#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	07:46:14 22 Feb 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	1_D6_ACAGTG_L004_R1_001.fastq
SNP	1	63	NC_007779	66457	A	frequency=1
SNP	2	68	NC_007779	97880	T	frequency=1
SNP	3	75	NC_007779	167632	A	frequency=1
SNP	4	83	NC_007779	274547	G	frequency=1
DEL	5	519,536	NC_007779	274733	97240	frequency=1
SNP	6	103	NC_007779	547694	G	frequency=1
INS	7	104	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	106	NC_007779	556858	T	frequency=1
SNP	9	107	NC_007779	569996	C	frequency=1
DEL	10	520,541	NC_007779	654214	1199	frequency=1
SNP	11	132	NC_007779	749354	A	frequency=1
SNP	12	133	NC_007779	758440	A	frequency=1
SNP	13	140	NC_007779	887234	A	frequency=1
SNP	14	146	NC_007779	987574	T	frequency=1
SNP	15	153	NC_007779	1093686	C	frequency=1
SNP	16	155	NC_007779	1097580	T	frequency=2.203088e-01
SNP	17	162	NC_007779	1170573	T	frequency=1
SNP	18	164	NC_007779	1213001	C	frequency=6.641483e-02
SNP	19	165	NC_007779	1213013	C	frequency=5.272532e-02
SNP	20	166	NC_007779	1213026	T	frequency=4.419804e-02
SNP	21	167	NC_007779	1213028	A	frequency=4.572964e-02
DEL	22	522,548	NC_007779	1301041	1336	frequency=1
SNP	23	176	NC_007779	1318876	A	frequency=1
DEL	24	523,551	NC_007779	1413639	23060	frequency=1
SNP	25	218	NC_007779	1483588	A	frequency=1
DEL	26	219	NC_007779	1496775	1	frequency=1
SNP	27	227	NC_007779	1615814	A	frequency=1
DEL	28	233	NC_007779	1669599	1	frequency=1
SNP	29	252	NC_007779	1844073	A	frequency=1
SNP	30	261	NC_007779	1918872	A	frequency=1
SNP	31	264	NC_007779	1973476	A	frequency=1
SNP	32	268	NC_007779	2005401	T	frequency=1
SNP	33	275	NC_007779	2170094	A	frequency=1
DEL	34	525,558	NC_007779	2320795	1336	frequency=1
SNP	35	291	NC_007779	2406075	T	frequency=1
SNP	36	294	NC_007779	2416102	A	frequency=1
SNP	37	304	NC_007779	2538628	T	frequency=1
INS	38	563	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=4.831288e-01
SNP	39	327	NC_007779	2866111	G	frequency=1
SNP	40	338	NC_007779	3003330	A	frequency=1
SNP	41	343	NC_007779	3049815	T	frequency=1
SNP	42	363	NC_007779	3397813	G	frequency=1
DEL	43	528,571	NC_007779	3742934	1336	frequency=1
DEL	44	529,573	NC_007779	3746911	1199	frequency=1
DEL	45	402	NC_007779	3750122	1	frequency=9.461536e-01
SNP	46	403	NC_007779	3750123	T	frequency=5.369616e-02
DEL	47	530,576	NC_007779	3750591	1199	frequency=1
SNP	48	417	NC_007779	3898657	G	frequency=1
DEL	49	531,578	NC_007779	3958123	34	frequency=1
SNP	50	439	NC_007779	4090749	T	frequency=1
SNP	51	443	NC_007779	4165991	C	frequency=1
DEL	52	532,581	NC_007779	4310363	1199	frequency=1
DEL	53	493,494	NC_007779	4371271	2	frequency=1
SNP	54	506	NC_007779	4546535	A	frequency=1
RA	55	.	NC_007779	301	1	.	T	bias_e_value=1683070	bias_p_value=0.362237	fisher_strand_p_value=0.573206	frequency=1.195240e-02	genotype_quality=1195.0	ks_quality_p_value=0.199428	log10_base_likelihood=-12.4438	log10_qual_likelihood_position_model=2.50307	log10_strand_likelihood_position_model=0.514116	new_cov=2/1	polymorphism_quality=7.1	quality=7.1	quality_position_model=1.92674e-11	ref_cov=103/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/146
RA	56	.	NC_007779	302	0	T	.	bias_e_value=4213680	bias_p_value=0.906882	fisher_strand_p_value=1	frequency=1.189613e-02	genotype_quality=975.1	ks_quality_p_value=0.600759	log10_base_likelihood=-8.1801	log10_qual_likelihood_position_model=1.42624	log10_strand_likelihood_position_model=0.369034	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.55278e-08	ref_cov=104/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/147
RA	57	.	NC_007779	5595	0	G	T	bias_e_value=2.18013	bias_p_value=4.69214e-07	fisher_strand_p_value=2.53775e-08	frequency=3.702068e-02	genotype_quality=952.2	ks_quality_p_value=1	log10_base_likelihood=-5.88816	log10_qual_likelihood_position_model=20.6925	log10_strand_likelihood_position_model=7.82839	new_cov=0/27	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=145/139	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/167
RA	58	.	NC_007779	11143	0	G	T	bias_e_value=0.0164331	bias_p_value=3.53678e-09	fisher_strand_p_value=1.49723e-10	frequency=5.757666e-02	genotype_quality=897.9	ks_quality_p_value=1	log10_base_likelihood=-9.08195	log10_qual_likelihood_position_model=19.1467	log10_strand_likelihood_position_model=9.82471	new_cov=0/27	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=149/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/127
RA	59	.	NC_007779	34111	1	.	T	bias_e_value=2881720	bias_p_value=0.620213	fisher_strand_p_value=0.498582	frequency=6.779671e-03	genotype_quality=1455.4	ks_quality_p_value=0.536488	log10_base_likelihood=-7.94984	log10_qual_likelihood_position_model=2.25693	log10_strand_likelihood_position_model=0.583101	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.33671e-07	ref_cov=149/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/144
RA	60	.	NC_007779	34112	0	T	.	bias_e_value=4635560	bias_p_value=0.997681	fisher_strand_p_value=1	frequency=1.323414e-02	genotype_quality=1198.5	ks_quality_p_value=0.932681	log10_base_likelihood=-10.7208	log10_qual_likelihood_position_model=4.50749	log10_strand_likelihood_position_model=0.423232	new_cov=2/2	polymorphism_quality=5.3	quality=5.3	quality_position_model=1.05123e-07	ref_cov=151/147	reject=INDEL_HOMOPOLYMER	tot_cov=153/149
RA	61	.	NC_007779	47305	0	G	T	bias_e_value=0.135969	bias_p_value=2.92638e-08	fisher_strand_p_value=1.36786e-09	frequency=6.870604e-02	genotype_quality=830.0	ks_quality_p_value=0.999205	log10_base_likelihood=-14.9861	log10_qual_likelihood_position_model=16.6592	log10_strand_likelihood_position_model=8.86396	new_cov=0/24	polymorphism_quality=9.6	quality=9.6	quality_position_model=Inf	ref_cov=141/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/117
RA	62	.	NC_007779	48338	0	T	G	bias_e_value=1144.34	bias_p_value=0.000246289	fisher_strand_p_value=2.09163e-05	frequency=2.779770e-02	genotype_quality=535.5	ks_quality_p_value=1	log10_base_likelihood=-6.15608	log10_qual_likelihood_position_model=4.29494	log10_strand_likelihood_position_model=4.67952	new_cov=4/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=7/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=11/130
RA	63	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1160.7	new_cov=154/139	quality=1160.7	ref_cov=0/0	tot_cov=154/139
RA	64	.	NC_007779	75074	0	T	G	bias_e_value=2.04521e-32	bias_p_value=4.40178e-39	fisher_strand_p_value=4.6897e-41	frequency=2.102795e-01	genotype_quality=701.4	ks_quality_p_value=1	log10_base_likelihood=-52.1073	log10_qual_likelihood_position_model=52.1788	log10_strand_likelihood_position_model=40.3289	new_cov=63/0	polymorphism_quality=47.0	quality=47.0	quality_position_model=Inf	ref_cov=22/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=85/168
RA	65	.	NC_007779	75079	0	C	T	bias_e_value=0.0327549	bias_p_value=7.04961e-09	fisher_strand_p_value=3.07823e-10	frequency=4.818344e-02	genotype_quality=762.5	ks_quality_p_value=1	log10_base_likelihood=-7.86923	log10_qual_likelihood_position_model=18.0412	log10_strand_likelihood_position_model=9.5117	new_cov=12/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=26/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=38/168
