.2824e-11	fisher_strand_p_value=4.35261e-13	frequency=9.956551e-02	genotype_quality=795.6	ks_quality_p_value=1	log10_base_likelihood=-18.7814	log10_qual_likelihood_position_model=20.2502	log10_strand_likelihood_position_model=12.3612	new_cov=0/34	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=136/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/121
RA	475	.	NC_007779	4131508	0	T	A	bias_e_value=195877	bias_p_value=0.0421573	fisher_strand_p_value=0.00708564	frequency=2.470303e-02	genotype_quality=1087.6	ks_quality_p_value=1	log10_base_likelihood=-11.59	log10_qual_likelihood_position_model=9.17821	log10_strand_likelihood_position_model=2.41476	new_cov=0/8	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=141/136	reject=POLYMORPHISM_STRAND	tot_cov=141/144
RA	476	.	NC_007779	4131519	0	T	G	bias_e_value=351851	bias_p_value=0.0757267	fisher_strand_p_value=0.0144621	frequency=1.606464e-02	genotype_quality=1025.4	ks_quality_p_value=1	log10_base_likelihood=-6.26467	log10_qual_likelihood_position_model=8.17329	log10_strand_likelihood_position_model=2.1187	new_cov=0/7	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=136/131	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=136/138
RA	477	.	NC_007779	4131522	0	C	T	bias_e_value=353513	bias_p_value=0.0760843	fisher_strand_p_value=0.0145491	frequency=2.174759e-02	genotype_quality=1104.2	ks_quality_p_value=0.999822	log10_base_likelihood=-8.16523	log10_qual_likelihood_position_model=8.18432	log10_strand_likelihood_position_model=2.09664	new_cov=0/7	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=140/137	reject=POLYMORPHISM_STRAND	tot_cov=140/144
RA	478	.	NC_007779	4148399	0	A	C	bias_e_value=3.47059e-10	bias_p_value=7.46954e-17	fisher_strand_p_value=1.78408e-18	frequency=9.290981e-02	genotype_quality=772.0	ks_quality_p_value=1	log10_base_likelihood=-11.4101	log10_qual_likelihood_position_model=32.1289	log10_strand_likelihood_position_model=17.7486	new_cov=0/39	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=148/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/100
RA	479	.	NC_007779	4152489	0	G	T	bias_e_value=4.77428	bias_p_value=1.02754e-06	fisher_strand_p_value=5.81857e-08	frequency=4.223156e-02	genotype_quality=1042.9	ks_quality_p_value=1	log10_base_likelihood=-9.18795	log10_qual_likelihood_position_model=16.4436	log10_strand_likelihood_position_model=7.23518	new_cov=0/22	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=160/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/152
RA	480	.	NC_007779	4157323	0	C	A	bias_e_value=0.00436937	bias_p_value=9.4039e-10	fisher_strand_p_value=3.99469e-11	frequency=5.587530e-02	genotype_quality=891.5	ks_quality_p_value=0.941499	log10_base_likelihood=-7.96426	log10_qual_likelihood_position_model=28.2126	log10_strand_likelihood_position_model=10.3985	new_cov=25/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=87/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/160
RA	481	.	NC_007779	4158580	1	.	A	bias_e_value=2664330	bias_p_value=0.573428	fisher_strand_p_value=0.233714	frequency=8.809090e-03	genotype_quality=1126.4	ks_quality_p_value=0.999922	log10_base_likelihood=-6.90135	log10_qual_likelihood_position_model=4.4091	log10_strand_likelihood_position_model=0.631315	new_cov=0/2	polymorphism_quality=1.4	quality=1.4	quality_position_model=0.00148681	ref_cov=117/108	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=117/110
RA	482	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1142.9	new_cov=133/136	quality=1142.9	ref_cov=0/0	tot_cov=133/136
RA	483	.	NC_007779	4174730	0	T	.	bias_e_value=2255110	bias_p_value=0.485353	fisher_strand_p_value=1	frequency=1.309204e-02	genotype_quality=910.3	ks_quality_p_value=0.178075	log10_base_likelihood=-8.33132	log10_qual_likelihood_position_model=2.64592	log10_strand_likelihood_position_model=0.411284	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.60229e-07	ref_cov=110/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/118
RA	484	.	NC_007779	4197139	0	T	G	bias_e_value=2.12146e-08	bias_p_value=4.56588e-15	fisher_strand_p_value=1.21277e-16	frequency=9.433317e-02	genotype_quality=659.8	ks_quality_p_value=1	log10_base_likelihood=-18.0093	log10_qual_likelihood_position_model=23.6693	log10_strand_likelihood_position_model=15.9162	new_cov=21/0	polymorphism_quality=12.7	quality=12.7	quality_position_model=Inf	ref_cov=21/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=42/148
RA	485	.	NC_007779	4207565	0	C	A	bias_e_value=0.681057	bias_p_value=1.4658e-07	fisher_strand_p_value=7.4341e-09	frequency=6.666613e-02	genotype_quality=796.5	ks_quality_p_value=1	log10_base_likelihood=-11.1359	log10_qual_likelihood_position_model=22.2101	log10_strand_likelihood_position_model=8.34263	new_cov=26/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=103/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/127
RA	486	.	NC_007779	4212758	0	A	C	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	487	.	NC_007779	4212760	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	488	.	NC_007779	4214141	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	489	.	NC_007779	4214142	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	490	.	NC_007779	4214143	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	491	.	NC_007779	4214144	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	492	.	NC_007779	4214148	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	493	.	NC_007779	4214149	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	494	.	NC_007779	4214150	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	495	.	NC_007779	4214151	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	496	.	NC_007779	4214152	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	497	.	NC_007779	4214153	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	498	.	NC_007779	4214155	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	499	.	NC_007779	4214156	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	500	.	NC_007779	4214157	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	501	.	NC_007779	4214159	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	502	.	NC_007779	4214162	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	503	.	NC_007779	4214163	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	504	.	NC_007779	4214165	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	505	.	NC_007779	4214166	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	506	.	NC_007779	4214167	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	507	.	