#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	05:15:34 07 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	4_D6_GCCAAT_L002_R2_001.fastq
SNP	1	59	NC_007779	66457	A	frequency=1
SNP	2	63	NC_007779	97880	T	frequency=1
SNP	3	74	NC_007779	167632	A	frequency=1
SNP	4	95	NC_007779	274547	G	frequency=1
DEL	5	702,722	NC_007779	274733	97240	frequency=1
SNP	6	125	NC_007779	547694	G	frequency=1
INS	7	126	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	127	NC_007779	556858	T	frequency=1
SNP	9	128	NC_007779	569996	C	frequency=1
DEL	10	703,728	NC_007779	654214	1199	frequency=1
SNP	11	150	NC_007779	749354	A	frequency=1
SNP	12	153	NC_007779	758440	A	frequency=1
SNP	13	161	NC_007779	887234	A	frequency=1
SNP	14	170	NC_007779	987574	T	frequency=1
SNP	15	198	NC_007779	1093686	C	frequency=1
SNP	16	200	NC_007779	1097580	T	frequency=1.725631e-01
SNP	17	206	NC_007779	1170573	T	frequency=1
DEL	18	705,735	NC_007779	1301041	1336	frequency=1
SNP	19	219	NC_007779	1318876	A	frequency=1
DEL	20	706,738	NC_007779	1413639	23060	frequency=1
SNP	21	240	NC_007779	1483588	A	frequency=1
DEL	22	242	NC_007779	1496775	1	frequency=1
SNP	23	264	NC_007779	1615814	A	frequency=1
DEL	24	270	NC_007779	1669599	1	frequency=1
SNP	25	290	NC_007779	1844073	A	frequency=1
SNP	26	298	NC_007779	1907281	A	frequency=1.035404e-02
SNP	27	299	NC_007779	1918872	A	frequency=1
SNP	28	302	NC_007779	1973476	A	frequency=1
SNP	29	306	NC_007779	2005401	T	frequency=1
SNP	30	319	NC_007779	2170094	A	frequency=1
DEL	31	708,745	NC_007779	2320795	1336	frequency=1
SNP	32	346	NC_007779	2406075	T	frequency=1
SNP	33	352	NC_007779	2416102	A	frequency=1
SNP	34	367	NC_007779	2538628	T	frequency=1
INS	35	750	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=7.044069e-01
SNP	36	404	NC_007779	2866111	G	frequency=1
SNP	37	418	NC_007779	3003330	A	frequency=1
SNP	38	425	NC_007779	3049815	T	frequency=1
SNP	39	461	NC_007779	3397813	G	frequency=1
DEL	40	711,758	NC_007779	3742936	1336	frequency=1
DEL	41	712,760	NC_007779	3746911	1199	frequency=1
DEL	42	549	NC_007779	3750122	1	frequency=9.418178e-01
SNP	43	550	NC_007779	3750123	T	frequency=5.728531e-02
DEL	44	713,763	NC_007779	3750591	1199	frequency=1
SNP	45	573	NC_007779	3898657	G	frequency=1
DEL	46	714,765	NC_007779	3958123	34	frequency=1
SNP	47	602	NC_007779	4090749	T	frequency=1
SNP	48	613	NC_007779	4165991	C	frequency=1
DEL	49	715,768	NC_007779	4310363	1199	frequency=1
DEL	50	669,670	NC_007779	4371271	2	frequency=1
SNP	51	685	NC_007779	4546535	A	frequency=1
RA	52	.	NC_007779	5595	0	G	T	bias_e_value=1.58293	bias_p_value=3.40683e-07	fisher_strand_p_value=1.80948e-08	frequency=8.767843e-02	genotype_quality=830.5	ks_quality_p_value=1	log10_base_likelihood=-17.0447	log10_qual_likelihood_position_model=21.3105	log10_strand_likelihood_position_model=7.97226	new_cov=0/29	polymorphism_quality=11.7	quality=11.7	quality_position_model=Inf	ref_cov=118/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/148
RA	53	.	NC_007779	17050	0	A	C	bias_e_value=6.38763e-05	bias_p_value=1.37477e-11	fisher_strand_p_value=4.67754e-13	frequency=1.116638e-01	genotype_quality=356.1	ks_quality_p_value=1	log10_base_likelihood=-8.14733	log10_qual_likelihood_position_model=19.0056	log10_strand_likelihood_position_model=12.33	new_cov=0/25	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=74/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=74/48
RA	54	.	NC_007779	29503	0	T	C	bias_e_value=0.000487169	bias_p_value=1.0485e-10	fisher_strand_p_value=3.8428e-12	frequency=9.029961e-02	genotype_quality=675.7	ks_quality_p_value=1	log10_base_likelihood=-11.8132	log10_qual_likelihood_position_model=21.3305	log10_strand_likelihood_position_model=11.4154	new_cov=0/29	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=129/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/102
RA	55	.	NC_007779	34112	0	T	.	bias_e_value=2565410	bias_p_value=0.552138	fisher_strand_p_value=0.616183	frequency=1.414299e-02	genotype_quality=853.6	ks_quality_p_value=0.355998	log10_base_likelihood=-8.5349	log10_qual_likelihood_position_model=1.64716	log10_strand_likelihood_position_model=0.432422	new_cov=1/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=2.15912e-08	ref_cov=107/102	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/104
RA	56	.	NC_007779	46842	0	T	.	bias_e_value=1723710	bias_p_value=0.370982	fisher_strand_p_value=1	frequency=1.208878e-02	genotype_quality=1007.9	ks_quality_p_value=0.118378	log10_base_likelihood=-8.25384	log10_qual_likelihood_position_model=2.93964	log10_strand_likelihood_position_model=0.38297	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=8.18499e-07	ref_cov=109/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/138
RA	57	.	NC_007779	47305	0	G	T	bias_e_value=1.62248	bias_p_value=3.49196e-07	fisher_strand_p_value=1.85727e-08	frequency=6.673098e-02	genotype_quality=869.3	ks_quality_p_value=1	log10_base_likelihood=-16.7778	log10_qual_likelihood_position_model=17.373	log10_strand_likelihood_position_model=7.92044	new_cov=0/25	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=135/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/138
RA	58	.	NC_007779	61542	0	C	G	bias_e_value=0.00146113	bias_p_value=3.14471e-10	fisher_strand_p_value=1.20285e-11	frequency=7.538128e-02	genotype_quality=578.9	ks_quality_p_value=1	log10_base_likelihood=-15.0756	log10_qual_likelihood_position_model=13.4897	log10_strand_likelihood_position_model=10.9198	new_cov=13/0	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=15/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=28/128
RA	59	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1087.5	new_cov=144/118	quality=1087.5	ref_cov=0/0	tot_cov=144/118
RA	60	.	NC_007779	70602	0	G	T	bias_e_value=0.281602	bias_p_value=6.06073e-08	fisher_strand_p_value=2.93549e-09	frequency=9.500170e-02	genotype_quality=654.5	ks_quality_p_value=1	log10_base_likelihood=-9.11705	log10_qual_likelihood_position_model=18.7309	log10_strand_likelihood_position_model=8.69988	new_cov=0/29	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=102/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/118
RA	61	.	NC_007779	75074	0	T	G	bias_e_value=4.48911e-27	bias_p_value=9.66161e-34	fisher_strand_p_value=1.18665e-35	frequency=2.386389e-01	genotype_quality=488.4	ks_quality_p_value=1	log10_base_likelihood=-40.5017	log10_qual_likelihood_position_model=45.6197	log10_strand_likelihood_position_model=34.9257	new_cov=61/0	polymorphism_quality=35.4	quality=35.4	quality_position_model=Inf	ref_cov=18/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/122
RA	62	.	NC_007779	89555	0	G	T	bias_e_value=6.18639	bias_p_value=1.33146e-06	fisher_strand_p_value=9.34224e-08	frequency=6.725502e-02	genotype_quality=797.0	ks_quality_p_value=0.819795	log10_base_likelihood=-16.9471	log10_qual_likelihood_position_model=23.6523	log10_strand_likelihood_position_model=7.02955	new_cov=18/0	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=84/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/136
RA	63	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=1200.2	new_cov=150/139	quality=1200.2	ref_cov=0/0	tot_cov=150/139
RA	64	.	NC_007779	101231	0	T	G	bias_e_value=7.2688e-06	bias_p_value=1.56442e-12	fisher_strand_p_value=4.94476e-14	frequency=7.652330e-02	genotype_quality=548.9	ks_quality_p_value=1	log10_base_likelihood=-6.51483	log10_qual_likelihood_position_model=23.065	log10_strand_likelihood_position_model=13.3059	new_cov=19/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=20/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=40/118
RA	65	.	NC_007779	101246	0	T	G	bias_e_value=3.9888	bias_p_value=8.58483e-07	fisher_strand_p_value=5.01197e-08	frequency=6.320381e-02	genotype_quality=533.4	ks_quality_p_value=0.959582	log10_base_likelihood=-24.2815	log10_qual_likelihood_position_model=9.42695	log10_strand_likelihood_position_model=7.29999	new_cov=10/0	polymorphism_quality=19.0	quality=19.0	quality_position_model=1.59493e-09	ref_cov=21/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=31/115
RA	66	.	NC_007779	107544	1	.	T	bias_e_value=1792650	bias_p_value=0.38582	fisher_strand_p_value=0.664192	frequency=2.040863e-02	genotype_quality=1173.9	ks_quality_p_value=0.188843	log10_base_likelihood=-22.9035	log10_qual_likelihood_position_model=2.69612	log10_strand_likelihood_position_model=0.54253	new_cov=3/2	polymorphism_quality=17.6	quality=17.6	quality_position_model=7.7936e-22	ref_cov=110/130	reject=INDEL_HOMOPOLYMER	tot_cov=113/132
RA	67	.	NC_007779	119384	0	T	G	bias_e_value=1.61976e-20	bias_p_value=3.48609e-27	fisher_strand_p_value=5.27298e-29	frequency=1.645303e-01	genotype_quality=623.2	ks_quality_p_value=1	log10_base_likelihood=-21.1389	log10_qual_likelihood_position_model=39.6467	log10_strand_likelihood_position_model=28.2779	new_cov=56/0	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=37/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=93/138
RA	68	.	NC_007779	119389	0	C	A	bias_e_value=0.0684218	bias_p_value=1.4726e-08	fisher_strand_p_value=6.65412e-10	frequency=5.930710e-02	genotype_quality=801.0	ks_quality_p_value=1	log10_base_likelihood=-7.86296	log10_qual_likelihood_position_model=15.4055	log10_strand_likelihood_position_model=9.17691	new_cov=22/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=75/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=97/139
RA	69	.	NC_007779	137009	0	G	T	bias_e_value=22.7033	bias_p_value=4.88628e-06	fisher_strand_p_value=3.08283e-07	frequency=6.824112e-02	genotype_quality=599.4	ks_quality_p_value=0.990513	log10_base_likelihood=-7.72966	log10_qual_likelihood_position_model=18.7463	log10_strand_likelihood_position_model=6.51105	new_cov=16/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=60/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=76/106
RA	70	.	NC_007779	149550	1	.	T	bias_e_value=594497	bias_p_value=0.12795	fisher_strand_p_value=0.511952	frequency=7.936478e-03	genotype_quality=1242.1	ks_quality_p_value=0.0546021	log10_base_likelihood=-8.29473	log10_qual_likelihood_position_model=1.94374	log10_strand_likelihood_position_model=0.469404	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=8.4528e-08	ref_cov=145/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/105
RA	71	.	NC_007779	151656	0	T	G	bias_e_value=0.0313175	bias_p_value=6.74027e-09	fisher_strand_p_value=2.93714e-10	frequency=8.078861e-02	genotype_quality=790.6	ks_quality_p_value=1	log10_base_likelihood=-8.68296	log10_qual_likelihood_position_model=28.7163	log10_strand_likelihood_position_model=9.53208	new_cov=28/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=91/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/125
RA	72	.	NC_007779	162886	0	C	A	bias_e_value=1134.03	bias_p_value=0.00024407	fisher_strand_p_value=2.07104e-05	frequency=3.649902e-02	genotype_quality=850.1	ks_quality_p_value=1	log10_base_likelihood=-7.68858	log10_qual_likelihood_position_model=13.3494	log10_strand_likelihood_position_model=4.83319	new_cov=16/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=121/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/130
RA	73	.	NC_007779	164596	1	.	A	bias_e_value=2293020	bias_p_value=0.493512	fisher_strand_p_value=0.182841	frequency=1.342010e-02	genotype_quality=669.2	ks_quality_p_value=1	log10_base_likelihood=-6.49262	log10_qual_likelihood_position_model=3.74139	log10_strand_likelihood_position_model=0.737927	new_cov=2/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=0.00101192	ref_cov=62/85	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=64/85
RA	74	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=980.2	new_cov=113/122	quality=980.2	ref_cov=0/0	tot_cov=113/122
RA	75	.	NC_007779	175694	0	T	G	bias_e_value=1.34192e-12	bias_p_value=2.88813e-19	fisher_strand_p_value=6.07385e-21	frequency=1.039920e-01	genotype_quality=711.6	ks_quality_p_value=1	log10_base_likelihood=-11.4844	log10_qual_likelihood_position_model=32.7336	log10_strand_likelihood_position_model=20.2165	new_cov=49/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=63/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/137
RA	76	.	NC_007779	193477	1	.	G	bias_e_value=1969330	bias_p_value=0.423846	fisher_strand_p_value=0.198669	frequency=9.216309e-03	genotype_quality=1080.7	ks_quality_p_value=0.726859	log10_base_likelihood=-8.22781	log10_qual_likelihood_position_model=1.15161	log10_strand_likelihood_position_model=0.701871	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.61727e-08	ref_cov=95/120	reject=POLYMORPHISM_STRAND	tot_cov=97/120
RA	77	.	NC_007779	193480	0	C	G	bias_e_value=7.31261e-07	bias_p_value=1.57385e-13	fisher_strand_p_value=4.62806e-15	frequency=1.412830e-01	genotype_quality=600.9	ks_quality_p_value=1	log10_base_likelihood=-25.69	log10_qual_likelihood_position_model=21.9383	log10_strand_likelihood_position_model=14.3346	new_cov=29/0	polymorphism_quality=20.5	quality=20.5	quality_position_model=Inf	ref_cov=41/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=70/117
RA	78	.	NC_007779	193483	0	C	G	bias_e_value=0.00520138	bias_p_value=1.11946e-09	fisher_strand_p_value=4.50992e-11	frequency=7.320118e-02	genotype_quality=580.7	ks_quality_p_value=1	log10_base_likelihood=-5.78063	log10_qual_likelihood_position_model=18.82	log10_strand_likelihood_position_model=10.3458	new_cov=20/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=41/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/117
RA	79	.	NC_007779	193489	0	G	T	bias_e_value=83.7238	bias_p_value=1.80193e-05	fisher_strand_p_value=1.23374e-06	frequency=7.104445e-02	genotype_quality=671.1	ks_quality_p_value=1	log10_base_likelihood=-9.42269	log10_qual_likelihood_position_model=15.5503	log10_strand_likelihood_position_model=5.92158	new_cov=16/1	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=60/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=76/118
RA	80	.	NC_007779	193496	0	A	T	bias_e_value=0.000109803	bias_p_value=2.36322e-11	fisher_strand_p_value=8.19713e-13	frequency=1.288414e-01	genotype_quality=643.3	ks_quality_p_value=1	log10_base_likelihood=-37.6337	log10_qual_likelihood_position_model=29.2798	log10_strand_likelihood_position_model=12.0863	new_cov=24/0	polymorphism_quality=32.5	quality=32.5	quality_position_model=Inf	ref_cov=42/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=66/118
RA	81	.	NC_007779	201737	1	.	G	bias_e_value=1948120	bias_p_value=0.41928	fisher_strand_p_value=0.155957	frequency=9.216309e-03	genotype_quality=1065.1	ks_quality_p_value=0.91086	log10_base_likelihood=-7.36423	log10_qual_likelihood_position_model=2.72643	log10_strand_likelihood_position_model=0.806996	new_cov=2/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.1583e-05	ref_cov=84/131	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=86/131
RA	82	.	NC_007779	212548	0	T	G	bias_e_value=3.97208e-08	bias_p_value=8.54884e-15	fisher_strand_p_value=2.31025e-16	frequency=1.149206e-01	genotype_quality=574.3	ks_quality_p_value=1	log10_base_likelihood=-10.3785	log10_qual_likelihood_position_model=36.5873	log10_strand_likelihood_position_model=15.6363	new_cov=37/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=49/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/110
RA	83	.	NC_007779	228004	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	84	.	NC_007779	228006	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	85	.	NC_007779	228007	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	86	.	NC_007779	228008	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	87	.	NC_007779	228009	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	88	.	NC_007779	228010	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	89	.	NC_007779	228011	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	90	.	NC_007779	228012	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	91	.	NC_007779	228013	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	92	.	NC_007779	228014	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	93	.	NC_007779	233118	0	T	C	bias_e_value=2.20546	bias_p_value=4.74666e-07	fisher_strand_p_value=2.56893e-08	frequency=5.137920e-02	genotype_quality=555.0	ks_quality_p_value=1	log10_base_likelihood=-5.71534	log10_qual_likelihood_position_model=14.466	log10_strand_likelihood_position_model=7.59025	new_cov=0/10	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=120/20	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/30
RA	94	.	NC_007779	265582	0	T	G	bias_e_value=1.13087	bias_p_value=2.43389e-07	fisher_strand_p_value=1.2688e-08	frequency=7.384682e-02	genotype_quality=608.0	ks_quality_p_value=1	log10_base_likelihood=-7.81786	log10_qual_likelihood_position_model=16.7377	log10_strand_likelihood_position_model=7.89661	new_cov=22/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=69/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=91/103
RA	95	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1057.0	new_cov=131/114	quality=1057.0	ref_cov=0/0	tot_cov=131/114
RA	96	.	NC_007779	306622	0	G	C	deleted=1	frequency=1	genotype_quality=1.0	new_cov=1/0	quality=1.0	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	97	.	NC_007779	335105	0	C	A	deleted=1	frequency=1	genotype_quality=1.5	new_cov=0/1	quality=1.5	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	98	.	NC_007779	374799	0	T	G	bias_e_value=1.50384e-13	bias_p_value=3.23662e-20	fisher_strand_p_value=6.50122e-22	frequency=9.975052e-02	genotype_quality=574.7	ks_quality_p_value=1	log10_base_likelihood=-6.62402	log10_qual_likelihood_position_model=33.3422	log10_strand_likelihood_position_model=21.187	new_cov=33/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=22/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=55/127
RA	99	.	NC_007779	375033	0	G	.	bias_e_value=2318150	bias_p_value=0.49892	fisher_strand_p_value=0.215638	frequency=9.798050e-03	genotype_quality=869.5	ks_quality_p_value=0.862741	log10_base_likelihood=-5.62589	log10_qual_likelihood_position_model=0.733124	log10_strand_likelihood_position_model=0.666275	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=4.45281e-06	ref_cov=93/109	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/109
RA	100	.	NC_007779	378715	0	T	.	bias_e_value=3423960	bias_p_value=0.736916	fisher_strand_p_value=0.62197	frequency=1.203728e-02	genotype_quality=1019.2	ks_quality_p_value=0.593338	log10_base_likelihood=-7.90792	log10_qual_likelihood_position_model=3.03598	log10_strand_likelihood_position_model=0.42599	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.6247e-06	ref_cov=124/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/124
RA	101	.	NC_007779	379237	0	G	.	bias_e_value=3289670	bias_p_value=0.708014	fisher_strand_p_value=1	frequency=1.226425e-02	genotype_quality=677.9	ks_quality_p_value=0.341132	log10_base_likelihood=-5.89782	log10_qual_likelihood_position_model=2.60216	log10_strand_likelihood_position_model=0.332787	new_cov=1/1	polymorphism_quality=0.3	quality=0.3	quality_position_model=9.59388e-05	ref_cov=103/58	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/59
RA	102	.	NC_007779	386657	0	G	.	bias_e_value=545509	bias_p_value=0.117406	fisher_strand_p_value=0.499139	frequency=7.688522e-03	genotype_quality=1083.6	ks_quality_p_value=0.0501865	log10_base_likelihood=-5.8414	log10_qual_likelihood_position_model=1.7279	log10_strand_likelihood_position_model=0.5644	new_cov=2/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=2.2939e-05	ref_cov=134/124	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=136/124
RA	103	.	NC_007779	386658	0	C	.	bias_e_value=482804	bias_p_value=0.103911	fisher_strand_p_value=0.499985	frequency=7.747650e-03	genotype_quality=1055.3	ks_quality_p_value=0.0429269	log10_base_likelihood=-5.66222	log10_qual_likelihood_position_model=1.88203	log10_strand_likelihood_position_model=0.551293	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=5.00356e-05	ref_cov=135/121	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=137/121
RA	104	.	NC_007779	387560	0	A	C	bias_e_value=2.01883e-07	bias_p_value=4.345e-14	fisher_strand_p_value=1.22977e-15	frequency=6.567860e-02	genotype_quality=726.5	ks_quality_p_value=1	log10_base_likelihood=-6.62801	log10_qual_likelihood_position_model=29.3365	log10_strand_likelihood_position_model=14.9102	new_cov=0/38	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=130/70	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/108
RA	105	.	NC_007779	387919	0	A	G	bias_e_value=14.9073	bias_p_value=3.2084e-06	fisher_strand_p_value=1.9972e-07	frequency=4.291153e-02	genotype_quality=464.3	ks_quality_p_value=0.976564	log10_base_likelihood=-9.01016	log10_qual_likelihood_position_model=6.88488	log10_strand_likelihood_position_model=6.69958	new_cov=0/6	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=125/7	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=125/13
RA	106	.	NC_007779	429744	1	.	T	bias_e_value=788627	bias_p_value=0.169731	fisher_strand_p_value=1	frequency=7.967949e-03	genotype_quality=1244.6	ks_quality_p_value=0.0403036	log10_base_likelihood=-8.29914	log10_qual_likelihood_position_model=1.95128	log10_strand_likelihood_position_model=0.302347	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.72098e-08	ref_cov=135/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/115
RA	107	.	NC_007779	432858	0	T	G	bias_e_value=9.36507e-11	bias_p_value=2.01558e-17	fisher_strand_p_value=4.66472e-19	frequency=1.379709e-01	genotype_quality=648.7	ks_quality_p_value=1	log10_base_likelihood=-15.9507	log10_qual_likelihood_position_model=35.0619	log10_strand_likelihood_position_model=18.3384	new_cov=53/0	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=70/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/116
RA	108	.	NC_007779	437543	0	G	.	bias_e_value=1060710	bias_p_value=0.228289	fisher_strand_p_value=0.501729	frequency=8.295059e-03	genotype_quality=1035.5	ks_quality_p_value=0.119221	log10_base_likelihood=-5.90754	log10_qual_likelihood_position_model=1.12977	log10_strand_likelihood_position_model=0.531014	new_cov=2/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=4.2405e-06	ref_cov=129/110	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=131/110
RA	109	.	NC_007779	437544	0	C	.	bias_e_value=1107810	bias_p_value=0.238427	fisher_strand_p_value=0.502236	frequency=8.470535e-03	genotype_quality=1032.2	ks_quality_p_value=0.126345	log10_base_likelihood=-5.73991	log10_qual_likelihood_position_model=1.09836	log10_strand_likelihood_position_model=0.52618	new_cov=2/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=5.82178e-06	ref_cov=127/107	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=129/107
RA	110	.	NC_007779	437545	0	C	.	bias_e_value=1173810	bias_p_value=0.252631	fisher_strand_p_value=0.501873	frequency=8.506775e-03	genotype_quality=1033.0	ks_quality_p_value=0.136851	log10_base_likelihood=-5.74361	log10_qual_likelihood_position_model=1.05634	log10_strand_likelihood_position_model=0.52927	new_cov=2/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=5.25258e-06	ref_cov=126/107	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=128/107
RA	111	.	NC_007779	440767	0	G	T	bias_e_value=0.0174353	bias_p_value=3.75249e-09	fisher_strand_p_value=1.59271e-10	frequency=1.243882e-01	genotype_quality=720.1	ks_quality_p_value=1	log10_base_likelihood=-17.8917	log10_qual_likelihood_position_model=27.5952	log10_strand_likelihood_position_model=9.96812	new_cov=1/36	polymorphism_quality=12.6	quality=12.6	quality_position_model=Inf	ref_cov=113/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/127
RA	112	.	NC_007779	450484	0	G	T	bias_e_value=45.6531	bias_p_value=9.82562e-06	fisher_strand_p_value=7.06171e-07	frequency=7.937050e-02	genotype_quality=596.9	ks_quality_p_value=0.912064	log10_base_likelihood=-13.6432	log10_qual_likelihood_position_model=19.269	log10_strand_likelihood_position_model=6.16247	new_cov=15/1	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=48/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=63/113
RA	113	.	NC_007779	450929	0	T	.	bias_e_value=4082540	bias_p_value=0.878659	fisher_strand_p_value=0.57713	frequency=1.362514e-02	genotype_quality=903.2	ks_quality_p_value=0.952552	log10_base_likelihood=-8.04627	log10_qual_likelihood_position_model=3.42166	log10_strand_likelihood_position_model=0.502221	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.72394e-06	ref_cov=92/125	reject=POLYMORPHISM_STRAND	tot_cov=94/126
RA	114	.	NC_007779	465801	0	C	A	bias_e_value=0.00574305	bias_p_value=1.23604e-09	fisher_strand_p_value=5.13074e-11	frequency=1.162000e-01	genotype_quality=571.3	ks_quality_p_value=0.974592	log10_base_likelihood=-27.4235	log10_qual_likelihood_position_model=23.7726	log10_strand_likelihood_position_model=10.2898	new_cov=0/23	polymorphism_quality=22.2	quality=22.2	quality_position_model=Inf	ref_cov=109/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/72
RA	115	.	NC_007779	487626	0	A	C	bias_e_value=2.61862	bias_p_value=5.63588e-07	fisher_strand_p_value=3.08046e-08	frequency=6.336451e-02	genotype_quality=682.9	ks_quality_p_value=1	log10_base_likelihood=-10.0954	log10_qual_likelihood_position_model=19.9265	log10_strand_likelihood_position_model=7.51138	new_cov=0/20	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=113/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/92
RA	116	.	NC_007779	492774	0	C	A	bias_e_value=48314.3	bias_p_value=0.0103984	fisher_strand_p_value=0.0013694	frequency=2.744865e-02	genotype_quality=783.4	ks_quality_p_value=1	log10_base_likelihood=-5.90275	log10_qual_likelihood_position_model=8.02688	log10_strand_likelihood_position_model=2.86347	new_cov=0/6	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=135/64	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=135/70
RA	117	.	NC_007779	494823	0	T	G	bias_e_value=3.54439e-12	bias_p_value=7.62837e-19	fisher_strand_p_value=1.63847e-20	frequency=1.051579e-01	genotype_quality=542.2	ks_quality_p_value=1	log10_base_likelihood=-7.7376	log10_qual_likelihood_position_model=29.3484	log10_strand_likelihood_position_model=19.7856	new_cov=27/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=15/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=42/122
RA	118	.	NC_007779	503058	0	T	C	bias_e_value=0.00451494	bias_p_value=9.71722e-10	fisher_strand_p_value=3.89162e-11	frequency=9.853697e-02	genotype_quality=583.6	ks_quality_p_value=1	log10_base_likelihood=-12.114	log10_qual_likelihood_position_model=21.8635	log10_strand_likelihood_position_model=10.4099	new_cov=0/24	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=108/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/75
RA	119	.	NC_007779	506363	1	.	A	bias_e_value=792054	bias_p_value=0.170469	fisher_strand_p_value=0.6386	frequency=1.606464e-02	genotype_quality=1218.3	ks_quality_p_value=0.0634723	log10_base_likelihood=-17.7922	log10_qual_likelihood_position_model=2.71163	log10_strand_likelihood_position_model=0.490074	new_cov=3/1	polymorphism_quality=12.5	quality=12.5	quality_position_model=1.06988e-16	ref_cov=140/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/106
RA	120	.	NC_007779	513848	0	A	C	bias_e_value=1.73661e-10	bias_p_value=3.7376e-17	fisher_strand_p_value=8.7785e-19	frequency=1.145687e-01	genotype_quality=557.3	ks_quality_p_value=1	log10_base_likelihood=-11.9876	log10_qual_likelihood_position_model=27.7197	log10_strand_likelihood_position_model=18.0566	new_cov=0/31	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=118/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/58
RA	121	.	NC_007779	522430	1	.	T	bias_e_value=4000360	bias_p_value=0.860972	fisher_strand_p_value=0.651196	frequency=2.000046e-02	genotype_quality=969.2	ks_quality_p_value=0.800719	log10_base_likelihood=-18.2304	log10_qual_likelihood_position_model=1.73863	log10_strand_likelihood_position_model=0.459254	new_cov=3/1	polymorphism_quality=12.9	quality=12.9	quality_position_model=3.69306e-18	ref_cov=117/79	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/80
RA	122	.	NC_007779	524490	0	T	G	bias_e_value=3.60566e-08	bias_p_value=7.76022e-15	fisher_strand_p_value=2.09151e-16	frequency=1.124210e-01	genotype_quality=702.8	ks_quality_p_value=1	log10_base_likelihood=-22.9211	log10_qual_likelihood_position_model=29.3146	log10_strand_likelihood_position_model=15.6795	new_cov=28/0	polymorphism_quality=17.7	quality=17.7	quality_position_model=Inf	ref_cov=41/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=69/144
RA	123	.	NC_007779	527270	0	A	C	bias_e_value=3.85697	bias_p_value=8.3011e-07	fisher_strand_p_value=4.64119e-08	frequency=1.032257e-01	genotype_quality=511.2	ks_quality_p_value=1	log10_base_likelihood=-8.00918	log10_qual_likelihood_position_model=22.9336	log10_strand_likelihood_position_model=7.35164	new_cov=2/22	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=96/47	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/69
RA	124	.	NC_007779	535125	0	T	G	bias_e_value=5.59809e-10	bias_p_value=1.20484e-16	fisher_strand_p_value=2.91181e-18	frequency=1.192169e-01	genotype_quality=615.4	ks_quality_p_value=1	log10_base_likelihood=-14.4251	log10_qual_likelihood_position_model=32.5953	log10_strand_likelihood_position_model=17.5358	new_cov=45/0	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=59/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/117
RA	125	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=964.1	new_cov=109/123	quality=964.1	ref_cov=0/0	tot_cov=109/123
RA	126	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=814.8	new_cov=93/97	quality=814.8	ref_cov=0/0	tot_cov=93/97
RA	127	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=979.8	new_cov=128/107	quality=979.8	ref_cov=0/0	tot_cov=128/107
RA	128	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=870.8	new_cov=115/82	quality=870.8	ref_cov=0/0	tot_cov=115/82
RA	129	.	NC_007779	589157	0	T	G	bias_e_value=3.32555e-14	bias_p_value=7.15736e-21	fisher_strand_p_value=1.39454e-22	frequency=1.083474e-01	genotype_quality=674.2	ks_quality_p_value=1	log10_base_likelihood=-13.836	log10_qual_likelihood_position_model=40.4945	log10_strand_likelihood_position_model=21.8556	new_cov=42/0	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=41/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=83/141
RA	130	.	NC_007779	593216	0	T	G	bias_e_value=7.27469e-05	bias_p_value=1.56568e-11	fisher_strand_p_value=5.35163e-13	frequency=5.705786e-02	genotype_quality=620.9	ks_quality_p_value=1	log10_base_likelihood=-8.34277	log10_qual_likelihood_position_model=19.7039	log10_strand_likelihood_position_model=12.2715	new_cov=16/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=20/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/136
RA	131	.	NC_007779	598799	0	T	G	bias_e_value=1.31956e-17	bias_p_value=2.84001e-24	fisher_strand_p_value=4.78915e-26	frequency=1.825776e-01	genotype_quality=515.0	ks_quality_p_value=1	log10_base_likelihood=-33.5719	log10_qual_likelihood_position_model=35.2753	log10_strand_likelihood_position_model=25.3197	new_cov=38/0	polymorphism_quality=28.4	quality=28.4	quality_position_model=Inf	ref_cov=17/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=55/125
RA	132	.	NC_007779	598802	0	T	G	bias_e_value=3.65976e-12	bias_p_value=7.87667e-19	fisher_strand_p_value=1.69299e-20	frequency=9.086037e-02	genotype_quality=567.0	ks_quality_p_value=1	log10_base_likelihood=-8.17869	log10_qual_likelihood_position_model=28.9	log10_strand_likelihood_position_model=19.7713	new_cov=31/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=23/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=54/126
RA	133	.	NC_007779	606911	1	.	G	bias_e_value=12768.7	bias_p_value=0.00274813	fisher_strand_p_value=0.000692598	frequency=2.654839e-02	genotype_quality=1108.4	ks_quality_p_value=0.435754	log10_base_likelihood=-27.8285	log10_qual_likelihood_position_model=2.7074	log10_strand_likelihood_position_model=3.15952	new_cov=6/0	polymorphism_quality=22.6	quality=22.6	quality_position_model=3.72817e-24	ref_cov=63/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=69/157
RA	134	.	NC_007779	606915	0	T	G	bias_e_value=63.5053	bias_p_value=1.36678e-05	fisher_strand_p_value=9.28711e-07	frequency=3.159142e-02	genotype_quality=748.2	ks_quality_p_value=0.987587	log10_base_likelihood=-11.8541	log10_qual_likelihood_position_model=6.64507	log10_strand_likelihood_position_model=6.03212	new_cov=6/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=15/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=21/168
RA	135	.	NC_007779	612991	0	C	G	bias_e_value=1.31998e-08	bias_p_value=2.8409e-15	fisher_strand_p_value=7.46006e-17	frequency=9.252739e-02	genotype_quality=598.1	ks_quality_p_value=0.998575	log10_base_likelihood=-18.4185	log10_qual_likelihood_position_model=18.7563	log10_strand_likelihood_position_model=16.1273	new_cov=0/16	polymorphism_quality=13.1	quality=13.1	quality_position_model=Inf	ref_cov=135/7	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=135/23
RA	136	.	NC_007779	616029	0	C	A	bias_e_value=1.27529	bias_p_value=2.74472e-07	fisher_strand_p_value=1.45685e-08	frequency=6.150484e-02	genotype_quality=732.6	ks_quality_p_value=0.988683	log10_base_likelihood=-11.6594	log10_qual_likelihood_position_model=18.0145	log10_strand_likelihood_position_model=7.83659	new_cov=0/15	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=144/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/69