RA	66	.	NC_007779	84006	0	T	.	bias_e_value=1718920	bias_p_value=0.369953	fisher_strand_p_value=0.174178	frequency=1.332474e-02	genotype_quality=899.7	ks_quality_p_value=0.676874	log10_base_likelihood=-8.29565	log10_qual_likelihood_position_model=1.48456	log10_strand_likelihood_position_model=0.807127	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.31577e-08	ref_cov=58/164	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=60/165
RA	67	.	NC_007779	89555	0	G	T	bias_e_value=324.464	bias_p_value=6.98323e-05	fisher_strand_p_value=5.70875e-06	frequency=3.497887e-02	genotype_quality=932.9	ks_quality_p_value=0.930547	log10_base_likelihood=-6.2339	log10_qual_likelihood_position_model=21.5077	log10_strand_likelihood_position_model=5.24346	new_cov=15/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=111/147	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/147
RA	68	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=1073.7	new_cov=147/120	quality=1073.7	ref_cov=0/0	tot_cov=147/120
RA	69	.	NC_007779	101246	0	T	G	bias_e_value=889.146	bias_p_value=0.000191365	fisher_strand_p_value=1.63652e-05	frequency=4.678011e-02	genotype_quality=472.7	ks_quality_p_value=0.970373	log10_base_likelihood=-14.306	log10_qual_likelihood_position_model=8.26744	log10_strand_likelihood_position_model=4.78608	new_cov=7/0	polymorphism_quality=8.9	quality=8.9	quality_position_model=0.00714693	ref_cov=23/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=30/103
RA	70	.	NC_007779	107544	1	.	T	bias_e_value=351323	bias_p_value=0.075613	fisher_strand_p_value=0.107486	frequency=1.127815e-02	genotype_quality=1290.3	ks_quality_p_value=0.134299	log10_base_likelihood=-12.6568	log10_qual_likelihood_position_model=2.91409	log10_strand_likelihood_position_model=0.968647	new_cov=3/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=8.95951e-11	ref_cov=124/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/139
RA	71	.	NC_007779	116855	0	G	T	bias_e_value=898.631	bias_p_value=0.000193406	fisher_strand_p_value=1.82068e-05	frequency=4.210186e-02	genotype_quality=827.1	ks_quality_p_value=0.882374	log10_base_likelihood=-7.4471	log10_qual_likelihood_position_model=16.6114	log10_strand_likelihood_position_model=5.0408	new_cov=0/16	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=124/108	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/125
RA	72	.	NC_007779	119384	0	T	G	bias_e_value=6.31761e-11	bias_p_value=1.3597e-17	fisher_strand_p_value=3.11771e-19	frequency=8.313847e-02	genotype_quality=750.1	ks_quality_p_value=1	log10_base_likelihood=-9.62438	log10_qual_likelihood_position_model=31.8796	log10_strand_likelihood_position_model=18.5062	new_cov=43/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=66/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/147
RA	73	.	NC_007779	134366	0	G	T	bias_e_value=10.6205	bias_p_value=2.28579e-06	fisher_strand_p_value=1.36032e-07	frequency=3.094387e-02	genotype_quality=1035.7	ks_quality_p_value=0.999549	log10_base_likelihood=-7.15488	log10_qual_likelihood_position_model=17.6789	log10_strand_likelihood_position_model=6.86636	new_cov=0/20	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=163/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/145
RA	74	.	NC_007779	164569	0	C	G	bias_e_value=1480.24	bias_p_value=0.000318583	fisher_strand_p_value=2.77187e-05	frequency=3.156948e-02	genotype_quality=519.4	ks_quality_p_value=1	log10_base_likelihood=-5.87573	log10_qual_likelihood_position_model=7.12005	log10_strand_likelihood_position_model=4.55723	new_cov=0/6	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=116/21	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/27
RA	75	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=1061.0	new_cov=139/127	quality=1061.0	ref_cov=0/0	tot_cov=139/127
RA	76	.	NC_007779	173073	0	A	C	bias_e_value=9.99731	bias_p_value=2.15166e-06	fisher_strand_p_value=1.27505e-07	frequency=3.094482e-02	genotype_quality=817.8	ks_quality_p_value=1	log10_base_likelihood=-6.67267	log10_qual_likelihood_position_model=16.9961	log10_strand_likelihood_position_model=6.89447	new_cov=0/18	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=142/91	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/111
RA	77	.	NC_007779	175694	0	T	G	bias_e_value=2.63848e-10	bias_p_value=5.67864e-17	fisher_strand_p_value=1.34729e-18	frequency=1.246457e-01	genotype_quality=686.1	ks_quality_p_value=1	log10_base_likelihood=-15.7143	log10_qual_likelihood_position_model=32.4601	log10_strand_likelihood_position_model=17.8705	new_cov=49/0	polymorphism_quality=10.4	quality=10.4	quality_position_model=Inf	ref_cov=73/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/127
RA	78	.	NC_007779	207536	0	G	T	bias_e_value=2.44378	bias_p_value=5.25959e-07	fisher_strand_p_value=2.86334e-08	frequency=5.387163e-02	genotype_quality=802.9	ks_quality_p_value=1	log10_base_likelihood=-9.59782	log10_qual_likelihood_position_model=20.6537	log10_strand_likelihood_position_model=7.60895	new_cov=0/27	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=123/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/148
RA	79	.	NC_007779	223974	0	G	T	frequency=1	genotype_quality=1.3	new_cov=1/0	quality=1.3	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	80	.	NC_007779	227943	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	81	.	NC_007779	227944	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	82	.	NC_007779	255885	0	T	.	bias_e_value=1893650	bias_p_value=0.407559	fisher_strand_p_value=0.6111	frequency=1.033020e-02	genotype_quality=1118.9	ks_quality_p_value=0.222735	log10_base_likelihood=-7.46867	log10_qual_likelihood_position_model=3.89697	log10_strand_likelihood_position_model=0.440333	new_cov=2/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=6.34997e-05	ref_cov=138/149	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/150
RA	83	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1330.5	new_cov=155/159	quality=1330.5	ref_cov=0/0	tot_cov=155/159
RA	84	.	NC_007779	365514	0	C	T	deleted=1	frequency=1	genotype_quality=114.5	new_cov=27/0	quality=114.5	ref_cov=0/0	tot_cov=27/0
RA	85	.	NC_007779	365524	0	G	.	deleted=1	frequency=1	genotype_quality=143.9	new_cov=28/1	quality=143.9	ref_cov=1/0	tot_cov=29/1
RA	86	.	NC_007779	379236	1	.	G	bias_e_value=1753290	bias_p_value=0.377348	fisher_strand_p_value=0.304742	frequency=1.860523e-02	genotype_quality=1013.1	ks_quality_p_value=0.398302	log10_base_likelihood=-18.3467	log10_qual_likelihood_position_model=2.97605	log10_strand_likelihood_position_model=0.702362	new_cov=4/0	polymorphism_quality=13.0	quality=13.0	quality_position_model=8.92105e-17	ref_cov=140/71	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/71
RA	87	.	NC_007779	379237	0	G	.	bias_e_value=3202790	bias_p_value=0.689316	fisher_strand_p_value=0.335926	frequency=4.802561e-02	genotype_quality=899.2	ks_quality_p_value=0.964934	log10_base_likelihood=-36.7282	log10_qual_likelihood_position_model=5.4759	log10_strand_likelihood_position_model=0.87568	new_cov=9/2	polymorphism_quality=31.6	quality=31.6	quality_position_model=1.22227e-32	ref_cov=139/79	reject=INDEL_HOMOPOLYMER	tot_cov=148/81