NC_007779	4214168	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	508	.	NC_007779	4214169	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	509	.	NC_007779	4214171	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	510	.	NC_007779	4214172	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	511	.	NC_007779	4214174	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	512	.	NC_007779	4214175	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	513	.	NC_007779	4214176	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	514	.	NC_007779	4214177	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	515	.	NC_007779	4215368	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	516	.	NC_007779	4215369	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	517	.	NC_007779	4215370	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	518	.	NC_007779	4215372	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	519	.	NC_007779	4215373	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	520	.	NC_007779	4215374	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	521	.	NC_007779	4215375	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	522	.	NC_007779	4215379	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	523	.	NC_007779	4215380	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	524	.	NC_007779	4215382	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	525	.	NC_007779	4215383	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	526	.	NC_007779	4215384	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	527	.	NC_007779	4215385	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	528	.	NC_007779	4215388	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	529	.	NC_007779	4215390	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	530	.	NC_007779	4215392	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	531	.	NC_007779	4226513	0	C	A	bias_e_value=0.00466274	bias_p_value=1.00353e-09	fisher_strand_p_value=4.02442e-11	frequency=8.415174e-02	genotype_quality=889.9	ks_quality_p_value=1	log10_base_likelihood=-22.5709	log10_qual_likelihood_position_model=20.8045	log10_strand_likelihood_position_model=10.3953	new_cov=31/0	polymorphism_quality=17.3	quality=17.3	quality_position_model=Inf	ref_cov=109/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/145
RA	532	.	NC_007779	4227183	0	T	G	bias_e_value=4.66777e-07	bias_p_value=1.00461e-13	fisher_strand_p_value=2.91454e-15	frequency=5.454111e-02	genotype_quality=981.6	ks_quality_p_value=1	log10_base_likelihood=-7.85645	log10_qual_likelihood_position_model=28.6203	log10_strand_likelihood_position_model=14.5354	new_cov=33/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=90/187	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/187
RA	533	.	NC_007779	4254117	0	T	.	bias_e_value=4519380	bias_p_value=0.972677	fisher_strand_p_value=1	frequency=1.023006e-02	genotype_quality=1178.1	ks_quality_p_value=0.775531	log10_base_likelihood=-7.95452	log10_qual_likelihood_position_model=2.39333	log10_strand_likelihood_position_model=0.414409	new_cov=2/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.88482e-07	ref_cov=148/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/143
RA	534	.	NC_007779	4289840	0	G	T	bias_e_value=3.58779	bias_p_value=7.72176e-07	fisher_strand_p_value=4.29886e-08	frequency=6.390667e-02	genotype_quality=808.7	ks_quality_p_value=1	log10_base_likelihood=-10.4708	log10_qual_likelihood_position_model=16.5526	log10_strand_likelihood_position_model=7.67765	new_cov=0/28	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=126/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/157
RA	535	.	NC_007779	4304641	0	T	G	bias_e_value=0.00011394	bias_p_value=2.45226e-11	fisher_strand_p_value=8.51732e-13	frequency=5.555439e-02	genotype_quality=727.0	ks_quality_p_value=1	log10_base_likelihood=-6.29316	log10_qual_likelihood_position_model=23.8185	log10_strand_likelihood_position_model=12.0697	new_cov=27/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=66/143	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=95/143
RA	536	.	NC_007779	4318994	0	A	G	bias_e_value=1.73791	bias_p_value=3.7404e-07	fisher_strand_p_value=2.02097e-08	frequency=3.605270e-02	genotype_quality=569.0	ks_quality_p_value=0.988199	log10_base_likelihood=-10.0158	log10_qual_likelihood_position_model=7.24648	log10_strand_likelihood_position_model=7.69444	new_cov=0/6	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=151/5	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=151/11
RA	537	.	NC_007779	4320637	0	C	A	bias_e_value=7032.11	bias_p_value=0.00151347	fisher_strand_p_value=0.000154863	frequency=3.190804e-02	genotype_quality=909.8	ks_quality_p_value=1	log10_base_likelihood=-6.45258	log10_qual_likelihood_position_model=17.1241	log10_strand_likelihood_position_model=3.84286	new_cov=14/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=131/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/123
RA	538	.	NC_007779	4337469	0	A	C	bias_e_value=1.05851e-15	bias_p_value=2.27816e-22	fisher_strand_p_value=4.15435e-24	frequency=1.215239e-01	genotype_quality=662.0	ks_quality_p_value=1	log10_base_likelihood=-17.6106	log10_qual_likelihood_position_model=32.9657	log10_strand_likelihood_position_model=23.3815	new_cov=0/34	polymorphism_quality=12.3	quality=12.3	quality_position_model=Inf	ref_cov=147/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/56
RA	539	.	NC_007779	4348862	0	G	C	bias_e_value=499959	bias_p_value=0.107603	fisher_strand_p_value=0.0224295	frequency=1.851749e-02	genotype_quality=1173.4	ks_quality_p_value=1	log10_base_likelihood=-6.19476	log10_qual_likelihood_position_model=10.4842	log10_strand_likelihood_position_model=1.69332	new_cov=7/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=157/120	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=164/120
RA	540	.	NC_007779	4351353	0	T	G	bias_e_value=1.93058e-06	bias_p_value=4.15507e-13	fisher_strand_p_value=1.25888e-14	frequency=6.242847e-02	genotype_quality=809.6	ks_quality_p_value=1	log10_base_likelihood=-9.75543	log10_qual_likelihood_position_model=34.4017	log10_strand_likelihood_position_model=13.9	new_cov=29/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=64/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/158
RA	541	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=1318.9	new_cov=133/129	quality=1318.9	ref_cov=0/0	tot_cov=133/129
RA	542	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=1318.9	new_cov=133/129	quality=1318.9	ref_cov=0/0	tot_cov=133/129