RA	137	.	NC_007779	623841	1	.	G	bias_e_value=2557380	bias_p_value=0.550408	fisher_strand_p_value=1	frequency=1.290321e-02	genotype_quality=776.5	ks_quality_p_value=0.218222	log10_base_likelihood=-8.918	log10_qual_likelihood_position_model=1.80036	log10_strand_likelihood_position_model=0.0113174	new_cov=2/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=4.60865e-09	ref_cov=151/2	reject=POLYMORPHISM_STRAND	tot_cov=153/2
RA	138	.	NC_007779	645484	0	A	C	bias_e_value=0.0354951	bias_p_value=7.63938e-09	fisher_strand_p_value=3.34804e-10	frequency=4.658079e-02	genotype_quality=970.8	ks_quality_p_value=1	log10_base_likelihood=-6.33561	log10_qual_likelihood_position_model=23.0499	log10_strand_likelihood_position_model=9.47521	new_cov=0/23	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=172/97	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/120
RA	139	.	NC_007779	645970	0	T	G	bias_e_value=1.19017e-14	bias_p_value=2.56153e-21	fisher_strand_p_value=4.89103e-23	frequency=1.489491e-01	genotype_quality=625.6	ks_quality_p_value=1	log10_base_likelihood=-44.5041	log10_qual_likelihood_position_model=32.3034	log10_strand_likelihood_position_model=22.3106	new_cov=35/0	polymorphism_quality=39.4	quality=39.4	quality_position_model=Inf	ref_cov=26/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/142
RA	140	.	NC_007779	645983	0	T	C	bias_e_value=0.772662	bias_p_value=1.66295e-07	fisher_strand_p_value=8.49128e-09	frequency=6.728029e-02	genotype_quality=722.2	ks_quality_p_value=1	log10_base_likelihood=-9.77985	log10_qual_likelihood_position_model=18.9846	log10_strand_likelihood_position_model=8.07103	new_cov=19/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=65/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/125
RA	141	.	NC_007779	646433	0	A	C	bias_e_value=0.170963	bias_p_value=3.67953e-08	fisher_strand_p_value=1.73804e-09	frequency=3.210640e-02	genotype_quality=765.4	ks_quality_p_value=1	log10_base_likelihood=-6.49624	log10_qual_likelihood_position_model=13.991	log10_strand_likelihood_position_model=8.75994	new_cov=0/9	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=175/16	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=175/25
RA	142	.	NC_007779	646440	0	C	A	bias_e_value=1.12692e-14	bias_p_value=2.4254e-21	fisher_strand_p_value=4.63184e-23	frequency=1.093826e-01	genotype_quality=764.1	ks_quality_p_value=0.998778	log10_base_likelihood=-65.3353	log10_qual_likelihood_position_model=19.4678	log10_strand_likelihood_position_model=22.3342	new_cov=0/22	polymorphism_quality=60.3	quality=60.3	quality_position_model=9.66155e-26	ref_cov=171/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/30
RA	143	.	NC_007779	649677	0	T	G	bias_e_value=1.24441e-10	bias_p_value=2.67827e-17	fisher_strand_p_value=6.24043e-19	frequency=6.658220e-02	genotype_quality=739.9	ks_quality_p_value=1	log10_base_likelihood=-6.1702	log10_qual_likelihood_position_model=27.9244	log10_strand_likelihood_position_model=18.2048	new_cov=32/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=41/153	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=73/153
RA	144	.	NC_007779	660356	0	T	G	bias_e_value=4.77944e-26	bias_p_value=1.02865e-32	fisher_strand_p_value=1.30169e-34	frequency=1.460729e-01	genotype_quality=746.1	ks_quality_p_value=1	log10_base_likelihood=-26.191	log10_qual_likelihood_position_model=47.3266	log10_strand_likelihood_position_model=33.8855	new_cov=58/0	polymorphism_quality=21.0	quality=21.0	quality_position_model=Inf	ref_cov=33/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/169
RA	145	.	NC_007779	665062	0	C	A	bias_e_value=0.0568302	bias_p_value=1.22312e-08	fisher_strand_p_value=5.85766e-10	frequency=6.942606e-02	genotype_quality=758.1	ks_quality_p_value=0.935307	log10_base_likelihood=-15.6297	log10_qual_likelihood_position_model=23.0975	log10_strand_likelihood_position_model=9.23228	new_cov=0/18	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=145/55	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/73
RA	146	.	NC_007779	686495	0	A	C	bias_e_value=1.79342e-16	bias_p_value=3.85986e-23	fisher_strand_p_value=6.81404e-25	frequency=1.532063e-01	genotype_quality=795.4	ks_quality_p_value=1	log10_base_likelihood=-54.128	log10_qual_likelihood_position_model=40.8091	log10_strand_likelihood_position_model=24.1666	new_cov=0/43	polymorphism_quality=49.1	quality=49.1	quality_position_model=Inf	ref_cov=168/43	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/86
RA	147	.	NC_007779	687133	0	A	C	bias_e_value=1.56837e-05	bias_p_value=3.37549e-12	fisher_strand_p_value=1.0944e-13	frequency=5.000162e-02	genotype_quality=1092.7	ks_quality_p_value=1	log10_base_likelihood=-15.1766	log10_qual_likelihood_position_model=30.6858	log10_strand_likelihood_position_model=12.9608	new_cov=0/28	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=200/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=200/119
RA	148	.	NC_007779	704668	0	T	G	bias_e_value=4.29926e-06	bias_p_value=9.25301e-13	fisher_strand_p_value=2.87539e-14	frequency=5.397606e-02	genotype_quality=613.0	ks_quality_p_value=1	log10_base_likelihood=-9.81429	log10_qual_likelihood_position_model=20.6395	log10_strand_likelihood_position_model=13.5413	new_cov=19/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=23/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=42/135
RA	149	.	NC_007779	706385	1	.	T	bias_e_value=2397150	bias_p_value=0.515922	fisher_strand_p_value=0.221053	frequency=9.523392e-03	genotype_quality=1038.7	ks_quality_p_value=0.888091	log10_base_likelihood=-8.54221	log10_qual_likelihood_position_model=1.72434	log10_strand_likelihood_position_model=0.655504	new_cov=0/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=4.33224e-08	ref_cov=111/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/99
RA	150	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=931.7	new_cov=119/105	quality=931.7	ref_cov=0/0	tot_cov=119/105
RA	151	.	NC_007779	752693	0	A	C	bias_e_value=2.1291e-20	bias_p_value=4.58232e-27	fisher_strand_p_value=6.96034e-29	frequency=2.104225e-01	genotype_quality=600.3	ks_quality_p_value=1	log10_base_likelihood=-48.3205	log10_qual_likelihood_position_model=45.2532	log10_strand_likelihood_position_model=28.1574	new_cov=0/56	polymorphism_quality=43.2	quality=43.2	quality_position_model=Inf	ref_cov=137/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/93
RA	152	.	NC_007779	753547	0	T	A	bias_e_value=0.815895	bias_p_value=1.756e-07	fisher_strand_p_value=8.99273e-09	frequency=7.378864e-02	genotype_quality=599.4	ks_quality_p_value=1	log10_base_likelihood=-10.483	log10_qual_likelihood_position_model=18.8566	log10_strand_likelihood_position_model=8.04611	new_cov=0/14	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=122/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/51
RA	153	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=877.7	new_cov=97/111	quality=877.7	ref_cov=0/0	tot_cov=97/111
RA	154	.	NC_007779	759019	0	C	G	bias_e_value=9.46837e-15	bias_p_value=2.03782e-21	fisher_strand_p_value=3.87379e-23	frequency=1.078343e-01	genotype_quality=654.9	ks_quality_p_value=1	log10_base_likelihood=-40.1104	log10_qual_likelihood_position_model=21.6114	log10_strand_likelihood_position_model=22.4119	new_cov=0/18	polymorphism_quality=35.0	quality=35.0	quality_position_model=Inf	ref_cov=146/1	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/19
RA	155	.	NC_007779	796581	0	G	T	bias_e_value=37.8876	bias_p_value=8.1543e-06	fisher_strand_p_value=5.2762e-07	frequency=5.483389e-02	genotype_quality=691.1	ks_quality_p_value=1	log10_base_likelihood=-6.81438	log10_qual_likelihood_position_model=15.5849	log10_strand_likelihood_position_model=6.27768	new_cov=0/17	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=115/77	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/94
RA	156	.	NC_007779	827921	0	T	G	bias_e_value=1.17507e-12	bias_p_value=2.52904e-19	fisher_strand_p_value=5.30353e-21	frequency=8.866119e-02	genotype_quality=577.5	ks_quality_p_value=1	log10_base_likelihood=-7.45603	log10_qual_likelihood_position_model=29.9142	log10_strand_likelihood_position_model=20.2754	new_cov=41/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=39/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=82/124
RA	157	.	NC_007779	829585	0	G	T	bias_e_value=0.00723954	bias_p_value=1.55812e-09	fisher_strand_p_value=6.36551e-11	frequency=9.737873e-02	genotype_quality=532.7	ks_quality_p_value=1	log10_base_likelihood=-15.4782	log10_qual_likelihood_position_model=19.6313	log10_strand_likelihood_position_model=10.1962	new_cov=17/0	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=28/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=45/109
RA	158	.	NC_007779	847635	0	A	C	bias_e_value=6.92777	bias_p_value=1.49102e-06	fisher_strand_p_value=8.63622e-08	frequency=5.813074e-02	genotype_quality=660.5	ks_quality_p_value=1	log10_base_likelihood=-8.00441	log10_qual_likelihood_position_model=21.4097	log10_strand_likelihood_position_model=7.06368	new_cov=15/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=53/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=68/119
RA	159	.	NC_007779	853114	0	C	G	bias_e_value=8.86028e-05	bias_p_value=1.90694e-11	fisher_strand_p_value=6.56389e-13	frequency=9.006357e-02	genotype_quality=570.8	ks_quality_p_value=1	log10_base_likelihood=-21.8461	log10_qual_likelihood_position_model=15.5902	log10_strand_likelihood_position_model=12.1828	new_cov=0/14	polymorphism_quality=16.6	quality=16.6	quality_position_model=Inf	ref_cov=122/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/26
RA	160	.	NC_007779	882863	0	A	.	bias_e_value=574343	bias_p_value=0.123612	fisher_strand_p_value=0.0787117	frequency=1.185036e-02	genotype_quality=1032.6	ks_quality_p_value=0.339828	log10_base_likelihood=-8.40676	log10_qual_likelihood_position_model=1.58269	log10_strand_likelihood_position_model=1.10396	new_cov=0/3	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.24203e-07	ref_cov=144/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/109
RA	161	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=695.6	new_cov=112/70	quality=695.6	ref_cov=0/0	tot_cov=112/70
RA	162	.	NC_007779	894943	0	T	G	bias_e_value=1.61907e-10	bias_p_value=3.48462e-17	fisher_strand_p_value=8.17055e-19	frequency=6.437492e-02	genotype_quality=703.0	ks_quality_p_value=1	log10_base_likelihood=-6.97906	log10_qual_likelihood_position_model=26.8924	log10_strand_likelihood_position_model=18.0877	new_cov=22/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=17/156	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=39/156
RA	163	.	NC_007779	901814	0	A	C	bias_e_value=27.8957	bias_p_value=6.00381e-06	fisher_strand_p_value=3.80422e-07	frequency=6.417131e-02	genotype_quality=707.4	ks_quality_p_value=1	log10_base_likelihood=-7.00048	log10_qual_likelihood_position_model=20.2462	log10_strand_likelihood_position_model=6.43619	new_cov=0/22	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=105/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/120
RA	164	.	NC_007779	904838	0	C	A	bias_e_value=1.09248e-05	bias_p_value=2.35128e-12	fisher_strand_p_value=8.48071e-14	frequency=1.002378e-01	genotype_quality=879.1	ks_quality_p_value=0.888139	log10_base_likelihood=-26.5271	log10_qual_likelihood_position_model=26.769	log10_strand_likelihood_position_model=13.0716	new_cov=32/0	polymorphism_quality=21.3	quality=21.3	quality_position_model=Inf	ref_cov=84/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/156
RA	165	.	NC_007779	947970	0	C	A	bias_e_value=228.342	bias_p_value=4.91446e-05	fisher_strand_p_value=3.63353e-06	frequency=5.469799e-02	genotype_quality=747.7	ks_quality_p_value=1	log10_base_likelihood=-9.48127	log10_qual_likelihood_position_model=13.1381	log10_strand_likelihood_position_model=5.43967	new_cov=17/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=94/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/112
RA	166	.	NC_007779	954820	0	A	C	bias_e_value=1.68904e-05	bias_p_value=3.63522e-12	fisher_strand_p_value=1.18154e-13	frequency=1.453614e-01	genotype_quality=433.3	ks_quality_p_value=1	log10_base_likelihood=-14.4883	log10_qual_likelihood_position_model=26.746	log10_strand_likelihood_position_model=12.9913	new_cov=0/39	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=78/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=78/88
RA	167	.	NC_007779	964573	1	.	G	bias_e_value=2554090	bias_p_value=0.549701	fisher_strand_p_value=0.247657	frequency=1.149368e-02	genotype_quality=1309.4	ks_quality_p_value=0.879269	log10_base_likelihood=-12.8473	log10_qual_likelihood_position_model=1.28787	log10_strand_likelihood_position_model=0.873383	new_cov=3/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=9.98239e-13	ref_cov=131/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/127
RA	168	.	NC_007779	969494	0	C	A	bias_e_value=17.8957	bias_p_value=3.85158e-06	fisher_strand_p_value=2.37139e-07	frequency=6.179810e-02	genotype_quality=714.7	ks_quality_p_value=0.999165	log10_base_likelihood=-9.8496	log10_qual_likelihood_position_model=16.0118	log10_strand_likelihood_position_model=6.625	new_cov=20/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=92/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/119
RA	169	.	NC_007779	987436	0	A	C	bias_e_value=0.0362227	bias_p_value=7.79598e-09	fisher_strand_p_value=3.41985e-10	frequency=1.087122e-01	genotype_quality=552.1	ks_quality_p_value=1	log10_base_likelihood=-10.6125	log10_qual_likelihood_position_model=28.1424	log10_strand_likelihood_position_model=9.59633	new_cov=0/33	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=87/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=87/108
RA	170	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=610.8	new_cov=49/98	quality=610.8	ref_cov=0/0	tot_cov=49/98
RA	171	.	NC_007779	987916	0	T	G	bias_e_value=1.34439e-08	bias_p_value=2.89345e-15	fisher_strand_p_value=7.59097e-17	frequency=1.096144e-01	genotype_quality=520.0	ks_quality_p_value=1	log10_base_likelihood=-30.3581	log10_qual_likelihood_position_model=20.3135	log10_strand_likelihood_position_model=16.1197	new_cov=18/0	polymorphism_quality=25.2	quality=25.2	quality_position_model=Inf	ref_cov=9/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/121
RA	172	.	NC_007779	1002413	0	T	G	bias_e_value=2.14388e-14	bias_p_value=4.61413e-21	fisher_strand_p_value=8.9124e-23	frequency=1.400785e-01	genotype_quality=738.7	ks_quality_p_value=1	log10_base_likelihood=-20.5842	log10_qual_likelihood_position_model=40.5289	log10_strand_likelihood_position_model=22.0531	new_cov=52/1	polymorphism_quality=15.3	quality=15.3	quality_position_model=Inf	ref_cov=56/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/149
RA	173	.	NC_007779	1003248	0	A	G	bias_e_value=1400970	bias_p_value=0.301521	fisher_strand_p_value=0.28257	frequency=1.420975e-02	genotype_quality=847.7	ks_quality_p_value=0.310909	log10_base_likelihood=-6.08131	log10_qual_likelihood_position_model=2.68232	log10_strand_likelihood_position_model=0.649045	new_cov=0/3	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.000161921	ref_cov=82/125	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=82/128
RA	174	.	NC_007779	1005103	0	T	.	bias_e_value=287698	bias_p_value=0.0619194	fisher_strand_p_value=0.234125	frequency=1.169014e-02	genotype_quality=689.3	ks_quality_p_value=0.0482287	log10_base_likelihood=-5.7514	log10_qual_likelihood_position_model=1.75929	log10_strand_likelihood_position_model=0.630553	new_cov=2/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=3.62043e-05	ref_cov=81/88	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=83/88
RA	175	.	NC_007779	1006080	0	C	A	bias_e_value=3114.11	bias_p_value=0.000670231	fisher_strand_p_value=6.52172e-05	frequency=3.990841e-02	genotype_quality=778.8	ks_quality_p_value=0.962628	log10_base_likelihood=-6.45151	log10_qual_likelihood_position_model=11.1195	log10_strand_likelihood_position_model=4.18564	new_cov=12/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=95/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/125
RA	176	.	NC_007779	1013042	0	G	C	bias_e_value=19.6192	bias_p_value=4.2225e-06	fisher_strand_p_value=2.61335e-07	frequency=5.565262e-02	genotype_quality=516.0	ks_quality_p_value=1	log10_base_likelihood=-6.62744	log10_qual_likelihood_position_model=9.50081	log10_strand_likelihood_position_model=6.5828	new_cov=0/9	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=109/20	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/29
RA	177	.	NC_007779	1019391	0	A	.	bias_e_value=4640440	bias_p_value=0.998732	fisher_strand_p_value=1	frequency=1.270294e-02	genotype_quality=972.5	ks_quality_p_value=0.950066	log10_base_likelihood=-8.20986	log10_qual_likelihood_position_model=2.11727	log10_strand_likelihood_position_model=0.40353	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.33749e-07	ref_cov=111/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/124
RA	178	.	NC_007779	1037604	0	C	G	bias_e_value=4.62904e-08	bias_p_value=9.96279e-15	fisher_strand_p_value=2.72972e-16	frequency=1.376615e-01	genotype_quality=486.9	ks_quality_p_value=0.990521	log10_base_likelihood=-29.4196	log10_qual_likelihood_position_model=20.2821	log10_strand_likelihood_position_model=15.5639	new_cov=20/0	polymorphism_quality=24.2	quality=24.2	quality_position_model=Inf	ref_cov=12/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=33/108
RA	179	.	NC_007779	1050711	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	180	.	NC_007779	1050712	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	181	.	NC_007779	1050713	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	182	.	NC_007779	1050714	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	183	.	NC_007779	1050715	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	184	.	NC_007779	1050716	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	185	.	NC_007779	1050717	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	186	.	NC_007779	1050718	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	187	.	NC_007779	1050719	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	188	.	NC_007779	1050720	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	189	.	NC_007779	1050722	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	190	.	NC_007779	1050723	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	191	.	NC_007779	1050724	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	192	.	NC_007779	1050725	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	193	.	NC_007779	1050726	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	194	.	NC_007779	1050727	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	195	.	NC_007779	1050728	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	196	.	NC_007779	1050730	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	197	.	NC_007779	1086017	0	A	C	bias_e_value=1.74846e-09	bias_p_value=3.7631e-16	fisher_strand_p_value=9.35855e-18	frequency=1.087861e-01	genotype_quality=670.7	ks_quality_p_value=1	log10_base_likelihood=-9.09663	log10_qual_likelihood_position_model=31.5222	log10_strand_likelihood_position_model=17.0288	new_cov=0/44	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=121/63	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/107
RA	198	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=896.3	new_cov=87/114	quality=896.3	ref_cov=0/0	tot_cov=87/114
RA	199	.	NC_007779	1096958	1	.	T	bias_e_value=4582600	bias_p_value=0.986282	fisher_strand_p_value=1	frequency=7.873535e-03	genotype_quality=1245.9	ks_quality_p_value=0.839003	log10_base_likelihood=-8.00997	log10_qual_likelihood_position_model=2.11776	log10_strand_likelihood_position_model=0.303212	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.69805e-07	ref_cov=114/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/139
RA	200	.	NC_007779	1097580	0	C	T	bias_e_value=2723310	bias_p_value=0.58612	fisher_strand_p_value=0.741309	frequency=1.725631e-01	genotype_quality=647.3	ks_quality_p_value=0.327178	log10_base_likelihood=-122.879	log10_qual_likelihood_position_model=16.9347	log10_strand_likelihood_position_model=0.911586	new_cov=19/25	polymorphism_quality=118.0	quality=118.0	quality_position_model=1.45815e-107	ref_cov=98/113	tot_cov=117/138
RA	201	.	NC_007779	1116582	0	G	C	bias_e_value=5.75936e-17	bias_p_value=1.23955e-23	fisher_strand_p_value=2.14449e-25	frequency=1.807976e-01	genotype_quality=401.6	ks_quality_p_value=1	log10_base_likelihood=-51.8719	log10_qual_likelihood_position_model=18.6031	log10_strand_likelihood_position_model=24.6687	new_cov=0/25	polymorphism_quality=46.8	quality=46.8	quality_position_model=1.35004e-10	ref_cov=110/2	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/27
RA	202	.	NC_007779	1120197	0	C	A	bias_e_value=915.315	bias_p_value=0.000196997	fisher_strand_p_value=1.63908e-05	frequency=4.601955e-02	genotype_quality=735.7	ks_quality_p_value=1	log10_base_likelihood=-6.50071	log10_qual_likelihood_position_model=11.2245	log10_strand_likelihood_position_model=4.7854	new_cov=15/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=100/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/117
RA	203	.	NC_007779	1158848	0	T	G	bias_e_value=2.20111e-19	bias_p_value=4.7373e-26	fisher_strand_p_value=7.46476e-28	frequency=1.967983e-01	genotype_quality=572.2	ks_quality_p_value=1	log10_base_likelihood=-34.0777	log10_qual_likelihood_position_model=39.6977	log10_strand_likelihood_position_model=27.127	new_cov=58/0	polymorphism_quality=28.9	quality=28.9	quality_position_model=Inf	ref_cov=37/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/123
RA	204	.	NC_007779	1163018	0	T	G	bias_e_value=0.000274004	bias_p_value=5.89722e-11	fisher_strand_p_value=2.11507e-12	frequency=1.012540e-01	genotype_quality=722.2	ks_quality_p_value=1	log10_base_likelihood=-13.9024	log10_qual_likelihood_position_model=27.3134	log10_strand_likelihood_position_model=11.6747	new_cov=33/0	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=83/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/125
RA	205	.	NC_007779	1164334	0	C	G	bias_e_value=29.5839	bias_p_value=6.36716e-06	fisher_strand_p_value=4.05055e-07	frequency=4.600239e-02	genotype_quality=524.4	ks_quality_p_value=1	log10_base_likelihood=-7.90792	log10_qual_likelihood_position_model=9.29547	log10_strand_likelihood_position_model=6.39249	new_cov=0/7	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=114/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/19
RA	206	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1045.4	new_cov=181/67	quality=1045.4	ref_cov=0/0	tot_cov=181/67
RA	207	.	NC_007779	1177683	0	A	G	bias_e_value=0.0396521	bias_p_value=8.53406e-09	fisher_strand_p_value=3.75923e-10	frequency=8.245754e-02	genotype_quality=468.7	ks_quality_p_value=1	log10_base_likelihood=-15.6825	log10_qual_likelihood_position_model=14.8077	log10_strand_likelihood_position_model=9.4249	new_cov=12/0	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=15/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/108
RA	208	.	NC_007779	1224173	0	G	A	bias_e_value=0.00376297	bias_p_value=8.09879e-10	fisher_strand_p_value=3.219e-11	frequency=1.486907e-01	genotype_quality=570.7	ks_quality_p_value=1	log10_base_likelihood=-31.3276	log10_qual_likelihood_position_model=28.0649	log10_strand_likelihood_position_model=10.5786	new_cov=0/32	polymorphism_quality=26.1	quality=26.1	quality_position_model=Inf	ref_cov=99/71	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/103
RA	209	.	NC_007779	1229345	1	.	A	bias_e_value=1619360	bias_p_value=0.348525	fisher_strand_p_value=0.166629	frequency=8.620262e-03	genotype_quality=1156.1	ks_quality_p_value=0.648571	log10_base_likelihood=-8.43978	log10_qual_likelihood_position_model=1.42807	log10_strand_likelihood_position_model=0.778249	new_cov=0/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.65831e-08	ref_cov=137/93	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/95
RA	210	.	NC_007779	1262472	0	A	C	bias_e_value=1.50859e-06	bias_p_value=3.24685e-13	fisher_strand_p_value=9.76195e-15	frequency=1.221476e-01	genotype_quality=584.0	ks_quality_p_value=1	log10_base_likelihood=-19.3099	log10_qual_likelihood_position_model=30.5231	log10_strand_likelihood_position_model=14.0264	new_cov=0/44	polymorphism_quality=14.0	quality=14.0	quality_position_model=Inf	ref_cov=101/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/117
RA	211	.	NC_007779	1273395	1	.	G	bias_e_value=632923	bias_p_value=0.13622	fisher_strand_p_value=0.0352403	frequency=1.224422e-02	genotype_quality=1221.4	ks_quality_p_value=0.859588	log10_base_likelihood=-12.5588	log10_qual_likelihood_position_model=1.98117	log10_strand_likelihood_position_model=1.45296	new_cov=3/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=3.92225e-11	ref_cov=78/164	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=81/164
RA	212	.	NC_007779	1273399	0	T	G	bias_e_value=2.60208e-23	bias_p_value=5.6003e-30	fisher_strand_p_value=7.70963e-32	frequency=1.369748e-01	genotype_quality=698.2	ks_quality_p_value=1	log10_base_likelihood=-26.2677	log10_qual_likelihood_position_model=39.8422	log10_strand_likelihood_position_model=31.113	new_cov=41/0	polymorphism_quality=21.0	quality=21.0	quality_position_model=Inf	ref_cov=16/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=57/164
RA	213	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=54.2	new_cov=7/10	quality=54.2	ref_cov=0/0	tot_cov=7/10
RA	214	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=16.5	new_cov=4/3	quality=16.5	ref_cov=0/0	tot_cov=4/3
RA	215	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=26.6	new_cov=10/7	quality=26.6	ref_cov=0/0	tot_cov=10/7
RA	216	.	NC_007779	1288911	0	T	G	bias_e_value=287.811	bias_p_value=6.19436e-05	fisher_strand_p_value=4.66612e-06	frequency=3.582287e-02	genotype_quality=754.2	ks_quality_p_value=1	log10_base_likelihood=-8.59242	log10_qual_likelihood_position_model=14.5535	log10_strand_likelihood_position_model=5.33104	new_cov=14/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=81/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/124
RA	217	.	NC_007779	1312244	0	C	T	bias_e_value=4091610	bias_p_value=0.88061	fisher_strand_p_value=0.610393	frequency=1.189709e-02	genotype_quality=1077.6	ks_quality_p_value=0.906013	log10_base_likelihood=-5.6995	log10_qual_likelihood_position_model=1.49721	log10_strand_likelihood_position_model=0.440782	new_cov=1/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=1.37001e-05	ref_cov=129/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=130/121
RA	218	.	NC_007779	1313924	0	C	A	bias_e_value=5.92751	bias_p_value=1.27574e-06	fisher_strand_p_value=7.31914e-08	frequency=4.708719e-02	genotype_quality=809.1	ks_quality_p_value=1	log10_base_likelihood=-12.1026	log10_qual_likelihood_position_model=15.9333	log10_strand_likelihood_position_model=7.13554	new_cov=11/0	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=37/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=48/148
RA	219	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1076.3	new_cov=145/113	quality=1076.3	ref_cov=0/0	tot_cov=145/113
RA	220	.	NC_007779	1324190	0	T	C	bias_e_value=1.99804e-05	bias_p_value=4.30024e-12	fisher_strand_p_value=1.40562e-13	frequency=7.896709e-02	genotype_quality=699.5	ks_quality_p_value=1	log10_base_likelihood=-8.44514	log10_qual_likelihood_position_model=21.5272	log10_strand_likelihood_position_model=12.8521	new_cov=0/26	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=142/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/80
RA	221	.	NC_007779	1325276	0	G	T	bias_e_value=23972.7	bias_p_value=0.00515949	fisher_strand_p_value=0.00061894	frequency=3.312016e-02	genotype_quality=784.9	ks_quality_p_value=0.993033	log10_base_likelihood=-6.61948	log10_qual_likelihood_position_model=12.9725	log10_strand_likelihood_position_model=3.20835	new_cov=0/10	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=112/97	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/107
RA	222	.	NC_007779	1330179	0	T	G	bias_e_value=8.22337	bias_p_value=1.76986e-06	fisher_strand_p_value=1.03606e-07	frequency=3.434467e-02	genotype_quality=805.0	ks_quality_p_value=1	log10_base_likelihood=-8.70275	log10_qual_likelihood_position_model=23.5832	log10_strand_likelihood_position_model=6.98462	new_cov=21/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=97/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/124
RA	223	.	NC_007779	1352913	1	.	T	bias_e_value=83283.2	bias_p_value=0.0179245	fisher_strand_p_value=0.00669788	frequency=2.439022e-02	genotype_quality=774.8	ks_quality_p_value=0.38439	log10_base_likelihood=-18.7983	log10_qual_likelihood_position_model=1.77507	log10_strand_likelihood_position_model=2.17406	new_cov=4/0	polymorphism_quality=13.5	quality=13.5	quality_position_model=5.84717e-17	ref_cov=44/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=48/116
RA	224	.	NC_007779	1352922	0	T	C	bias_e_value=0.358678	bias_p_value=7.7196e-08	fisher_strand_p_value=3.83686e-09	frequency=5.500841e-02	genotype_quality=487.5	ks_quality_p_value=0.986636	log10_base_likelihood=-11.7856	log10_qual_likelihood_position_model=8.82942	log10_strand_likelihood_position_model=8.41602	new_cov=8/0	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=8/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/126
RA	225	.	NC_007779	1352924	0	A	C	bias_e_value=11.6505	bias_p_value=2.50746e-06	fisher_strand_p_value=1.50036e-07	frequency=5.386066e-02	genotype_quality=478.7	ks_quality_p_value=1	log10_base_likelihood=-10.5019	log10_qual_likelihood_position_model=10.2259	log10_strand_likelihood_position_model=6.82796	new_cov=8/1	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=11/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=19/127
RA	226	.	NC_007779	1371749	1	.	T	bias_e_value=1911400	bias_p_value=0.411379	fisher_strand_p_value=0.220311	frequency=2.597427e-02	genotype_quality=1091.9	ks_quality_p_value=0.626546	log10_base_likelihood=-27.2507	log10_qual_likelihood_position_model=4.03066	log10_strand_likelihood_position_model=0.914056	new_cov=5/1	polymorphism_quality=22.0	quality=22.0	quality_position_model=1.67408e-24	ref_cov=119/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/107
RA	227	.	NC_007779	1378219	0	A	C	bias_e_value=1.4179e-08	bias_p_value=3.05165e-15	fisher_strand_p_value=8.0175e-17	frequency=1.160693e-01	genotype_quality=598.4	ks_quality_p_value=1	log10_base_likelihood=-18.0827	log10_qual_likelihood_position_model=36.5376	log10_strand_likelihood_position_model=16.096	new_cov=0/36	polymorphism_quality=12.8	quality=12.8	quality_position_model=Inf	ref_cov=114/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/82
RA	228	.	NC_007779	1378854	0	A	C	bias_e_value=7.42359e-07	bias_p_value=1.59773e-13	fisher_strand_p_value=4.70044e-15	frequency=1.096840e-01	genotype_quality=543.1	ks_quality_p_value=1	log10_base_likelihood=-9.05513	log10_qual_likelihood_position_model=26.674	log10_strand_likelihood_position_model=14.3279	new_cov=0/40	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=99/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/98
RA	229	.	NC_007779	1405508	0	G	T	bias_e_value=1.58282e-06	bias_p_value=3.40661e-13	fisher_strand_p_value=1.03529e-14	frequency=1.300249e-01	genotype_quality=476.8	ks_quality_p_value=0.990785	log10_base_likelihood=-38.9182	log10_qual_likelihood_position_model=19.5309	log10_strand_likelihood_position_model=13.9849	new_cov=17/0	polymorphism_quality=33.8	quality=33.8	quality_position_model=2.65122e-07	ref_cov=10/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=27/103
RA	230	.	NC_007779	1409137	0	G	T	bias_e_value=4.96661e-10	bias_p_value=1.06893e-16	fisher_strand_p_value=2.57571e-18	frequency=1.869674e-01	genotype_quality=652.2	ks_quality_p_value=1	log10_base_likelihood=-42.1015	log10_qual_likelihood_position_model=26.532	log10_strand_likelihood_position_model=17.6048	new_cov=0/51	polymorphism_quality=37.0	quality=37.0	quality_position_model=Inf	ref_cov=117/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/123
RA	231	.	NC_007779	1410956	1	.	T	bias_e_value=1331000	bias_p_value=0.286461	fisher_strand_p_value=1	frequency=7.299423e-03	genotype_quality=1342.7	ks_quality_p_value=0.0817509	log10_base_likelihood=-8.31482	log10_qual_likelihood_position_model=2.0414	log10_strand_likelihood_position_model=0.30468	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.86838e-08	ref_cov=151/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/122
RA	232	.	NC_007779	1429390	1	.	C	bias_e_value=3418580	bias_p_value=0.735759	deleted=1	fisher_strand_p_value=1	frequency=1	genotype_quality=4.5	ks_quality_p_value=0.367879	log10_base_likelihood=-6.54222	log10_qual_likelihood_position_model=0.30103	log10_strand_likelihood_position_model=0.30103	new_cov=1/0	polymorphism_changed_to_consensus=1	polymorphism_quality=1.0	quality=1.0	quality_position_model=7.35204e-08	ref_cov=0/1	reject=EVALUE	tot_cov=1/1
RA	233	.	NC_007779	1429455	0	G	A	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	234	.	NC_007779	1429463	0	C	G	deleted=1	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	235	.	NC_007779	1437441	0	G	A	bias_e_value=6.47644	bias_p_value=1.39388e-06	fisher_strand_p_value=8.04029e-08	frequency=3.972626e-02	genotype_quality=707.1	ks_quality_p_value=1	log10_base_likelihood=-8.79524	log10_qual_likelihood_position_model=12.2093	log10_strand_likelihood_position_model=7.09473	new_cov=0/8	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=150/18	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=150/26