RA	88	.	NC_007779	387917	0	T	G	bias_e_value=0.922392	bias_p_value=1.9852e-07	fisher_strand_p_value=1.02343e-08	frequency=4.607105e-02	genotype_quality=451.7	ks_quality_p_value=1	log10_base_likelihood=-5.82937	log10_qual_likelihood_position_model=12.1209	log10_strand_likelihood_position_model=7.98994	new_cov=0/10	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=118/17	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/27
RA	89	.	NC_007779	387919	0	A	G	bias_e_value=0.000291689	bias_p_value=6.27784e-11	fisher_strand_p_value=2.25683e-12	frequency=9.233284e-02	genotype_quality=435.0	ks_quality_p_value=1	log10_base_likelihood=-17.786	log10_qual_likelihood_position_model=13.7992	log10_strand_likelihood_position_model=11.6465	new_cov=0/14	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=116/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=117/27
RA	90	.	NC_007779	398675	0	T	G	bias_e_value=1193330	bias_p_value=0.256833	fisher_strand_p_value=0.0722078	frequency=8.730888e-03	genotype_quality=1363.9	ks_quality_p_value=0.972995	log10_base_likelihood=-6.2239	log10_qual_likelihood_position_model=3.18826	log10_strand_likelihood_position_model=1.14142	new_cov=3/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=0.00136662	ref_cov=140/199	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=143/199
RA	91	.	NC_007779	407306	0	C	A	bias_e_value=6.43578	bias_p_value=1.38513e-06	fisher_strand_p_value=7.98674e-08	frequency=5.957270e-02	genotype_quality=734.2	ks_quality_p_value=1	log10_base_likelihood=-7.44409	log10_qual_likelihood_position_model=15.5837	log10_strand_likelihood_position_model=7.28441	new_cov=23/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=101/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/121
RA	92	.	NC_007779	432858	0	T	G	bias_e_value=8.44837e-07	bias_p_value=1.81829e-13	fisher_strand_p_value=5.37035e-15	frequency=7.885838e-02	genotype_quality=703.3	ks_quality_p_value=1	log10_base_likelihood=-6.50399	log10_qual_likelihood_position_model=27.8167	log10_strand_likelihood_position_model=14.27	new_cov=38/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=76/130	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/130
RA	93	.	NC_007779	440767	0	G	T	bias_e_value=0.0135085	bias_p_value=2.90734e-09	fisher_strand_p_value=1.2202e-10	frequency=9.344625e-02	genotype_quality=820.3	ks_quality_p_value=1	log10_base_likelihood=-20.3122	log10_qual_likelihood_position_model=24.0456	log10_strand_likelihood_position_model=10.0446	new_cov=1/35	polymorphism_quality=15.0	quality=15.0	quality_position_model=Inf	ref_cov=136/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/142
RA	94	.	NC_007779	467487	1	.	T	bias_e_value=4646230	bias_p_value=0.999979	fisher_strand_p_value=1	frequency=7.298470e-03	genotype_quality=1334.0	ks_quality_p_value=0.993527	log10_base_likelihood=-7.74628	log10_qual_likelihood_position_model=1.97082	log10_strand_likelihood_position_model=0.310788	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.28477e-07	ref_cov=114/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/159
RA	95	.	NC_007779	468787	1	.	A	bias_e_value=2776980	bias_p_value=0.597672	fisher_strand_p_value=1	frequency=1.293087e-02	genotype_quality=1119.0	ks_quality_p_value=0.250794	log10_base_likelihood=-12.9635	log10_qual_likelihood_position_model=1.85058	log10_strand_likelihood_position_model=0.40976	new_cov=1/2	polymorphism_quality=7.6	quality=7.6	quality_position_model=9.58916e-13	ref_cov=111/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/120
RA	96	.	NC_007779	497096	0	T	G	bias_e_value=11874.2	bias_p_value=0.00255561	fisher_strand_p_value=0.000278168	frequency=2.609730e-02	genotype_quality=787.1	ks_quality_p_value=1	log10_base_likelihood=-5.69045	log10_qual_likelihood_position_model=13.4077	log10_strand_likelihood_position_model=3.55569	new_cov=0/11	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=127/109	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=128/120
RA	97	.	NC_007779	506363	1	.	A	bias_e_value=3999560	bias_p_value=0.860799	fisher_strand_p_value=1	frequency=7.246017e-03	genotype_quality=1355.9	ks_quality_p_value=0.52116	log10_base_likelihood=-8.2094	log10_qual_likelihood_position_model=1.25575	log10_strand_likelihood_position_model=0.302222	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.35533e-08	ref_cov=148/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/127
RA	98	.	NC_007779	513848	0	A	C	bias_e_value=3.61618e-13	bias_p_value=7.78286e-20	fisher_strand_p_value=1.59193e-21	frequency=1.274090e-01	genotype_quality=654.1	ks_quality_p_value=1	log10_base_likelihood=-19.412	log10_qual_likelihood_position_model=32.3081	log10_strand_likelihood_position_model=20.7981	new_cov=0/39	polymorphism_quality=14.1	quality=14.1	quality_position_model=Inf	ref_cov=139/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/78
RA	99	.	NC_007779	522430	1	.	T	bias_e_value=3942870	bias_p_value=0.848598	fisher_strand_p_value=0.570426	frequency=1.200008e-02	genotype_quality=1217.8	ks_quality_p_value=0.881679	log10_base_likelihood=-13.209	log10_qual_likelihood_position_model=2.10294	log10_strand_likelihood_position_model=0.522715	new_cov=1/2	polymorphism_quality=7.8	quality=7.8	quality_position_model=1.27044e-12	ref_cov=146/101	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/103
RA	100	.	NC_007779	522431	0	T	.	bias_e_value=1812010	bias_p_value=0.389986	fisher_strand_p_value=1	frequency=2.399063e-02	genotype_quality=991.9	ks_quality_p_value=0.127443	log10_base_likelihood=-17.9228	log10_qual_likelihood_position_model=3.0195	log10_strand_likelihood_position_model=0.51246	new_cov=4/2	polymorphism_quality=12.6	quality=12.6	quality_position_model=1.70566e-16	ref_cov=143/101	reject=INDEL_HOMOPOLYMER	tot_cov=147/103
RA	101	.	NC_007779	524490	0	T	G	bias_e_value=0.00598236	bias_p_value=1.28755e-09	fisher_strand_p_value=5.21773e-11	frequency=6.502533e-02	genotype_quality=748.0	ks_quality_p_value=1	log10_base_likelihood=-11.9663	log10_qual_likelihood_position_model=23.2983	log10_strand_likelihood_position_model=10.2825	new_cov=20/0	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=56/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=76/150
RA	102	.	NC_007779	528272	0	T	.	bias_e_value=777174	bias_p_value=0.167266	fisher_strand_p_value=1	frequency=1.249313e-02	genotype_quality=968.3	ks_quality_p_value=0.0395383	log10_base_likelihood=-8.39567	log10_qual_likelihood_position_model=1.71675	log10_strand_likelihood_position_model=0.41028	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.36477e-08	ref_cov=122/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/116
RA	103	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=1113.2	new_cov=131/142	quality=1113.2	ref_cov=0/0	tot_cov=131/142
RA	104	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=841.6	new_cov=110/91	quality=841.6	ref_cov=0/0	tot_cov=110/91
RA	105	.	NC_007779	556653	0	A	C	bias_e_value=3.82781e-06	bias_p_value=8.23835e-13	fisher_strand_p_value=2.55058e-14	frequency=6.985855e-02	genotype_quality=653.1	ks_quality_p_value=1	log10_base_likelihood=-7.94642	log10_qual_likelihood_position_model=22.9984	log10_strand_likelihood_position_model=13.5934	new_cov=0/26	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=135/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/71