RA	543	.	NC_007779	4396933	1	.	A	bias_e_value=4645900	bias_p_value=0.999906	fisher_strand_p_value=1	frequency=6.493568e-03	genotype_quality=1526.8	ks_quality_p_value=0.986343	log10_base_likelihood=-8.1721	log10_qual_likelihood_position_model=1.89004	log10_strand_likelihood_position_model=0.299911	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=6.65252e-08	ref_cov=157/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=158/150
RA	544	.	NC_007779	4403831	0	G	T	bias_e_value=22.8756	bias_p_value=4.92337e-06	fisher_strand_p_value=3.07831e-07	frequency=4.049397e-02	genotype_quality=944.9	ks_quality_p_value=1	log10_base_likelihood=-5.98483	log10_qual_likelihood_position_model=19.3042	log10_strand_likelihood_position_model=6.51169	new_cov=0/20	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=141/116	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/137
RA	545	.	NC_007779	4414725	0	T	.	bias_e_value=4087440	bias_p_value=0.879714	fisher_strand_p_value=1	frequency=1.715946e-02	genotype_quality=913.3	ks_quality_p_value=0.551515	log10_base_likelihood=-11.6285	log10_qual_likelihood_position_model=2.57522	log10_strand_likelihood_position_model=0.386448	new_cov=1/3	polymorphism_quality=6.2	quality=6.2	quality_position_model=1.15363e-10	ref_cov=71/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=72/161
RA	546	.	NC_007779	4419586	0	T	G	bias_e_value=10.2298	bias_p_value=2.2017e-06	fisher_strand_p_value=1.30659e-07	frequency=6.069851e-02	genotype_quality=724.0	ks_quality_p_value=1	log10_base_likelihood=-5.92632	log10_qual_likelihood_position_model=22.1003	log10_strand_likelihood_position_model=6.88386	new_cov=20/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=89/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=109/120
RA	547	.	NC_007779	4420066	0	C	A	bias_e_value=3.5664	bias_p_value=7.67573e-07	fisher_strand_p_value=4.27173e-08	frequency=3.601646e-02	genotype_quality=866.7	ks_quality_p_value=1	log10_base_likelihood=-5.90354	log10_qual_likelihood_position_model=14.273	log10_strand_likelihood_position_model=7.3694	new_cov=20/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=99/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/146
RA	548	.	NC_007779	4429120	0	G	T	bias_e_value=2.70966	bias_p_value=5.83183e-07	fisher_strand_p_value=4.90164e-08	frequency=4.126072e-02	genotype_quality=922.3	ks_quality_p_value=0.651593	log10_base_likelihood=-6.79628	log10_qual_likelihood_position_model=25.6719	log10_strand_likelihood_position_model=7.30966	new_cov=0/22	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=152/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/143
RA	549	.	NC_007779	4429130	0	A	.	bias_e_value=4006260	bias_p_value=0.862241	fisher_strand_p_value=0.680817	frequency=1.784992e-02	genotype_quality=1126.2	ks_quality_p_value=0.768752	log10_base_likelihood=-14.667	log10_qual_likelihood_position_model=2.14291	log10_strand_likelihood_position_model=0.50855	new_cov=2/3	polymorphism_quality=9.3	quality=9.3	quality_position_model=4.41744e-14	ref_cov=140/135	reject=INDEL_HOMOPOLYMER	tot_cov=142/138
RA	550	.	NC_007779	4477098	1	.	A	bias_e_value=4307420	bias_p_value=0.927059	fisher_strand_p_value=1	frequency=7.194519e-03	genotype_quality=1358.7	ks_quality_p_value=0.643234	log10_base_likelihood=-8.09512	log10_qual_likelihood_position_model=1.52291	log10_strand_likelihood_position_model=0.326259	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.55128e-08	ref_cov=172/104	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=173/105
RA	551	.	NC_007779	4487705	0	T	.	bias_e_value=4532930	bias_p_value=0.975594	fisher_strand_p_value=1	frequency=1.166439e-02	genotype_quality=1019.7	ks_quality_p_value=0.78736	log10_base_likelihood=-8.02096	log10_qual_likelihood_position_model=1.84027	log10_strand_likelihood_position_model=0.40673	new_cov=2/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.09239e-07	ref_cov=132/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/123
RA	552	.	NC_007779	4508941	0	T	.	bias_e_value=2962750	bias_p_value=0.637654	fisher_strand_p_value=0.565567	frequency=1.118565e-02	genotype_quality=1035.1	ks_quality_p_value=0.496781	log10_base_likelihood=-8.14265	log10_qual_likelihood_position_model=2.88817	log10_strand_likelihood_position_model=0.540891	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.37954e-06	ref_cov=160/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=161/107
RA	553	.	NC_007779	4510865	1	.	A	bias_e_value=353538	bias_p_value=0.0760897	fisher_strand_p_value=0.208827	frequency=7.633209e-03	genotype_quality=1299.2	ks_quality_p_value=0.0696646	log10_base_likelihood=-8.34713	log10_qual_likelihood_position_model=1.4635	log10_strand_likelihood_position_model=0.680214	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.92931e-08	ref_cov=118/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/142
RA	554	.	NC_007779	4540870	0	T	G	bias_e_value=2.89781e-13	bias_p_value=6.23677e-20	fisher_strand_p_value=1.26982e-21	frequency=1.055665e-01	genotype_quality=743.3	ks_quality_p_value=1	log10_base_likelihood=-14.8193	log10_qual_likelihood_position_model=33.6871	log10_strand_likelihood_position_model=20.8963	new_cov=38/0	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=43/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=81/156
RA	555	.	NC_007779	4540877	0	A	T	bias_e_value=1.80325e-10	bias_p_value=3.88101e-17	fisher_strand_p_value=9.12358e-19	frequency=1.327386e-01	genotype_quality=732.9	ks_quality_p_value=1	log10_base_likelihood=-26.3959	log10_qual_likelihood_position_model=26.0269	log10_strand_likelihood_position_model=18.0398	new_cov=34/0	polymorphism_quality=21.2	quality=21.2	quality_position_model=Inf	ref_cov=47/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=81/152
RA	556	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=849.2	new_cov=119/86	quality=849.2	ref_cov=0/0	tot_cov=119/86
RA	557	.	NC_007779	4573184	0	T	G	bias_e_value=0.00813552	bias_p_value=1.75096e-09	fisher_strand_p_value=7.18905e-11	frequency=6.743240e-02	genotype_quality=767.6	ks_quality_p_value=1	log10_base_likelihood=-11.1011	log10_qual_likelihood_position_model=22.9925	log10_strand_likelihood_position_model=10.3629	new_cov=36/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=114/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/124
RA	558	.	NC_007779	4583430	1	.	T	bias_e_value=3476480	bias_p_value=0.74822	fisher_strand_p_value=1	frequency=8.510590e-03	genotype_quality=1156.3	ks_quality_p_value=0.380556	log10_base_likelihood=-8.39496	log10_qual_likelihood_position_model=1.6042	log10_strand_likelihood_position_model=0.300131	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.9854e-08	ref_cov=122/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/112