RA	236	.	NC_007779	1437447	0	G	C	bias_e_value=6.08697e-10	bias_p_value=1.31006e-16	fisher_strand_p_value=3.17267e-18	frequency=1.068578e-01	genotype_quality=711.3	ks_quality_p_value=1	log10_base_likelihood=-16.458	log10_qual_likelihood_position_model=25.317	log10_strand_likelihood_position_model=17.4986	new_cov=0/29	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=151/36	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/65
RA	237	.	NC_007779	1438937	0	T	.	bias_e_value=4646010	bias_p_value=0.999931	fisher_strand_p_value=1	frequency=1.647282e-02	genotype_quality=749.6	ks_quality_p_value=0.988282	log10_base_likelihood=-8.3534	log10_qual_likelihood_position_model=2.31092	log10_strand_likelihood_position_model=0.376837	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.41432e-07	ref_cov=101/78	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=103/79
RA	238	.	NC_007779	1442205	0	G	C	bias_e_value=1.98252	bias_p_value=4.26685e-07	fisher_strand_p_value=2.29526e-08	frequency=4.982996e-02	genotype_quality=669.6	ks_quality_p_value=1	log10_base_likelihood=-8.04217	log10_qual_likelihood_position_model=10.8961	log10_strand_likelihood_position_model=7.63917	new_cov=0/10	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=141/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/34
RA	239	.	NC_007779	1479548	0	G	T	bias_e_value=1309890	bias_p_value=0.281918	fisher_strand_p_value=0.250923	frequency=1.103687e-02	genotype_quality=1171.9	ks_quality_p_value=0.318603	log10_base_likelihood=-6.17787	log10_qual_likelihood_position_model=2.02111	log10_strand_likelihood_position_model=0.819019	new_cov=0/3	polymorphism_quality=0.6	quality=0.6	quality_position_model=3.83674e-05	ref_cov=126/142	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=126/145
RA	240	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=635.5	new_cov=124/34	quality=635.5	ref_cov=0/0	tot_cov=124/34
RA	241	.	NC_007779	1483616	0	C	G	bias_e_value=7.90141e-06	bias_p_value=1.70057e-12	fisher_strand_p_value=5.41866e-14	frequency=9.553432e-02	genotype_quality=610.9	ks_quality_p_value=0.994672	log10_base_likelihood=-23.0682	log10_qual_likelihood_position_model=18.6692	log10_strand_likelihood_position_model=13.2661	new_cov=0/16	polymorphism_quality=17.8	quality=17.8	quality_position_model=Inf	ref_cov=132/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/31
RA	242	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1199.7	new_cov=112/126	quality=1199.7	ref_cov=0/0	tot_cov=112/126
RA	243	.	NC_007779	1498414	1	.	A	bias_e_value=908955	bias_p_value=0.195629	fisher_strand_p_value=0.501436	frequency=7.843018e-03	genotype_quality=1272.5	ks_quality_p_value=0.0969584	log10_base_likelihood=-8.2844	log10_qual_likelihood_position_model=1.5475	log10_strand_likelihood_position_model=0.534774	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=3.94136e-08	ref_cov=117/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/138
RA	244	.	NC_007779	1502095	1	.	T	bias_e_value=4625020	bias_p_value=0.995413	fisher_strand_p_value=1	frequency=1.117325e-02	genotype_quality=885.2	ks_quality_p_value=0.90576	log10_base_likelihood=-8.58186	log10_qual_likelihood_position_model=1.42409	log10_strand_likelihood_position_model=0.300894	new_cov=1/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=8.32452e-09	ref_cov=82/95	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=83/96
RA	245	.	NC_007779	1507752	0	A	C	bias_e_value=1.38342e-06	bias_p_value=2.97745e-13	fisher_strand_p_value=8.928e-15	frequency=9.973860e-02	genotype_quality=624.2	ks_quality_p_value=1	log10_base_likelihood=-12.1394	log10_qual_likelihood_position_model=27.1788	log10_strand_likelihood_position_model=14.0492	new_cov=0/31	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=118/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/80
RA	246	.	NC_007779	1512930	0	T	C	bias_e_value=0.00315401	bias_p_value=6.78816e-10	fisher_strand_p_value=2.6785e-11	frequency=8.511734e-02	genotype_quality=593.6	ks_quality_p_value=1	log10_base_likelihood=-6.99098	log10_qual_likelihood_position_model=20.4042	log10_strand_likelihood_position_model=10.5721	new_cov=0/24	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=116/54	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/78
RA	247	.	NC_007779	1515709	0	A	G	bias_e_value=5.03396e-13	bias_p_value=1.08343e-19	fisher_strand_p_value=2.23149e-21	frequency=2.412915e-01	genotype_quality=477.7	ks_quality_p_value=1	log10_base_likelihood=-66.5751	log10_qual_likelihood_position_model=44.5369	log10_strand_likelihood_position_model=20.8262	new_cov=56/0	polymorphism_quality=61.6	quality=61.6	quality_position_model=0.0079556	ref_cov=55/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/110
RA	248	.	NC_007779	1515714	0	A	T	bias_e_value=5.60743	bias_p_value=1.20685e-06	fisher_strand_p_value=6.90061e-08	frequency=9.383392e-02	genotype_quality=669.5	ks_quality_p_value=1	log10_base_likelihood=-18.6859	log10_qual_likelihood_position_model=22.3295	log10_strand_likelihood_position_model=7.16111	new_cov=21/0	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=79/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=100/107
RA	249	.	NC_007779	1527466	0	T	A	bias_e_value=328.157	bias_p_value=7.06271e-05	fisher_strand_p_value=5.37774e-06	frequency=5.701303e-02	genotype_quality=774.8	ks_quality_p_value=1	log10_base_likelihood=-12.4547	log10_qual_likelihood_position_model=17.5799	log10_strand_likelihood_position_model=5.2694	new_cov=0/14	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=126/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/98
RA	250	.	NC_007779	1527474	0	G	A	bias_e_value=2.00112e-08	bias_p_value=4.30687e-15	fisher_strand_p_value=1.14215e-16	frequency=1.659532e-01	genotype_quality=644.9	ks_quality_p_value=1	log10_base_likelihood=-52.2912	log10_qual_likelihood_position_model=34.1749	log10_strand_likelihood_position_model=15.9423	new_cov=0/42	polymorphism_quality=47.2	quality=47.2	quality_position_model=0.000676025	ref_cov=129/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/114
RA	251	.	NC_007779	1527479	0	C	A	bias_e_value=1.11337	bias_p_value=2.39623e-07	fisher_strand_p_value=1.40729e-08	frequency=8.032751e-02	genotype_quality=796.3	ks_quality_p_value=0.886878	log10_base_likelihood=-19.5002	log10_qual_likelihood_position_model=25.1538	log10_strand_likelihood_position_model=7.85162	new_cov=0/22	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=129/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/112
RA	252	.	NC_007779	1531018	0	A	C	bias_e_value=1.31923e-05	bias_p_value=2.8393e-12	fisher_strand_p_value=9.1525e-14	frequency=7.390451e-02	genotype_quality=597.9	ks_quality_p_value=1	log10_base_likelihood=-5.73965	log10_qual_likelihood_position_model=20.2649	log10_strand_likelihood_position_model=13.0385	new_cov=0/19	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=129/24	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/43
RA	253	.	NC_007779	1537499	0	A	G	bias_e_value=1.41808e-07	bias_p_value=3.05205e-14	fisher_strand_p_value=8.55026e-16	frequency=1.667500e-01	genotype_quality=517.5	ks_quality_p_value=1	log10_base_likelihood=-26.3192	log10_qual_likelihood_position_model=31.1685	log10_strand_likelihood_position_model=15.068	new_cov=37/0	polymorphism_quality=21.1	quality=21.1	quality_position_model=Inf	ref_cov=51/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=88/107
RA	254	.	NC_007779	1539616	0	G	T	bias_e_value=1022980	bias_p_value=0.220169	fisher_strand_p_value=0.250587	frequency=1.229668e-02	genotype_quality=1038.2	ks_quality_p_value=0.227301	log10_base_likelihood=-6.01472	log10_qual_likelihood_position_model=2.18301	log10_strand_likelihood_position_model=0.819696	new_cov=0/3	polymorphism_quality=0.5	quality=0.5	quality_position_model=8.50493e-05	ref_cov=113/127	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=113/130
RA	255	.	NC_007779	1552367	0	G	T	bias_e_value=0.00127587	bias_p_value=2.74598e-10	fisher_strand_p_value=1.04471e-11	frequency=6.764078e-02	genotype_quality=704.9	ks_quality_p_value=1	log10_base_likelihood=-6.54435	log10_qual_likelihood_position_model=15.5372	log10_strand_likelihood_position_model=10.981	new_cov=0/22	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=136/52	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/74
RA	256	.	NC_007779	1552377	0	A	C	bias_e_value=8.25021e-26	bias_p_value=1.77564e-32	fisher_strand_p_value=2.26279e-34	frequency=2.082615e-01	genotype_quality=547.3	ks_quality_p_value=1	log10_base_likelihood=-38.2562	log10_qual_likelihood_position_model=40.2212	log10_strand_likelihood_position_model=33.6454	new_cov=0/56	polymorphism_quality=33.1	quality=33.1	quality_position_model=Inf	ref_cov=134/20	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/76
RA	257	.	NC_007779	1562465	0	T	G	bias_e_value=0.00136107	bias_p_value=2.92934e-10	fisher_strand_p_value=1.11732e-11	frequency=1.108174e-01	genotype_quality=525.9	ks_quality_p_value=1	log10_base_likelihood=-12.5261	log10_qual_likelihood_position_model=19.438	log10_strand_likelihood_position_model=10.9518	new_cov=25/0	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=49/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/107
RA	258	.	NC_007779	1562518	0	A	C	bias_e_value=8.06859e-05	bias_p_value=1.73655e-11	fisher_strand_p_value=5.95751e-13	frequency=1.395435e-01	genotype_quality=334.9	ks_quality_p_value=1	log10_base_likelihood=-10.7005	log10_qual_likelihood_position_model=21.4774	log10_strand_likelihood_position_model=12.2249	new_cov=0/28	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=70/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=70/55
RA	259	.	NC_007779	1569435	1	.	G	bias_e_value=3002550	bias_p_value=0.64622	fisher_strand_p_value=0.497908	frequency=8.474350e-03	genotype_quality=1178.9	ks_quality_p_value=0.577966	log10_base_likelihood=-7.99957	log10_qual_likelihood_position_model=2.34953	log10_strand_likelihood_position_model=0.596551	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=6.10701e-07	ref_cov=117/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/117
RA	260	.	NC_007779	1578837	0	A	C	bias_e_value=0.000263858	bias_p_value=5.67884e-11	fisher_strand_p_value=2.03389e-12	frequency=5.727673e-02	genotype_quality=648.0	ks_quality_p_value=1	log10_base_likelihood=-8.44783	log10_qual_likelihood_position_model=21.7316	log10_strand_likelihood_position_model=11.6917	new_cov=0/28	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=121/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/89
RA	261	.	NC_007779	1592766	1	.	A	bias_e_value=3822450	bias_p_value=0.822682	fisher_strand_p_value=0.498104	frequency=9.009361e-03	genotype_quality=1108.1	ks_quality_p_value=0.937808	log10_base_likelihood=-8.52733	log10_qual_likelihood_position_model=0.994389	log10_strand_likelihood_position_model=0.580762	new_cov=0/2	polymorphism_quality=3.1	quality=3.1	quality_position_model=6.64082e-09	ref_cov=108/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/114
RA	262	.	NC_007779	1595838	1	.	C	bias_e_value=3944840	bias_p_value=0.849022	fisher_strand_p_value=1	frequency=1.004982e-02	genotype_quality=976.9	ks_quality_p_value=0.503551	log10_base_likelihood=-8.46307	log10_qual_likelihood_position_model=0.773219	log10_strand_likelihood_position_model=0.302023	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.36633e-09	ref_cov=90/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=91/108
RA	263	.	NC_007779	1595962	1	.	C	bias_e_value=1106230	bias_p_value=0.238088	fisher_strand_p_value=0.501449	frequency=9.803772e-03	genotype_quality=990.7	ks_quality_p_value=0.126298	log10_base_likelihood=-9.0318	log10_qual_likelihood_position_model=2.01943	log10_strand_likelihood_position_model=0.530411	new_cov=2/0	polymorphism_quality=3.6	quality=3.6	quality_position_model=2.02673e-08	ref_cov=109/93	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/93
RA	264	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=792.0	new_cov=93/110	quality=792.0	ref_cov=0/0	tot_cov=93/110
RA	265	.	NC_007779	1628027	0	G	T	bias_e_value=17.5579	bias_p_value=3.77887e-06	fisher_strand_p_value=2.36144e-07	frequency=1.621923e-01	genotype_quality=296.5	ks_quality_p_value=0.983203	log10_base_likelihood=-35.0581	log10_qual_likelihood_position_model=12.688	log10_strand_likelihood_position_model=6.62682	new_cov=15/0	polymorphism_quality=29.9	quality=29.9	quality_position_model=7.25153e-18	ref_cov=23/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=38/54
RA	266	.	NC_007779	1640426	1	.	A	bias_e_value=4597230	bias_p_value=0.989432	fisher_strand_p_value=1	frequency=1.111031e-02	genotype_quality=897.4	ks_quality_p_value=0.858187	log10_base_likelihood=-7.8002	log10_qual_likelihood_position_model=2.46673	log10_strand_likelihood_position_model=0.304006	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=6.46872e-07	ref_cov=79/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=80/100
RA	267	.	NC_007779	1642159	0	A	.	bias_e_value=1803800	bias_p_value=0.388221	fisher_strand_p_value=0.563775	frequency=1.259708e-02	genotype_quality=984.7	ks_quality_p_value=0.224535	log10_base_likelihood=-8.34988	log10_qual_likelihood_position_model=2.32739	log10_strand_likelihood_position_model=0.547143	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.22723e-07	ref_cov=143/92	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/94
RA	268	.	NC_007779	1651009	0	T	G	bias_e_value=6.14336e-10	bias_p_value=1.3222e-16	fisher_strand_p_value=3.2028e-18	frequency=1.818190e-01	genotype_quality=378.7	ks_quality_p_value=1	log10_base_likelihood=-29.7895	log10_qual_likelihood_position_model=26.7967	log10_strand_likelihood_position_model=17.4945	new_cov=27/0	polymorphism_quality=24.6	quality=24.6	quality_position_model=Inf	ref_cov=13/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=40/88
RA	269	.	NC_007779	1660545	0	G	T	bias_e_value=1935.3	bias_p_value=0.000416522	fisher_strand_p_value=3.71913e-05	frequency=3.470898e-02	genotype_quality=843.9	ks_quality_p_value=1	log10_base_likelihood=-6.11999	log10_qual_likelihood_position_model=10.601	log10_strand_likelihood_position_model=4.42956	new_cov=0/14	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=128/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/127
RA	270	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=976.2	new_cov=90/104	quality=976.2	ref_cov=0/0	tot_cov=90/104
RA	271	.	NC_007779	1671093	0	G	T	bias_e_value=154.533	bias_p_value=3.32592e-05	fisher_strand_p_value=2.39298e-06	frequency=6.224966e-02	genotype_quality=734.7	ks_quality_p_value=0.996574	log10_base_likelihood=-8.79948	log10_qual_likelihood_position_model=18.5743	log10_strand_likelihood_position_model=5.69537	new_cov=0/21	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=103/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/129
RA	272	.	NC_007779	1681402	0	T	G	bias_e_value=1.75532e-05	bias_p_value=3.77786e-12	fisher_strand_p_value=1.22949e-13	frequency=9.662104e-02	genotype_quality=590.2	ks_quality_p_value=1	log10_base_likelihood=-14.4373	log10_qual_likelihood_position_model=24.2411	log10_strand_likelihood_position_model=12.9103	new_cov=27/0	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=44/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=71/115
RA	273	.	NC_007779	1686463	0	A	C	bias_e_value=2.47953e-05	bias_p_value=5.33654e-12	fisher_strand_p_value=1.75718e-13	frequency=8.965874e-02	genotype_quality=521.8	ks_quality_p_value=1	log10_base_likelihood=-9.58733	log10_qual_likelihood_position_model=23.2906	log10_strand_likelihood_position_model=12.7552	new_cov=0/29	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=102/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/73
RA	274	.	NC_007779	1703335	0	G	C	bias_e_value=2.61787e-08	bias_p_value=5.63427e-15	fisher_strand_p_value=1.58551e-16	frequency=1.355972e-01	genotype_quality=538.1	ks_quality_p_value=0.949338	log10_base_likelihood=-37.4756	log10_qual_likelihood_position_model=20.7639	log10_strand_likelihood_position_model=15.7998	new_cov=21/0	polymorphism_quality=32.3	quality=32.3	quality_position_model=0.0179286	ref_cov=15/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=36/117
RA	275	.	NC_007779	1703849	1	.	T	bias_e_value=2057820	bias_p_value=0.44289	fisher_strand_p_value=0.184173	frequency=8.196831e-03	genotype_quality=1205.8	ks_quality_p_value=0.838454	log10_base_likelihood=-8.61893	log10_qual_likelihood_position_model=1.3017	log10_strand_likelihood_position_model=0.734773	new_cov=2/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=1.59644e-08	ref_cov=103/139	reject=POLYMORPHISM_STRAND	tot_cov=105/139
RA	276	.	NC_007779	1709966	0	C	A	bias_e_value=3253560	bias_p_value=0.700243	fisher_strand_p_value=0.630635	frequency=1.309776e-02	genotype_quality=1070.7	ks_quality_p_value=0.529587	log10_base_likelihood=-6.12694	log10_qual_likelihood_position_model=4.9279	log10_strand_likelihood_position_model=0.517974	new_cov=3/1	polymorphism_quality=0.6	quality=0.6	quality_position_model=0.0345919	ref_cov=137/112	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=140/114
RA	277	.	NC_007779	1710558	0	C	G	bias_e_value=687.447	bias_p_value=0.000147955	fisher_strand_p_value=1.19989e-05	frequency=6.707096e-02	genotype_quality=758.4	ks_quality_p_value=1	log10_base_likelihood=-10.0216	log10_qual_likelihood_position_model=22.1608	log10_strand_likelihood_position_model=4.99536	new_cov=2/19	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=126/89	reject=FISHER_STRAND_P_VALUE	tot_cov=128/108
RA	278	.	NC_007779	1713510	0	A	C	bias_e_value=5.05742e-10	bias_p_value=1.08848e-16	fisher_strand_p_value=2.62398e-18	frequency=1.155267e-01	genotype_quality=735.4	ks_quality_p_value=1	log10_base_likelihood=-19.8984	log10_qual_likelihood_position_model=36.4753	log10_strand_likelihood_position_model=17.581	new_cov=0/42	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=140/66	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/109
RA	279	.	NC_007779	1716031	1	.	T	bias_e_value=2133660	bias_p_value=0.459214	fisher_strand_p_value=0.624746	frequency=1.886749e-02	genotype_quality=1013.3	ks_quality_p_value=0.261375	log10_base_likelihood=-17.702	log10_qual_likelihood_position_model=2.35245	log10_strand_likelihood_position_model=0.547669	new_cov=3/1	polymorphism_quality=12.4	quality=12.4	quality_position_model=6.52991e-17	ref_cov=110/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/99
RA	280	.	NC_007779	1732512	0	T	G	bias_e_value=0.0485572	bias_p_value=1.04506e-08	fisher_strand_p_value=4.64687e-10	frequency=7.622004e-02	genotype_quality=542.2	ks_quality_p_value=1	log10_base_likelihood=-7.78335	log10_qual_likelihood_position_model=18.6932	log10_strand_likelihood_position_model=9.33284	new_cov=25/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=58/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=83/96
RA	281	.	NC_007779	1763744	0	C	A	bias_e_value=4.45782	bias_p_value=9.59429e-07	fisher_strand_p_value=5.41062e-08	frequency=5.403996e-02	genotype_quality=831.7	ks_quality_p_value=1	log10_base_likelihood=-9.94608	log10_qual_likelihood_position_model=16.8229	log10_strand_likelihood_position_model=7.26675	new_cov=20/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=99/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/143
RA	282	.	NC_007779	1771362	0	C	T	bias_e_value=578087	bias_p_value=0.124418	fisher_strand_p_value=0.612321	frequency=1.284027e-02	genotype_quality=959.3	ks_quality_p_value=0.0440476	log10_base_likelihood=-6.24539	log10_qual_likelihood_position_model=2.34407	log10_strand_likelihood_position_model=0.437857	new_cov=2/1	polymorphism_quality=0.7	quality=0.7	quality_position_model=2.82489e-05	ref_cov=111/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=113/120
RA	283	.	NC_007779	1772183	1	.	T	bias_e_value=959122	bias_p_value=0.206426	fisher_strand_p_value=1	frequency=1.639366e-02	genotype_quality=1173.7	ks_quality_p_value=0.0522326	log10_base_likelihood=-17.9863	log10_qual_likelihood_position_model=3.04965	log10_strand_likelihood_position_model=0.423329	new_cov=2/2	polymorphism_quality=12.7	quality=12.7	quality_position_model=1.28122e-16	ref_cov=116/124	reject=INDEL_HOMOPOLYMER	tot_cov=118/126
RA	284	.	NC_007779	1781198	0	T	.	bias_e_value=4187970	bias_p_value=0.901351	fisher_strand_p_value=0.593422	frequency=1.303005e-02	genotype_quality=948.1	ks_quality_p_value=0.994385	log10_base_likelihood=-7.71529	log10_qual_likelihood_position_model=4.97913	log10_strand_likelihood_position_model=0.467244	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=0.000533347	ref_cov=103/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/125
RA	285	.	NC_007779	1801443	0	A	C	bias_e_value=1.49957e-07	bias_p_value=3.22743e-14	fisher_strand_p_value=9.05617e-16	frequency=9.386969e-02	genotype_quality=586.6	ks_quality_p_value=1	log10_base_likelihood=-5.8952	log10_qual_likelihood_position_model=31.4741	log10_strand_likelihood_position_model=15.0431	new_cov=0/36	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=109/50	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=109/86
RA	286	.	NC_007779	1801456	0	C	G	bias_e_value=90.039	bias_p_value=1.93785e-05	fisher_strand_p_value=1.39777e-06	frequency=8.087778e-02	genotype_quality=659.1	ks_quality_p_value=0.954326	log10_base_likelihood=-16.4533	log10_qual_likelihood_position_model=17.4995	log10_strand_likelihood_position_model=5.88375	new_cov=0/20	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=101/94	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=101/114
RA	287	.	NC_007779	1820099	0	A	C	bias_e_value=2.26208e-15	bias_p_value=4.86852e-22	fisher_strand_p_value=9.00506e-24	frequency=1.782279e-01	genotype_quality=579.3	ks_quality_p_value=1	log10_base_likelihood=-43.9873	log10_qual_likelihood_position_model=32.9216	log10_strand_likelihood_position_model=23.0455	new_cov=0/41	polymorphism_quality=38.9	quality=38.9	quality_position_model=Inf	ref_cov=133/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/73
RA	288	.	NC_007779	1826775	0	G	A	bias_e_value=48078.4	bias_p_value=0.0103476	fisher_strand_p_value=0.0013617	frequency=4.543114e-02	genotype_quality=754.9	ks_quality_p_value=1	log10_base_likelihood=-9.59381	log10_qual_likelihood_position_model=14.3144	log10_strand_likelihood_position_model=2.89695	new_cov=0/11	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=95/108	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=95/119
RA	289	.	NC_007779	1837206	0	G	T	bias_e_value=0.395465	bias_p_value=8.51134e-08	fisher_strand_p_value=4.24024e-09	frequency=8.408260e-02	genotype_quality=591.5	ks_quality_p_value=0.989324	log10_base_likelihood=-19.6004	log10_qual_likelihood_position_model=19.4029	log10_strand_likelihood_position_model=8.37261	new_cov=16/0	polymorphism_quality=14.3	quality=14.3	quality_position_model=Inf	ref_cov=41/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=57/115
RA	290	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=947.8	new_cov=125/105	quality=947.8	ref_cov=0/0	tot_cov=126/105
RA	291	.	NC_007779	1846634	0	A	.	bias_e_value=4204690	bias_p_value=0.904948	fisher_strand_p_value=0.66741	frequency=2.211571e-02	genotype_quality=934.0	ks_quality_p_value=0.89448	log10_base_likelihood=-15.0471	log10_qual_likelihood_position_model=3.92137	log10_strand_likelihood_position_model=0.53294	new_cov=2/3	polymorphism_quality=9.7	quality=9.7	quality_position_model=1.24257e-12	ref_cov=118/103	reject=INDEL_HOMOPOLYMER	tot_cov=120/106
RA	292	.	NC_007779	1879404	0	A	C	bias_e_value=2.57553e-15	bias_p_value=5.54314e-22	fisher_strand_p_value=1.0278e-23	frequency=1.078787e-01	genotype_quality=648.3	ks_quality_p_value=1	log10_base_likelihood=-19.5349	log10_qual_likelihood_position_model=31.9783	log10_strand_likelihood_position_model=22.9881	new_cov=0/27	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=150/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/39
RA	293	.	NC_007779	1879996	0	G	T	bias_e_value=617.552	bias_p_value=0.000132912	fisher_strand_p_value=1.06779e-05	frequency=4.687357e-02	genotype_quality=727.0	ks_quality_p_value=1	log10_base_likelihood=-6.22233	log10_qual_likelihood_position_model=12.2423	log10_strand_likelihood_position_model=4.97151	new_cov=11/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=64/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=75/128
RA	294	.	NC_007779	1906475	1	.	C	bias_e_value=2413860	bias_p_value=0.519519	fisher_strand_p_value=0.217774	frequency=9.174347e-03	genotype_quality=1068.4	ks_quality_p_value=0.911642	log10_base_likelihood=-8.20327	log10_qual_likelihood_position_model=1.90554	log10_strand_likelihood_position_model=0.661995	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.51889e-07	ref_cov=100/116	reject=POLYMORPHISM_STRAND	tot_cov=102/116
RA	295	.	NC_007779	1906477	1	.	G	bias_e_value=41470.2	bias_p_value=0.00892537	fisher_strand_p_value=0.00116753	frequency=4.144859e-02	genotype_quality=882.4	ks_quality_p_value=0.983997	log10_base_likelihood=-30.8348	log10_qual_likelihood_position_model=10.4198	log10_strand_likelihood_position_model=2.93273	new_cov=8/0	polymorphism_quality=25.6	quality=25.6	quality_position_model=1.25676e-19	ref_cov=77/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=85/108
RA	296	.	NC_007779	1906488	0	G	T	bias_e_value=30.5938	bias_p_value=6.58452e-06	fisher_strand_p_value=4.1984e-07	frequency=5.612040e-02	genotype_quality=693.9	ks_quality_p_value=1	log10_base_likelihood=-6.45046	log10_qual_likelihood_position_model=14.8536	log10_strand_likelihood_position_model=6.37692	new_cov=15/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=62/116	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=77/116
RA	297	.	NC_007779	1906502	0	A	T	bias_e_value=12414.6	bias_p_value=0.00267192	fisher_strand_p_value=0.000292418	frequency=4.049683e-02	genotype_quality=673.7	ks_quality_p_value=1	log10_base_likelihood=-8.13315	log10_qual_likelihood_position_model=11.6002	log10_strand_likelihood_position_model=3.534	new_cov=8/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=59/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=67/112
RA	298	.	NC_007779	1907281	0	C	A	bias_e_value=4224850	bias_p_value=0.909286	fisher_strand_p_value=0.678684	frequency=1.035404e-02	genotype_quality=2098.5	ks_quality_p_value=0.892188	log10_base_likelihood=-9.93413	log10_qual_likelihood_position_model=3.74858	log10_strand_likelihood_position_model=0.514969	new_cov=3/2	polymorphism_quality=4.5	quality=4.5	quality_position_model=1.39773e-07	ref_cov=231/244	tot_cov=234/246
RA	299	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=809.1	new_cov=114/91	quality=809.1	ref_cov=0/0	tot_cov=114/92
RA	300	.	NC_007779	1956118	0	C	A	bias_e_value=909.442	bias_p_value=0.000195733	fisher_strand_p_value=1.71183e-05	frequency=5.402327e-02	genotype_quality=443.4	ks_quality_p_value=0.950801	log10_base_likelihood=-16.1006	log10_qual_likelihood_position_model=6.40068	log10_strand_likelihood_position_model=4.76654	new_cov=0/6	polymorphism_quality=10.8	quality=10.8	quality_position_model=8.143e-07	ref_cov=91/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/20
RA	301	.	NC_007779	1971508	0	A	C	bias_e_value=4.51264e-10	bias_p_value=9.71226e-17	fisher_strand_p_value=2.33476e-18	frequency=1.414919e-01	genotype_quality=489.6	ks_quality_p_value=1	log10_base_likelihood=-30.6808	log10_qual_likelihood_position_model=22.886	log10_strand_likelihood_position_model=17.6318	new_cov=0/24	polymorphism_quality=25.5	quality=25.5	quality_position_model=Inf	ref_cov=117/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/39
RA	302	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=842.4	new_cov=103/104	quality=842.4	ref_cov=0/0	tot_cov=103/104
RA	303	.	NC_007779	1993894	0	A	C	bias_e_value=0.490272	bias_p_value=1.05518e-07	fisher_strand_p_value=5.25926e-09	frequency=9.252214e-02	genotype_quality=696.2	ks_quality_p_value=1	log10_base_likelihood=-14.7327	log10_qual_likelihood_position_model=30.3177	log10_strand_likelihood_position_model=8.52275	new_cov=0/30	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=96/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=96/120
RA	304	.	NC_007779	1999251	0	T	G	bias_e_value=0.143919	bias_p_value=3.09747e-08	fisher_strand_p_value=1.45072e-09	frequency=9.447956e-02	genotype_quality=504.8	ks_quality_p_value=1	log10_base_likelihood=-8.51046	log10_qual_likelihood_position_model=23.7716	log10_strand_likelihood_position_model=8.8707	new_cov=33/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=69/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/73
RA	305	.	NC_007779	2004055	0	A	C	bias_e_value=3.53402e-23	bias_p_value=7.60605e-30	fisher_strand_p_value=1.05158e-31	frequency=2.060924e-01	genotype_quality=621.0	ks_quality_p_value=1	log10_base_likelihood=-41.0408	log10_qual_likelihood_position_model=42.5914	log10_strand_likelihood_position_model=30.9782	new_cov=0/65	polymorphism_quality=35.9	quality=35.9	quality_position_model=Inf	ref_cov=139/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/105
RA	306	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=997.3	new_cov=109/126	quality=997.3	ref_cov=0/0	tot_cov=109/126
RA	307	.	NC_007779	2027359	0	T	A	bias_e_value=272239	bias_p_value=0.0585923	fisher_strand_p_value=0.0107361	frequency=2.369881e-02	genotype_quality=935.5	ks_quality_p_value=0.983125	log10_base_likelihood=-6.28507	log10_qual_likelihood_position_model=9.91328	log10_strand_likelihood_position_model=1.96915	new_cov=0/6	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=127/109	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=127/115
RA	308	.	NC_007779	2060392	0	T	G	bias_e_value=1.97753e-08	bias_p_value=4.25611e-15	fisher_strand_p_value=1.12832e-16	frequency=1.663218e-01	genotype_quality=529.6	ks_quality_p_value=1	log10_base_likelihood=-21.722	log10_qual_likelihood_position_model=50.377	log10_strand_likelihood_position_model=15.9913	new_cov=59/0	polymorphism_quality=16.5	quality=16.5	quality_position_model=Inf	ref_cov=76/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/90
RA	309	.	NC_007779	2065611	0	C	A	bias_e_value=559.817	bias_p_value=0.000120486	fisher_strand_p_value=9.60281e-06	frequency=4.016304e-02	genotype_quality=804.7	ks_quality_p_value=0.999435	log10_base_likelihood=-7.04927	log10_qual_likelihood_position_model=16.4344	log10_strand_likelihood_position_model=5.0176	new_cov=15/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=99/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/124
RA	310	.	NC_007779	2082881	0	A	.	bias_e_value=4082460	bias_p_value=0.878642	fisher_strand_p_value=0.606015	frequency=1.309299e-02	genotype_quality=940.5	ks_quality_p_value=0.907103	log10_base_likelihood=-8.4627	log10_qual_likelihood_position_model=1.37936	log10_strand_likelihood_position_model=0.446643	new_cov=1/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.40357e-08	ref_cov=119/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/109
RA	311	.	NC_007779	2089418	0	G	.	bias_e_value=3720240	bias_p_value=0.800684	fisher_strand_p_value=0.521445	frequency=8.158684e-03	genotype_quality=1069.9	ks_quality_p_value=0.842531	log10_base_likelihood=-5.68339	log10_qual_likelihood_position_model=0.955436	log10_strand_likelihood_position_model=0.433108	new_cov=0/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=3.77644e-06	ref_cov=96/147	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=96/149
RA	312	.	NC_007779	2089543	0	A	C	bias_e_value=1.18348e-08	bias_p_value=2.54713e-15	fisher_strand_p_value=6.65952e-17	frequency=1.125383e-01	genotype_quality=784.4	ks_quality_p_value=1	log10_base_likelihood=-17.9607	log10_qual_likelihood_position_model=34.7337	log10_strand_likelihood_position_model=16.1766	new_cov=0/37	polymorphism_quality=12.7	quality=12.7	quality_position_model=Inf	ref_cov=146/66	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/103
RA	313	.	NC_007779	2098223	0	T	G	bias_e_value=2.34089e-05	bias_p_value=5.03814e-12	fisher_strand_p_value=1.65568e-13	frequency=7.281542e-02	genotype_quality=626.8	ks_quality_p_value=1	log10_base_likelihood=-7.03512	log10_qual_likelihood_position_model=23.2342	log10_strand_likelihood_position_model=12.781	new_cov=33/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=63/114	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=96/114
RA	314	.	NC_007779	2101941	0	A	.	bias_e_value=1676150	bias_p_value=0.360748	fisher_strand_p_value=0.272176	frequency=1.249313e-02	genotype_quality=992.4	ks_quality_p_value=0.417478	log10_base_likelihood=-8.45337	log10_qual_likelihood_position_model=1.31461	log10_strand_likelihood_position_model=0.687551	new_cov=3/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.1803e-08	ref_cov=139/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/98
RA	315	.	NC_007779	2106207	0	T	.	bias_e_value=1370280	bias_p_value=0.294917	fisher_strand_p_value=1	frequency=1.378727e-02	genotype_quality=603.7	ks_quality_p_value=0.0851556	log10_base_likelihood=-5.83404	log10_qual_likelihood_position_model=1.32322	log10_strand_likelihood_position_model=0.301529	new_cov=1/1	polymorphism_quality=0.3	quality=0.3	quality_position_model=4.64136e-06	ref_cov=78/65	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=79/66