RA	106	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=1148.7	new_cov=135/155	quality=1148.7	ref_cov=0/0	tot_cov=135/155
RA	107	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1178.4	new_cov=124/148	quality=1178.4	ref_cov=0/0	tot_cov=124/148
RA	108	.	NC_007779	589157	0	T	G	bias_e_value=0.000254412	bias_p_value=5.47553e-11	fisher_strand_p_value=1.95842e-12	frequency=6.949520e-02	genotype_quality=598.0	ks_quality_p_value=1	log10_base_likelihood=-6.71334	log10_qual_likelihood_position_model=30.4992	log10_strand_likelihood_position_model=11.7081	new_cov=28/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=59/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=87/118
RA	109	.	NC_007779	593216	0	T	G	bias_e_value=3.58833e-10	bias_p_value=7.72293e-17	fisher_strand_p_value=1.84611e-18	frequency=9.083557e-02	genotype_quality=623.2	ks_quality_p_value=1	log10_base_likelihood=-10.7621	log10_qual_likelihood_position_model=26.3794	log10_strand_likelihood_position_model=17.7337	new_cov=28/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=28/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=56/137
RA	110	.	NC_007779	598799	0	T	G	bias_e_value=2.29701e-21	bias_p_value=4.9437e-28	fisher_strand_p_value=7.25998e-30	frequency=1.813931e-01	genotype_quality=591.5	ks_quality_p_value=1	log10_base_likelihood=-22.4547	log10_qual_likelihood_position_model=39.8483	log10_strand_likelihood_position_model=29.1391	new_cov=47/0	polymorphism_quality=17.2	quality=17.2	quality_position_model=Inf	ref_cov=21/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=68/134
RA	111	.	NC_007779	615779	0	T	G	bias_e_value=1.18964e-05	bias_p_value=2.56038e-12	fisher_strand_p_value=8.22507e-14	frequency=6.819820e-02	genotype_quality=556.5	ks_quality_p_value=1	log10_base_likelihood=-12.1871	log10_qual_likelihood_position_model=19.1614	log10_strand_likelihood_position_model=13.0849	new_cov=16/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=15/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=31/128
RA	112	.	NC_007779	617601	0	C	A	bias_e_value=90.1593	bias_p_value=1.94044e-05	fisher_strand_p_value=1.33584e-06	frequency=4.799509e-02	genotype_quality=801.4	ks_quality_p_value=1	log10_base_likelihood=-8.67241	log10_qual_likelihood_position_model=14.1128	log10_strand_likelihood_position_model=5.87424	new_cov=15/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=83/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/133
RA	113	.	NC_007779	631234	0	G	.	bias_e_value=3979900	bias_p_value=0.856569	fisher_strand_p_value=1	frequency=1.153278e-02	genotype_quality=1065.4	ks_quality_p_value=0.51473	log10_base_likelihood=-8.61739	log10_qual_likelihood_position_model=1.92965	log10_strand_likelihood_position_model=0.397092	new_cov=2/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=3.19323e-08	ref_cov=137/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/121
RA	114	.	NC_007779	645970	0	T	G	bias_e_value=3.2456e-18	bias_p_value=6.9853e-25	fisher_strand_p_value=1.15028e-26	frequency=1.601424e-01	genotype_quality=620.0	ks_quality_p_value=1	log10_base_likelihood=-30.3583	log10_qual_likelihood_position_model=35.9182	log10_strand_likelihood_position_model=25.9392	new_cov=37/0	polymorphism_quality=25.2	quality=25.2	quality_position_model=Inf	ref_cov=18/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=55/141
RA	115	.	NC_007779	646440	0	C	A	bias_e_value=0.000121961	bias_p_value=2.62488e-11	fisher_strand_p_value=9.1873e-13	frequency=5.377960e-02	genotype_quality=823.1	ks_quality_p_value=0.994768	log10_base_likelihood=-19.7388	log10_qual_likelihood_position_model=16.5533	log10_strand_likelihood_position_model=12.0368	new_cov=0/12	polymorphism_quality=14.5	quality=14.5	quality_position_model=Inf	ref_cov=183/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=183/26
RA	116	.	NC_007779	660356	0	T	G	bias_e_value=9.26544e-12	bias_p_value=1.99414e-18	fisher_strand_p_value=4.37545e-20	frequency=9.035873e-02	genotype_quality=710.8	ks_quality_p_value=1	log10_base_likelihood=-9.74754	log10_qual_likelihood_position_model=29.9258	log10_strand_likelihood_position_model=19.359	new_cov=40/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=53/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/148
RA	117	.	NC_007779	665062	0	C	A	bias_e_value=0.893642	bias_p_value=1.92333e-07	fisher_strand_p_value=1.02784e-08	frequency=2.843857e-02	genotype_quality=1669.0	ks_quality_p_value=0.963017	log10_base_likelihood=-9.92777	log10_qual_likelihood_position_model=27.1944	log10_strand_likelihood_position_model=7.98807	new_cov=0/21	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=273/184	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=273/205
RA	118	.	NC_007779	667452	0	G	T	bias_e_value=3.23348	bias_p_value=6.95922e-07	fisher_strand_p_value=3.85074e-08	frequency=4.793024e-02	genotype_quality=1967.7	ks_quality_p_value=1	log10_base_likelihood=-31.272	log10_qual_likelihood_position_model=37.8473	log10_strand_likelihood_position_model=7.68905	new_cov=29/0	polymorphism_quality=26.1	quality=26.1	quality_position_model=Inf	ref_cov=255/227	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=285/227
RA	119	.	NC_007779	667899	1	.	G	bias_e_value=2649170	bias_p_value=0.570164	fisher_strand_p_value=0.239945	frequency=3.006935e-03	genotype_quality=3302.8	ks_quality_p_value=0.964632	log10_base_likelihood=-6.80534	log10_qual_likelihood_position_model=2.8361	log10_strand_likelihood_position_model=0.619889	new_cov=2/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=3.72972e-05	ref_cov=324/339	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=326/339
RA	120	.	NC_007779	674072	0	T	.	bias_e_value=2710720	bias_p_value=0.583412	fisher_strand_p_value=0.248658	frequency=5.382538e-03	genotype_quality=2223.1	ks_quality_p_value=0.967729	log10_base_likelihood=-6.59807	log10_qual_likelihood_position_model=4.13003	log10_strand_likelihood_position_model=0.900749	new_cov=0/3	polymorphism_quality=1.1	quality=1.1	quality_position_model=0.00314658	ref_cov=277/276	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=277/279
RA	121	.	NC_007779	686495	0	A	C	bias_e_value=3.9876e-39	bias_p_value=8.58225e-46	fisher_strand_p_value=7.84019e-48	frequency=1.068082e-01	genotype_quality=1534.8	ks_quality_p_value=1	log10_base_likelihood=-33.3354	log10_qual_likelihood_position_model=75.9583	log10_strand_likelihood_position_model=47.1057	new_cov=0/74	polymorphism_quality=28.2	quality=28.2	quality_position_model=Inf	ref_cov=332/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=332/139
RA	122	.	NC_007779	687133	0	A	C	bias_e_value=2.26109e-08	bias_p_value=4.86641e-15	fisher_strand_p_value=1.29484e-16	frequency=2.857876e-02	genotype_quality=1917.2	ks_quality_p_value=1	log10_base_likelihood=-9.82498	log10_qual_likelihood_position_model=46.4481	log10_strand_likelihood_position_model=15.8878	new_cov=0/36	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=351/181	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=351/219