RA	559	.	NC_007779	4584556	0	C	A	bias_e_value=3.71563	bias_p_value=7.99692e-07	fisher_strand_p_value=4.46126e-08	frequency=3.755856e-02	genotype_quality=965.6	ks_quality_p_value=1	log10_base_likelihood=-6.35352	log10_qual_likelihood_position_model=19.5923	log10_strand_likelihood_position_model=7.35054	new_cov=19/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=105/165	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/165
RA	560	.	NC_007779	4584731	0	G	T	bias_e_value=37.2125	bias_p_value=8.00901e-06	fisher_strand_p_value=5.17575e-07	frequency=3.432560e-02	genotype_quality=861.1	ks_quality_p_value=1	log10_base_likelihood=-5.60245	log10_qual_likelihood_position_model=13.1845	log10_strand_likelihood_position_model=6.28603	new_cov=0/15	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=159/90	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/106
RA	561	.	NC_007779	4599760	0	C	A	bias_e_value=7.337e-06	bias_p_value=1.5791e-12	fisher_strand_p_value=4.99268e-14	frequency=9.441280e-02	genotype_quality=950.5	ks_quality_p_value=1	log10_base_likelihood=-18.9948	log10_qual_likelihood_position_model=24.1325	log10_strand_likelihood_position_model=13.4932	new_cov=41/0	polymorphism_quality=13.7	quality=13.7	quality_position_model=Inf	ref_cov=120/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/159
RA	562	.	NC_007779	4610781	0	A	C	bias_e_value=0.0297665	bias_p_value=6.40646e-09	fisher_strand_p_value=2.78523e-10	frequency=7.668209e-02	genotype_quality=797.8	ks_quality_p_value=1	log10_base_likelihood=-20.0374	log10_qual_likelihood_position_model=21.5255	log10_strand_likelihood_position_model=9.55514	new_cov=0/25	polymorphism_quality=14.8	quality=14.8	quality_position_model=Inf	ref_cov=142/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/113
RA	563	.	NC_007779	4613456	0	C	A	bias_e_value=45.3836	bias_p_value=9.76763e-06	fisher_strand_p_value=1.21627e-06	frequency=4.879522e-02	genotype_quality=728.9	ks_quality_p_value=0.526204	log10_base_likelihood=-6.704	log10_qual_likelihood_position_model=19.4323	log10_strand_likelihood_position_model=5.97349	new_cov=20/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=109/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/118
RA	564	.	NC_007779	4635770	0	G	T	bias_e_value=127.317	bias_p_value=2.74016e-05	fisher_strand_p_value=1.93583e-06	frequency=4.812527e-02	genotype_quality=678.1	ks_quality_p_value=1	log10_base_likelihood=-8.92768	log10_qual_likelihood_position_model=11.9478	log10_strand_likelihood_position_model=5.84026	new_cov=0/19	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=112/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/118
RA	565	.	NC_007779	4636470	0	C	G	bias_e_value=0.0247121	bias_p_value=5.31862e-09	fisher_strand_p_value=2.2929e-10	frequency=9.589195e-02	genotype_quality=622.1	ks_quality_p_value=1	log10_base_likelihood=-16.2533	log10_qual_likelihood_position_model=19.2757	log10_strand_likelihood_position_model=9.64618	new_cov=20/1	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=39/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=59/122
RA	566	.	NC_007779	4636473	0	A	G	bias_e_value=3.62152	bias_p_value=7.79435e-07	fisher_strand_p_value=4.34167e-08	frequency=5.189991e-02	genotype_quality=566.1	ks_quality_p_value=1	log10_base_likelihood=-6.1949	log10_qual_likelihood_position_model=14.5506	log10_strand_likelihood_position_model=7.36234	new_cov=10/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=23/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=33/126
RA	567	.	NC_007779	4642414	1	.	A	bias_e_value=2884270	bias_p_value=0.620763	fisher_strand_p_value=0.57625	frequency=1.158333e-02	genotype_quality=1255.1	ks_quality_p_value=0.464903	log10_base_likelihood=-13.0344	log10_qual_likelihood_position_model=1.87898	log10_strand_likelihood_position_model=0.505726	new_cov=2/1	polymorphism_quality=7.7	quality=7.7	quality_position_model=1.08716e-12	ref_cov=108/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/149
MC	568	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=279	right_inside_cov=0	right_outside_cov=279
MC	569	.	NC_007779	1288311	1288512	67	53	left_inside_cov=190	left_outside_cov=196	right_inside_cov=190	right_outside_cov=192
MC	570	.	NC_007779	1301041	1302376	1328	0	left_inside_cov=0	left_outside_cov=256	right_inside_cov=0	right_outside_cov=257
MC	571	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=337	right_inside_cov=1	right_outside_cov=339
MC	572	.	NC_007779	2176983	2178208	0	0	left_inside_cov=0	left_outside_cov=316	right_inside_cov=0	right_outside_cov=264
MC	573	.	NC_007779	2320795	2322130	1328	0	left_inside_cov=0	left_outside_cov=299	right_inside_cov=0	right_outside_cov=302
MC	574	.	NC_007779	3128826	3147473	1176	0	left_inside_cov=190	left_outside_cov=194	right_inside_cov=0	right_outside_cov=243
MC	575	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=297	right_inside_cov=0	right_outside_cov=368
MC	576	.	NC_007779	3742936	3744271	1326	0	left_inside_cov=0	left_outside_cov=326	right_inside_cov=0	right_outside_cov=327
MC	577	.	NC_007779	3746911	3748109	0	1197	left_inside_cov=0	left_outside_cov=297	right_inside_cov=0	right_outside_cov=297
MC	578	.	NC_007779	3750591	3751789	1194	0	left_inside_cov=0	left_outside_cov=319	right_inside_cov=0	right_outside_cov=317
MC	579	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=293	right_inside_cov=0	right_outside_cov=294
MC	580	.	NC_007779	4310363	4311561	0	1197	left_inside_cov=0	left_outside_cov=298	right_inside_cov=0	right_outside_cov=295
JC	581	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=124	coverage_plus=134	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=47	max_min_left_plus=50	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=259	pos_hash_score=131	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=258
JC	582	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=10	coverage_minus=112	coverage_plus=102	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371963__1__10____101__101__0__0	max_left=85	max_left_minus=85	max_left_plus=85	max_min_left=45	max_min_left_minus=45	max_min_left_plus=45	max_min_right=46	max_min_right_minus=46	max_min_right_plus=44	max_pos_hash_score=160	max_right=85	max_right_minus=84	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=214	pos_hash_score=112	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=214