RA	316	.	NC_007779	2107010	1	.	A	bias_e_value=1665150	bias_p_value=0.358379	fisher_strand_p_value=0.177815	frequency=9.614944e-03	genotype_quality=1018.1	ks_quality_p_value=0.632908	log10_base_likelihood=-8.51124	log10_qual_likelihood_position_model=1.27954	log10_strand_likelihood_position_model=0.750032	new_cov=0/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=2.02813e-08	ref_cov=120/86	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/88
RA	317	.	NC_007779	2138003	0	A	C	bias_e_value=2802970	bias_p_value=0.603264	fisher_strand_p_value=1	frequency=8.276939e-03	genotype_quality=1050.4	ks_quality_p_value=0.25486	log10_base_likelihood=-6.06337	log10_qual_likelihood_position_model=3.36594	log10_strand_likelihood_position_model=0.397954	new_cov=2/1	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.000494212	ref_cov=134/118	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=136/119
RA	318	.	NC_007779	2156216	0	G	A	bias_e_value=4092390	bias_p_value=0.880778	fisher_strand_p_value=0.600295	frequency=1.382160e-02	genotype_quality=906.6	ks_quality_p_value=0.921726	log10_base_likelihood=-5.67964	log10_qual_likelihood_position_model=1.99748	log10_strand_likelihood_position_model=0.455166	new_cov=1/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=5.0268e-05	ref_cov=114/99	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=115/101
RA	319	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=979.5	new_cov=104/128	quality=979.5	ref_cov=0/1	tot_cov=104/129
RA	320	.	NC_007779	2174678	0	C	G	bias_e_value=2.02355e-09	bias_p_value=4.35515e-16	fisher_strand_p_value=1.08916e-17	frequency=1.448240e-01	genotype_quality=660.3	ks_quality_p_value=0.998148	log10_base_likelihood=-43.1147	log10_qual_likelihood_position_model=27.0725	log10_strand_likelihood_position_model=16.9629	new_cov=0/29	polymorphism_quality=38.0	quality=38.0	quality_position_model=Inf	ref_cov=131/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/61
RA	321	.	NC_007779	2199432	0	G	C	bias_e_value=7.53615e-13	bias_p_value=1.62196e-19	fisher_strand_p_value=3.36928e-21	frequency=1.411071e-01	genotype_quality=642.7	ks_quality_p_value=1	log10_base_likelihood=-46.2794	log10_qual_likelihood_position_model=26.5811	log10_strand_likelihood_position_model=20.4725	new_cov=0/26	polymorphism_quality=41.2	quality=41.2	quality_position_model=Inf	ref_cov=140/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=140/42
RA	322	.	NC_007779	2211749	0	G	C	bias_e_value=10.9514	bias_p_value=2.357e-06	fisher_strand_p_value=1.40576e-07	frequency=5.082417e-02	genotype_quality=688.2	ks_quality_p_value=0.999317	log10_base_likelihood=-10.4168	log10_qual_likelihood_position_model=11.6384	log10_strand_likelihood_position_model=6.85209	new_cov=11/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=37/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=48/137
RA	323	.	NC_007779	2212417	0	G	T	bias_e_value=0.104339	bias_p_value=2.24562e-08	fisher_strand_p_value=1.03941e-09	frequency=6.341314e-02	genotype_quality=567.4	ks_quality_p_value=0.996139	log10_base_likelihood=-20.2927	log10_qual_likelihood_position_model=11.0468	log10_strand_likelihood_position_model=8.98321	new_cov=9/0	polymorphism_quality=15.0	quality=15.0	quality_position_model=0.137492	ref_cov=9/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=18/123
RA	324	.	NC_007779	2213136	0	G	T	bias_e_value=1.75934e-11	bias_p_value=3.78652e-18	fisher_strand_p_value=8.44158e-20	frequency=1.854572e-01	genotype_quality=512.2	ks_quality_p_value=0.998568	log10_base_likelihood=-71.112	log10_qual_likelihood_position_model=26.2327	log10_strand_likelihood_position_model=19.0736	new_cov=30/0	polymorphism_quality=66.1	quality=66.1	quality_position_model=4.93124e-28	ref_cov=19/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/110
RA	325	.	NC_007779	2213138	0	C	G	bias_e_value=2042.67	bias_p_value=0.00043963	fisher_strand_p_value=4.0442e-05	frequency=4.134369e-02	genotype_quality=516.7	ks_quality_p_value=0.975808	log10_base_likelihood=-5.79967	log10_qual_likelihood_position_model=7.50709	log10_strand_likelihood_position_model=4.39317	new_cov=7/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=30/110	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=37/110
RA	326	.	NC_007779	2222886	0	T	G	bias_e_value=3862.72	bias_p_value=0.000831347	fisher_strand_p_value=7.96996e-05	frequency=3.471470e-02	genotype_quality=454.9	ks_quality_p_value=0.999339	log10_base_likelihood=-7.24836	log10_qual_likelihood_position_model=6.19109	log10_strand_likelihood_position_model=4.09854	new_cov=4/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=8/100	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=12/100
RA	327	.	NC_007779	2226744	0	T	G	bias_e_value=3.91402e-10	bias_p_value=8.42389e-17	fisher_strand_p_value=2.01797e-18	frequency=1.182823e-01	genotype_quality=735.3	ks_quality_p_value=1	log10_base_likelihood=-16.3334	log10_qual_likelihood_position_model=37.7221	log10_strand_likelihood_position_model=17.6951	new_cov=40/0	polymorphism_quality=11.0	quality=11.0	quality_position_model=Inf	ref_cov=62/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=103/144
RA	328	.	NC_007779	2245262	0	G	C	bias_e_value=9.699	bias_p_value=2.08745e-06	fisher_strand_p_value=1.24069e-07	frequency=6.288433e-02	genotype_quality=473.4	ks_quality_p_value=0.995128	log10_base_likelihood=-7.09208	log10_qual_likelihood_position_model=9.43499	log10_strand_likelihood_position_model=6.90634	new_cov=0/9	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=101/16	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=101/25
RA	329	.	NC_007779	2249963	0	T	G	bias_e_value=3.74037e-20	bias_p_value=8.05016e-27	fisher_strand_p_value=1.2335e-28	frequency=2.615151e-01	genotype_quality=503.1	ks_quality_p_value=1	log10_base_likelihood=-44.7299	log10_qual_likelihood_position_model=47.3424	log10_strand_likelihood_position_model=27.9089	new_cov=69/0	polymorphism_quality=39.6	quality=39.6	quality_position_model=Inf	ref_cov=41/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/111
RA	330	.	NC_007779	2264339	0	A	C	bias_e_value=0.0147006	bias_p_value=3.16391e-09	fisher_strand_p_value=1.33281e-10	frequency=8.405399e-02	genotype_quality=648.7	ks_quality_p_value=1	log10_base_likelihood=-11.2212	log10_qual_likelihood_position_model=22.4178	log10_strand_likelihood_position_model=9.87523	new_cov=0/23	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=114/56	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/79
RA	331	.	NC_007779	2278635	0	C	A	bias_e_value=22.8756	bias_p_value=4.92337e-06	fisher_strand_p_value=3.07831e-07	frequency=4.782677e-02	genotype_quality=932.0	ks_quality_p_value=1	log10_base_likelihood=-9.117	log10_qual_likelihood_position_model=18.1165	log10_strand_likelihood_position_model=6.51169	new_cov=20/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=116/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/141
RA	332	.	NC_007779	2278884	0	T	G	bias_e_value=8.49505e-09	bias_p_value=1.82833e-15	fisher_strand_p_value=4.73805e-17	frequency=1.242485e-01	genotype_quality=672.0	ks_quality_p_value=1	log10_base_likelihood=-14.359	log10_qual_likelihood_position_model=41.2083	log10_strand_likelihood_position_model=16.4579	new_cov=47/0	polymorphism_quality=9.0	quality=9.0	quality_position_model=Inf	ref_cov=71/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/116
RA	333	.	NC_007779	2287114	0	C	A	bias_e_value=13.644	bias_p_value=2.93651e-06	fisher_strand_p_value=1.99061e-07	frequency=5.601883e-02	genotype_quality=824.1	ks_quality_p_value=0.891653	log10_base_likelihood=-11.4509	log10_qual_likelihood_position_model=21.6918	log10_strand_likelihood_position_model=6.70101	new_cov=0/16	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=145/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/97
RA	334	.	NC_007779	2307309	0	T	C	bias_e_value=0.000328596	bias_p_value=7.07217e-11	fisher_strand_p_value=2.55373e-12	frequency=7.095909e-02	genotype_quality=598.1	ks_quality_p_value=1	log10_base_likelihood=-15.1476	log10_qual_likelihood_position_model=15.6096	log10_strand_likelihood_position_model=11.5928	new_cov=0/14	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=144/18	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/32
RA	335	.	NC_007779	2331120	0	T	G	bias_e_value=6.09159e-19	bias_p_value=1.31105e-25	fisher_strand_p_value=2.10011e-27	frequency=1.578627e-01	genotype_quality=633.4	ks_quality_p_value=1	log10_base_likelihood=-28.2317	log10_qual_likelihood_position_model=38.5075	log10_strand_likelihood_position_model=26.6778	new_cov=49/0	polymorphism_quality=23.0	quality=23.0	quality_position_model=Inf	ref_cov=34/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/142
RA	336	.	NC_007779	2332580	0	A	C	bias_e_value=1.39862e-18	bias_p_value=3.01016e-25	fisher_strand_p_value=4.88796e-27	frequency=1.896682e-01	genotype_quality=499.4	ks_quality_p_value=1	log10_base_likelihood=-24.826	log10_qual_likelihood_position_model=40.7426	log10_strand_likelihood_position_model=26.3109	new_cov=0/51	polymorphism_quality=19.6	quality=19.6	quality_position_model=Inf	ref_cov=112/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/77
RA	337	.	NC_007779	2337256	0	G	C	bias_e_value=5.81519	bias_p_value=1.25156e-06	fisher_strand_p_value=7.17771e-08	frequency=4.626942e-02	genotype_quality=579.0	ks_quality_p_value=0.999217	log10_base_likelihood=-5.90858	log10_qual_likelihood_position_model=12.1717	log10_strand_likelihood_position_model=7.14401	new_cov=8/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=14/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=22/125
RA	338	.	NC_007779	2342393	0	A	C	bias_e_value=9.02907e-12	bias_p_value=1.94327e-18	fisher_strand_p_value=4.26135e-20	frequency=1.692586e-01	genotype_quality=570.0	ks_quality_p_value=1	log10_base_likelihood=-18.808	log10_qual_likelihood_position_model=34.0373	log10_strand_likelihood_position_model=19.3705	new_cov=0/45	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=114/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/91
RA	339	.	NC_007779	2344586	0	C	A	bias_e_value=1997.15	bias_p_value=0.000429834	fisher_strand_p_value=3.84988e-05	frequency=3.724957e-02	genotype_quality=954.0	ks_quality_p_value=1	log10_base_likelihood=-8.2141	log10_qual_likelihood_position_model=13.8171	log10_strand_likelihood_position_model=4.41455	new_cov=14/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=121/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/138
RA	340	.	NC_007779	2347976	0	A	C	bias_e_value=9.10011e-11	bias_p_value=1.95856e-17	fisher_strand_p_value=4.52967e-19	frequency=1.005650e-01	genotype_quality=624.2	ks_quality_p_value=1	log10_base_likelihood=-11.217	log10_qual_likelihood_position_model=28.802	log10_strand_likelihood_position_model=18.3439	new_cov=0/40	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=124/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/87
RA	341	.	NC_007779	2348480	0	G	T	bias_e_value=1752.21	bias_p_value=0.000377116	fisher_strand_p_value=3.3348e-05	frequency=3.800964e-02	genotype_quality=792.8	ks_quality_p_value=1	log10_base_likelihood=-6.31826	log10_qual_likelihood_position_model=13.8769	log10_strand_likelihood_position_model=4.47693	new_cov=0/10	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=127/65	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/75
RA	342	.	NC_007779	2353815	0	A	C	bias_e_value=0.000107413	bias_p_value=2.31178e-11	fisher_strand_p_value=8.01239e-13	frequency=8.527708e-02	genotype_quality=474.2	ks_quality_p_value=1	log10_base_likelihood=-14.5936	log10_qual_likelihood_position_model=17.1335	log10_strand_likelihood_position_model=12.0962	new_cov=0/14	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=107/10	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/24
RA	343	.	NC_007779	2354264	0	A	C	bias_e_value=2.24146e-12	bias_p_value=4.82416e-19	fisher_strand_p_value=1.02584e-20	frequency=6.363726e-02	genotype_quality=912.5	ks_quality_p_value=1	log10_base_likelihood=-7.7634	log10_qual_likelihood_position_model=44.9473	log10_strand_likelihood_position_model=19.9889	new_cov=0/42	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=170/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/109
RA	344	.	NC_007779	2354291	0	A	C	bias_e_value=4.18738e-16	bias_p_value=9.01224e-23	fisher_strand_p_value=1.61561e-24	frequency=1.637726e-01	genotype_quality=722.0	ks_quality_p_value=1	log10_base_likelihood=-35.9909	log10_qual_likelihood_position_model=41.0481	log10_strand_likelihood_position_model=23.7917	new_cov=0/49	polymorphism_quality=30.8	quality=30.8	quality_position_model=Inf	ref_cov=157/53	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/102
RA	345	.	NC_007779	2373239	0	A	C	bias_e_value=0.00175725	bias_p_value=3.78201e-10	fisher_strand_p_value=1.45732e-11	frequency=5.809212e-02	genotype_quality=482.3	ks_quality_p_value=1	log10_base_likelihood=-6.1067	log10_qual_likelihood_position_model=16.9816	log10_strand_likelihood_position_model=10.8364	new_cov=0/15	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=105/17	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/32
RA	346	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=893.2	new_cov=107/112	quality=893.2	ref_cov=0/0	tot_cov=107/112
RA	347	.	NC_007779	2409404	0	A	C	bias_e_value=1.60078e-06	bias_p_value=3.44525e-13	fisher_strand_p_value=1.03775e-14	frequency=1.811113e-01	genotype_quality=467.6	ks_quality_p_value=1	log10_base_likelihood=-34.3665	log10_qual_likelihood_position_model=25.2355	log10_strand_likelihood_position_model=13.9839	new_cov=0/36	polymorphism_quality=29.2	quality=29.2	quality_position_model=Inf	ref_cov=93/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/83
RA	348	.	NC_007779	2409820	1	.	A	bias_e_value=3187270	bias_p_value=0.685974	fisher_strand_p_value=1	frequency=7.272720e-03	genotype_quality=1379.4	ks_quality_p_value=0.321192	log10_base_likelihood=-8.10175	log10_qual_likelihood_position_model=1.28602	log10_strand_likelihood_position_model=0.303655	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.88681e-08	ref_cov=123/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/151
RA	349	.	NC_007779	2410289	0	T	A	bias_e_value=117319	bias_p_value=0.0252497	fisher_strand_p_value=0.00384909	frequency=3.172112e-02	genotype_quality=927.4	ks_quality_p_value=1	log10_base_likelihood=-7.07506	log10_qual_likelihood_position_model=14.7664	log10_strand_likelihood_position_model=2.534	new_cov=0/9	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=114/120	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=114/129
RA	350	.	NC_007779	2410289	1	.	A	bias_e_value=4361330	bias_p_value=0.938662	fisher_strand_p_value=1	frequency=9.049416e-03	genotype_quality=1077.0	ks_quality_p_value=0.670855	log10_base_likelihood=-8.45929	log10_qual_likelihood_position_model=1.35803	log10_strand_likelihood_position_model=0.299781	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=9.49329e-09	ref_cov=105/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/115
RA	351	.	NC_007779	2410316	0	A	C	bias_e_value=0.000801571	bias_p_value=1.72517e-10	fisher_strand_p_value=6.44496e-12	frequency=1.249256e-01	genotype_quality=705.4	ks_quality_p_value=1	log10_base_likelihood=-31.1465	log10_qual_likelihood_position_model=31.6801	log10_strand_likelihood_position_model=11.3279	new_cov=1/40	polymorphism_quality=26.0	quality=26.0	quality_position_model=Inf	ref_cov=117/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/131
RA	352	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=904.0	new_cov=105/119	quality=904.0	ref_cov=0/0	tot_cov=105/119
RA	353	.	NC_007779	2417605	0	C	A	bias_e_value=11.1811	bias_p_value=2.40644e-06	fisher_strand_p_value=1.96462e-07	frequency=7.493210e-02	genotype_quality=759.0	ks_quality_p_value=0.731007	log10_base_likelihood=-15.4807	log10_qual_likelihood_position_model=27.1515	log10_strand_likelihood_position_model=6.7215	new_cov=23/0	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=106/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/113
RA	354	.	NC_007779	2418070	1	.	A	bias_e_value=4111940	bias_p_value=0.884986	fisher_strand_p_value=1	frequency=8.657455e-03	genotype_quality=1153.1	ks_quality_p_value=0.560496	log10_base_likelihood=-8.30552	log10_qual_likelihood_position_model=1.83102	log10_strand_likelihood_position_model=0.300132	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=4.21039e-08	ref_cov=109/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/121
RA	355	.	NC_007779	2418806	0	A	.	bias_e_value=2799710	bias_p_value=0.602564	fisher_strand_p_value=0.360727	frequency=1.549721e-02	genotype_quality=1077.2	ks_quality_p_value=0.705099	log10_base_likelihood=-11.7624	log10_qual_likelihood_position_model=1.43435	log10_strand_likelihood_position_model=0.622997	new_cov=1/3	polymorphism_quality=6.4	quality=6.4	quality_position_model=1.00075e-11	ref_cov=131/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/126
RA	356	.	NC_007779	2419465	0	A	C	bias_e_value=0.389825	bias_p_value=8.38994e-08	fisher_strand_p_value=4.13206e-09	frequency=6.294107e-02	genotype_quality=680.0	ks_quality_p_value=1	log10_base_likelihood=-6.40061	log10_qual_likelihood_position_model=21.1852	log10_strand_likelihood_position_model=8.38383	new_cov=0/22	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=114/70	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/92
RA	357	.	NC_007779	2420902	0	G	C	bias_e_value=0.00818624	bias_p_value=1.76187e-09	fisher_strand_p_value=7.72173e-11	frequency=6.884003e-02	genotype_quality=770.8	ks_quality_p_value=0.937069	log10_base_likelihood=-15.1136	log10_qual_likelihood_position_model=20.641	log10_strand_likelihood_position_model=10.1123	new_cov=18/0	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=49/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=67/154
RA	358	.	NC_007779	2446437	0	A	C	bias_e_value=0.653457	bias_p_value=1.40639e-07	fisher_strand_p_value=7.1171e-09	frequency=7.149649e-02	genotype_quality=684.1	ks_quality_p_value=1	log10_base_likelihood=-9.6887	log10_qual_likelihood_position_model=20.3461	log10_strand_likelihood_position_model=8.1477	new_cov=0/21	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=115/69	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/90
RA	359	.	NC_007779	2454650	1	.	C	bias_e_value=3907580	bias_p_value=0.841003	fisher_strand_p_value=1	frequency=1.162720e-02	genotype_quality=810.2	ks_quality_p_value=0.492055	log10_base_likelihood=-7.82405	log10_qual_likelihood_position_model=2.11828	log10_strand_likelihood_position_model=0.335881	new_cov=0/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.86524e-07	ref_cov=55/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=55/117
RA	360	.	NC_007779	2465370	0	C	A	bias_e_value=0.000142245	bias_p_value=3.06146e-11	fisher_strand_p_value=1.08662e-12	frequency=9.744787e-02	genotype_quality=545.3	ks_quality_p_value=0.986432	log10_base_likelihood=-31.3974	log10_qual_likelihood_position_model=15.8484	log10_strand_likelihood_position_model=11.9639	new_cov=0/14	polymorphism_quality=26.2	quality=26.2	quality_position_model=2.10202e-05	ref_cov=117/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/26
RA	361	.	NC_007779	2466047	0	G	A	bias_e_value=14770.2	bias_p_value=0.00317889	fisher_strand_p_value=0.000355502	frequency=3.349113e-02	genotype_quality=995.6	ks_quality_p_value=1	log10_base_likelihood=-11.1347	log10_qual_likelihood_position_model=11.9541	log10_strand_likelihood_position_model=3.44916	new_cov=0/10	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=140/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=140/120
RA	362	.	NC_007779	2468326	1	.	C	bias_e_value=1357910	bias_p_value=0.292253	fisher_strand_p_value=0.3	frequency=1.428604e-02	genotype_quality=985.2	ks_quality_p_value=0.280257	log10_base_likelihood=-12.2688	log10_qual_likelihood_position_model=2.34779	log10_strand_likelihood_position_model=0.598732	new_cov=0/3	polymorphism_quality=6.9	quality=6.9	quality_position_model=2.46309e-11	ref_cov=77/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=77/133
RA	363	.	NC_007779	2468327	0	C	.	bias_e_value=3889010	bias_p_value=0.837007	fisher_strand_p_value=0.557372	frequency=1.401329e-02	genotype_quality=903.9	ks_quality_p_value=0.872784	log10_base_likelihood=-9.03387	log10_qual_likelihood_position_model=1.46485	log10_strand_likelihood_position_model=0.580186	new_cov=2/1	polymorphism_quality=3.6	quality=3.6	quality_position_model=6.08818e-09	ref_cov=78/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=80/134
RA	364	.	NC_007779	2485817	0	T	G	bias_e_value=0.806987	bias_p_value=1.73682e-07	fisher_strand_p_value=8.88928e-09	frequency=7.905531e-02	genotype_quality=428.0	ks_quality_p_value=1	log10_base_likelihood=-8.85004	log10_qual_likelihood_position_model=15.4133	log10_strand_likelihood_position_model=8.05113	new_cov=14/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=24/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=38/86
RA	365	.	NC_007779	2517218	0	A	C	bias_e_value=2.51092e-15	bias_p_value=5.4041e-22	fisher_strand_p_value=1.00154e-23	frequency=1.140933e-01	genotype_quality=539.2	ks_quality_p_value=1	log10_base_likelihood=-14.4477	log10_qual_likelihood_position_model=33.4436	log10_strand_likelihood_position_model=22.9993	new_cov=0/31	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=128/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/45
RA	366	.	NC_007779	2536601	0	T	G	bias_e_value=0.00249301	bias_p_value=5.36555e-10	fisher_strand_p_value=2.0969e-11	frequency=7.735205e-02	genotype_quality=711.5	ks_quality_p_value=1	log10_base_likelihood=-10.3583	log10_qual_likelihood_position_model=23.2633	log10_strand_likelihood_position_model=10.6784	new_cov=22/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=55/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=78/136
RA	367	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=924.8	new_cov=100/126	quality=924.8	ref_cov=0/0	tot_cov=100/126
RA	368	.	NC_007779	2556426	0	G	T	bias_e_value=0.0218919	bias_p_value=4.71166e-09	fisher_strand_p_value=2.34044e-10	frequency=7.425785e-02	genotype_quality=831.2	ks_quality_p_value=0.863174	log10_base_likelihood=-13.5728	log10_qual_likelihood_position_model=29.1879	log10_strand_likelihood_position_model=9.6307	new_cov=0/28	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=139/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/129
RA	369	.	NC_007779	2577537	0	G	.	bias_e_value=1265270	bias_p_value=0.272317	fisher_strand_p_value=1	frequency=7.572174e-03	genotype_quality=1139.9	ks_quality_p_value=0.0761798	log10_base_likelihood=-5.73514	log10_qual_likelihood_position_model=1.40128	log10_strand_likelihood_position_model=0.301405	new_cov=1/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=7.11233e-06	ref_cov=140/122	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=141/123
RA	370	.	NC_007779	2581401	1	.	A	bias_e_value=4448000	bias_p_value=0.957314	fisher_strand_p_value=1	frequency=8.474350e-03	genotype_quality=1174.9	ks_quality_p_value=0.72242	log10_base_likelihood=-8.26635	log10_qual_likelihood_position_model=1.20692	log10_strand_likelihood_position_model=0.299186	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.04688e-08	ref_cov=117/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/118
RA	371	.	NC_007779	2581900	0	G	T	bias_e_value=2978.8	bias_p_value=0.000641109	fisher_strand_p_value=5.97777e-05	frequency=4.383183e-02	genotype_quality=828.7	ks_quality_p_value=1	log10_base_likelihood=-8.49577	log10_qual_likelihood_position_model=15.715	log10_strand_likelihood_position_model=4.27115	new_cov=0/17	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=108/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/146
RA	372	.	NC_007779	2593271	0	A	C	bias_e_value=0.0164204	bias_p_value=3.53406e-09	fisher_strand_p_value=1.49602e-10	frequency=5.713701e-02	genotype_quality=700.4	ks_quality_p_value=1	log10_base_likelihood=-6.66864	log10_qual_likelihood_position_model=32.633	log10_strand_likelihood_position_model=9.82506	new_cov=0/29	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=114/82	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/112
RA	373	.	NC_007779	2598509	1	.	T	bias_e_value=549918	bias_p_value=0.118355	fisher_strand_p_value=0.498062	frequency=8.264542e-03	genotype_quality=1199.8	ks_quality_p_value=0.0508124	log10_base_likelihood=-8.35386	log10_qual_likelihood_position_model=1.71584	log10_strand_likelihood_position_model=0.589567	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=5.68113e-08	ref_cov=121/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/119
RA	374	.	NC_007779	2601998	0	A	C	bias_e_value=0.0872766	bias_p_value=1.8784e-08	fisher_strand_p_value=8.58672e-10	frequency=5.509853e-02	genotype_quality=595.9	ks_quality_p_value=1	log10_base_likelihood=-12.6765	log10_qual_likelihood_position_model=14.5408	log10_strand_likelihood_position_model=9.06617	new_cov=0/11	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=129/17	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/28
RA	375	.	NC_007779	2604001	0	T	G	bias_e_value=0.00107357	bias_p_value=2.31057e-10	fisher_strand_p_value=8.73095e-12	frequency=5.643845e-02	genotype_quality=596.3	ks_quality_p_value=1	log10_base_likelihood=-5.60885	log10_qual_likelihood_position_model=18.9349	log10_strand_likelihood_position_model=11.0589	new_cov=19/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=33/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=52/120
RA	376	.	NC_007779	2610583	0	G	C	bias_e_value=0.140226	bias_p_value=3.01798e-08	fisher_strand_p_value=1.41169e-09	frequency=6.480694e-02	genotype_quality=651.5	ks_quality_p_value=1	log10_base_likelihood=-9.48698	log10_qual_likelihood_position_model=15.1264	log10_strand_likelihood_position_model=8.85026	new_cov=0/14	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=129/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/46
RA	377	.	NC_007779	2623159	0	T	G	bias_e_value=2.58871e-22	bias_p_value=5.57152e-29	fisher_strand_p_value=7.92419e-31	frequency=2.420964e-01	genotype_quality=424.9	ks_quality_p_value=1	log10_base_likelihood=-43.1258	log10_qual_likelihood_position_model=37.7154	log10_strand_likelihood_position_model=30.101	new_cov=54/0	polymorphism_quality=38.0	quality=38.0	quality_position_model=Inf	ref_cov=18/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/109
RA	378	.	NC_007779	2640922	0	T	G	bias_e_value=6.54362e-08	bias_p_value=1.40834e-14	fisher_strand_p_value=3.85944e-16	frequency=1.002803e-01	genotype_quality=733.4	ks_quality_p_value=1	log10_base_likelihood=-17.4364	log10_qual_likelihood_position_model=37.9419	log10_strand_likelihood_position_model=15.4135	new_cov=40/0	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=75/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/135
RA	379	.	NC_007779	2641345	0	T	G	bias_e_value=2.17353	bias_p_value=4.67795e-07	fisher_strand_p_value=2.52963e-08	frequency=5.249453e-02	genotype_quality=502.6	ks_quality_p_value=1	log10_base_likelihood=-10.1834	log10_qual_likelihood_position_model=10.2046	log10_strand_likelihood_position_model=7.59694	new_cov=8/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=10/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=18/113
RA	380	.	NC_007779	2646804	0	A	C	bias_e_value=2.69878e-09	bias_p_value=5.80842e-16	fisher_strand_p_value=1.46068e-17	frequency=6.299877e-02	genotype_quality=864.4	ks_quality_p_value=1	log10_base_likelihood=-8.85094	log10_qual_likelihood_position_model=39.0436	log10_strand_likelihood_position_model=16.8354	new_cov=0/37	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=165/71	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=165/109
RA	381	.	NC_007779	2648595	0	A	C	bias_e_value=2.77763e-08	bias_p_value=5.97811e-15	fisher_strand_p_value=1.59964e-16	frequency=7.884836e-02	genotype_quality=550.2	ks_quality_p_value=1	log10_base_likelihood=-9.47956	log10_qual_likelihood_position_model=21.1854	log10_strand_likelihood_position_model=15.796	new_cov=0/16	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=128/7	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/23
RA	382	.	NC_007779	2672817	0	A	C	bias_e_value=3.32575e-11	bias_p_value=7.15779e-18	fisher_strand_p_value=1.6169e-19	frequency=1.369433e-01	genotype_quality=530.3	ks_quality_p_value=1	log10_base_likelihood=-21.4519	log10_qual_likelihood_position_model=29.7387	log10_strand_likelihood_position_model=18.7913	new_cov=0/34	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=116/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/63
RA	383	.	NC_007779	2690409	1	.	C	bias_e_value=1603930	bias_p_value=0.345203	fisher_strand_p_value=0.106583	frequency=1.286983e-02	genotype_quality=1121.7	ks_quality_p_value=1	log10_base_likelihood=-9.22027	log10_qual_likelihood_position_model=4.33603	log10_strand_likelihood_position_model=0.972314	new_cov=0/3	polymorphism_quality=3.8	quality=3.8	quality_position_model=9.51823e-06	ref_cov=122/108	reject=POLYMORPHISM_STRAND	tot_cov=122/111
RA	384	.	NC_007779	2700681	0	T	G	bias_e_value=0.000196912	bias_p_value=4.23801e-11	fisher_strand_p_value=1.50154e-12	frequency=1.100988e-01	genotype_quality=651.2	ks_quality_p_value=1	log10_base_likelihood=-9.14881	log10_qual_likelihood_position_model=28.271	log10_strand_likelihood_position_model=11.8321	new_cov=37/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=82/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/109
RA	385	.	NC_007779	2708935	0	A	C	bias_e_value=4.04174e-10	bias_p_value=8.69877e-17	fisher_strand_p_value=2.08546e-18	frequency=1.759701e-01	genotype_quality=596.7	ks_quality_p_value=1	log10_base_likelihood=-25.6515	log10_qual_likelihood_position_model=32.6552	log10_strand_likelihood_position_model=17.708	new_cov=0/51	polymorphism_quality=20.4	quality=20.4	quality_position_model=Inf	ref_cov=118/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/123
RA	386	.	NC_007779	2733192	0	C	.	bias_e_value=2727040	bias_p_value=0.586924	fisher_strand_p_value=0.498786	frequency=8.192062e-03	genotype_quality=1027.7	ks_quality_p_value=0.4874	log10_base_likelihood=-5.68696	log10_qual_likelihood_position_model=1.09979	log10_strand_likelihood_position_model=0.568822	new_cov=2/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=7.35891e-06	ref_cov=125/117	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/117
RA	387	.	NC_007779	2753288	0	G	A	bias_e_value=4047420	bias_p_value=0.8711	fisher_strand_p_value=0.607704	frequency=1.415920e-02	genotype_quality=896.5	ks_quality_p_value=0.884228	log10_base_likelihood=-5.81999	log10_qual_likelihood_position_model=1.66782	log10_strand_likelihood_position_model=0.443813	new_cov=2/1	polymorphism_quality=0.3	quality=0.3	quality_position_model=1.55838e-05	ref_cov=99/109	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=101/110
RA	388	.	NC_007779	2753432	1	.	A	bias_e_value=831027	bias_p_value=0.178857	fisher_strand_p_value=0.501479	frequency=8.474350e-03	genotype_quality=1178.3	ks_quality_p_value=0.0860982	log10_base_likelihood=-8.33	log10_qual_likelihood_position_model=1.32041	log10_strand_likelihood_position_model=0.532966	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.05255e-08	ref_cov=126/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/108
RA	389	.	NC_007779	2756311	0	T	.	bias_e_value=661614	bias_p_value=0.142395	fisher_strand_p_value=0.177173	frequency=9.702682e-03	genotype_quality=864.7	ks_quality_p_value=0.181025	log10_base_likelihood=-5.58888	log10_qual_likelihood_position_model=0.91703	log10_strand_likelihood_position_model=0.751603	new_cov=2/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=9.32851e-06	ref_cov=85/119	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=87/119
RA	390	.	NC_007779	2771144	0	G	T	bias_e_value=2.38449	bias_p_value=5.13199e-07	fisher_strand_p_value=3.57288e-08	frequency=7.129431e-02	genotype_quality=732.0	ks_quality_p_value=0.780864	log10_base_likelihood=-15.007	log10_qual_likelihood_position_model=23.1468	log10_strand_likelihood_position_model=7.44698	new_cov=0/22	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=123/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/115
RA	391	.	NC_007779	2774179	0	A	T	bias_e_value=111306	bias_p_value=0.0239558	fisher_strand_p_value=0.00361764	frequency=3.095341e-02	genotype_quality=931.7	ks_quality_p_value=1	log10_base_likelihood=-7.02666	log10_qual_likelihood_position_model=14.3211	log10_strand_likelihood_position_model=2.60063	new_cov=9/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=122/120	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=131/120
RA	392	.	NC_007779	2783852	1	.	A	bias_e_value=4646310	bias_p_value=0.999994	fisher_strand_p_value=1	frequency=9.661674e-03	genotype_quality=1033.4	ks_quality_p_value=0.996612	log10_base_likelihood=-8.12799	log10_qual_likelihood_position_model=2.9486	log10_strand_likelihood_position_model=0.32833	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.9194e-07	ref_cov=140/65	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/65
RA	393	.	NC_007779	2791171	0	G	T	bias_e_value=5.44575	bias_p_value=1.17205e-06	fisher_strand_p_value=6.68977e-08	frequency=8.206987e-02	genotype_quality=703.7	ks_quality_p_value=1	log10_base_likelihood=-16.4183	log10_qual_likelihood_position_model=17.9294	log10_strand_likelihood_position_model=7.17459	new_cov=0/22	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=111/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/111