RA	123	.	NC_007779	704593	0	T	G	bias_e_value=0.0026101	bias_p_value=5.61756e-10	fisher_strand_p_value=2.19949e-11	frequency=4.997492e-02	genotype_quality=731.5	ks_quality_p_value=1	log10_base_likelihood=-6.41501	log10_qual_likelihood_position_model=19.7158	log10_strand_likelihood_position_model=10.6577	new_cov=24/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=66/139	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=91/139
RA	124	.	NC_007779	704668	0	T	G	bias_e_value=2.26934e-08	bias_p_value=4.88415e-15	fisher_strand_p_value=1.29969e-16	frequency=8.191490e-02	genotype_quality=618.9	ks_quality_p_value=1	log10_base_likelihood=-6.97743	log10_qual_likelihood_position_model=26.6382	log10_strand_likelihood_position_model=15.8862	new_cov=28/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=35/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=64/132
RA	125	.	NC_007779	706385	1	.	T	bias_e_value=2023370	bias_p_value=0.435476	fisher_strand_p_value=0.229489	frequency=7.272720e-03	genotype_quality=1344.7	ks_quality_p_value=0.655714	log10_base_likelihood=-8.4408	log10_qual_likelihood_position_model=1.61606	log10_strand_likelihood_position_model=0.639238	new_cov=0/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=4.10029e-08	ref_cov=143/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/132
RA	126	.	NC_007779	723942	1	.	T	bias_e_value=1085100	bias_p_value=0.233538	fisher_strand_p_value=0.516965	frequency=7.604599e-03	genotype_quality=1270.2	ks_quality_p_value=0.119333	log10_base_likelihood=-7.98664	log10_qual_likelihood_position_model=1.89874	log10_strand_likelihood_position_model=0.449233	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.5083e-07	ref_cov=155/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/106
RA	127	.	NC_007779	732511	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	128	.	NC_007779	732512	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	129	.	NC_007779	732513	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	130	.	NC_007779	732515	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	131	.	NC_007779	742822	0	C	A	bias_e_value=125.116	bias_p_value=2.69279e-05	fisher_strand_p_value=1.89984e-06	frequency=3.778839e-02	genotype_quality=859.6	ks_quality_p_value=1	log10_base_likelihood=-6.25474	log10_qual_likelihood_position_model=16.2124	log10_strand_likelihood_position_model=5.95933	new_cov=19/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=112/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/129
RA	132	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=1106.0	new_cov=110/165	quality=1106.0	ref_cov=0/0	tot_cov=110/165
RA	133	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=1105.5	new_cov=126/149	quality=1105.5	ref_cov=0/0	tot_cov=126/149
RA	134	.	NC_007779	759019	0	C	G	bias_e_value=4.22425e-06	bias_p_value=9.09158e-13	fisher_strand_p_value=2.82363e-14	frequency=7.535839e-02	genotype_quality=651.4	ks_quality_p_value=1	log10_base_likelihood=-23.212	log10_qual_likelihood_position_model=16.5233	log10_strand_likelihood_position_model=13.5492	new_cov=0/13	polymorphism_quality=18.0	quality=18.0	quality_position_model=Inf	ref_cov=145/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/21
RA	135	.	NC_007779	817515	0	G	T	bias_e_value=0.160426	bias_p_value=3.45274e-08	fisher_strand_p_value=1.62579e-09	frequency=5.888939e-02	genotype_quality=916.0	ks_quality_p_value=1	log10_base_likelihood=-9.06903	log10_qual_likelihood_position_model=26.1082	log10_strand_likelihood_position_model=8.83348	new_cov=0/31	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=135/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/161
RA	136	.	NC_007779	842195	0	C	A	bias_e_value=196.037	bias_p_value=4.21917e-05	fisher_strand_p_value=3.08362e-06	frequency=4.602242e-02	genotype_quality=965.0	ks_quality_p_value=0.999459	log10_base_likelihood=-9.22043	log10_qual_likelihood_position_model=23.9548	log10_strand_likelihood_position_model=5.72133	new_cov=24/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=160/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=186/126
RA	137	.	NC_007779	853114	0	C	G	bias_e_value=210.127	bias_p_value=4.52243e-05	fisher_strand_p_value=3.32164e-06	frequency=4.841185e-02	genotype_quality=680.1	ks_quality_p_value=1	log10_base_likelihood=-13.0765	log10_qual_likelihood_position_model=9.78596	log10_strand_likelihood_position_model=5.47865	new_cov=0/10	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=125/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=125/54
RA	138	.	NC_007779	868836	1	.	C	bias_e_value=4023300	bias_p_value=0.865908	fisher_strand_p_value=0.571885	frequency=1.132011e-02	genotype_quality=1286.7	ks_quality_p_value=0.925171	log10_base_likelihood=-12.2693	log10_qual_likelihood_position_model=3.46795	log10_strand_likelihood_position_model=0.518533	new_cov=1/2	polymorphism_quality=6.9	quality=6.9	quality_position_model=2.85416e-10	ref_cov=154/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=155/110
RA	139	.	NC_007779	884191	1	.	T	bias_e_value=1680370	bias_p_value=0.361656	fisher_strand_p_value=0.114241	frequency=1.260281e-02	genotype_quality=1153.5	ks_quality_p_value=0.998285	log10_base_likelihood=-10.0134	log10_qual_likelihood_position_model=5.56793	log10_strand_likelihood_position_model=0.942177	new_cov=0/3	polymorphism_quality=4.6	quality=4.6	quality_position_model=2.56409e-05	ref_cov=122/113	reject=POLYMORPHISM_STRAND	tot_cov=122/116
RA	140	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=762.3	new_cov=120/82	quality=762.3	ref_cov=0/0	tot_cov=120/82
RA	141	.	NC_007779	889983	1	.	A	bias_e_value=4320480	bias_p_value=0.929869	fisher_strand_p_value=1	frequency=7.434845e-03	genotype_quality=1319.5	ks_quality_p_value=0.649675	log10_base_likelihood=-8.4669	log10_qual_likelihood_position_model=1.48867	log10_strand_likelihood_position_model=0.299467	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.27019e-08	ref_cov=132/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/136
RA	142	.	NC_007779	889984	0	A	.	bias_e_value=4228330	bias_p_value=0.910037	fisher_strand_p_value=0.620939	frequency=1.070213e-02	genotype_quality=1100.5	ks_quality_p_value=0.977574	log10_base_likelihood=-7.64223	log10_qual_likelihood_position_model=2.45991	log10_strand_likelihood_position_model=0.427585	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.2498e-06	ref_cov=136/139	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/141
RA	143	.	NC_007779	904838	0	C	A	bias_e_value=1.76445e-05	bias_p_value=3.79751e-12	fisher_strand_p_value=1.38512e-13	frequency=7.345963e-02	genotype_quality=946.4	ks_quality_p_value=0.892417	log10_base_likelihood=-14.7345	log10_qual_likelihood_position_model=27.0589	log10_strand_likelihood_position_model=12.8585	new_cov=32/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=97/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/172
RA	144	.	NC_007779	960579	1	.	T	bias_e_value=4098880	bias_p_value=0.882176	fisher_strand_p_value=1	frequency=8.771896e-03	genotype_quality=1110.8	ks_quality_p_value=0.555679	log10_base_likelihood=-8.10985	log10_qual_likelihood_position_model=1.87511	log10_strand_likelihood_position_model=0.300762	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=7.4611e-08	ref_cov=106/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/121