JC	583	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=109	coverage_plus=85	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=57	key=NC_007779__289856__1__NC_007779__2176982__-1__-33__CTATTGCAATACCGCATTGTGAGGCGATTCATG__101__101__1__0	max_left=62	max_left_minus=62	max_left_plus=62	max_min_left=33	max_min_left_minus=32	max_min_left_plus=33	max_min_right=34	max_min_right_minus=34	max_min_right_plus=34	max_pos_hash_score=114	max_right=62	max_right_minus=62	max_right_plus=61	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.22	new_junction_frequency=1.000000e+00	new_junction_read_count=195	pos_hash_score=92	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=194	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	584	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=156	coverage_plus=104	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=90	key=NC_007779__380484__1__NC_007779__381407__-1__0____101__101__1__1	max_left=90	max_left_minus=90	max_left_plus=90	max_min_left=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=1.03	new_junction_frequency=NA	new_junction_read_count=261	pos_hash_score=131	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=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=260
JC	585	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=104	coverage_plus=126	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=88	key=NC_007779__381401__1__NC_007779__381814__-1__2____101__101__1__1	max_left=93	max_left_minus=92	max_left_plus=93	max_min_left=49	max_min_left_minus=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=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=NA	new_junction_read_count=231	pos_hash_score=133	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=2	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=230
JC	586	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=118	coverage_plus=154	flanking_left=101	flanking_right=101	frequency=9.827278e-01	junction_possible_overlap_registers=87	key=NC_007779__608573__-1__NC_007779__1305025__1__3____101__101__1__0	max_left=92	max_left_minus=92	max_left_plus=91	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=1.13	new_junction_frequency=9.827278e-01	new_junction_read_count=275	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=0.02	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=5	side_2_redundant=0	total_non_overlap_reads=272
JC	587	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=4	coverage_minus=98	coverage_plus=98	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=85	key=NC_007779__654213__-1__NC_007779__655409__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=170	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.80	new_junction_frequency=1.000000e+00	new_junction_read_count=192	pos_hash_score=114	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=1	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=196
JC	588	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=19	coverage_plus=26	flanking_left=101	flanking_right=101	frequency=2.482908e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=78	max_left_minus=78	max_left_plus=76	max_min_left=41	max_min_left_minus=41	max_min_left_plus=39	max_min_right=42	max_min_right_minus=42	max_min_right_plus=34	max_pos_hash_score=148	max_right=76	max_right_minus=72	max_right_plus=76	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.22	new_junction_frequency=2.482908e-01	new_junction_read_count=46	pos_hash_score=39	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.70	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=177	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=74	side_2_read_count=133	side_2_redundant=0	total_non_overlap_reads=45
JC	589	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=24	coverage_plus=28	flanking_left=101	flanking_right=101	frequency=2.712886e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=79	max_left_minus=79	max_left_plus=79	max_min_left=42	max_min_left_minus=42	max_min_left_plus=37	max_min_right=42	max_min_right_minus=36	max_min_right_plus=42	max_pos_hash_score=148	max_right=79	max_right_minus=79	max_right_plus=79	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.25	new_junction_frequency=2.712886e-01	new_junction_read_count=52	pos_hash_score=45	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.70	side_1_overlap=16	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=0.64	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=133	side_2_redundant=0	total_non_overlap_reads=52
JC	590	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=111	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=9.872979e-01	junction_possible_overlap_registers=88	key=NC_007779__1221489__1__NC_007779__1301039__1__2____101__101__0__1	max_left=93	max_left_minus=92	max_left_plus=93	max_min_left=49	max_min_left_minus=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=85	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=9.872979e-01	new_junction_read_count=228	pos_hash_score=112	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=3	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=224
JC	591	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=123	coverage_plus=96	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=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=180	max_right=88	max_right_minus=88	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=219	pos_hash_score=113	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=219
JC	592	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=110	coverage_plus=95	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=87	max_min_left=46	max_min_left_minus=46	max_min_left_plus=45	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=0.88	new_junction_frequency=1.000000e+00	new_junction_read_count=206	pos_hash_score=113	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=205
JC	593	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=112	coverage_plus=123	flanking_left=101	flanking_right=101	frequency=9.393993e-01	junction_possible_overlap_registers=86	key=NC_007779__1305037__-1__NC_007779__2519719__1__4____101__101__0__1	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=47	max_min_left_plus=48	max_min_right=48	max_min_right_minus=44	max_min_right_plus=48	max_pos_hash_score=172	max_right=90	max_right_minus=90	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=9.393993e-01	new_junction_read_count=237	pos_hash_score=122	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.06	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=16	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	594	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=115	coverage_plus=116	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1397758__1__NC_007779__1672777__1__0____101__101__1__0	max_left=89	max_left_minus=89	max_left_plus=87	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=232	pos_hash_score=124	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=231