RA	394	.	NC_007779	2791635	0	C	T	bias_e_value=0.000129539	bias_p_value=2.78798e-11	fisher_strand_p_value=9.72826e-13	frequency=1.066971e-01	genotype_quality=552.5	ks_quality_p_value=1	log10_base_likelihood=-16.4755	log10_qual_likelihood_position_model=19.7236	log10_strand_likelihood_position_model=12.012	new_cov=0/21	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=116/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/53
RA	395	.	NC_007779	2791639	0	C	G	bias_e_value=0.000554123	bias_p_value=1.1926e-10	fisher_strand_p_value=4.39246e-12	frequency=1.100092e-01	genotype_quality=607.6	ks_quality_p_value=1	log10_base_likelihood=-23.408	log10_qual_likelihood_position_model=21.836	log10_strand_likelihood_position_model=11.3573	new_cov=0/20	polymorphism_quality=18.2	quality=18.2	quality_position_model=Inf	ref_cov=116/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/54
RA	396	.	NC_007779	2797644	0	C	A	bias_e_value=438.574	bias_p_value=9.43915e-05	fisher_strand_p_value=7.3665e-06	frequency=3.910160e-02	genotype_quality=790.0	ks_quality_p_value=0.999582	log10_base_likelihood=-6.81619	log10_qual_likelihood_position_model=9.56968	log10_strand_likelihood_position_model=5.13274	new_cov=0/9	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=152/51	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=152/60
RA	397	.	NC_007779	2816615	0	G	C	bias_e_value=3.15835e-16	bias_p_value=6.79751e-23	fisher_strand_p_value=1.4117e-24	frequency=1.996675e-01	genotype_quality=626.8	ks_quality_p_value=0.85878	log10_base_likelihood=-65.8818	log10_qual_likelihood_position_model=36.3374	log10_strand_likelihood_position_model=23.8503	new_cov=46/0	polymorphism_quality=60.9	quality=60.9	quality_position_model=1.32149e-07	ref_cov=38/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=84/137
RA	398	.	NC_007779	2817030	0	G	C	bias_e_value=1.73292e-20	bias_p_value=3.72965e-27	fisher_strand_p_value=6.40537e-29	frequency=2.299438e-01	genotype_quality=651.5	ks_quality_p_value=0.881642	log10_base_likelihood=-90.4914	log10_qual_likelihood_position_model=43.7906	log10_strand_likelihood_position_model=28.1935	new_cov=57/0	polymorphism_quality=85.5	quality=85.5	quality_position_model=1.15379e-20	ref_cov=41/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/143
RA	399	.	NC_007779	2830767	0	G	T	bias_e_value=6154.27	bias_p_value=0.00132454	fisher_strand_p_value=0.000133504	frequency=3.806400e-02	genotype_quality=987.2	ks_quality_p_value=1	log10_base_likelihood=-11.2395	log10_qual_likelihood_position_model=14.954	log10_strand_likelihood_position_model=3.92527	new_cov=0/14	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=131/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/152
RA	400	.	NC_007779	2833875	0	A	C	bias_e_value=0.00015265	bias_p_value=3.2854e-11	fisher_strand_p_value=1.15324e-12	frequency=7.795238e-02	genotype_quality=731.5	ks_quality_p_value=1	log10_base_likelihood=-7.94721	log10_qual_likelihood_position_model=29.4286	log10_strand_likelihood_position_model=11.9381	new_cov=0/33	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=120/76	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/109
RA	401	.	NC_007779	2833989	0	A	C	bias_e_value=1.70762	bias_p_value=3.6752e-07	fisher_strand_p_value=1.96036e-08	frequency=2.641487e-02	genotype_quality=631.0	ks_quality_p_value=1	log10_base_likelihood=-6.33302	log10_qual_likelihood_position_model=10.8401	log10_strand_likelihood_position_model=7.70766	new_cov=0/8	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=142/13	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/21
RA	402	.	NC_007779	2839296	0	A	G	bias_e_value=1.55978e-06	bias_p_value=3.35701e-13	fisher_strand_p_value=1.01036e-14	frequency=1.069331e-01	genotype_quality=636.4	ks_quality_p_value=1	log10_base_likelihood=-23.9843	log10_qual_likelihood_position_model=23.8829	log10_strand_likelihood_position_model=13.9955	new_cov=23/0	polymorphism_quality=18.7	quality=18.7	quality_position_model=Inf	ref_cov=35/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=59/142
RA	403	.	NC_007779	2847445	0	G	T	bias_e_value=1.51517	bias_p_value=3.26099e-07	fisher_strand_p_value=1.72778e-08	frequency=8.846331e-02	genotype_quality=772.5	ks_quality_p_value=1	log10_base_likelihood=-16.5763	log10_qual_likelihood_position_model=21.4402	log10_strand_likelihood_position_model=7.93638	new_cov=0/29	polymorphism_quality=11.2	quality=11.2	quality_position_model=Inf	ref_cov=112/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/142
RA	404	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1163.0	new_cov=130/137	quality=1163.0	ref_cov=0/0	tot_cov=130/137
RA	405	.	NC_007779	2872916	0	T	G	bias_e_value=1.76303e-06	bias_p_value=3.79445e-13	fisher_strand_p_value=1.14637e-14	frequency=7.915878e-02	genotype_quality=752.8	ks_quality_p_value=1	log10_base_likelihood=-11.0989	log10_qual_likelihood_position_model=35.2929	log10_strand_likelihood_position_model=13.9407	new_cov=32/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=63/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/136
RA	406	.	NC_007779	2895131	0	A	C	bias_e_value=1.32267e-07	bias_p_value=2.84669e-14	fisher_strand_p_value=7.95897e-16	frequency=7.484961e-02	genotype_quality=707.0	ks_quality_p_value=1	log10_base_likelihood=-11.929	log10_qual_likelihood_position_model=28.1934	log10_strand_likelihood_position_model=15.0991	new_cov=0/22	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=146/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/49
RA	407	.	NC_007779	2895144	0	G	C	bias_e_value=3.55491	bias_p_value=7.651e-07	fisher_strand_p_value=4.30558e-08	frequency=5.192614e-02	genotype_quality=679.4	ks_quality_p_value=0.988753	log10_base_likelihood=-9.89992	log10_qual_likelihood_position_model=13.0643	log10_strand_likelihood_position_model=7.36597	new_cov=0/11	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=139/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/43
RA	408	.	NC_007779	2905200	0	C	G	bias_e_value=5880.79	bias_p_value=0.00126569	fisher_strand_p_value=0.000127953	frequency=3.100300e-02	genotype_quality=527.7	ks_quality_p_value=0.991968	log10_base_likelihood=-7.29921	log10_qual_likelihood_position_model=4.69363	log10_strand_likelihood_position_model=3.89295	new_cov=4/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=11/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=15/113
RA	409	.	NC_007779	2926157	0	T	G	bias_e_value=1.27327e-13	bias_p_value=2.74038e-20	fisher_strand_p_value=5.48573e-22	frequency=7.956076e-02	genotype_quality=667.4	ks_quality_p_value=1	log10_base_likelihood=-12.7136	log10_qual_likelihood_position_model=27.2449	log10_strand_likelihood_position_model=21.2608	new_cov=23/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=10/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=33/154
RA	410	.	NC_007779	2939008	0	A	C	bias_e_value=1.15822e-07	bias_p_value=2.49276e-14	fisher_strand_p_value=6.94293e-16	frequency=1.083789e-01	genotype_quality=761.0	ks_quality_p_value=1	log10_base_likelihood=-16.3578	log10_qual_likelihood_position_model=29.1641	log10_strand_likelihood_position_model=15.1585	new_cov=0/35	polymorphism_quality=11.0	quality=11.0	quality_position_model=Inf	ref_cov=144/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/102
RA	411	.	NC_007779	2974960	0	A	.	bias_e_value=1987270	bias_p_value=0.427708	fisher_strand_p_value=1	frequency=1.286697e-02	genotype_quality=971.9	ks_quality_p_value=0.146407	log10_base_likelihood=-8.25475	log10_qual_likelihood_position_model=2.84118	log10_strand_likelihood_position_model=0.398581	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.69693e-07	ref_cov=122/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/109
RA	412	.	NC_007779	2983097	0	A	C	bias_e_value=6.10878e-12	bias_p_value=1.31475e-18	fisher_strand_p_value=2.85806e-20	frequency=1.182208e-01	genotype_quality=531.6	ks_quality_p_value=1	log10_base_likelihood=-8.22886	log10_qual_likelihood_position_model=36.4549	log10_strand_likelihood_position_model=19.5439	new_cov=0/42	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=105/35	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/77
RA	413	.	NC_007779	2987535	0	A	C	bias_e_value=6.49842e-25	bias_p_value=1.39861e-31	fisher_strand_p_value=1.83112e-33	frequency=2.881532e-01	genotype_quality=462.9	ks_quality_p_value=1	log10_base_likelihood=-63.3552	log10_qual_likelihood_position_model=51.7035	log10_strand_likelihood_position_model=32.7373	new_cov=0/70	polymorphism_quality=58.3	quality=58.3	quality_position_model=Inf	ref_cov=116/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/99
RA	414	.	NC_007779	2987971	1	.	A	bias_e_value=422010	bias_p_value=0.0908264	fisher_strand_p_value=0.0448872	frequency=1.796436e-02	genotype_quality=821.1	ks_quality_p_value=0.403855	log10_base_likelihood=-13.2251	log10_qual_likelihood_position_model=2.14936	log10_strand_likelihood_position_model=1.34788	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=9.48477e-12	ref_cov=57/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=60/107
RA	415	.	NC_007779	2988137	0	A	.	bias_e_value=4081260	bias_p_value=0.878384	fisher_strand_p_value=0.561075	frequency=1.828575e-02	genotype_quality=680.1	ks_quality_p_value=0.97899	log10_base_likelihood=-8.91826	log10_qual_likelihood_position_model=3.05905	log10_strand_likelihood_position_model=0.553905	new_cov=1/2	polymorphism_quality=3.5	quality=3.5	quality_position_model=3.3435e-07	ref_cov=99/62	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=100/64
RA	416	.	NC_007779	2993110	0	T	.	bias_e_value=3087950	bias_p_value=0.664599	fisher_strand_p_value=0.508271	frequency=1.046467e-02	genotype_quality=798.3	ks_quality_p_value=0.595827	log10_base_likelihood=-5.56934	log10_qual_likelihood_position_model=0.964151	log10_strand_likelihood_position_model=0.484365	new_cov=2/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=5.74563e-06	ref_cov=107/81	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/82
RA	417	.	NC_007779	2999826	0	A	C	bias_e_value=1.21032e-09	bias_p_value=2.60489e-16	fisher_strand_p_value=6.41797e-18	frequency=7.873869e-02	genotype_quality=598.7	ks_quality_p_value=1	log10_base_likelihood=-6.26188	log10_qual_likelihood_position_model=30.7283	log10_strand_likelihood_position_model=17.1926	new_cov=0/34	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=122/39	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/73
RA	418	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=958.1	new_cov=101/128	quality=958.1	ref_cov=0/0	tot_cov=101/128
RA	419	.	NC_007779	3029385	0	C	A	bias_e_value=5.20603e-11	bias_p_value=1.12046e-17	fisher_strand_p_value=2.64452e-19	frequency=1.100211e-01	genotype_quality=697.0	ks_quality_p_value=0.967109	log10_base_likelihood=-46.7726	log10_qual_likelihood_position_model=25.6879	log10_strand_likelihood_position_model=18.5777	new_cov=0/21	polymorphism_quality=41.7	quality=41.7	quality_position_model=0.000295035	ref_cov=154/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=154/34
RA	420	.	NC_007779	3034413	0	A	C	bias_e_value=1.05823e-20	bias_p_value=2.27756e-27	fisher_strand_p_value=3.42261e-29	frequency=1.679301e-01	genotype_quality=594.7	ks_quality_p_value=1	log10_base_likelihood=-34.0949	log10_qual_likelihood_position_model=39.1198	log10_strand_likelihood_position_model=28.4656	new_cov=0/48	polymorphism_quality=28.9	quality=28.9	quality_position_model=Inf	ref_cov=140/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/75
RA	421	.	NC_007779	3035390	0	T	C	bias_e_value=6.79872e-14	bias_p_value=1.46324e-20	fisher_strand_p_value=2.89208e-22	frequency=1.530681e-01	genotype_quality=458.8	ks_quality_p_value=1	log10_base_likelihood=-50.3199	log10_qual_likelihood_position_model=20.103	log10_strand_likelihood_position_model=21.5388	new_cov=0/30	polymorphism_quality=45.2	quality=45.2	quality_position_model=1.12329e-10	ref_cov=140/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/49
RA	422	.	NC_007779	3044712	0	T	C	bias_e_value=0.562847	bias_p_value=1.21138e-07	fisher_strand_p_value=6.08826e-09	frequency=6.873035e-02	genotype_quality=487.4	ks_quality_p_value=0.998946	log10_base_likelihood=-12.4271	log10_qual_likelihood_position_model=13.3707	log10_strand_likelihood_position_model=8.21551	new_cov=12/0	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=25/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=37/120
RA	423	.	NC_007779	3044714	0	A	C	bias_e_value=170.896	bias_p_value=3.67809e-05	fisher_strand_p_value=2.65798e-06	frequency=5.851984e-02	genotype_quality=450.1	ks_quality_p_value=1	log10_base_likelihood=-7.90395	log10_qual_likelihood_position_model=13.0852	log10_strand_likelihood_position_model=5.59192	new_cov=11/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=26/113	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=38/116
RA	424	.	NC_007779	3044718	0	T	C	bias_e_value=3859.45	bias_p_value=0.000830645	fisher_strand_p_value=7.95725e-05	frequency=3.301620e-02	genotype_quality=574.9	ks_quality_p_value=1	log10_base_likelihood=-6.68631	log10_qual_likelihood_position_model=8.77812	log10_strand_likelihood_position_model=4.09924	new_cov=6/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=29/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/124
RA	425	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=1036.6	new_cov=127/125	quality=1036.6	ref_cov=0/0	tot_cov=127/125
RA	426	.	NC_007779	3074129	0	G	T	bias_e_value=31.0193	bias_p_value=6.67608e-06	fisher_strand_p_value=4.26079e-07	frequency=6.180382e-02	genotype_quality=862.9	ks_quality_p_value=1	log10_base_likelihood=-12.9376	log10_qual_likelihood_position_model=15.9189	log10_strand_likelihood_position_model=6.39004	new_cov=0/22	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=124/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/141
RA	427	.	NC_007779	3084663	0	C	A	bias_e_value=263.354	bias_p_value=5.668e-05	fisher_strand_p_value=4.23897e-06	frequency=3.682041e-02	genotype_quality=951.8	ks_quality_p_value=1	log10_base_likelihood=-5.62473	log10_qual_likelihood_position_model=15.1005	log10_strand_likelihood_position_model=5.6171	new_cov=18/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=120/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/136
RA	428	.	NC_007779	3085177	1	.	A	bias_e_value=2711800	bias_p_value=0.583642	fisher_strand_p_value=0.498134	frequency=7.936478e-03	genotype_quality=1258.7	ks_quality_p_value=0.483395	log10_base_likelihood=-8.14071	log10_qual_likelihood_position_model=3.17782	log10_strand_likelihood_position_model=0.590061	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=3.12979e-06	ref_cov=126/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/124
RA	429	.	NC_007779	3093172	0	C	T	bias_e_value=4162860	bias_p_value=0.895946	fisher_strand_p_value=0.600725	frequency=1.132107e-02	genotype_quality=1113.7	ks_quality_p_value=0.965511	log10_base_likelihood=-5.61856	log10_qual_likelihood_position_model=1.66333	log10_strand_likelihood_position_model=0.455383	new_cov=2/1	polymorphism_quality=0.1	quality=0.1	quality_position_model=2.58561e-05	ref_cov=121/139	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=124/140
RA	430	.	NC_007779	3110532	0	C	A	bias_e_value=0.000150215	bias_p_value=3.23298e-11	fisher_strand_p_value=1.13977e-12	frequency=8.238411e-02	genotype_quality=591.2	ks_quality_p_value=0.99509	log10_base_likelihood=-21.2576	log10_qual_likelihood_position_model=16.7964	log10_strand_likelihood_position_model=11.9432	new_cov=0/13	polymorphism_quality=16.0	quality=16.0	quality_position_model=Inf	ref_cov=128/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/24
RA	431	.	NC_007779	3124070	0	G	.	bias_e_value=1969880	bias_p_value=0.423965	fisher_strand_p_value=0.239471	frequency=9.428024e-03	genotype_quality=873.2	ks_quality_p_value=0.60327	log10_base_likelihood=-5.59234	log10_qual_likelihood_position_model=1.11634	log10_strand_likelihood_position_model=0.620748	new_cov=2/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=1.09172e-05	ref_cov=102/108	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=104/108
RA	432	.	NC_007779	3124071	0	C	.	bias_e_value=2118970	bias_p_value=0.456053	fisher_strand_p_value=0.241673	frequency=9.565353e-03	genotype_quality=856.9	ks_quality_p_value=0.668482	log10_base_likelihood=-5.79809	log10_qual_likelihood_position_model=1.10393	log10_strand_likelihood_position_model=0.616772	new_cov=2/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=6.38084e-06	ref_cov=101/106	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=103/106
RA	433	.	NC_007779	3126794	0	T	.	bias_e_value=3038660	bias_p_value=0.653992	fisher_strand_p_value=0.576718	frequency=1.019669e-02	genotype_quality=1203.8	ks_quality_p_value=0.509901	log10_base_likelihood=-8.15831	log10_qual_likelihood_position_model=1.45421	log10_strand_likelihood_position_model=0.505258	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=3.97224e-08	ref_cov=123/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/169
RA	434	.	NC_007779	3152854	1	.	A	bias_e_value=2333910	bias_p_value=0.502312	fisher_strand_p_value=1	frequency=1.321602e-02	genotype_quality=1112.2	ks_quality_p_value=0.188063	log10_base_likelihood=-13.0561	log10_qual_likelihood_position_model=2.38544	log10_strand_likelihood_position_model=0.383594	new_cov=2/1	polymorphism_quality=7.7	quality=7.7	quality_position_model=2.54778e-12	ref_cov=124/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/101
RA	435	.	NC_007779	3152855	0	A	.	bias_e_value=3642110	bias_p_value=0.783868	fisher_strand_p_value=0.584715	frequency=1.297951e-02	genotype_quality=939.7	ks_quality_p_value=0.717348	log10_base_likelihood=-8.46654	log10_qual_likelihood_position_model=2.00878	log10_strand_likelihood_position_model=0.484543	new_cov=1/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=6.79552e-08	ref_cov=128/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/102
RA	436	.	NC_007779	3157655	0	T	.	bias_e_value=1175510	bias_p_value=0.252996	fisher_strand_p_value=0.0958731	frequency=1.148605e-02	genotype_quality=1062.1	ks_quality_p_value=0.717809	log10_base_likelihood=-8.19062	log10_qual_likelihood_position_model=1.28464	log10_strand_likelihood_position_model=1.0183	new_cov=0/3	polymorphism_quality=2.7	quality=2.7	quality_position_model=8.33109e-08	ref_cov=141/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/120
RA	437	.	NC_007779	3160153	0	G	C	bias_e_value=1.76907e-11	bias_p_value=3.80746e-18	fisher_strand_p_value=8.47716e-20	frequency=1.543632e-01	genotype_quality=550.8	ks_quality_p_value=1	log10_base_likelihood=-55.4342	log10_qual_likelihood_position_model=23.3275	log10_strand_likelihood_position_model=19.0717	new_cov=26/0	polymorphism_quality=50.4	quality=50.4	quality_position_model=4.06123e-15	ref_cov=16/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=42/125
RA	438	.	NC_007779	3162929	0	G	C	bias_e_value=4.12195	bias_p_value=8.8714e-07	fisher_strand_p_value=6.06085e-08	frequency=7.932329e-02	genotype_quality=646.8	ks_quality_p_value=0.821609	log10_base_likelihood=-12.2476	log10_qual_likelihood_position_model=24.0268	log10_strand_likelihood_position_model=7.21747	new_cov=20/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=77/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=97/114
RA	439	.	NC_007779	3195467	0	A	C	bias_e_value=0.00216783	bias_p_value=4.66568e-10	fisher_strand_p_value=1.81308e-11	frequency=7.846928e-02	genotype_quality=714.5	ks_quality_p_value=1	log10_base_likelihood=-8.03508	log10_qual_likelihood_position_model=26.1847	log10_strand_likelihood_position_model=10.7416	new_cov=0/25	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=131/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/90
RA	440	.	NC_007779	3212355	0	G	C	bias_e_value=1.37087e-06	bias_p_value=2.95043e-13	fisher_strand_p_value=9.37419e-15	frequency=1.366138e-01	genotype_quality=666.8	ks_quality_p_value=0.943492	log10_base_likelihood=-36.9637	log10_qual_likelihood_position_model=24.9191	log10_strand_likelihood_position_model=14.0281	new_cov=31/0	polymorphism_quality=31.8	quality=31.8	quality_position_model=Inf	ref_cov=54/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/127
RA	441	.	NC_007779	3212363	0	T	A	bias_e_value=1594.89	bias_p_value=0.000343257	fisher_strand_p_value=3.00795e-05	frequency=3.597736e-02	genotype_quality=700.1	ks_quality_p_value=1	log10_base_likelihood=-6.27097	log10_qual_likelihood_position_model=13.886	log10_strand_likelihood_position_model=4.52173	new_cov=9/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=57/135	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=66/135
RA	442	.	NC_007779	3220025	0	C	A	bias_e_value=0.766712	bias_p_value=1.65015e-07	fisher_strand_p_value=8.42239e-09	frequency=5.714703e-02	genotype_quality=883.6	ks_quality_p_value=1	log10_base_likelihood=-8.41371	log10_qual_likelihood_position_model=24.744	log10_strand_likelihood_position_model=8.07456	new_cov=23/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=100/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/139
RA	443	.	NC_007779	3231302	0	C	G	bias_e_value=0.480398	bias_p_value=1.03393e-07	fisher_strand_p_value=5.14785e-09	frequency=6.994295e-02	genotype_quality=675.5	ks_quality_p_value=1	log10_base_likelihood=-13.366	log10_qual_likelihood_position_model=18.4599	log10_strand_likelihood_position_model=8.28837	new_cov=0/15	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=133/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/59
RA	444	.	NC_007779	3231439	1	.	A	bias_e_value=2324750	bias_p_value=0.500342	fisher_strand_p_value=0.242948	frequency=8.096695e-03	genotype_quality=1228.1	ks_quality_p_value=0.769243	log10_base_likelihood=-8.36131	log10_qual_likelihood_position_model=1.15097	log10_strand_likelihood_position_model=0.614487	new_cov=0/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.54646e-08	ref_cov=125/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/122
RA	445	.	NC_007779	3231832	1	.	G	bias_e_value=157957	bias_p_value=0.0339961	fisher_strand_p_value=0.00553719	frequency=2.336407e-02	genotype_quality=1044.7	ks_quality_p_value=0.989104	log10_base_likelihood=-22.0573	log10_qual_likelihood_position_model=2.84104	log10_strand_likelihood_position_model=2.25671	new_cov=5/0	polymorphism_quality=16.8	quality=16.8	quality_position_model=4.25058e-19	ref_cov=72/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=77/137
RA	446	.	NC_007779	3238315	1	.	T	bias_e_value=2737510	bias_p_value=0.589177	fisher_strand_p_value=0.247114	frequency=1.999950e-02	genotype_quality=676.4	ks_quality_p_value=0.990252	log10_base_likelihood=-12.9331	log10_qual_likelihood_position_model=3.09794	log10_strand_likelihood_position_model=0.843327	new_cov=3/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=5.36315e-11	ref_cov=76/71	reject=POLYMORPHISM_STRAND	tot_cov=79/71
RA	447	.	NC_007779	3258181	0	G	C	bias_e_value=5585	bias_p_value=0.00120202	fisher_strand_p_value=0.000132296	frequency=2.565384e-02	genotype_quality=591.3	ks_quality_p_value=0.90594	log10_base_likelihood=-7.43566	log10_qual_likelihood_position_model=4.80307	log10_strand_likelihood_position_model=3.87845	new_cov=4/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=14/137	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=18/137
RA	448	.	NC_007779	3266843	0	C	G	bias_e_value=0.147484	bias_p_value=3.17421e-08	fisher_strand_p_value=1.48846e-09	frequency=7.569075e-02	genotype_quality=565.8	ks_quality_p_value=1	log10_base_likelihood=-10.6128	log10_qual_likelihood_position_model=12.6529	log10_strand_likelihood_position_model=8.82726	new_cov=0/13	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=116/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/37
RA	449	.	NC_007779	3272305	0	C	A	bias_e_value=816.79	bias_p_value=0.000175792	fisher_strand_p_value=1.5001e-05	frequency=3.898525e-02	genotype_quality=903.2	ks_quality_p_value=0.96506	log10_base_likelihood=-7.04473	log10_qual_likelihood_position_model=13.8638	log10_strand_likelihood_position_model=4.82388	new_cov=15/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=117/137	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/137
RA	450	.	NC_007779	3280326	0	A	C	bias_e_value=1.68899e-18	bias_p_value=3.63509e-25	fisher_strand_p_value=5.92119e-27	frequency=1.698895e-01	genotype_quality=551.0	ks_quality_p_value=1	log10_base_likelihood=-24.5398	log10_qual_likelihood_position_model=38.2585	log10_strand_likelihood_position_model=26.2276	new_cov=0/47	polymorphism_quality=19.3	quality=19.3	quality_position_model=Inf	ref_cov=127/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/76
RA	451	.	NC_007779	3300073	0	T	G	bias_e_value=1.56307e-14	bias_p_value=3.3641e-21	fisher_strand_p_value=6.45772e-23	frequency=1.788187e-01	genotype_quality=552.3	ks_quality_p_value=1	log10_base_likelihood=-24.2068	log10_qual_likelihood_position_model=47.0959	log10_strand_likelihood_position_model=22.1899	new_cov=57/0	polymorphism_quality=19.0	quality=19.0	quality_position_model=Inf	ref_cov=50/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/111
RA	452	.	NC_007779	3310088	0	G	C	bias_e_value=0.203179	bias_p_value=4.37288e-08	fisher_strand_p_value=2.08339e-09	frequency=3.921795e-02	genotype_quality=768.9	ks_quality_p_value=1	log10_base_likelihood=-8.04873	log10_qual_likelihood_position_model=10.4805	log10_strand_likelihood_position_model=8.68123	new_cov=0/8	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=171/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=171/19
RA	453	.	NC_007779	3333612	0	T	G	bias_e_value=0.0275668	bias_p_value=5.93303e-09	fisher_strand_p_value=2.57044e-10	frequency=4.832745e-02	genotype_quality=634.2	ks_quality_p_value=1	log10_base_likelihood=-10.9963	log10_qual_likelihood_position_model=13.0215	log10_strand_likelihood_position_model=9.58999	new_cov=9/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=9/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=18/146
RA	454	.	NC_007779	3350708	0	A	C	bias_e_value=1.16876e-09	bias_p_value=2.51544e-16	fisher_strand_p_value=6.19213e-18	frequency=9.571505e-02	genotype_quality=744.5	ks_quality_p_value=1	log10_base_likelihood=-11.2887	log10_qual_likelihood_position_model=35.0928	log10_strand_likelihood_position_model=17.2082	new_cov=0/42	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=137/67	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/109
RA	455	.	NC_007779	3362867	0	A	.	bias_e_value=1300550	bias_p_value=0.279908	fisher_strand_p_value=0.614308	frequency=1.082325e-02	genotype_quality=1150.5	ks_quality_p_value=0.128845	log10_base_likelihood=-8.23688	log10_qual_likelihood_position_model=1.79693	log10_strand_likelihood_position_model=0.435873	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.31403e-08	ref_cov=141/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/135
RA	456	.	NC_007779	3385700	1	.	T	bias_e_value=543576	bias_p_value=0.11699	fisher_strand_p_value=0.50313	frequency=7.379532e-03	genotype_quality=1321.9	ks_quality_p_value=0.0495642	log10_base_likelihood=-8.07378	log10_qual_likelihood_position_model=2.04479	log10_strand_likelihood_position_model=0.520885	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.05969e-07	ref_cov=122/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/149
RA	457	.	NC_007779	3387541	0	G	A	bias_e_value=11.04	bias_p_value=2.37607e-06	fisher_strand_p_value=1.41689e-07	frequency=5.235481e-02	genotype_quality=855.9	ks_quality_p_value=1	log10_base_likelihood=-6.62169	log10_qual_likelihood_position_model=15.8948	log10_strand_likelihood_position_model=6.84867	new_cov=0/17	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=148/88	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=148/105
RA	458	.	NC_007779	3389914	0	A	C	bias_e_value=9.68711e-10	bias_p_value=2.08489e-16	fisher_strand_p_value=5.10807e-18	frequency=1.551528e-01	genotype_quality=551.4	ks_quality_p_value=1	log10_base_likelihood=-12.192	log10_qual_likelihood_position_model=36.8264	log10_strand_likelihood_position_model=17.5792	new_cov=0/62	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=95/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/136
RA	459	.	NC_007779	3389914	1	.	C	bias_e_value=2869440	bias_p_value=0.617572	fisher_strand_p_value=0.281827	frequency=1.349449e-02	genotype_quality=978.8	ks_quality_p_value=0.942018	log10_base_likelihood=-7.98284	log10_qual_likelihood_position_model=3.43547	log10_strand_likelihood_position_model=0.651878	new_cov=0/3	polymorphism_quality=2.5	quality=2.5	quality_position_model=9.90428e-06	ref_cov=87/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=87/135
RA	460	.	NC_007779	3397405	0	A	C	bias_e_value=4.06686e-19	bias_p_value=8.75283e-26	fisher_strand_p_value=1.39291e-27	frequency=1.448908e-01	genotype_quality=593.5	ks_quality_p_value=1	log10_base_likelihood=-13.5034	log10_qual_likelihood_position_model=41.4622	log10_strand_likelihood_position_model=26.8561	new_cov=0/51	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=131/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/83
RA	461	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1217.6	new_cov=127/153	quality=1217.6	ref_cov=0/0	tot_cov=127/153
RA	462	.	NC_007779	3404070	0	T	G	bias_e_value=2.9838e-07	bias_p_value=6.42183e-14	fisher_strand_p_value=1.8385e-15	frequency=1.521616e-01	genotype_quality=513.6	ks_quality_p_value=1	log10_base_likelihood=-23.8526	log10_qual_likelihood_position_model=32.6148	log10_strand_likelihood_position_model=14.8067	new_cov=42/0	polymorphism_quality=18.6	quality=18.6	quality_position_model=Inf	ref_cov=55/94	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/94
RA	463	.	NC_007779	3412753	0	C	T	bias_e_value=0.869934	bias_p_value=1.8723e-07	fisher_strand_p_value=9.62166e-09	frequency=5.276966e-02	genotype_quality=772.6	ks_quality_p_value=1	log10_base_likelihood=-7.93047	log10_qual_likelihood_position_model=17.2832	log10_strand_likelihood_position_model=8.01675	new_cov=0/13	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=150/41	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/54
RA	464	.	NC_007779	3421203	0	T	C	bias_e_value=1.03916e-05	bias_p_value=2.23651e-12	fisher_strand_p_value=7.15255e-14	frequency=7.138395e-02	genotype_quality=715.3	ks_quality_p_value=1	log10_base_likelihood=-10.2206	log10_qual_likelihood_position_model=22.9197	log10_strand_likelihood_position_model=13.1455	new_cov=0/20	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=156/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/54
RA	465	.	NC_007779	3421217	0	C	G	bias_e_value=0.0356363	bias_p_value=7.66977e-09	fisher_strand_p_value=3.84518e-10	frequency=5.388594e-02	genotype_quality=887.1	ks_quality_p_value=0.874332	log10_base_likelihood=-9.87928	log10_qual_likelihood_position_model=24.1361	log10_strand_likelihood_position_model=9.41508	new_cov=0/19	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=172/71	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=172/90
RA	466	.	NC_007779	3423128	1	.	G	bias_e_value=532031	bias_p_value=0.114506	fisher_strand_p_value=0.12135	frequency=1.941776e-02	genotype_quality=740.0	ks_quality_p_value=0.199971	log10_base_likelihood=-18.3504	log10_qual_likelihood_position_model=3.30739	log10_strand_likelihood_position_model=1.21699	new_cov=4/0	polymorphism_quality=13.0	quality=13.0	quality_position_model=6.38503e-16	ref_cov=99/103	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=103/103
RA	467	.	NC_007779	3440270	0	C	A	bias_e_value=231.906	bias_p_value=4.99115e-05	fisher_strand_p_value=3.6948e-06	frequency=6.417322e-02	genotype_quality=828.1	ks_quality_p_value=1	log10_base_likelihood=-14.3705	log10_qual_likelihood_position_model=15.8003	log10_strand_likelihood_position_model=5.66678	new_cov=22/0	polymorphism_quality=9.0	quality=9.0	quality_position_model=Inf	ref_cov=132/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/116
RA	468	.	NC_007779	3440600	0	A	C	bias_e_value=8.63484e-13	bias_p_value=1.85842e-19	fisher_strand_p_value=3.87166e-21	frequency=1.004777e-01	genotype_quality=737.6	ks_quality_p_value=1	log10_base_likelihood=-13.5796	log10_qual_likelihood_position_model=32.99	log10_strand_likelihood_position_model=20.4121	new_cov=0/43	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=148/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/97
RA	469	.	NC_007779	3447060	0	T	A	bias_e_value=31503.9	bias_p_value=0.00678038	fisher_strand_p_value=0.000838787	frequency=3.787613e-02	genotype_quality=910.1	ks_quality_p_value=1	log10_base_likelihood=-9.27794	log10_qual_likelihood_position_model=16.5886	log10_strand_likelihood_position_model=3.23718	new_cov=0/11	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=124/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/133