RA	145	.	NC_007779	969494	0	C	A	bias_e_value=0.0112058	bias_p_value=2.41175e-09	fisher_strand_p_value=1.00398e-10	frequency=1.000853e-01	genotype_quality=709.4	ks_quality_p_value=1	log10_base_likelihood=-22.0972	log10_qual_likelihood_position_model=18.6518	log10_strand_likelihood_position_model=9.99827	new_cov=30/0	polymorphism_quality=16.8	quality=16.8	quality_position_model=Inf	ref_cov=89/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/120
RA	146	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=798.3	new_cov=69/127	quality=798.3	ref_cov=0/0	tot_cov=69/127
RA	147	.	NC_007779	987916	0	T	G	bias_e_value=3.79114e-07	bias_p_value=8.15942e-14	fisher_strand_p_value=2.35255e-15	frequency=9.644604e-02	genotype_quality=524.0	ks_quality_p_value=1	log10_base_likelihood=-17.7901	log10_qual_likelihood_position_model=19.2063	log10_strand_likelihood_position_model=14.6285	new_cov=16/0	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=9/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=25/121
RA	148	.	NC_007779	991407	0	G	T	bias_e_value=1.38733	bias_p_value=2.98585e-07	fisher_strand_p_value=1.82309e-08	frequency=4.287815e-02	genotype_quality=936.9	ks_quality_p_value=0.863501	log10_base_likelihood=-8.32352	log10_qual_likelihood_position_model=23.9017	log10_strand_likelihood_position_model=7.73919	new_cov=0/23	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=153/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/144
RA	149	.	NC_007779	1035834	0	C	A	bias_e_value=1824.46	bias_p_value=0.000392667	fisher_strand_p_value=3.48598e-05	frequency=3.414345e-02	genotype_quality=917.8	ks_quality_p_value=1	log10_base_likelihood=-8.90716	log10_qual_likelihood_position_model=11.7581	log10_strand_likelihood_position_model=4.45767	new_cov=13/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=117/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/149
RA	150	.	NC_007779	1037529	0	T	G	bias_e_value=623.45	bias_p_value=0.000134181	fisher_strand_p_value=1.13593e-05	frequency=2.420712e-02	genotype_quality=624.1	ks_quality_p_value=0.94978	log10_base_likelihood=-6.58719	log10_qual_likelihood_position_model=5.8611	log10_strand_likelihood_position_model=4.94465	new_cov=4/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=7/153	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=11/153
RA	151	.	NC_007779	1079013	0	C	A	bias_e_value=118.101	bias_p_value=2.5418e-05	fisher_strand_p_value=1.7855e-06	frequency=4.395580e-02	genotype_quality=773.4	ks_quality_p_value=1	log10_base_likelihood=-6.16583	log10_qual_likelihood_position_model=12.7622	log10_strand_likelihood_position_model=5.74824	new_cov=18/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=103/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/122
RA	152	.	NC_007779	1085002	1	.	T	bias_e_value=2395220	bias_p_value=0.515508	fisher_strand_p_value=0.505278	frequency=6.733894e-03	genotype_quality=1447.7	ks_quality_p_value=0.388024	log10_base_likelihood=-8.2509	log10_qual_likelihood_position_model=1.07003	log10_strand_likelihood_position_model=0.506456	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.28337e-08	ref_cov=164/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/131
RA	153	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1188.5	new_cov=126/148	quality=1188.5	ref_cov=0/0	tot_cov=126/148
RA	154	.	NC_007779	1097403	0	A	.	bias_e_value=671551	bias_p_value=0.144534	fisher_strand_p_value=0.0867643	frequency=7.782936e-03	genotype_quality=1365.9	ks_quality_p_value=0.37684	log10_base_likelihood=-7.54171	log10_qual_likelihood_position_model=1.56154	log10_strand_likelihood_position_model=1.06166	new_cov=0/3	polymorphism_quality=2.0	quality=2.0	quality_position_model=8.43841e-07	ref_cov=214/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=214/171
RA	155	.	NC_007779	1097580	0	C	T	bias_e_value=261434	bias_p_value=0.0562667	fisher_strand_p_value=0.514878	frequency=2.203088e-01	genotype_quality=766.3	ks_quality_p_value=0.0195128	log10_base_likelihood=-217.648	log10_qual_likelihood_position_model=19.7244	log10_strand_likelihood_position_model=1.11525	new_cov=38/38	polymorphism_quality=212.9	quality=212.9	quality_position_model=1.78751e-199	ref_cov=121/148	tot_cov=159/187
RA	156	.	NC_007779	1097583	1	.	A	bias_e_value=3913250	bias_p_value=0.842223	fisher_strand_p_value=0.501133	frequency=6.059647e-03	genotype_quality=1211.0	ks_quality_p_value=0.985327	log10_base_likelihood=-7.35289	log10_qual_likelihood_position_model=2.33328	log10_strand_likelihood_position_model=0.542224	new_cov=0/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=2.43351e-06	ref_cov=153/175	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/177
RA	157	.	NC_007779	1099918	1	.	T	bias_e_value=4093370	bias_p_value=0.88099	fisher_strand_p_value=0.553667	frequency=1.275921e-02	genotype_quality=1139.8	ks_quality_p_value=1	log10_base_likelihood=-9.30107	log10_qual_likelihood_position_model=5.4264	log10_strand_likelihood_position_model=0.495297	new_cov=3/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=3.46659e-05	ref_cov=158/74	reject=POLYMORPHISM_STRAND	tot_cov=161/74
RA	158	.	NC_007779	1116582	0	G	C	bias_e_value=3.92178e-08	bias_p_value=8.4406e-15	fisher_strand_p_value=2.28019e-16	frequency=1.074185e-01	genotype_quality=518.2	ks_quality_p_value=1	log10_base_likelihood=-26.2803	log10_qual_likelihood_position_model=12.7208	log10_strand_likelihood_position_model=15.642	new_cov=0/17	polymorphism_quality=21.1	quality=21.1	quality_position_model=Inf	ref_cov=126/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/26
RA	159	.	NC_007779	1142633	1	.	T	bias_e_value=2110320	bias_p_value=0.45419	fisher_strand_p_value=0.190227	frequency=6.622314e-03	genotype_quality=1481.4	ks_quality_p_value=0.843907	log10_base_likelihood=-8.10059	log10_qual_likelihood_position_model=1.22876	log10_strand_likelihood_position_model=0.720728	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=4.44995e-08	ref_cov=130/170	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/170
RA	160	.	NC_007779	1148417	0	C	A	bias_e_value=1347.42	bias_p_value=0.000289997	fisher_strand_p_value=2.85028e-05	frequency=3.383923e-02	genotype_quality=865.2	ks_quality_p_value=0.877375	log10_base_likelihood=-7.18883	log10_qual_likelihood_position_model=18.8647	log10_strand_likelihood_position_model=4.60118	new_cov=16/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=129/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/129
RA	161	.	NC_007779	1158848	0	T	G	bias_e_value=2.14573e-15	bias_p_value=4.61812e-22	fisher_strand_p_value=8.53342e-24	frequency=1.182761e-01	genotype_quality=748.7	ks_quality_p_value=1	log10_base_likelihood=-15.5681	log10_qual_likelihood_position_model=36.9372	log10_strand_likelihood_position_model=23.0689	new_cov=51/0	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=56/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/147
RA	162	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1212.3	new_cov=188/110	quality=1212.3	ref_cov=0/1	tot_cov=188/111
RA	163	.	NC_007779	1177683	0	A	G	bias_e_value=28.4809	bias_p_value=6.12977e-06	fisher_strand_p_value=3.88949e-07	frequency=5.066967e-02	genotype_quality=670.6	ks_quality_p_value=1	log10_base_likelihood=-9.238	log10_qual_likelihood_position_model=11.4456	log10_strand_likelihood_position_model=6.41011	new_cov=13/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=58/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=71/137