JC	595	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=98	coverage_plus=105	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=64	key=NC_007779__1413638__-1__NC_007779__1436673__1__26____101__101__0__0	max_left=69	max_left_minus=69	max_left_plus=68	max_min_left=37	max_min_left_minus=37	max_min_left_plus=37	max_min_right=37	max_min_right_minus=37	max_min_right_plus=35	max_pos_hash_score=128	max_right=69	max_right_minus=69	max_right_plus=69	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=204	pos_hash_score=95	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=26	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=64	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=203
JC	596	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=110	coverage_plus=109	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=94	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=85	max_right_minus=85	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=219	pos_hash_score=114	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=219
JC	597	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=112	coverage_plus=102	flanking_left=101	flanking_right=101	frequency=9.601770e-01	junction_possible_overlap_registers=90	key=NC_007779__1907280__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=9.601770e-01	new_junction_read_count=217	pos_hash_score=115	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=9	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=214
JC	598	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=115	coverage_plus=134	flanking_left=101	flanking_right=101	frequency=9.541985e-01	junction_possible_overlap_registers=90	key=NC_007779__1907288__-1__NC_007779__2411458__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=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=0.99	new_junction_frequency=9.541985e-01	new_junction_read_count=250	pos_hash_score=136	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.05	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=12	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=249
JC	599	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=140	coverage_plus=59	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=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=0.79	new_junction_frequency=1.000000e+00	new_junction_read_count=200	pos_hash_score=101	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=199
JC	600	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=132	coverage_plus=137	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__1980095__-1__NC_007779__2176983__1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=269	pos_hash_score=137	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=269
JC	601	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=123	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=239	pos_hash_score=127	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=238
JC	602	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=135	coverage_plus=111	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=84	key=NC_007779__2320794__-1__NC_007779__2322125__1__6____101__101__0__0	max_left=89	max_left_minus=88	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=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=89	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=123	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=246
JC	603	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=69	coverage_plus=122	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=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=0.76	new_junction_frequency=1.000000e+00	new_junction_read_count=191	pos_hash_score=114	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=191
JC	604	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=126	coverage_plus=127	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=86	max_left_minus=85	max_left_plus=86	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=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=253	pos_hash_score=124	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=253
JC	605	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=137	coverage_plus=135	flanking_left=101	flanking_right=101	frequency=9.611307e-01	junction_possible_overlap_registers=90	key=NC_007779__2411458__1__NC_007779__2985055__-1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=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=1.08	new_junction_frequency=9.611307e-01	new_junction_read_count=272	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=0.04	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=272
JC	606	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=110	coverage_plus=139	flanking_left=101	flanking_right=101	frequency=9.363296e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=49	max_min_right_minus=46	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=9.363296e-01	new_junction_read_count=250	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=0.07	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=17	side_2_redundant=0	total_non_overlap_reads=249
JC	607	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=144	coverage_plus=125	flanking_left=101	flanking_right=101	frequency=6.924067e-01	junction_possible_overlap_registers=86	key=NC_007779__2865229__1__NC_007779__2865278__-1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=6.924067e-01	new_junction_read_count=269	pos_hash_score=128	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.53	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=135	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.46	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=110	side_2_redundant=0	total_non_overlap_reads=269
JC	608	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=101	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3147474__1__NC_007779__3262328__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.85	new_junction_frequency=1.000000e+00	new_junction_read_count=215	pos_hash_score=122	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=214