RA	470	.	NC_007779	3459894	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	471	.	NC_007779	3459896	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	472	.	NC_007779	3459897	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	473	.	NC_007779	3459899	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	474	.	NC_007779	3459900	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	475	.	NC_007779	3459901	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	476	.	NC_007779	3459903	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	477	.	NC_007779	3459904	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	478	.	NC_007779	3459906	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	479	.	NC_007779	3459909	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	480	.	NC_007779	3459911	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	481	.	NC_007779	3459912	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	482	.	NC_007779	3459913	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	483	.	NC_007779	3459915	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	484	.	NC_007779	3459916	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	485	.	NC_007779	3459917	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	486	.	NC_007779	3459918	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	487	.	NC_007779	3459919	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	488	.	NC_007779	3459920	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	489	.	NC_007779	3459921	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	3459923	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	491	.	NC_007779	3459924	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	492	.	NC_007779	3459926	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	493	.	NC_007779	3459927	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	3459929	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	495	.	NC_007779	3459930	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	496	.	NC_007779	3459931	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	3459932	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	498	.	NC_007779	3459933	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	3459934	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	500	.	NC_007779	3459935	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	3459936	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	3459937	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	3459938	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=1/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	504	.	NC_007779	3459939	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	505	.	NC_007779	3459940	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	506	.	NC_007779	3459942	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	3459943	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	508	.	NC_007779	3459945	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	3459946	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	510	.	NC_007779	3459947	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	511	.	NC_007779	3459948	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	512	.	NC_007779	3459949	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	3459950	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	3459951	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	515	.	NC_007779	3459952	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	516	.	NC_007779	3459955	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=1/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	517	.	NC_007779	3459957	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	518	.	NC_007779	3459958	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	519	.	NC_007779	3459959	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	520	.	NC_007779	3459960	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	521	.	NC_007779	3475527	0	T	G	bias_e_value=8.20852e-13	bias_p_value=1.76667e-19	fisher_strand_p_value=3.67655e-21	frequency=2.097116e-01	genotype_quality=504.3	ks_quality_p_value=1	log10_base_likelihood=-44.2509	log10_qual_likelihood_position_model=37.6224	log10_strand_likelihood_position_model=20.4488	new_cov=60/0	polymorphism_quality=39.1	quality=39.1	quality_position_model=Inf	ref_cov=56/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/100
RA	522	.	NC_007779	3475533	0	C	T	bias_e_value=2.73841e-09	bias_p_value=5.89371e-16	fisher_strand_p_value=1.48269e-17	frequency=2.214704e-01	genotype_quality=543.1	ks_quality_p_value=1	log10_base_likelihood=-63.1185	log10_qual_likelihood_position_model=48.8217	log10_strand_likelihood_position_model=17.0675	new_cov=52/0	polymorphism_quality=58.1	quality=58.1	quality_position_model=Inf	ref_cov=70/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/107
RA	523	.	NC_007779	3475539	0	G	T	bias_e_value=8826.01	bias_p_value=0.00189957	fisher_strand_p_value=0.000199545	frequency=5.660772e-02	genotype_quality=612.0	ks_quality_p_value=1	log10_base_likelihood=-11.2649	log10_qual_likelihood_position_model=8.97971	log10_strand_likelihood_position_model=3.69996	new_cov=10/0	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=66/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=76/96
RA	524	.	NC_007779	3481746	0	T	G	bias_e_value=3.12932e-07	bias_p_value=6.73503e-14	fisher_strand_p_value=1.93087e-15	frequency=8.486700e-02	genotype_quality=871.6	ks_quality_p_value=1	log10_base_likelihood=-9.93023	log10_qual_likelihood_position_model=29.7863	log10_strand_likelihood_position_model=14.7142	new_cov=34/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=78/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/162
RA	525	.	NC_007779	3499066	0	A	C	bias_e_value=4.60741e-07	bias_p_value=9.91624e-14	fisher_strand_p_value=2.87573e-15	frequency=8.839226e-02	genotype_quality=673.2	ks_quality_p_value=1	log10_base_likelihood=-16.0955	log10_qual_likelihood_position_model=24.8047	log10_strand_likelihood_position_model=14.5413	new_cov=0/20	polymorphism_quality=10.8	quality=10.8	quality_position_model=Inf	ref_cov=147/24	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/44
RA	526	.	NC_007779	3520391	0	C	G	bias_e_value=1.40278e-10	bias_p_value=3.01911e-17	fisher_strand_p_value=7.05474e-19	frequency=1.108732e-01	genotype_quality=549.0	ks_quality_p_value=1	log10_base_likelihood=-25.4111	log10_qual_likelihood_position_model=17.4692	log10_strand_likelihood_position_model=18.1515	new_cov=17/0	polymorphism_quality=20.2	quality=20.2	quality_position_model=Inf	ref_cov=4/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=21/127
RA	527	.	NC_007779	3530293	1	.	A	bias_e_value=3888650	bias_p_value=0.836929	fisher_strand_p_value=0.499199	frequency=8.928299e-03	genotype_quality=1106.8	ks_quality_p_value=0.974275	log10_base_likelihood=-7.86141	log10_qual_likelihood_position_model=2.98255	log10_strand_likelihood_position_model=0.558485	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.55117e-06	ref_cov=116/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/106
RA	528	.	NC_007779	3543542	0	G	T	bias_e_value=510.196	bias_p_value=0.000109806	fisher_strand_p_value=8.67702e-06	frequency=4.141331e-02	genotype_quality=678.3	ks_quality_p_value=1	log10_base_likelihood=-5.64198	log10_qual_likelihood_position_model=14.9126	log10_strand_likelihood_position_model=5.06163	new_cov=0/13	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=113/71	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/84
RA	529	.	NC_007779	3543547	0	A	C	bias_e_value=1.20956e-25	bias_p_value=2.60325e-32	fisher_strand_p_value=3.33392e-34	frequency=3.015213e-01	genotype_quality=503.2	ks_quality_p_value=1	log10_base_likelihood=-66.8802	log10_qual_likelihood_position_model=54.5715	log10_strand_likelihood_position_model=33.5251	new_cov=0/86	polymorphism_quality=61.9	quality=61.9	quality_position_model=Inf	ref_cov=118/43	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/131
RA	530	.	NC_007779	3553973	1	.	C	bias_e_value=1732350	bias_p_value=0.372843	fisher_strand_p_value=0.293735	frequency=1.538467e-02	genotype_quality=932.9	ks_quality_p_value=0.405984	log10_base_likelihood=-13.6827	log10_qual_likelihood_position_model=1.86871	log10_strand_likelihood_position_model=0.615067	new_cov=3/0	polymorphism_quality=8.3	quality=8.3	quality_position_model=2.99599e-13	ref_cov=119/73	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/73
RA	531	.	NC_007779	3558662	0	T	.	bias_e_value=4568080	bias_p_value=0.983158	fisher_strand_p_value=1	frequency=1.281357e-02	genotype_quality=958.5	ks_quality_p_value=0.822173	log10_base_likelihood=-8.52335	log10_qual_likelihood_position_model=1.31276	log10_strand_likelihood_position_model=0.394234	new_cov=2/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=9.16421e-09	ref_cov=124/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/108
RA	532	.	NC_007779	3571074	0	A	G	bias_e_value=0.249661	bias_p_value=5.37329e-08	fisher_strand_p_value=2.58669e-09	frequency=6.055021e-02	genotype_quality=680.3	ks_quality_p_value=1	log10_base_likelihood=-7.87772	log10_qual_likelihood_position_model=15.5226	log10_strand_likelihood_position_model=8.58726	new_cov=19/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=64/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=83/135
RA	533	.	NC_007779	3586831	1	.	T	bias_e_value=1932060	bias_p_value=0.415825	fisher_strand_p_value=0.244465	frequency=6.348610e-03	genotype_quality=1587.6	ks_quality_p_value=0.573864	log10_base_likelihood=-8.03449	log10_qual_likelihood_position_model=1.95227	log10_strand_likelihood_position_model=0.611784	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.25353e-07	ref_cov=159/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/156
RA	534	.	NC_007779	3673380	0	G	T	bias_e_value=1406.92	bias_p_value=0.000302802	fisher_strand_p_value=2.90852e-05	frequency=3.857517e-02	genotype_quality=808.7	ks_quality_p_value=0.901449	log10_base_likelihood=-5.92573	log10_qual_likelihood_position_model=19.1734	log10_strand_likelihood_position_model=4.58424	new_cov=0/16	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=119/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/135
RA	535	.	NC_007779	3676780	0	A	C	bias_e_value=0.147209	bias_p_value=3.16828e-08	fisher_strand_p_value=1.48554e-09	frequency=8.307076e-02	genotype_quality=745.4	ks_quality_p_value=1	log10_base_likelihood=-11.5074	log10_qual_likelihood_position_model=22.5658	log10_strand_likelihood_position_model=8.96086	new_cov=0/28	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=121/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/126
RA	536	.	NC_007779	3684449	0	C	G	bias_e_value=6466.22	bias_p_value=0.00139168	fisher_strand_p_value=0.000141294	frequency=4.062653e-02	genotype_quality=818.7	ks_quality_p_value=0.998291	log10_base_likelihood=-7.99083	log10_qual_likelihood_position_model=14.8536	log10_strand_likelihood_position_model=3.84987	new_cov=0/12	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=124/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/119
RA	537	.	NC_007779	3686205	0	A	.	bias_e_value=4646150	bias_p_value=0.99996	fisher_strand_p_value=1	frequency=1.281071e-02	genotype_quality=966.4	ks_quality_p_value=0.991049	log10_base_likelihood=-8.07419	log10_qual_likelihood_position_model=2.21738	log10_strand_likelihood_position_model=0.388619	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.26562e-07	ref_cov=126/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/106
RA	538	.	NC_007779	3688858	0	A	C	bias_e_value=1.14915e-27	bias_p_value=2.47324e-34	fisher_strand_p_value=2.98705e-36	frequency=2.687063e-01	genotype_quality=428.2	ks_quality_p_value=1	log10_base_likelihood=-50.6098	log10_qual_likelihood_position_model=45.9431	log10_strand_likelihood_position_model=35.5248	new_cov=0/62	polymorphism_quality=45.5	quality=45.5	quality_position_model=Inf	ref_cov=114/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/77
RA	539	.	NC_007779	3701118	0	G	T	bias_e_value=0.388046	bias_p_value=8.35167e-08	fisher_strand_p_value=4.11224e-09	frequency=7.423496e-02	genotype_quality=774.3	ks_quality_p_value=1	log10_base_likelihood=-10.1667	log10_qual_likelihood_position_model=18.0457	log10_strand_likelihood_position_model=8.38592	new_cov=0/24	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=125/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/113
RA	540	.	NC_007779	3709260	1	.	C	bias_e_value=2391090	bias_p_value=0.514619	fisher_strand_p_value=0.246606	frequency=9.049416e-03	genotype_quality=1063.9	ks_quality_p_value=0.792824	log10_base_likelihood=-7.14686	log10_qual_likelihood_position_model=2.3646	log10_strand_likelihood_position_model=0.607996	new_cov=0/2	polymorphism_quality=1.6	quality=1.6	quality_position_model=5.05046e-06	ref_cov=111/108	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/110
RA	541	.	NC_007779	3710315	0	T	G	bias_e_value=1.34484	bias_p_value=2.89441e-07	fisher_strand_p_value=1.52339e-08	frequency=3.973484e-02	genotype_quality=878.7	ks_quality_p_value=1	log10_base_likelihood=-6.57076	log10_qual_likelihood_position_model=23.0606	log10_strand_likelihood_position_model=7.81719	new_cov=23/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=102/135	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/135
RA	542	.	NC_007779	3727557	0	A	G	bias_e_value=0.000969351	bias_p_value=2.08627e-10	fisher_strand_p_value=7.8519e-12	frequency=6.931782e-02	genotype_quality=562.7	ks_quality_p_value=1	log10_base_likelihood=-10.2342	log10_qual_likelihood_position_model=17.1221	log10_strand_likelihood_position_model=11.105	new_cov=13/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=15/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=28/133
RA	543	.	NC_007779	3728146	1	.	T	bias_e_value=193167	bias_p_value=0.0415741	fisher_strand_p_value=0.00962715	frequency=1.990032e-02	genotype_quality=958.6	ks_quality_p_value=0.723788	log10_base_likelihood=-18.0096	log10_qual_likelihood_position_model=2.49593	log10_strand_likelihood_position_model=2.0165	new_cov=4/0	polymorphism_quality=12.7	quality=12.7	quality_position_model=1.37747e-15	ref_cov=60/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=64/137
RA	544	.	NC_007779	3728155	0	T	C	bias_e_value=3.81929e-08	bias_p_value=8.22e-15	fisher_strand_p_value=2.21896e-16	frequency=8.991098e-02	genotype_quality=543.7	ks_quality_p_value=1	log10_base_likelihood=-21.0952	log10_qual_likelihood_position_model=19.2829	log10_strand_likelihood_position_model=15.6538	new_cov=16/0	polymorphism_quality=15.8	quality=15.8	quality_position_model=Inf	ref_cov=9/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=25/143
RA	545	.	NC_007779	3728157	0	A	C	bias_e_value=0.000950459	bias_p_value=2.04561e-10	fisher_strand_p_value=7.69295e-12	frequency=7.737827e-02	genotype_quality=508.8	ks_quality_p_value=1	log10_base_likelihood=-9.59872	log10_qual_likelihood_position_model=20.9592	log10_strand_likelihood_position_model=11.1205	new_cov=15/3	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=11/135	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=26/138
RA	546	.	NC_007779	3731042	0	T	.	bias_e_value=3989240	bias_p_value=0.858577	fisher_strand_p_value=1	frequency=1.265049e-02	genotype_quality=946.3	ks_quality_p_value=0.517768	log10_base_likelihood=-8.36937	log10_qual_likelihood_position_model=1.61578	log10_strand_likelihood_position_model=0.411764	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.82744e-08	ref_cov=114/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/122
RA	547	.	NC_007779	3732310	0	G	T	bias_e_value=0.166516	bias_p_value=3.58382e-08	fisher_strand_p_value=1.69063e-09	frequency=7.694674e-02	genotype_quality=778.6	ks_quality_p_value=1	log10_base_likelihood=-11.0215	log10_qual_likelihood_position_model=17.326	log10_strand_likelihood_position_model=8.77195	new_cov=0/26	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=127/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/121
RA	548	.	NC_007779	3734364	1	.	A	bias_e_value=3103260	bias_p_value=0.667896	fisher_strand_p_value=0.498352	frequency=7.220268e-03	genotype_quality=1380.1	ks_quality_p_value=0.613244	log10_base_likelihood=-8.28519	log10_qual_likelihood_position_model=1.1266	log10_strand_likelihood_position_model=0.588042	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.64221e-08	ref_cov=136/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/141
RA	549	.	NC_007779	3750122	0	C	.	bias_e_value=189237	bias_p_value=0.0407282	fisher_strand_p_value=0.798759	frequency=9.418178e-01	genotype_quality=1234.8	ks_quality_p_value=0.00851083	log10_base_likelihood=-78.4884	log10_qual_likelihood_position_model=9.42804	log10_strand_likelihood_position_model=0.727387	new_cov=132/127	polymorphism_quality=73.5	quality=73.5	quality_position_model=9.04568e-71	ref_cov=9/7	tot_cov=141/134
RA	550	.	NC_007779	3750123	0	C	T	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=5.728531e-02	genotype_quality=1035.1	ks_quality_p_value=0.999551	log10_base_likelihood=-35.618	log10_qual_likelihood_position_model=9.86187	log10_strand_likelihood_position_model=0.696282	new_cov=8/8	polymorphism_quality=30.5	quality=30.5	quality_position_model=2.78661e-27	ref_cov=133/126	tot_cov=141/134
RA	551	.	NC_007779	3762475	0	T	G	bias_e_value=9.19336e-06	bias_p_value=1.97863e-12	fisher_strand_p_value=6.30231e-14	frequency=1.170754e-01	genotype_quality=639.2	ks_quality_p_value=1	log10_base_likelihood=-13.1307	log10_qual_likelihood_position_model=30.6895	log10_strand_likelihood_position_model=13.2005	new_cov=34/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=65/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=99/118
RA	552	.	NC_007779	3763528	0	A	C	bias_e_value=320.814	bias_p_value=6.90466e-05	fisher_strand_p_value=5.32434e-06	frequency=3.101635e-02	genotype_quality=616.0	ks_quality_p_value=0.985589	log10_base_likelihood=-9.68119	log10_qual_likelihood_position_model=5.85144	log10_strand_likelihood_position_model=5.27373	new_cov=0/5	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=144/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/16
RA	553	.	NC_007779	3773157	0	T	G	bias_e_value=21.702	bias_p_value=4.67077e-06	fisher_strand_p_value=2.91016e-07	frequency=3.756237e-02	genotype_quality=995.4	ks_quality_p_value=1	log10_base_likelihood=-5.89705	log10_qual_likelihood_position_model=24.1076	log10_strand_likelihood_position_model=6.53608	new_cov=20/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=118/144	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/144
RA	554	.	NC_007779	3788380	0	G	T	bias_e_value=0.751365	bias_p_value=1.61711e-07	fisher_strand_p_value=8.25157e-09	frequency=7.880640e-02	genotype_quality=823.9	ks_quality_p_value=0.999183	log10_base_likelihood=-16.05	log10_qual_likelihood_position_model=23.423	log10_strand_likelihood_position_model=8.10758	new_cov=0/29	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=118/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/146
RA	555	.	NC_007779	3789663	0	T	.	bias_e_value=3737200	bias_p_value=0.804334	fisher_strand_p_value=0.581261	frequency=1.179218e-02	genotype_quality=1009.5	ks_quality_p_value=0.76351	log10_base_likelihood=-7.50955	log10_qual_likelihood_position_model=4.2442	log10_strand_likelihood_position_model=0.492918	new_cov=1/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=0.000153198	ref_cov=142/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/110
RA	556	.	NC_007779	3812429	0	G	T	bias_e_value=309.522	bias_p_value=6.66165e-05	fisher_strand_p_value=5.04804e-06	frequency=4.302025e-02	genotype_quality=749.5	ks_quality_p_value=1	log10_base_likelihood=-5.85298	log10_qual_likelihood_position_model=13.8927	log10_strand_likelihood_position_model=5.29688	new_cov=0/16	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=117/94	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/111
RA	557	.	NC_007779	3813810	0	T	G	bias_e_value=2.51282e-11	bias_p_value=5.40818e-18	fisher_strand_p_value=1.21381e-19	frequency=1.232977e-01	genotype_quality=514.5	ks_quality_p_value=1	log10_base_likelihood=-18.7386	log10_qual_likelihood_position_model=26.9554	log10_strand_likelihood_position_model=18.9158	new_cov=34/0	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=27/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/112
RA	558	.	NC_007779	3820146	0	T	G	bias_e_value=0.673536	bias_p_value=1.44961e-07	fisher_strand_p_value=7.34764e-09	frequency=7.125425e-02	genotype_quality=664.6	ks_quality_p_value=1	log10_base_likelihood=-7.04445	log10_qual_likelihood_position_model=21.3337	log10_strand_likelihood_position_model=8.14314	new_cov=21/1	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=58/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=79/122
RA	559	.	NC_007779	3824606	1	.	T	bias_e_value=4571850	bias_p_value=0.98397	fisher_strand_p_value=1	frequency=1.339245e-02	genotype_quality=1076.3	ks_quality_p_value=0.826376	log10_base_likelihood=-12.594	log10_qual_likelihood_position_model=2.69388	log10_strand_likelihood_position_model=0.420165	new_cov=2/1	polymorphism_quality=7.2	quality=7.2	quality_position_model=1.69947e-11	ref_cov=111/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/111
RA	560	.	NC_007779	3828029	0	G	T	bias_e_value=4.93917e-05	bias_p_value=1.06303e-11	fisher_strand_p_value=4.21297e-13	frequency=1.352124e-01	genotype_quality=659.6	ks_quality_p_value=0.850802	log10_base_likelihood=-32.1354	log10_qual_likelihood_position_model=32.5015	log10_strand_likelihood_position_model=12.3754	new_cov=31/0	polymorphism_quality=27.0	quality=27.0	quality_position_model=Inf	ref_cov=63/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=94/118
RA	561	.	NC_007779	3845596	0	G	T	bias_e_value=1.43595	bias_p_value=3.0905e-07	fisher_strand_p_value=1.63255e-08	frequency=5.462170e-02	genotype_quality=960.2	ks_quality_p_value=1	log10_base_likelihood=-12.9057	log10_qual_likelihood_position_model=17.2428	log10_strand_likelihood_position_model=7.78713	new_cov=0/23	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=152/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/140
RA	562	.	NC_007779	3846240	0	G	C	bias_e_value=5.37984e-05	bias_p_value=1.15787e-11	fisher_strand_p_value=3.92203e-13	frequency=9.603643e-02	genotype_quality=497.5	ks_quality_p_value=0.998431	log10_base_likelihood=-13.5061	log10_qual_likelihood_position_model=15.0816	log10_strand_likelihood_position_model=12.4065	new_cov=0/16	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=119/16	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/32
RA	563	.	NC_007779	3855255	0	C	A	bias_e_value=2001.53	bias_p_value=0.000430777	fisher_strand_p_value=3.90451e-05	frequency=2.503872e-02	genotype_quality=650.8	ks_quality_p_value=0.988382	log10_base_likelihood=-8.60949	log10_qual_likelihood_position_model=5.14642	log10_strand_likelihood_position_model=4.40843	new_cov=0/4	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=145/10	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/14
RA	564	.	NC_007779	3859254	1	.	T	bias_e_value=51476.5	bias_p_value=0.011079	fisher_strand_p_value=0.00149397	frequency=2.884579e-02	genotype_quality=979.8	ks_quality_p_value=0.986103	log10_base_likelihood=-28.5618	log10_qual_likelihood_position_model=2.10058	log10_strand_likelihood_position_model=2.82566	new_cov=6/0	polymorphism_quality=23.4	quality=23.4	quality_position_model=7.61824e-26	ref_cov=66/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=72/136
RA	565	.	NC_007779	3859263	0	T	C	bias_e_value=0.00752802	bias_p_value=1.62021e-09	fisher_strand_p_value=6.63019e-11	frequency=7.896996e-02	genotype_quality=572.8	ks_quality_p_value=1	log10_base_likelihood=-20.3912	log10_qual_likelihood_position_model=18.5035	log10_strand_likelihood_position_model=10.1785	new_cov=16/0	polymorphism_quality=15.1	quality=15.1	quality_position_model=Inf	ref_cov=33/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=49/137
RA	566	.	NC_007779	3859265	0	A	C	bias_e_value=6.11162	bias_p_value=1.31536e-06	fisher_strand_p_value=7.56054e-08	frequency=5.882263e-02	genotype_quality=540.3	ks_quality_p_value=1	log10_base_likelihood=-11.6582	log10_qual_likelihood_position_model=12.425	log10_strand_likelihood_position_model=7.13648	new_cov=15/2	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=38/136	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=53/138
RA	567	.	NC_007779	3859270	0	G	C	bias_e_value=5.30413	bias_p_value=1.14157e-06	fisher_strand_p_value=6.50542e-08	frequency=5.163431e-02	genotype_quality=699.8	ks_quality_p_value=1	log10_base_likelihood=-10.8343	log10_qual_likelihood_position_model=12.3009	log10_strand_likelihood_position_model=7.18672	new_cov=11/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=33/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=44/136
RA	568	.	NC_007779	3885601	0	G	T	bias_e_value=252.844	bias_p_value=5.44181e-05	fisher_strand_p_value=4.05645e-06	frequency=3.552437e-02	genotype_quality=1056.7	ks_quality_p_value=1	log10_base_likelihood=-5.85014	log10_qual_likelihood_position_model=15.4859	log10_strand_likelihood_position_model=5.39185	new_cov=0/17	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=158/138	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/155
RA	569	.	NC_007779	3888878	0	T	G	bias_e_value=0.0886203	bias_p_value=1.90732e-08	fisher_strand_p_value=8.7253e-10	frequency=7.515907e-02	genotype_quality=702.3	ks_quality_p_value=1	log10_base_likelihood=-9.76194	log10_qual_likelihood_position_model=21.8935	log10_strand_likelihood_position_model=9.05922	new_cov=26/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=82/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/117
RA	570	.	NC_007779	3891907	0	T	.	bias_e_value=2756900	bias_p_value=0.59335	fisher_strand_p_value=0.250208	frequency=1.113796e-02	genotype_quality=1091.6	ks_quality_p_value=0.989905	log10_base_likelihood=-7.62349	log10_qual_likelihood_position_model=2.92853	log10_strand_likelihood_position_model=0.827555	new_cov=0/3	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.06007e-05	ref_cov=126/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/143
RA	571	.	NC_007779	3895373	0	T	G	bias_e_value=3.0775e-07	bias_p_value=6.6235e-14	fisher_strand_p_value=1.89796e-15	frequency=1.015410e-01	genotype_quality=588.8	ks_quality_p_value=1	log10_base_likelihood=-13.6265	log10_qual_likelihood_position_model=37.2914	log10_strand_likelihood_position_model=14.7217	new_cov=35/0	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=57/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/121
RA	572	.	NC_007779	3897683	0	C	.	bias_e_value=2837080	bias_p_value=0.610606	fisher_strand_p_value=1	frequency=8.616447e-03	genotype_quality=1010.9	ks_quality_p_value=0.260272	log10_base_likelihood=-5.75711	log10_qual_likelihood_position_model=1.38747	log10_strand_likelihood_position_model=0.309739	new_cov=1/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=6.65604e-06	ref_cov=97/133	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=98/134
RA	573	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1258.4	new_cov=157/133	quality=1258.4	ref_cov=0/0	tot_cov=157/133
RA	574	.	NC_007779	3898897	0	G	T	bias_e_value=1681.21	bias_p_value=0.000361835	fisher_strand_p_value=3.29766e-05	frequency=4.859638e-02	genotype_quality=475.0	ks_quality_p_value=0.966408	log10_base_likelihood=-7.73574	log10_qual_likelihood_position_model=9.57946	log10_strand_likelihood_position_model=4.48179	new_cov=7/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=24/94	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=31/94
RA	575	.	NC_007779	3900676	1	.	G	bias_e_value=457768	bias_p_value=0.0985224	fisher_strand_p_value=0.205346	frequency=7.633209e-03	genotype_quality=1321.5	ks_quality_p_value=0.0977476	log10_base_likelihood=-8.49618	log10_qual_likelihood_position_model=1.24321	log10_strand_likelihood_position_model=0.687513	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.66218e-08	ref_cov=117/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/143
RA	576	.	NC_007779	3900680	0	T	G	bias_e_value=1.39881e-16	bias_p_value=3.01056e-23	fisher_strand_p_value=5.29109e-25	frequency=1.085925e-01	genotype_quality=603.7	ks_quality_p_value=1	log10_base_likelihood=-22.3045	log10_qual_likelihood_position_model=27.5665	log10_strand_likelihood_position_model=24.2765	new_cov=23/0	polymorphism_quality=17.0	quality=17.0	quality_position_model=Inf	ref_cov=4/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/148
RA	577	.	NC_007779	3900687	0	G	T	bias_e_value=229.846	bias_p_value=4.94682e-05	fisher_strand_p_value=3.65937e-06	frequency=3.313541e-02	genotype_quality=727.9	ks_quality_p_value=1	log10_base_likelihood=-7.89077	log10_qual_likelihood_position_model=11.6627	log10_strand_likelihood_position_model=5.43659	new_cov=7/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=25/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=32/144
RA	578	.	NC_007779	3912297	0	G	.	bias_e_value=3807270	bias_p_value=0.819413	fisher_strand_p_value=0.621674	frequency=1.321030e-02	genotype_quality=946.5	ks_quality_p_value=0.744534	log10_base_likelihood=-8.92665	log10_qual_likelihood_position_model=1.07546	log10_strand_likelihood_position_model=0.425994	new_cov=2/1	polymorphism_quality=3.5	quality=3.5	quality_position_model=2.16602e-09	ref_cov=111/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/114
RA	579	.	NC_007779	3926942	0	G	T	bias_e_value=18389.8	bias_p_value=0.00395791	fisher_strand_p_value=0.000455434	frequency=3.496552e-02	genotype_quality=629.7	ks_quality_p_value=0.999501	log10_base_likelihood=-5.58633	log10_qual_likelihood_position_model=11.1755	log10_strand_likelihood_position_model=3.34157	new_cov=7/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=52/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=59/112
RA	580	.	NC_007779	3930443	0	T	G	bias_e_value=3.35912e-11	bias_p_value=7.22961e-18	fisher_strand_p_value=1.6335e-19	frequency=6.873655e-02	genotype_quality=537.8	ks_quality_p_value=1	log10_base_likelihood=-6.64187	log10_qual_likelihood_position_model=28.2167	log10_strand_likelihood_position_model=18.7869	new_cov=28/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=19/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=47/119
RA	581	.	NC_007779	3933153	0	G	T	bias_e_value=26843	bias_p_value=0.00577726	fisher_strand_p_value=0.000727542	frequency=3.814411e-02	genotype_quality=966.1	ks_quality_p_value=0.960659	log10_base_likelihood=-7.33385	log10_qual_likelihood_position_model=14.9109	log10_strand_likelihood_position_model=3.44385	new_cov=1/14	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=139/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/141
RA	582	.	NC_007779	3942675	0	A	C	bias_e_value=0.0533219	bias_p_value=1.14761e-08	fisher_strand_p_value=5.12517e-10	frequency=6.349325e-02	genotype_quality=768.6	ks_quality_p_value=1	log10_base_likelihood=-5.64344	log10_qual_likelihood_position_model=23.4706	log10_strand_likelihood_position_model=9.29029	new_cov=0/25	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=128/82	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/107
RA	583	.	NC_007779	3952095	1	.	G	bias_e_value=224109	bias_p_value=0.0482336	fisher_strand_p_value=0.0146094	frequency=2.138996e-02	genotype_quality=915.7	ks_quality_p_value=0.570471	log10_base_likelihood=-17.9289	log10_qual_likelihood_position_model=1.56175	log10_strand_likelihood_position_model=1.83537	new_cov=4/0	polymorphism_quality=12.6	quality=12.6	quality_position_model=1.22713e-16	ref_cov=62/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=66/121
RA	584	.	NC_007779	3981333	0	A	.	bias_e_value=2789450	bias_p_value=0.600356	fisher_strand_p_value=0.274529	frequency=1.249313e-02	genotype_quality=1003.2	ks_quality_p_value=0.920627	log10_base_likelihood=-8.38974	log10_qual_likelihood_position_model=1.39621	log10_strand_likelihood_position_model=0.678343	new_cov=0/3	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.01226e-08	ref_cov=97/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=97/143
RA	585	.	NC_007779	3985138	0	T	G	bias_e_value=1200.49	bias_p_value=0.000258373	fisher_strand_p_value=2.20405e-05	frequency=5.683756e-02	genotype_quality=618.9	ks_quality_p_value=1	log10_base_likelihood=-8.83202	log10_qual_likelihood_position_model=18.1394	log10_strand_likelihood_position_model=4.74516	new_cov=21/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=105/79	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/79
RA	586	.	NC_007779	4000222	0	C	G	bias_e_value=53.874	bias_p_value=1.1595e-05	fisher_strand_p_value=8.26739e-07	frequency=4.072094e-02	genotype_quality=993.6	ks_quality_p_value=0.930147	log10_base_likelihood=-6.12379	log10_qual_likelihood_position_model=19.2521	log10_strand_likelihood_position_model=6.08263	new_cov=0/18	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=157/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/142
RA	587	.	NC_007779	4010407	0	C	A	bias_e_value=4.10712	bias_p_value=8.83948e-07	fisher_strand_p_value=4.99845e-08	frequency=6.904888e-02	genotype_quality=678.5	ks_quality_p_value=0.992442	log10_base_likelihood=-14.1057	log10_qual_likelihood_position_model=18.893	log10_strand_likelihood_position_model=7.30117	new_cov=0/16	polymorphism_quality=8.7	quality=8.7	quality_position_model=Inf	ref_cov=127/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/76
RA	588	.	NC_007779	4022073	0	A	C	bias_e_value=1.8995e-07	bias_p_value=4.08816e-14	fisher_strand_p_value=1.15502e-15	frequency=5.617094e-02	genotype_quality=706.9	ks_quality_p_value=1	log10_base_likelihood=-5.83568	log10_qual_likelihood_position_model=24.8516	log10_strand_likelihood_position_model=14.9374	new_cov=0/28	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=142/45	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/73
RA	589	.	NC_007779	4023064	1	.	G	bias_e_value=1699210	bias_p_value=0.365709	fisher_strand_p_value=0.135569	frequency=2.051258e-02	genotype_quality=956.8	ks_quality_p_value=0.855059	log10_base_likelihood=-17.5317	log10_qual_likelihood_position_model=1.42669	log10_strand_likelihood_position_model=0.989129	new_cov=4/0	polymorphism_quality=12.2	quality=12.2	quality_position_model=3.1367e-17	ref_cov=107/84	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/84