RA	164	.	NC_007779	1213001	0	T	C	bias_e_value=1836720	bias_p_value=0.395306	fisher_strand_p_value=0.635814	frequency=6.641483e-02	genotype_quality=1020.5	ks_quality_p_value=0.204522	log10_base_likelihood=-54.691	log10_qual_likelihood_position_model=5.52601	log10_strand_likelihood_position_model=0.809927	new_cov=9/10	polymorphism_quality=49.6	quality=49.6	quality_position_model=1.02068e-50	ref_cov=146/121	tot_cov=155/131
RA	165	.	NC_007779	1213013	0	T	C	bias_e_value=3137520	bias_p_value=0.675267	fisher_strand_p_value=0.426202	frequency=5.272532e-02	genotype_quality=1051.8	ks_quality_p_value=0.731774	log10_base_likelihood=-39.8315	log10_qual_likelihood_position_model=5.27075	log10_strand_likelihood_position_model=0.912289	new_cov=6/9	polymorphism_quality=34.7	quality=34.7	quality_position_model=6.21434e-36	ref_cov=145/124	tot_cov=151/133
RA	166	.	NC_007779	1213026	0	C	T	bias_e_value=4388410	bias_p_value=0.944489	fisher_strand_p_value=0.775979	frequency=4.419804e-02	genotype_quality=1089.5	ks_quality_p_value=0.883876	log10_base_likelihood=-27.5599	log10_qual_likelihood_position_model=3.83575	log10_strand_likelihood_position_model=0.656436	new_cov=6/6	polymorphism_quality=22.3	quality=22.3	quality_position_model=2.85029e-25	ref_cov=141/118	tot_cov=147/124
RA	167	.	NC_007779	1213028	0	G	A	bias_e_value=4541590	bias_p_value=0.977457	fisher_strand_p_value=1	frequency=4.572964e-02	genotype_quality=1043.2	ks_quality_p_value=0.795322	log10_base_likelihood=-28.1512	log10_qual_likelihood_position_model=4.13843	log10_strand_likelihood_position_model=0.646652	new_cov=6/6	polymorphism_quality=22.9	quality=22.9	quality_position_model=1.42475e-25	ref_cov=133/117	tot_cov=139/123
RA	168	.	NC_007779	1213058	0	T	C	bias_e_value=4640550	bias_p_value=0.998755	fisher_strand_p_value=1	frequency=1.739883e-02	genotype_quality=894.5	ks_quality_p_value=0.950514	log10_base_likelihood=-7.44477	log10_qual_likelihood_position_model=3.7247	log10_strand_likelihood_position_model=0.423821	new_cov=2/2	polymorphism_quality=1.9	quality=1.9	quality_position_model=4.24518e-05	ref_cov=107/117	reject=EVALUE	tot_cov=109/119
RA	169	.	NC_007779	1213061	0	C	G	bias_e_value=4187420	bias_p_value=0.901231	fisher_strand_p_value=1	frequency=1.238728e-02	genotype_quality=1022.5	ks_quality_p_value=0.589863	log10_base_likelihood=-7.84499	log10_qual_likelihood_position_model=1.75247	log10_strand_likelihood_position_model=0.395171	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.3113e-07	ref_cov=111/128	reject=POLYMORPHISM_STRAND	tot_cov=112/130
RA	170	.	NC_007779	1262466	0	A	.	bias_e_value=4416770	bias_p_value=0.950592	fisher_strand_p_value=1	frequency=1.184845e-02	genotype_quality=998.4	ks_quality_p_value=0.702591	log10_base_likelihood=-8.04324	log10_qual_likelihood_position_model=2.38422	log10_strand_likelihood_position_model=0.375949	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.52595e-07	ref_cov=142/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/109
RA	171	.	NC_007779	1273399	0	T	G	bias_e_value=3.30658e-18	bias_p_value=7.11653e-25	fisher_strand_p_value=1.17225e-26	frequency=1.061311e-01	genotype_quality=759.8	ks_quality_p_value=1	log10_base_likelihood=-16.4513	log10_qual_likelihood_position_model=34.0325	log10_strand_likelihood_position_model=25.931	new_cov=36/0	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=24/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=60/174
RA	172	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=86.9	new_cov=15/11	quality=86.9	ref_cov=0/1	tot_cov=15/12
RA	173	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=19.3	new_cov=6/3	quality=19.3	ref_cov=0/1	tot_cov=6/4
RA	174	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=59.3	new_cov=15/11	quality=59.3	ref_cov=0/0	tot_cov=15/11
RA	175	.	NC_007779	1306089	0	G	C	bias_e_value=1623.78	bias_p_value=0.000349476	fisher_strand_p_value=3.07409e-05	frequency=3.916740e-02	genotype_quality=729.9	ks_quality_p_value=0.997931	log10_base_likelihood=-7.84301	log10_qual_likelihood_position_model=12.7103	log10_strand_likelihood_position_model=4.51228	new_cov=9/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=54/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=63/128
RA	176	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1207.2	new_cov=152/150	quality=1207.2	ref_cov=0/0	tot_cov=152/150
RA	177	.	NC_007779	1345021	0	T	.	bias_e_value=462391	bias_p_value=0.0995174	fisher_strand_p_value=0.045189	frequency=1.586342e-02	genotype_quality=997.5	ks_quality_p_value=0.449824	log10_base_likelihood=-11.087	log10_qual_likelihood_position_model=2.85488	log10_strand_likelihood_position_model=1.34497	new_cov=4/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=7.74775e-09	ref_cov=113/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/135
RA	178	.	NC_007779	1371749	1	.	T	bias_e_value=1857300	bias_p_value=0.399735	fisher_strand_p_value=0.7171	frequency=2.491093e-02	genotype_quality=1314.3	ks_quality_p_value=0.184379	log10_base_likelihood=-31.6569	log10_qual_likelihood_position_model=5.08693	log10_strand_likelihood_position_model=0.570482	new_cov=4/3	polymorphism_quality=26.5	quality=26.5	quality_position_model=3.14465e-28	ref_cov=133/141	reject=INDEL_HOMOPOLYMER	tot_cov=137/144
RA	179	.	NC_007779	1378219	0	A	C	bias_e_value=1.31757e-07	bias_p_value=2.83571e-14	fisher_strand_p_value=7.9274e-16	frequency=8.325958e-02	genotype_quality=675.7	ks_quality_p_value=1	log10_base_likelihood=-6.2125	log10_qual_likelihood_position_model=44.3311	log10_strand_likelihood_position_model=15.1009	new_cov=0/42	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=119/72	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/115
RA	180	.	NC_007779	1405508	0	G	T	bias_e_value=0.855084	bias_p_value=1.84034e-07	fisher_strand_p_value=9.49617e-09	frequency=7.427120e-02	genotype_quality=508.0	ks_quality_p_value=0.994991	log10_base_likelihood=-17.3236	log10_qual_likelihood_position_model=12.0732	log10_strand_likelihood_position_model=8.02245	new_cov=11/0	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=19/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=30/108
RA	181	.	NC_007779	1409137	0	G	T	bias_e_value=4.38422e-07	bias_p_value=9.43587e-14	fisher_strand_p_value=2.73237e-15	frequency=1.152582e-01	genotype_quality=702.1	ks_quality_p_value=1	log10_base_likelihood=-23.558	log10_qual_likelihood_position_model=22.4478	log10_strand_likelihood_position_model=14.5635	new_cov=0/40	polymorphism_quality=18.3	quality=18.3	quality_position_model=Inf	ref_cov=128/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/119
RA	182	.	NC_007779	1410956	1	.	T	bias_e_value=2218590	bias_p_value=0.477492	fisher_strand_p_value=0.214124	frequency=6.919861e-03	genotype_quality=1398.1	ks_quality_p_value=0.810526	log10_base_likelihood=-7.5765	log10_qual_likelihood_position_model=1.80903	log10_strand_likelihood_position_model=0.669334	new_cov=2/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=5.48792e-07	ref_cov=132/155	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/155