JC	609	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=158	coverage_plus=107	flanking_left=101	flanking_right=101	frequency=9.926471e-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=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=48	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.07	new_junction_frequency=9.926471e-01	new_junction_read_count=267	pos_hash_score=133	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.01	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=2	side_2_redundant=0	total_non_overlap_reads=265
JC	610	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=146	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=84	key=NC_007779__3261133__-1__NC_007779__3748109__-1__-6__CTTTGC__101__101__0__1	max_left=89	max_left_minus=89	max_left_plus=88	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=47	max_min_right_minus=47	max_min_right_plus=46	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=260	pos_hash_score=134	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=259	unique_read_sequence=CTTTGC
JC	611	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=86	coverage_plus=112	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0	max_left=85	max_left_minus=85	max_left_plus=85	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.79	new_junction_frequency=1.000000e+00	new_junction_read_count=200	pos_hash_score=105	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=198
JC	612	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=120	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3261134__1__NC_007779__3262338__1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=252	pos_hash_score=134	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=252
JC	613	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=154	coverage_plus=109	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=48	max_min_right=50	max_min_right_minus=48	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=263	pos_hash_score=141	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=263
JC	614	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=132	coverage_plus=158	flanking_left=101	flanking_right=101	frequency=9.932494e-01	junction_possible_overlap_registers=89	key=NC_007779__3512759__-1__NC_007779__3744263__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.16	new_junction_frequency=9.932494e-01	new_junction_read_count=291	pos_hash_score=140	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=2	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=290
JC	615	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=155	coverage_plus=105	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=86	max_left_plus=87	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=46	max_min_right_minus=46	max_min_right_plus=46	max_pos_hash_score=164	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=263	pos_hash_score=127	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=260
JC	616	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=138	coverage_plus=142	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3744263__-1__NC_007779__3903274__1__0____101__101__1__0	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=1.000000e+00	new_junction_read_count=280	pos_hash_score=142	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=280
JC	617	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=140	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3746910__-1__NC_007779__3748106__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.09	new_junction_frequency=1.000000e+00	new_junction_read_count=264	pos_hash_score=127	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=264
JC	618	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=127	coverage_plus=134	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3746911__1__NC_007779__3748646__-1__0____101__101__1__0	max_left=92	max_left_minus=92	max_left_plus=91	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=273	pos_hash_score=125	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=261
JC	619	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=139	coverage_plus=159	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=93	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=1.19	new_junction_frequency=1.000000e+00	new_junction_read_count=300	pos_hash_score=139	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=298
JC	620	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=139	coverage_plus=140	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=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=90	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=279	pos_hash_score=140	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=279
JC	621	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=122	coverage_plus=101	flanking_left=101	flanking_right=101	frequency=9.826477e-01	junction_possible_overlap_registers=89	key=NC_007779__3903279__-1__NC_007779__4504191__-1__1____101__101__0__1	max_left=94	max_left_minus=93	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=93	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=9.826477e-01	new_junction_read_count=224	pos_hash_score=131	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=4	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=223
JC	622	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=141	coverage_plus=114	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=88	key=NC_007779__3958122__-1__NC_007779__3958155__1__2____101__101__0__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=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=93	max_right_minus=93	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=257	pos_hash_score=139	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=88	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=255
JC	623	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=110	coverage_plus=128	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=93	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=238	pos_hash_score=125	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=238
JC	624	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=105	coverage_plus=124	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=85	max_left_minus=85	max_left_plus=84	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=230	pos_hash_score=116	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=229