RA	590	.	NC_007779	4023068	0	T	G	bias_e_value=0.198919	bias_p_value=4.2812e-08	fisher_strand_p_value=2.03755e-09	frequency=5.461979e-02	genotype_quality=436.1	ks_quality_p_value=1	log10_base_likelihood=-6.79094	log10_qual_likelihood_position_model=15.0859	log10_strand_likelihood_position_model=8.69089	new_cov=12/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=15/91	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/91
RA	591	.	NC_007779	4029633	0	T	G	bias_e_value=1.79966e-08	bias_p_value=3.87329e-15	fisher_strand_p_value=1.03186e-16	frequency=1.141920e-01	genotype_quality=587.9	ks_quality_p_value=0.992579	log10_base_likelihood=-19.4216	log10_qual_likelihood_position_model=26.6375	log10_strand_likelihood_position_model=15.9864	new_cov=24/0	polymorphism_quality=14.1	quality=14.1	quality_position_model=Inf	ref_cov=23/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=47/126
RA	592	.	NC_007779	4031691	1	.	T	bias_e_value=348025	bias_p_value=0.0749031	fisher_strand_p_value=0.016637	frequency=1.587296e-02	genotype_quality=911.6	ks_quality_p_value=0.857607	log10_base_likelihood=-13.175	log10_qual_likelihood_position_model=1.69843	log10_strand_likelihood_position_model=1.77893	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=1.01833e-11	ref_cov=46/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=49/140
RA	593	.	NC_007779	4043703	0	C	A	bias_e_value=2645.02	bias_p_value=0.00056927	fisher_strand_p_value=5.24389e-05	frequency=4.296875e-02	genotype_quality=758.4	ks_quality_p_value=1	log10_base_likelihood=-9.62017	log10_qual_likelihood_position_model=12.4143	log10_strand_likelihood_position_model=4.34664	new_cov=15/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=107/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/109
RA	594	.	NC_007779	4055100	0	G	T	bias_e_value=4.7382e-09	bias_p_value=1.01977e-15	fisher_strand_p_value=2.68709e-17	frequency=1.244731e-01	genotype_quality=702.8	ks_quality_p_value=0.968439	log10_base_likelihood=-36.3357	log10_qual_likelihood_position_model=33.5507	log10_strand_likelihood_position_model=16.5707	new_cov=29/0	polymorphism_quality=31.2	quality=31.2	quality_position_model=Inf	ref_cov=39/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=68/145
RA	595	.	NC_007779	4055329	0	T	G	bias_e_value=3.05615e-12	bias_p_value=6.57755e-19	fisher_strand_p_value=1.40818e-20	frequency=1.151147e-01	genotype_quality=559.6	ks_quality_p_value=1	log10_base_likelihood=-18.6941	log10_qual_likelihood_position_model=27.0004	log10_strand_likelihood_position_model=19.8513	new_cov=26/0	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=15/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=41/131
RA	596	.	NC_007779	4059485	0	T	.	bias_e_value=4632010	bias_p_value=0.996917	fisher_strand_p_value=1	frequency=1.362610e-02	genotype_quality=912.1	ks_quality_p_value=0.922508	log10_base_likelihood=-8.1908	log10_qual_likelihood_position_model=2.39758	log10_strand_likelihood_position_model=0.42399	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.86977e-07	ref_cov=108/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/110
RA	597	.	NC_007779	4062114	0	T	G	bias_e_value=5.82699e-16	bias_p_value=1.25411e-22	fisher_strand_p_value=2.26186e-24	frequency=1.521211e-01	genotype_quality=598.4	ks_quality_p_value=1	log10_base_likelihood=-20.5181	log10_qual_likelihood_position_model=38.9045	log10_strand_likelihood_position_model=23.6455	new_cov=45/0	polymorphism_quality=15.2	quality=15.2	quality_position_model=Inf	ref_cov=33/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=78/127
RA	598	.	NC_007779	4064463	0	G	T	bias_e_value=922.49	bias_p_value=0.000198541	fisher_strand_p_value=1.6531e-05	frequency=3.562641e-02	genotype_quality=787.6	ks_quality_p_value=1	log10_base_likelihood=-5.70099	log10_qual_likelihood_position_model=13.8733	log10_strand_likelihood_position_model=4.7817	new_cov=0/14	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=126/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/112
RA	599	.	NC_007779	4065564	0	C	G	bias_e_value=1321.52	bias_p_value=0.000284422	fisher_strand_p_value=2.44954e-05	frequency=4.341316e-02	genotype_quality=746.2	ks_quality_p_value=0.999458	log10_base_likelihood=-9.10694	log10_qual_likelihood_position_model=11.502	log10_strand_likelihood_position_model=4.61092	new_cov=11/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=71/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=82/125
RA	600	.	NC_007779	4076934	0	A	C	bias_e_value=9.97691e-08	bias_p_value=2.14727e-14	fisher_strand_p_value=5.95518e-16	frequency=1.381726e-01	genotype_quality=713.4	ks_quality_p_value=1	log10_base_likelihood=-30.3563	log10_qual_likelihood_position_model=30.5652	log10_strand_likelihood_position_model=15.2251	new_cov=0/42	polymorphism_quality=25.2	quality=25.2	quality_position_model=Inf	ref_cov=131/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/122
RA	601	.	NC_007779	4078140	0	C	G	bias_e_value=0.00821339	bias_p_value=1.76771e-09	fisher_strand_p_value=7.26082e-11	frequency=7.848883e-02	genotype_quality=600.1	ks_quality_p_value=1	log10_base_likelihood=-11.398	log10_qual_likelihood_position_model=15.6055	log10_strand_likelihood_position_model=10.139	new_cov=16/0	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=30/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=46/126
RA	602	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1086.7	new_cov=126/137	quality=1086.7	ref_cov=0/0	tot_cov=126/137
RA	603	.	NC_007779	4098730	0	G	T	bias_e_value=1.02804	bias_p_value=2.21259e-07	fisher_strand_p_value=1.14742e-08	frequency=6.262398e-02	genotype_quality=797.8	ks_quality_p_value=1	log10_base_likelihood=-7.15764	log10_qual_likelihood_position_model=19.8681	log10_strand_likelihood_position_model=7.99847	new_cov=0/26	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=129/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/139
RA	604	.	NC_007779	4114690	0	C	A	bias_e_value=18825.7	bias_p_value=0.00405174	fisher_strand_p_value=0.000467421	frequency=2.993679e-02	genotype_quality=892.7	ks_quality_p_value=1	log10_base_likelihood=-5.82458	log10_qual_likelihood_position_model=11.6852	log10_strand_likelihood_position_model=3.42046	new_cov=12/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=124/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/121
RA	605	.	NC_007779	4115400	0	T	C	bias_e_value=28.5376	bias_p_value=6.14196e-06	fisher_strand_p_value=3.9012e-07	frequency=6.076574e-02	genotype_quality=595.0	ks_quality_p_value=0.999118	log10_base_likelihood=-7.5726	log10_qual_likelihood_position_model=13.0356	log10_strand_likelihood_position_model=6.4088	new_cov=0/12	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=117/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/54
RA	606	.	NC_007779	4115400	1	.	C	bias_e_value=2612.13	bias_p_value=0.000562192	fisher_strand_p_value=5.17213e-05	frequency=4.905128e-02	genotype_quality=736.9	ks_quality_p_value=1	log10_base_likelihood=-23.0821	log10_qual_likelihood_position_model=10.6148	log10_strand_likelihood_position_model=4.28633	new_cov=0/8	polymorphism_quality=17.8	quality=17.8	quality_position_model=3.62985e-10	ref_cov=113/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=113/50
RA	607	.	NC_007779	4126202	0	A	G	bias_e_value=224724	bias_p_value=0.0483658	fisher_strand_p_value=0.25281	frequency=1.274681e-02	genotype_quality=937.7	ks_quality_p_value=0.0330759	log10_base_likelihood=-6.82869	log10_qual_likelihood_position_model=2.78098	log10_strand_likelihood_position_model=0.796255	new_cov=0/3	polymorphism_quality=1.3	quality=1.3	quality_position_model=4.73539e-05	ref_cov=107/125	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=107/128
RA	608	.	NC_007779	4128669	1	.	T	bias_e_value=1642840	bias_p_value=0.353577	fisher_strand_p_value=0.498966	frequency=7.843018e-03	genotype_quality=1262.4	ks_quality_p_value=0.221162	log10_base_likelihood=-8.21406	log10_qual_likelihood_position_model=2.25507	log10_strand_likelihood_position_model=0.566948	new_cov=0/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.71757e-07	ref_cov=122/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/133
RA	609	.	NC_007779	4147012	0	A	C	bias_e_value=0.00113394	bias_p_value=2.4405e-10	fisher_strand_p_value=9.24175e-12	frequency=1.020174e-01	genotype_quality=696.2	ks_quality_p_value=1	log10_base_likelihood=-12.9119	log10_qual_likelihood_position_model=25.9009	log10_strand_likelihood_position_model=11.0342	new_cov=0/31	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=116/76	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/107
RA	610	.	NC_007779	4148399	0	A	C	bias_e_value=1.7943e-09	bias_p_value=3.86175e-16	fisher_strand_p_value=9.61024e-18	frequency=1.154146e-01	genotype_quality=624.5	ks_quality_p_value=1	log10_base_likelihood=-12.8662	log10_qual_likelihood_position_model=31.6195	log10_strand_likelihood_position_model=17.0173	new_cov=0/39	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=119/50	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/89
RA	611	.	NC_007779	4148399	1	.	C	bias_e_value=680880	bias_p_value=0.146541	fisher_strand_p_value=0.0332848	frequency=1.957989e-02	genotype_quality=930.9	ks_quality_p_value=1	log10_base_likelihood=-9.97955	log10_qual_likelihood_position_model=4.09188	log10_strand_likelihood_position_model=1.47775	new_cov=0/4	polymorphism_quality=4.5	quality=4.5	quality_position_model=2.86245e-06	ref_cov=116/84	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/88
RA	612	.	NC_007779	4157323	0	C	A	bias_e_value=8820.2	bias_p_value=0.00189831	fisher_strand_p_value=0.000211905	frequency=3.708839e-02	genotype_quality=768.0	ks_quality_p_value=0.940979	log10_base_likelihood=-6.21138	log10_qual_likelihood_position_model=14.4233	log10_strand_likelihood_position_model=3.76887	new_cov=13/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=110/111	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/112
RA	613	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1118.7	new_cov=142/114	quality=1118.7	ref_cov=0/0	tot_cov=142/114
RA	614	.	NC_007779	4190480	0	A	C	bias_e_value=0.34242	bias_p_value=7.36967e-08	fisher_strand_p_value=3.60803e-09	frequency=4.891682e-02	genotype_quality=820.6	ks_quality_p_value=0.999262	log10_base_likelihood=-5.71888	log10_qual_likelihood_position_model=21.0755	log10_strand_likelihood_position_model=8.44273	new_cov=0/20	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=145/78	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/98
RA	615	.	NC_007779	4197139	0	T	G	bias_e_value=2.24706	bias_p_value=4.83621e-07	fisher_strand_p_value=2.6202e-08	frequency=5.009413e-02	genotype_quality=568.6	ks_quality_p_value=1	log10_base_likelihood=-14.8544	log10_qual_likelihood_position_model=11.8127	log10_strand_likelihood_position_model=7.58167	new_cov=9/0	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=16/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=25/124
RA	616	.	NC_007779	4211222	0	C	A	bias_e_value=236.281	bias_p_value=5.08531e-05	fisher_strand_p_value=3.77014e-06	frequency=4.529667e-02	genotype_quality=868.7	ks_quality_p_value=1	log10_base_likelihood=-7.25893	log10_qual_likelihood_position_model=14.1964	log10_strand_likelihood_position_model=5.42364	new_cov=17/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=111/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/130
RA	617	.	NC_007779	4212619	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	618	.	NC_007779	4212620	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	619	.	NC_007779	4212623	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	620	.	NC_007779	4212624	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	621	.	NC_007779	4212625	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	622	.	NC_007779	4212626	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	623	.	NC_007779	4212629	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	624	.	NC_007779	4212632	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	625	.	NC_007779	4212633	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	626	.	NC_007779	4212634	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	627	.	NC_007779	4212635	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	628	.	NC_007779	4212637	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	629	.	NC_007779	4212638	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	630	.	NC_007779	4212639	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	631	.	NC_007779	4212640	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	632	.	NC_007779	4212641	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	633	.	NC_007779	4212642	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	634	.	NC_007779	4212643	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	635	.	NC_007779	4212644	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	636	.	NC_007779	4212645	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	637	.	NC_007779	4212646	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	638	.	NC_007779	4212648	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	639	.	NC_007779	4212650	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	640	.	NC_007779	4212651	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	641	.	NC_007779	4212652	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	642	.	NC_007779	4212654	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	643	.	NC_007779	4212655	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	644	.	NC_007779	4212656	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	645	.	NC_007779	4212659	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	646	.	NC_007779	4212808	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	647	.	NC_007779	4214450	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	648	.	NC_007779	4214454	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	649	.	NC_007779	4214455	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	650	.	NC_007779	4214456	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	651	.	NC_007779	4220019	0	A	C	bias_e_value=1.70552e-05	bias_p_value=3.67068e-12	fisher_strand_p_value=1.19345e-13	frequency=1.304188e-01	genotype_quality=564.7	ks_quality_p_value=1	log10_base_likelihood=-16.2729	log10_qual_likelihood_position_model=39.4267	log10_strand_likelihood_position_model=13.0216	new_cov=0/44	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=94/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/120
RA	652	.	NC_007779	4224248	1	.	T	bias_e_value=4587640	bias_p_value=0.987369	fisher_strand_p_value=1	frequency=8.968353e-03	genotype_quality=1113.7	ks_quality_p_value=0.845329	log10_base_likelihood=-8.31578	log10_qual_likelihood_position_model=1.30691	log10_strand_likelihood_position_model=0.300136	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.18299e-08	ref_cov=105/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/117
RA	653	.	NC_007779	4226513	0	C	A	bias_e_value=2.01165e-05	bias_p_value=4.32955e-12	fisher_strand_p_value=1.41553e-13	frequency=9.058857e-02	genotype_quality=898.6	ks_quality_p_value=1	log10_base_likelihood=-16.7375	log10_qual_likelihood_position_model=25.2406	log10_strand_likelihood_position_model=12.8491	new_cov=31/0	polymorphism_quality=11.4	quality=11.4	quality_position_model=Inf	ref_cov=81/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/154
RA	654	.	NC_007779	4227183	0	T	G	bias_e_value=9.94181e-18	bias_p_value=2.13971e-24	fisher_strand_p_value=3.59079e-26	frequency=1.460996e-01	genotype_quality=632.2	ks_quality_p_value=1	log10_base_likelihood=-21.5204	log10_qual_likelihood_position_model=41.2273	log10_strand_likelihood_position_model=25.4448	new_cov=52/0	polymorphism_quality=16.3	quality=16.3	quality_position_model=Inf	ref_cov=41/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/136
RA	655	.	NC_007779	4244592	0	G	C	bias_e_value=104.821	bias_p_value=2.25599e-05	fisher_strand_p_value=1.57058e-06	frequency=4.030228e-02	genotype_quality=390.6	ks_quality_p_value=1	log10_base_likelihood=-5.77706	log10_qual_likelihood_position_model=4.94661	log10_strand_likelihood_position_model=5.80394	new_cov=0/4	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=90/1	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=90/5
RA	656	.	NC_007779	4294403	0	C	G	bias_e_value=7.67058	bias_p_value=1.65089e-06	fisher_strand_p_value=9.63046e-08	frequency=6.376886e-02	genotype_quality=760.2	ks_quality_p_value=0.999173	log10_base_likelihood=-6.6216	log10_qual_likelihood_position_model=18.4891	log10_strand_likelihood_position_model=7.01635	new_cov=19/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=82/123	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=101/123
RA	657	.	NC_007779	4304641	0	T	G	bias_e_value=0.00567012	bias_p_value=1.22034e-09	fisher_strand_p_value=4.93422e-11	frequency=7.523155e-02	genotype_quality=537.5	ks_quality_p_value=1	log10_base_likelihood=-7.34898	log10_qual_likelihood_position_model=18.6563	log10_strand_likelihood_position_model=10.3068	new_cov=23/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=45/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=69/102
RA	658	.	NC_007779	4312218	0	T	G	bias_e_value=6.2448e-05	bias_p_value=1.34403e-11	fisher_strand_p_value=4.56931e-13	frequency=8.133268e-02	genotype_quality=644.3	ks_quality_p_value=1	log10_base_likelihood=-11.034	log10_qual_likelihood_position_model=29.6157	log10_strand_likelihood_position_model=12.3401	new_cov=29/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=56/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=85/117
RA	659	.	NC_007779	4318992	0	T	G	bias_e_value=3297.36	bias_p_value=0.000709669	fisher_strand_p_value=6.68694e-05	frequency=3.439236e-02	genotype_quality=479.7	ks_quality_p_value=1	log10_base_likelihood=-7.24939	log10_qual_likelihood_position_model=7.05017	log10_strand_likelihood_position_model=4.18145	new_cov=1/5	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=128/12	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/17
RA	660	.	NC_007779	4318994	0	A	G	bias_e_value=4.24058	bias_p_value=9.12673e-07	fisher_strand_p_value=5.14497e-08	frequency=4.225636e-02	genotype_quality=498.2	ks_quality_p_value=0.997407	log10_base_likelihood=-7.71437	log10_qual_likelihood_position_model=7.74914	log10_strand_likelihood_position_model=7.28862	new_cov=0/6	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=128/5	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/11
RA	661	.	NC_007779	4318999	1	.	C	bias_e_value=289406	bias_p_value=0.062287	fisher_strand_p_value=0.0113736	frequency=1.574612e-02	genotype_quality=610.1	ks_quality_p_value=1	log10_base_likelihood=-6.85218	log10_qual_likelihood_position_model=2.82396	log10_strand_likelihood_position_model=1.9441	new_cov=0/2	polymorphism_quality=1.3	quality=1.3	quality_position_model=0.000846923	ref_cov=113/12	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=113/14
RA	662	.	NC_007779	4321435	0	G	C	bias_e_value=0.00526483	bias_p_value=1.13311e-09	fisher_strand_p_value=4.57174e-11	frequency=6.369066e-02	genotype_quality=563.2	ks_quality_p_value=0.999019	log10_base_likelihood=-19.7005	log10_qual_likelihood_position_model=9.11649	log10_strand_likelihood_position_model=10.3399	new_cov=9/0	polymorphism_quality=14.4	quality=14.4	quality_position_model=0.148157	ref_cov=5/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=14/126
RA	663	.	NC_007779	4322023	0	T	.	bias_e_value=2712440	bias_p_value=0.58378	fisher_strand_p_value=0.622018	frequency=1.180363e-02	genotype_quality=1007.6	ks_quality_p_value=0.387276	log10_base_likelihood=-8.27833	log10_qual_likelihood_position_model=1.82618	log10_strand_likelihood_position_model=0.425989	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.99076e-08	ref_cov=126/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/126
RA	664	.	NC_007779	4337469	0	A	C	bias_e_value=2.41279e-09	bias_p_value=5.19289e-16	fisher_strand_p_value=1.30213e-17	frequency=1.423502e-01	genotype_quality=486.0	ks_quality_p_value=1	log10_base_likelihood=-19.2932	log10_qual_likelihood_position_model=28.5566	log10_strand_likelihood_position_model=16.8853	new_cov=0/32	polymorphism_quality=14.0	quality=14.0	quality_position_model=Inf	ref_cov=100/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=100/59
RA	665	.	NC_007779	4346532	0	G	T	bias_e_value=350.728	bias_p_value=7.54849e-05	fisher_strand_p_value=5.77931e-06	frequency=3.175163e-02	genotype_quality=847.0	ks_quality_p_value=1	log10_base_likelihood=-5.8116	log10_qual_likelihood_position_model=14.4993	log10_strand_likelihood_position_model=5.23812	new_cov=0/12	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=141/75	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/87
RA	666	.	NC_007779	4348529	0	T	G	bias_e_value=6.63343e-09	bias_p_value=1.42767e-15	fisher_strand_p_value=3.67556e-17	frequency=1.054273e-01	genotype_quality=649.0	ks_quality_p_value=1	log10_base_likelihood=-17.2095	log10_qual_likelihood_position_model=33.2047	log10_strand_likelihood_position_model=16.4347	new_cov=31/0	polymorphism_quality=11.9	quality=11.9	quality_position_model=Inf	ref_cov=41/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=72/134
RA	667	.	NC_007779	4357170	1	.	A	bias_e_value=3302160	bias_p_value=0.710703	fisher_strand_p_value=0.49875	frequency=9.346008e-03	genotype_quality=1062.5	ks_quality_p_value=0.689003	log10_base_likelihood=-8.51024	log10_qual_likelihood_position_model=0.895665	log10_strand_likelihood_position_model=0.564252	new_cov=0/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=5.26258e-09	ref_cov=102/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=102/112
RA	668	.	NC_007779	4361112	1	.	G	bias_e_value=2750030	bias_p_value=0.591871	fisher_strand_p_value=0.24717	frequency=1.144886e-02	genotype_quality=1283.1	ks_quality_p_value=0.997792	log10_base_likelihood=-11.0804	log10_qual_likelihood_position_model=4.82831	log10_strand_likelihood_position_model=0.898127	new_cov=3/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=2.97641e-07	ref_cov=129/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/130
RA	669	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=1035.0	new_cov=100/103	quality=1035.0	ref_cov=0/0	tot_cov=100/103
RA	670	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=1035.0	new_cov=100/103	quality=1035.0	ref_cov=0/0	tot_cov=100/103
RA	671	.	NC_007779	4403831	0	G	T	bias_e_value=2535.98	bias_p_value=0.000545802	fisher_strand_p_value=5.00634e-05	frequency=4.199219e-02	genotype_quality=855.7	ks_quality_p_value=1	log10_base_likelihood=-8.5384	log10_qual_likelihood_position_model=15.5901	log10_strand_likelihood_position_model=4.3857	new_cov=0/15	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=119/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/131
RA	672	.	NC_007779	4419586	0	T	G	bias_e_value=2.15121e-12	bias_p_value=4.6299e-19	fisher_strand_p_value=9.83658e-21	frequency=1.578040e-01	genotype_quality=647.1	ks_quality_p_value=1	log10_base_likelihood=-23.384	log10_qual_likelihood_position_model=36.2798	log10_strand_likelihood_position_model=20.0072	new_cov=44/0	polymorphism_quality=18.1	quality=18.1	quality_position_model=Inf	ref_cov=52/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=96/135
RA	673	.	NC_007779	4429120	0	G	T	bias_e_value=1.23613	bias_p_value=2.66044e-07	fisher_strand_p_value=2.22725e-08	frequency=4.340076e-02	genotype_quality=948.3	ks_quality_p_value=0.625762	log10_base_likelihood=-6.08659	log10_qual_likelihood_position_model=28.473	log10_strand_likelihood_position_model=7.65223	new_cov=0/23	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=154/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/145
RA	674	.	NC_007779	4455463	0	T	G	bias_e_value=1.25863e-15	bias_p_value=2.70888e-22	fisher_strand_p_value=4.96381e-24	frequency=1.221471e-01	genotype_quality=690.1	ks_quality_p_value=0.998372	log10_base_likelihood=-18.2886	log10_qual_likelihood_position_model=31.3713	log10_strand_likelihood_position_model=23.3042	new_cov=34/0	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=26/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=60/162
RA	675	.	NC_007779	4479134	0	G	T	bias_e_value=3068.21	bias_p_value=0.000660351	fisher_strand_p_value=6.1791e-05	frequency=3.542519e-02	genotype_quality=740.2	ks_quality_p_value=0.999494	log10_base_likelihood=-5.67813	log10_qual_likelihood_position_model=12.3105	log10_strand_likelihood_position_model=4.25654	new_cov=0/15	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=117/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/134
RA	676	.	NC_007779	4487705	0	T	.	bias_e_value=1944230	bias_p_value=0.418443	fisher_strand_p_value=0.25778	frequency=1.244068e-02	genotype_quality=971.9	ks_quality_p_value=0.549406	log10_base_likelihood=-8.30273	log10_qual_likelihood_position_model=2.27983	log10_strand_likelihood_position_model=0.759336	new_cov=0/3	polymorphism_quality=2.8	quality=2.8	quality_position_model=3.69435e-07	ref_cov=106/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/135
RA	677	.	NC_007779	4510865	1	.	A	bias_e_value=2721200	bias_p_value=0.585667	fisher_strand_p_value=0.24874	frequency=1.239681e-02	genotype_quality=1196.4	ks_quality_p_value=0.973793	log10_base_likelihood=-13.1468	log10_qual_likelihood_position_model=2.29143	log10_strand_likelihood_position_model=0.844959	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=4.88103e-12	ref_cov=124/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/115
RA	678	.	NC_007779	4512615	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	679	.	NC_007779	4515413	0	T	G	bias_e_value=1.26326e-09	bias_p_value=2.71883e-16	fisher_strand_p_value=6.70595e-18	frequency=6.796312e-02	genotype_quality=743.0	ks_quality_p_value=1	log10_base_likelihood=-7.78381	log10_qual_likelihood_position_model=26.2847	log10_strand_likelihood_position_model=17.1735	new_cov=27/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=34/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/157
RA	680	.	NC_007779	4516697	0	T	G	bias_e_value=17548.2	bias_p_value=0.00377678	fisher_strand_p_value=0.000431747	frequency=5.392885e-02	genotype_quality=664.9	ks_quality_p_value=1	log10_base_likelihood=-7.15179	log10_qual_likelihood_position_model=16.9154	log10_strand_likelihood_position_model=3.64647	new_cov=17/2	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=93/106	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/108
RA	681	.	NC_007779	4522175	0	T	G	bias_e_value=0.000259676	bias_p_value=5.58885e-11	fisher_strand_p_value=2.00047e-12	frequency=8.149529e-02	genotype_quality=567.4	ks_quality_p_value=1	log10_base_likelihood=-10.8574	log10_qual_likelihood_position_model=23.9545	log10_strand_likelihood_position_model=11.6989	new_cov=26/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=46/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=72/107
RA	682	.	NC_007779	4540870	0	T	G	bias_e_value=3.65855e-30	bias_p_value=7.87405e-37	fisher_strand_p_value=8.88555e-39	frequency=2.423301e-01	genotype_quality=547.7	ks_quality_p_value=1	log10_base_likelihood=-37.5095	log10_qual_likelihood_position_model=50.1512	log10_strand_likelihood_position_model=38.0513	new_cov=70/0	polymorphism_quality=32.4	quality=32.4	quality_position_model=Inf	ref_cov=22/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=92/131
RA	683	.	NC_007779	4540877	0	A	T	bias_e_value=5.493e-09	bias_p_value=1.18222e-15	fisher_strand_p_value=3.02856e-17	frequency=1.502771e-01	genotype_quality=667.8	ks_quality_p_value=1	log10_base_likelihood=-31.4842	log10_qual_likelihood_position_model=27.3071	log10_strand_likelihood_position_model=16.5188	new_cov=32/0	polymorphism_quality=26.3	quality=26.3	quality_position_model=Inf	ref_cov=41/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/129
RA	684	.	NC_007779	4540892	0	T	A	bias_e_value=0.00465481	bias_p_value=1.00183e-09	fisher_strand_p_value=4.01729e-11	frequency=1.042972e-01	genotype_quality=719.3	ks_quality_p_value=1	log10_base_likelihood=-16.7684	log10_qual_likelihood_position_model=27.4637	log10_strand_likelihood_position_model=10.3961	new_cov=25/0	polymorphism_quality=11.4	quality=11.4	quality_position_model=Inf	ref_cov=61/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/118
RA	685	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=753.2	new_cov=93/85	quality=753.2	ref_cov=0/0	tot_cov=93/85
RA	686	.	NC_007779	4554532	0	T	C	bias_e_value=546.109	bias_p_value=0.000117536	fisher_strand_p_value=9.37161e-06	frequency=5.528545e-02	genotype_quality=523.0	ks_quality_p_value=0.996877	log10_base_likelihood=-9.36445	log10_qual_likelihood_position_model=10.1264	log10_strand_likelihood_position_model=5.02819	new_cov=10/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=45/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=55/111
RA	687	.	NC_007779	4554534	0	A	C	bias_e_value=174.572	bias_p_value=3.7572e-05	fisher_strand_p_value=2.71965e-06	frequency=6.923962e-02	genotype_quality=457.1	ks_quality_p_value=1	log10_base_likelihood=-9.33518	log10_qual_likelihood_position_model=17.2636	log10_strand_likelihood_position_model=5.58725	new_cov=15/2	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=43/106	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=59/109
RA	688	.	NC_007779	4555389	0	C	A	bias_e_value=33420	bias_p_value=0.00719277	fisher_strand_p_value=0.0010271	frequency=3.016567e-02	genotype_quality=834.9	ks_quality_p_value=0.873608	log10_base_likelihood=-6.80864	log10_qual_likelihood_position_model=11.8963	log10_strand_likelihood_position_model=3.06341	new_cov=11/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=122/115	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=133/115
RA	689	.	NC_007779	4571094	0	A	C	bias_e_value=2197.8	bias_p_value=0.000473018	fisher_strand_p_value=4.27696e-05	frequency=3.288174e-02	genotype_quality=745.0	ks_quality_p_value=1	log10_base_likelihood=-5.99162	log10_qual_likelihood_position_model=13.1173	log10_strand_likelihood_position_model=4.36886	new_cov=11/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=79/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/127
RA	690	.	NC_007779	4573184	0	T	G	bias_e_value=1.74256e-16	bias_p_value=3.7504e-23	fisher_strand_p_value=6.61739e-25	frequency=1.122222e-01	genotype_quality=772.5	ks_quality_p_value=1	log10_base_likelihood=-12.624	log10_qual_likelihood_position_model=44.065	log10_strand_likelihood_position_model=24.1793	new_cov=60/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=71/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/152
RA	691	.	NC_007779	4578176	0	A	G	bias_e_value=0.0825338	bias_p_value=1.77632e-08	fisher_strand_p_value=8.09842e-10	frequency=6.679821e-02	genotype_quality=549.8	ks_quality_p_value=1	log10_base_likelihood=-7.31004	log10_qual_likelihood_position_model=15.929	log10_strand_likelihood_position_model=9.0916	new_cov=13/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=23/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=36/119
RA	692	.	NC_007779	4599760	0	C	A	bias_e_value=8381.82	bias_p_value=0.00180397	fisher_strand_p_value=0.000188361	frequency=2.498436e-02	genotype_quality=982.9	ks_quality_p_value=1	log10_base_likelihood=-5.80092	log10_qual_likelihood_position_model=13.3118	log10_strand_likelihood_position_model=3.72501	new_cov=11/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=116/144	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/144
RA	693	.	NC_007779	4610781	0	A	C	bias_e_value=1.83355	bias_p_value=3.94622e-07	fisher_strand_p_value=2.1134e-08	frequency=4.547882e-02	genotype_quality=785.8	ks_quality_p_value=1	log10_base_likelihood=-8.59723	log10_qual_likelihood_position_model=20.2666	log10_strand_likelihood_position_model=7.67502	new_cov=0/21	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=129/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/109
RA	694	.	NC_007779	4610781	1	.	C	bias_e_value=2106220	bias_p_value=0.453308	fisher_strand_p_value=0.199049	frequency=8.769989e-03	genotype_quality=1051.3	ks_quality_p_value=0.80408	log10_base_likelihood=-6.43019	log10_qual_likelihood_position_model=2.85663	log10_strand_likelihood_position_model=0.701039	new_cov=0/2	polymorphism_quality=0.9	quality=0.9	quality_position_model=0.000119765	ref_cov=126/100	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/102
RA	695	.	NC_007779	4611002	1	.	G	bias_e_value=2886580	bias_p_value=0.621261	fisher_strand_p_value=0.498981	frequency=9.389877e-03	genotype_quality=1041.5	ks_quality_p_value=0.537653	log10_base_likelihood=-8.13682	log10_qual_likelihood_position_model=1.64953	log10_strand_likelihood_position_model=0.560174	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=7.58411e-08	ref_cov=110/101	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/101
RA	696	.	NC_007779	4622730	0	G	T	bias_e_value=95.518	bias_p_value=2.05577e-05	fisher_strand_p_value=1.53187e-06	frequency=4.503345e-02	genotype_quality=786.0	ks_quality_p_value=0.927825	log10_base_likelihood=-7.30978	log10_qual_likelihood_position_model=19.5425	log10_strand_likelihood_position_model=5.81478	new_cov=0/17	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=128/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/115
RA	697	.	NC_007779	4636467	1	.	G	bias_e_value=2568670	bias_p_value=0.552837	fisher_strand_p_value=0.23443	frequency=9.708405e-03	genotype_quality=1028.8	ks_quality_p_value=0.937682	log10_base_likelihood=-7.94961	log10_qual_likelihood_position_model=1.54644	log10_strand_likelihood_position_model=0.629986	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.09442e-07	ref_cov=98/106	reject=POLYMORPHISM_STRAND	tot_cov=100/106
RA	698	.	NC_007779	4636470	0	C	G	bias_e_value=3.95781e-20	bias_p_value=8.51814e-27	fisher_strand_p_value=1.30636e-28	frequency=2.893925e-01	genotype_quality=440.6	ks_quality_p_value=1	log10_base_likelihood=-83.1036	log10_qual_likelihood_position_model=36.2119	log10_strand_likelihood_position_model=27.8854	new_cov=54/1	polymorphism_quality=78.1	quality=78.1	quality_position_model=3.61019e-21	ref_cov=20/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=74/111
RA	699	.	NC_007779	4636473	0	A	G	bias_e_value=0.00765081	bias_p_value=1.64663e-09	fisher_strand_p_value=6.74299e-11	frequency=7.240486e-02	genotype_quality=474.0	ks_quality_p_value=1	log10_base_likelihood=-11.0008	log10_qual_likelihood_position_model=13.5569	log10_strand_likelihood_position_model=10.1711	new_cov=10/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=7/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=17/114
RA	700	.	NC_007779	4639643	1	.	G	bias_e_value=1521430	bias_p_value=0.327448	fisher_strand_p_value=0.10437	frequency=1.226997e-02	genotype_quality=809.2	ks_quality_p_value=0.946462	log10_base_likelihood=-8.15408	log10_qual_likelihood_position_model=1.22747	log10_strand_likelihood_position_model=0.981423	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=7.26448e-08	ref_cov=51/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=53/110
RA	701	.	NC_007779	4640524	0	C	A	bias_e_value=16.0608	bias_p_value=3.45666e-06	fisher_strand_p_value=2.11149e-07	frequency=6.900597e-02	genotype_quality=792.8	ks_quality_p_value=1	log10_base_likelihood=-14.079	log10_qual_likelihood_position_model=16.1455	log10_strand_likelihood_position_model=6.68963	new_cov=23/0	polymorphism_quality=8.7	quality=8.7	quality_position_model=Inf	ref_cov=112/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/118
MC	702	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=258	right_inside_cov=1	right_outside_cov=258
MC	703	.	NC_007779	654214	655412	1196	0	left_inside_cov=0	left_outside_cov=292	right_inside_cov=0	right_outside_cov=290
MC	704	.	NC_007779	1288302	1288521	73	62	left_inside_cov=174	left_outside_cov=177	right_inside_cov=175	right_outside_cov=177
MC	705	.	NC_007779	1301041	1302376	1326	0	left_inside_cov=0	left_outside_cov=238	right_inside_cov=0	right_outside_cov=240
MC	706	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=279	right_inside_cov=0	right_outside_cov=281
MC	707	.	NC_007779	2176983	2178208	0	0	left_inside_cov=0	left_outside_cov=294	right_inside_cov=0	right_outside_cov=229
MC	708	.	NC_007779	2320795	2322130	1327	0	left_inside_cov=0	left_outside_cov=257	right_inside_cov=0	right_outside_cov=259
MC	709	.	NC_007779	3128826	3147473	1176	0	left_inside_cov=174	left_outside_cov=180	right_inside_cov=0	right_outside_cov=265
MC	710	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=260	right_inside_cov=0	right_outside_cov=273
MC	711	.	NC_007779	3742936	3744271	1325	0	left_inside_cov=0	left_outside_cov=318	right_inside_cov=0	right_outside_cov=318
MC	712	.	NC_007779	3746911	3748109	0	0	left_inside_cov=0	left_outside_cov=266	right_inside_cov=0	right_outside_cov=267
MC	713	.	NC_007779	3750591	3751789	1197	0	left_inside_cov=0	left_outside_cov=290	right_inside_cov=0	right_outside_cov=290
MC	714	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=245	right_inside_cov=0	right_outside_cov=246
MC	715	.	NC_007779	4310363	4311561	0	0	left_inside_cov=1	left_outside_cov=252	right_inside_cov=0	right_outside_cov=250
JC	716	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=116	coverage_plus=123	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=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=239	pos_hash_score=124	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=239
JC	717	.	NC_007779	49661	1	NC_007779	273179	1	0	alignment_overlap=0	coverage_minus=6	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=3.750000e-02	junction_possible_overlap_registers=90	key=NC_007779__49661__1__NC_007779__273179__1__0____101__101__0__1	max_left=92	max_left_minus=77	max_left_plus=92	max_min_left=36	max_min_left_minus=36	max_min_left_plus=0	max_min_right=45	max_min_right_minus=45	max_min_right_plus=37	max_pos_hash_score=180	max_right=92	max_right_minus=92	max_right_plus=37	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.04	new_junction_frequency=3.750000e-02	new_junction_read_count=9	pos_hash_score=8	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.99	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=231	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=8
JC	718	.	NC_007779	49664	-1	NC_007779	274373	-1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=3	flanking_left=101	flanking_right=101	frequency=2.489627e-02	junction_possible_overlap_registers=90	key=NC_007779__49664__-1__NC_007779__274373__-1__0____101__101__0__1	max_left=76	max_left_minus=72	max_left_plus=76	max_min_left=47	max_min_left_minus=47	max_min_left_plus=39	max_min_right=46	max_min_right_minus=29	max_min_right_plus=46	max_pos_hash_score=180	max_right=62	max_right_minus=58	max_right_plus=62	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.03	new_junction_frequency=2.489627e-02	new_junction_read_count=6	pos_hash_score=6	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=235	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=6
JC	719	.	NC_007779	273179	1	NC_007779	657877	1	0	alignment_overlap=0	coverage_minus=6	coverage_plus=7	flanking_left=101	flanking_right=101	frequency=5.098039e-02	junction_possible_overlap_registers=90	key=NC_007779__273179__1__NC_007779__657877__1__0____101__101__1__0	max_left=90	max_left_minus=84	max_left_plus=90	max_min_left=43	max_min_left_minus=43	max_min_left_plus=25	max_min_right=44	max_min_right_minus=44	max_min_right_plus=11	max_pos_hash_score=180	max_right=95	max_right_minus=91	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.06	new_junction_frequency=5.098039e-02	new_junction_read_count=13	pos_hash_score=13	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.03	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=242	side_2_redundant=0	total_non_overlap_reads=13
JC	720	.	NC_007779	274373	-1	NC_007779	657880	-1	0	alignment_overlap=0	coverage_minus=6	coverage_plus=6	flanking_left=101	flanking_right=101	frequency=4.743083e-02	junction_possible_overlap_registers=90	key=NC_007779__274373__-1__NC_007779__657880__-1__0____101__101__1__0	max_left=82	max_left_minus=82	max_left_plus=79	max_min_left=40	max_min_left_minus=40	max_min_left_plus=39	max_min_right=50	max_min_right_minus=50	max_min_right_plus=34	max_pos_hash_score=180	max_right=77	max_right_minus=61	max_right_plus=77	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.05	new_junction_frequency=4.743083e-02	new_junction_read_count=12	pos_hash_score=12	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.03	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=241	side_2_redundant=0	total_non_overlap_reads=12
JC	721	.	NC_007779	274373	-1	NC_007779	675375	1	0	alignment_overlap=0	coverage_minus=14	coverage_plus=17	flanking_left=101	flanking_right=101	frequency=9.841270e-02	junction_possible_overlap_registers=90	key=NC_007779__274373__-1__NC_007779__675375__1__0____101__101__1__0	max_left=79	max_left_minus=79	max_left_plus=78	max_min_left=48	max_min_left_minus=48	max_min_left_plus=45	max_min_right=42	max_min_right_minus=42	max_min_right_plus=36	max_pos_hash_score=180	max_right=95	max_right_minus=89	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.13	new_junction_frequency=9.841270e-02	new_junction_read_count=31	pos_hash_score=26	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.21	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=284	side_2_redundant=0	total_non_overlap_reads=31
JC	722	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=8	coverage_minus=102	coverage_plus=108	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371965__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=83	max_min_left=46	max_min_left_minus=46	max_min_left_plus=45	max_min_right=46	max_min_right_minus=45	max_min_right_plus=46	max_pos_hash_score=160	max_right=87	max_right_minus=86	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=208	pos_hash_score=116	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=2	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=80	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=210
JC	723	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=105	coverage_plus=79	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=57	key=NC_007779__289856__1__NC_007779__2176982__-1__-33__CTATTGCAATACCGCATTGTGAGGCGATTCATG__101__101__1__0	max_left=62	max_left_minus=62	max_left_plus=62	max_min_left=33	max_min_left_minus=33	max_min_left_plus=33	max_min_right=33	max_min_right_minus=33	max_min_right_plus=33	max_pos_hash_score=114	max_right=62	max_right_minus=62	max_right_plus=60	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.24	new_junction_frequency=1.000000e+00	new_junction_read_count=184	pos_hash_score=94	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=184	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	724	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=89	coverage_plus=92	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=48	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.77	new_junction_frequency=NA	new_junction_read_count=181	pos_hash_score=109	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=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=181
JC	725	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=77	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=88	key=NC_007779__381401__1__NC_007779__381814__-1__2____101__101__1__1	max_left=93	max_left_minus=93	max_left_plus=92	max_min_left=49	max_min_left_minus=47	max_min_left_plus=49	max_min_right=48	max_min_right_minus=48	max_min_right_plus=47	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.83	new_junction_frequency=NA	new_junction_read_count=190	pos_hash_score=114	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=190
JC	726	.	NC_007779	400327	-1	NC_007779	575008	-1	0	alignment_overlap=4	coverage_minus=0	coverage_plus=3	flanking_left=101	flanking_right=101	frequency=1.494024e-02	junction_possible_overlap_registers=86	key=NC_007779__400327__-1__NC_007779__575012__-1__4____101__101__0__1	max_left=89	max_left_minus=0	max_left_plus=89	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=23	max_min_right_minus=0	max_min_right_plus=23	max_pos_hash_score=172	max_right=23	max_right_minus=0	max_right_plus=23	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.01	new_junction_frequency=1.494024e-02	new_junction_read_count=3	pos_hash_score=3	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.88	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=207	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=3
JC	727	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=99	coverage_plus=112	flanking_left=101	flanking_right=101	frequency=9.689270e-01	junction_possible_overlap_registers=87	key=NC_007779__608573__-1__NC_007779__1305025__1__3____101__101__1__0	max_left=92	max_left_minus=91	max_left_plus=92	max_min_left=48	max_min_left_minus=46	max_min_left_plus=48	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=174	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=9.689270e-01	new_junction_read_count=211	pos_hash_score=118	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.03	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=7	side_2_redundant=0	total_non_overlap_reads=211
JC	728	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=128	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=85	key=NC_007779__654213__-1__NC_007779__655408__1__5____101__101__0__0	max_left=90	max_left_minus=90	max_left_plus=90	max_min_left=47	max_min_left_minus=46	max_min_left_plus=47	max_min_right=48	max_min_right_minus=48	max_min_right_plus=46	max_pos_hash_score=170	max_right=90	max_right_minus=90	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.15	new_junction_frequency=1.000000e+00	new_junction_read_count=254	pos_hash_score=126	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=5	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=85	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=252
JC	729	.	NC_007779	654213	1	NC_007779	669383	1	0	alignment_overlap=0	coverage_minus=2	coverage_plus=3	flanking_left=101	flanking_right=101	frequency=1.792115e-02	junction_possible_overlap_registers=90	key=NC_007779__654213__1__NC_007779__669383__1__0____101__101__1__0	max_left=58	max_left_minus=50	max_left_plus=58	max_min_left=50	max_min_left_minus=50	max_min_left_plus=10	max_min_right=50	max_min_right_minus=0	max_min_right_plus=50	max_pos_hash_score=180	max_right=91	max_right_minus=83	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=1.792115e-02	new_junction_read_count=5	pos_hash_score=5	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.17	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=274	side_2_redundant=0	total_non_overlap_reads=5
JC	730	.	NC_007779	679235	1	NC_007779	689467	-1	0	alignment_overlap=0	coverage_minus=1	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.023891e-02	junction_possible_overlap_registers=90	key=NC_007779__679235__1__NC_007779__689467__-1__0____101__101__0__1	max_left=75	max_left_minus=48	max_left_plus=75	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=26	max_min_right_minus=0	max_min_right_plus=26	max_pos_hash_score=180	max_right=54	max_right_minus=53	max_right_plus=54	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.01	new_junction_frequency=1.023891e-02	new_junction_read_count=3	pos_hash_score=3	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.24	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=290	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=3
JC	731	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=19	coverage_plus=37	flanking_left=101	flanking_right=101	frequency=3.208352e-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=72	max_min_left=40	max_min_left_minus=37	max_min_left_plus=40	max_min_right=42	max_min_right_minus=33	max_min_right_plus=42	max_pos_hash_score=148	max_right=76	max_right_minus=73	max_right_plus=76	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.29	new_junction_frequency=3.208352e-01	new_junction_read_count=56	pos_hash_score=46	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.67	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=157	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.56	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=108	side_2_redundant=0	total_non_overlap_reads=56
JC	732	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=39	coverage_plus=29	flanking_left=101	flanking_right=101	frequency=3.677664e-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=78	max_left_plus=79	max_min_left=42	max_min_left_minus=42	max_min_left_plus=42	max_min_right=42	max_min_right_minus=42	max_min_right_plus=40	max_pos_hash_score=148	max_right=79	max_right_minus=79	max_right_plus=76	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.35	new_junction_frequency=3.677664e-01	new_junction_read_count=68	pos_hash_score=50	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.65	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=153	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.56	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=108	side_2_redundant=0	total_non_overlap_reads=68
JC	733	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=89	coverage_plus=108	flanking_left=101	flanking_right=101	frequency=9.853284e-01	junction_possible_overlap_registers=88	key=NC_007779__1221489__1__NC_007779__1301039__1__2____101__101__0__1	max_left=93	max_left_minus=93	max_left_plus=92	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=88	max_right_minus=84	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=9.853284e-01	new_junction_read_count=197	pos_hash_score=116	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=197
JC	734	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=127	coverage_plus=83	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1221495__-1__NC_007779__1302369__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=91	max_right_minus=91	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=1.000000e+00	new_junction_read_count=210	pos_hash_score=115	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=210
JC	735	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=95	coverage_plus=101	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=83	key=NC_007779__1301040__-1__NC_007779__1302370__1__7____101__101__0__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=46	max_min_left_minus=46	max_min_left_plus=44	max_min_right=47	max_min_right_minus=47	max_min_right_plus=46	max_pos_hash_score=166	max_right=88	max_right_minus=88	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=196	pos_hash_score=110	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=196
JC	736	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=100	coverage_plus=108	flanking_left=101	flanking_right=101	frequency=9.479891e-01	junction_possible_overlap_registers=86	key=NC_007779__1305037__-1__NC_007779__2519719__1__4____101__101__0__1	max_left=91	max_left_minus=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=90	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=9.479891e-01	new_junction_read_count=209	pos_hash_score=121	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.05	side_1_overlap=4	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=208
JC	737	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=131	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1397758__1__NC_007779__1672777__1__0____101__101__1__0	max_left=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=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=244	pos_hash_score=131	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=244
JC	738	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=90	coverage_plus=85	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=36	max_min_right=37	max_min_right_minus=37	max_min_right_plus=37	max_pos_hash_score=128	max_right=69	max_right_minus=69	max_right_plus=69	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=175	pos_hash_score=97	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=175
JC	739	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=99	coverage_plus=103	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=48	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=84	max_right_minus=83	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.87	new_junction_frequency=1.000000e+00	new_junction_read_count=204	pos_hash_score=107	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=202
JC	740	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=111	coverage_plus=112	flanking_left=101	flanking_right=101	frequency=9.570815e-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=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=9.570815e-01	new_junction_read_count=223	pos_hash_score=127	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=10	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	741	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=106	coverage_plus=105	flanking_left=101	flanking_right=101	frequency=9.636364e-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=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=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=9.636364e-01	new_junction_read_count=212	pos_hash_score=128	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.03	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=8	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=211
JC	742	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=106	coverage_plus=47	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1980091__1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=49	max_min_left_minus=49	max_min_left_plus=45	max_min_right=49	max_min_right_minus=49	max_min_right_plus=38	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=0.66	new_junction_frequency=1.000000e+00	new_junction_read_count=154	pos_hash_score=89	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=153
JC	743	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=103	coverage_plus=99	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__1980095__-1__NC_007779__2176983__1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=92	max_right_minus=92	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.87	new_junction_frequency=1.000000e+00	new_junction_read_count=202	pos_hash_score=111	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=202
JC	744	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=99	coverage_plus=114	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=86	max_right_minus=84	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=213	pos_hash_score=110	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=213
JC	745	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=97	coverage_plus=110	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=88	max_left_minus=87	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=88	max_right_minus=88	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=207	pos_hash_score=111	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=207
JC	746	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=67	coverage_plus=125	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=87	max_left_minus=84	max_left_plus=87	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=48	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.83	new_junction_frequency=1.000000e+00	new_junction_read_count=194	pos_hash_score=101	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=192
JC	747	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=106	coverage_plus=141	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2322124__-1__NC_007779__2589830__1__0____101__101__1__0	max_left=90	max_left_minus=90	max_left_plus=83	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.06	new_junction_frequency=1.000000e+00	new_junction_read_count=248	pos_hash_score=122	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=247
JC	748	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=126	coverage_plus=119	flanking_left=101	flanking_right=101	frequency=9.570312e-01	junction_possible_overlap_registers=90	key=NC_007779__2411458__1__NC_007779__2985055__-1__0____101__101__1__0	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=9.570312e-01	new_junction_read_count=245	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=0.05	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=245
JC	749	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=80	coverage_plus=93	flanking_left=101	flanking_right=101	frequency=9.402174e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=88	max_left_minus=87	max_left_plus=88	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.74	new_junction_frequency=9.402174e-01	new_junction_read_count=173	pos_hash_score=102	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.05	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=173
JC	750	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=120	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=7.044069e-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=47	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=47	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=7.044069e-01	new_junction_read_count=249	pos_hash_score=131	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.48	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=113	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.45	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=101	side_2_redundant=0	total_non_overlap_reads=249
JC	751	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=114	coverage_plus=132	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=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=87	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=246	pos_hash_score=124	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=246
JC	752	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=136	coverage_plus=135	flanking_left=101	flanking_right=101	frequency=9.856138e-01	junction_possible_overlap_registers=89	key=NC_007779__3186082__-1__NC_007779__3512753__1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=9.856138e-01	new_junction_read_count=271	pos_hash_score=130	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=271
JC	753	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=129	coverage_plus=98	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=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=227	pos_hash_score=124	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=227	unique_read_sequence=CTTTGC
JC	754	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=81	coverage_plus=98	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=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.78	new_junction_frequency=1.000000e+00	new_junction_read_count=182	pos_hash_score=108	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=179
JC	755	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=114	coverage_plus=114	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=47	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=228	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=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=228
JC	756	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=158	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.21	new_junction_frequency=1.000000e+00	new_junction_read_count=282	pos_hash_score=145	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=282
JC	757	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=116	coverage_plus=130	flanking_left=101	flanking_right=101	frequency=9.880841e-01	junction_possible_overlap_registers=89	key=NC_007779__3512759__-1__NC_007779__3744263__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=48	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=90	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.06	new_junction_frequency=9.880841e-01	new_junction_read_count=246	pos_hash_score=143	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=3	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=246
JC	758	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=140	coverage_plus=122	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=82	key=NC_007779__3742935__-1__NC_007779__3744264__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=87	max_min_left=46	max_min_left_minus=45	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=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.23	new_junction_frequency=1.000000e+00	new_junction_read_count=262	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=262
JC	759	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=119	coverage_plus=101	flanking_left=101	flanking_right=101	frequency=9.821429e-01	junction_possible_overlap_registers=90	key=NC_007779__3744263__-1__NC_007779__3903274__1__0____101__101__1__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.94	new_junction_frequency=9.821429e-01	new_junction_read_count=220	pos_hash_score=121	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=220
JC	760	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=124	coverage_plus=100	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=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=224	pos_hash_score=126	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=224
JC	761	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=141	coverage_plus=129	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3746911__1__NC_007779__3748646__-1__0____101__101__1__0	max_left=92	max_left_minus=92	max_left_plus=92	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.23	new_junction_frequency=1.000000e+00	new_junction_read_count=288	pos_hash_score=135	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=270
JC	762	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=138	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3748105__-1__NC_007779__3748643__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=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=1.15	new_junction_frequency=1.000000e+00	new_junction_read_count=270	pos_hash_score=140	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=270
JC	763	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=110	coverage_plus=134	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3750590__-1__NC_007779__3751786__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=90	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=46	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=245	pos_hash_score=130	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=244
JC	764	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=136	coverage_plus=122	flanking_left=101	flanking_right=101	frequency=9.923925e-01	junction_possible_overlap_registers=89	key=NC_007779__3903279__-1__NC_007779__4504191__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.12	new_junction_frequency=9.923925e-01	new_junction_read_count=258	pos_hash_score=132	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=258
JC	765	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=108	coverage_plus=100	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=88	key=NC_007779__3958122__-1__NC_007779__3958155__1__2____101__101__0__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=47	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=209	pos_hash_score=118	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=208
JC	766	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=110	coverage_plus=120	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=93	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=230	pos_hash_score=126	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=230
JC	767	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=117	coverage_plus=117	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=86	max_left_minus=86	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=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=234	pos_hash_score=113	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=234
JC	768	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=119	coverage_plus=108	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=47	max_min_right=48	max_min_right_minus=46	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=228	pos_hash_score=121	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=227
JC	769	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=119	coverage_plus=104	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4310363__1__NC_007779__4353540__1__0____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=49	max_min_right_minus=49	max_min_right_plus=48	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=231	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=223
JC	770	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=98	coverage_plus=130	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4311557__-1__NC_007779__4353543__-1__0____101__101__1__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=239	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=228
JC	771	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=144	coverage_plus=152	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4355060__1__NC_007779__4502861__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.27	new_junction_frequency=1.000000e+00	new_junction_read_count=297	pos_hash_score=151	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=296
JC	772	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=107	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=9.912681e-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=90	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=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=9.912681e-01	new_junction_read_count=222	pos_hash_score=116	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=2	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=222
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JC	774	.	NC_007779	4547370	-1	NC_007779	4547666	-1	0	alignment_overlap=9	coverage_minus=9	coverage_plus=6	flanking_left=101	flanking_right=101	frequency=7.562390e-02	junction_possible_overlap_registers=81	key=NC_007779__4547370__-1__NC_007779__4547675__-1__9____101__101__0__0	max_left=68	max_left_minus=61	max_left_plus=68	max_min_left=36	max_min_left_minus=36	max_min_left_plus=25	max_min_right=41	max_min_right_minus=41	max_min_right_plus=27	max_pos_hash_score=162	max_right=82	max_right_minus=82	max_right_plus=81	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.07	new_junction_frequency=7.562390e-02	new_junction_read_count=15	pos_hash_score=15	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.82	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=193	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.92	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=193	side_2_redundant=0	total_non_overlap_reads=15
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