JC	625	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=138	coverage_plus=119	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=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=46	max_min_right=48	max_min_right_minus=47	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.06	new_junction_frequency=1.000000e+00	new_junction_read_count=257	pos_hash_score=131	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	626	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=113	coverage_plus=140	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=93	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=256	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=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=253
JC	627	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=111	coverage_plus=148	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=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=270	pos_hash_score=132	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=259
JC	628	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=132	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=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=1.23	new_junction_frequency=1.000000e+00	new_junction_read_count=311	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=310
JC	629	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=131	coverage_plus=133	flanking_left=101	flanking_right=101	frequency=9.677419e-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=1.07	new_junction_frequency=9.677419e-01	new_junction_read_count=264	pos_hash_score=137	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=9	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=264
JC	630	.	NC_007779	4547362	1	NC_007779	4547676	1	0	alignment_overlap=9	coverage_minus=26	coverage_plus=19	flanking_left=101	flanking_right=101	frequency=2.147459e-01	junction_possible_overlap_registers=81	key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0	max_left=86	max_left_minus=86	max_left_plus=78	max_min_left=45	max_min_left_minus=44	max_min_left_plus=45	max_min_right=46	max_min_right_minus=46	max_min_right_plus=38	max_pos_hash_score=162	max_right=85	max_right_minus=85	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.20	new_junction_frequency=2.147459e-01	new_junction_read_count=45	pos_hash_score=37	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.63	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=159	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.82	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=186	side_2_redundant=0	total_non_overlap_reads=45
JC	631	.	NC_007779	4547370	-1	NC_007779	4547666	-1	0	alignment_overlap=9	coverage_minus=14	coverage_plus=18	flanking_left=101	flanking_right=101	frequency=1.631820e-01	junction_possible_overlap_registers=81	key=NC_007779__4547370__-1__NC_007779__4547675__-1__9____101__101__0__0	max_left=85	max_left_minus=82	max_left_plus=85	max_min_left=44	max_min_left_minus=43	max_min_left_plus=44	max_min_right=46	max_min_right_minus=34	max_min_right_plus=46	max_pos_hash_score=162	max_right=86	max_right_minus=86	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.14	new_junction_frequency=1.631820e-01	new_junction_read_count=32	pos_hash_score=29	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.63	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=158	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.82	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=186	side_2_redundant=0	total_non_overlap_reads=32
UN	632	.	NC_007779	15485	16634
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UN	645	.	NC_007779	273275	274275
UN	646	.	NC_007779	274733	371972
UN	647	.	NC_007779	380576	381723
UN	648	.	NC_007779	391029	392101
UN	649	.	NC_007779	525194	525848
UN	650	.	NC_007779	566089	567161
UN	651	.	NC_007779	573905	574918
UN	652	.	NC_007779	580439	580490
UN	653	.	NC_007779	607325	608476
UN	654	.	NC_007779	654214	655412
UN	655	.	NC_007779	688366	689375
UN	656	.	NC_007779	730322	730468
UN	657	.	NC_007779	730826	730860
UN	658	.	NC_007779	732503	732614
UN	659	.	NC_007779	733123	733151
UN	660	.	NC_007779	734994	735022
UN	661	.	NC_007779	1050345	1050399
UN	662	.	NC_007779	1050560	1050736
UN	663	.	NC_007779	1094763	1095829
UN	664	.	NC_007779	1105719	1106860
UN	665	.	NC_007779	1270768	1270800
UN	666	.	NC_007779	1271838	1271871
UN	667	.	NC_007779	1288372	1288460
UN	668	.	NC_007779	1301041	1302376
UN	669	.	NC_007779	1397851	1398859
UN	670	.	NC_007779	1413639	1436698
UN	671	.	NC_007779	1469721	1470864
UN	672	.	NC_007779	1471108	1472133
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UN	675	.	NC_007779	1572480	1572486
UN	676	.	NC_007779	1572681	1572965
UN	677	.	NC_007779	1573215	1573420
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UN	679	.	NC_007779	1635030	1635030
UN	680	.	NC_007779	1635032	1635032
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UN	682	.	NC_007779	1635439	1635539
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UN	688	.	NC_007779	2068409	2068504
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UN	700	.	NC_007779	2519816	2520967
UN	701	.	NC_007779	2724816	2727806
UN	702	.	NC_007779	2728090	2728121
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UN	705	.	NC_007779	2995112	2996257
UN	706	.	NC_007779	3128894	3147473
UN	707	.	NC_007779	3184842	3185985
UN	708	.	NC_007779	3261134	3262337
UN	709	.	NC_007779	3365505	3366515
UN	710	.	NC_007779	3423614	3424411
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UN	713	.	NC_007779	3427045	3428592
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UN	719	.	NC_007779	3596172	3597193
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UN	721	.	NC_007779	3598088	3598749
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UN	723	.	NC_007779	3599296	3599491
UN	724	.	NC_007779	3599687	3600848
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UN	728	.	NC_007779	3690552	3690668
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UN	730	.	NC_007779	3691208	3692523
UN	731	.	NC_007779	3692789	3693186
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UN	735	.	NC_007779	3746911	3748109
UN	736	.	NC_007779	3750591	3751789
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UN	748	.	NC_007779	4019429	4021044
UN	749	.	NC_007779	4056314	4056890
UN	750	.	NC_007779	4169476	4169587
UN	751	.	NC_007779	4169782	4170156
UN	752	.	NC_007779	4211520	4211762
UN	753	.	NC_007779	4211959	4213508
UN	754	.	NC_007779	4213667	4215791
UN	755	.	NC_007779	4215987	4216658
UN	756	.	NC_007779	4299523	4299551
UN	757	.	NC_007779	4299747	4299777
UN	758	.	NC_007779	4310363	4311561
UN	759	.	NC_007779	4502953	4504094
UN	760	.	NC_007779	4512231	4513265