RA	183	.	NC_007779	1412694	0	C	A	bias_e_value=0.714934	bias_p_value=1.53871e-07	fisher_strand_p_value=7.82418e-09	frequency=5.458784e-02	genotype_quality=762.1	ks_quality_p_value=1	log10_base_likelihood=-6.05114	log10_qual_likelihood_position_model=17.2125	log10_strand_likelihood_position_model=8.10656	new_cov=23/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=89/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/126
RA	184	.	NC_007779	1429766	0	T	C	deleted=1	frequency=1	genotype_quality=1.3	new_cov=0/1	quality=1.3	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	185	.	NC_007779	1430138	0	A	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	186	.	NC_007779	1430146	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	187	.	NC_007779	1430165	0	T	C	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	188	.	NC_007779	1433509	0	C	T	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	189	.	NC_007779	1433522	0	T	C	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	190	.	NC_007779	1433525	0	T	C	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	191	.	NC_007779	1433527	0	C	T	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	192	.	NC_007779	1433546	0	T	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	193	.	NC_007779	1433558	0	T	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	194	.	NC_007779	1433561	0	T	C	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	195	.	NC_007779	1433567	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	196	.	NC_007779	1433576	0	A	T	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	197	.	NC_007779	1433578	0	C	T	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	198	.	NC_007779	1433582	0	T	G	deleted=1	frequency=1	genotype_quality=4.7	new_cov=1/1	quality=4.7	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	199	.	NC_007779	1433588	0	G	A	deleted=1	frequency=1	genotype_quality=7.9	new_cov=1/1	quality=7.9	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	200	.	NC_007779	1433591	0	A	G	deleted=1	frequency=1	genotype_quality=8.7	new_cov=1/1	quality=8.7	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	201	.	NC_007779	1433594	0	C	T	deleted=1	frequency=1	genotype_quality=8.1	new_cov=1/1	quality=8.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	202	.	NC_007779	1433598	0	A	C	deleted=1	frequency=1	genotype_quality=7.6	new_cov=1/1	quality=7.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	203	.	NC_007779	1433600	0	C	T	deleted=1	frequency=1	genotype_quality=8.0	new_cov=1/1	quality=8.0	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	204	.	NC_007779	1433612	0	T	A	deleted=1	frequency=1	genotype_quality=7.9	new_cov=1/1	quality=7.9	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	205	.	NC_007779	1433621	0	G	A	deleted=1	frequency=1	genotype_quality=7.4	new_cov=1/1	quality=7.4	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	206	.	NC_007779	1433624	0	T	C	deleted=1	frequency=1	genotype_quality=8.9	new_cov=1/1	quality=8.9	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	207	.	NC_007779	1433630	0	C	G	deleted=1	frequency=1	genotype_quality=8.8	new_cov=1/1	quality=8.8	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	208	.	NC_007779	1433636	0	T	C	deleted=1	frequency=1	genotype_quality=8.9	new_cov=1/1	quality=8.9	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	209	.	NC_007779	1433642	0	T	C	deleted=1	frequency=1	genotype_quality=8.3	new_cov=1/1	quality=8.3	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	210	.	NC_007779	1433648	0	G	T	deleted=1	frequency=1	genotype_quality=8.2	new_cov=1/1	quality=8.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	211	.	NC_007779	1433651	0	C	T	deleted=1	frequency=1	genotype_quality=8.2	new_cov=1/1	quality=8.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	212	.	NC_007779	1433672	0	C	T	deleted=1	frequency=1	genotype_quality=7.5	new_cov=1/1	quality=7.5	ref_cov=0/0	reject=EVALUE	tot_cov=1/1
RA	213	.	NC_007779	1433675	0	C	A	deleted=1	frequency=1	genotype_quality=3.9	new_cov=1/0	quality=3.9	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	214	.	NC_007779	1437441	0	G	A	bias_e_value=8.32903	bias_p_value=1.7926e-06	fisher_strand_p_value=1.0502e-07	frequency=4.101658e-02	genotype_quality=786.1	ks_quality_p_value=1	log10_base_likelihood=-5.96955	log10_qual_likelihood_position_model=14.9262	log10_strand_likelihood_position_model=6.97873	new_cov=0/10	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=157/34	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/44
RA	215	.	NC_007779	1437447	0	G	C	bias_e_value=1.2923e-05	bias_p_value=2.78134e-12	fisher_strand_p_value=8.9595e-14	frequency=6.684542e-02	genotype_quality=813.0	ks_quality_p_value=1	log10_base_likelihood=-8.63851	log10_qual_likelihood_position_model=23.2798	log10_strand_likelihood_position_model=13.0477	new_cov=0/26	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=161/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/87
RA	216	.	NC_007779	1472740	0	A	.	bias_e_value=2707640	bias_p_value=0.582747	fisher_strand_p_value=0.25035	frequency=1.040649e-02	genotype_quality=1156.9	ks_quality_p_value=0.959329	log10_base_likelihood=-7.7207	log10_qual_likelihood_position_model=3.22277	log10_strand_likelihood_position_model=0.827617	new_cov=0/3	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.70903e-05	ref_cov=134/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/154
RA	217	.	NC_007779	1476017	0	T	.	bias_e_value=3845610	bias_p_value=0.827666	fisher_strand_p_value=0.575903	frequency=1.248360e-02	genotype_quality=865.6	ks_quality_p_value=0.822595	log10_base_likelihood=-7.59422	log10_qual_likelihood_position_model=2.826	log10_strand_likelihood_position_model=0.506074	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=4.08603e-06	ref_cov=99/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=103/137
RA	218	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=818.8	new_cov=159/49	quality=818.8	ref_cov=0/0	tot_cov=159/49
RA	219	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1375.4	new_cov=143/135	quality=1375.4	ref_cov=0/0	tot_cov=143/135
RA	220	.	NC_007779	1515709	0	A	G	bias_e_value=2.64775e-05	bias_p_value=5.69858e-12	fisher_strand_p_value=1.88059e-13	frequency=1.040435e-01	genotype_quality=732.5	ks_quality_p_value=1	log10_base_likelihood=-17.6089	log10_qual_likelihood_position_model=36.604	log10_strand_likelihood_position_model=12.7257	new_cov=34/0	polymorphism_quality=12.3	quality=12.3	quality_position_model=Inf	ref_cov=87/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/142
RA	221	.	NC_007779	1527474	0	G	A	bias_e_value=0.241217	bias_p_value=5.19156e-08	fisher_strand_p_value=2.49486e-09	frequency=7.769680e-02	genotype_quality=932.0	ks_quality_p_value=1	log10_base_likelihood=-21.2275	log10_qual_likelihood_position_model=30.0121	log10_strand_likelihood_position_model=8.60295	new_cov=0/26	polymorphism_quality=16.0	quality=16.0	quality_position_model=Inf	ref_cov=151/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/145
RA	222	.	NC_007779	1537499	0	A	G	bias_e_value=0.0308227	bias_p_value=6.63378e-09	fisher_strand_p_value=2.88864e-10	frequency=1.243386e-01	genotype_quality=597.0	ks_quality_p_value=1	log10_base_likelihood=-15.0261	log10_qual_likelihood_position_model=24.3841	log10_strand_likelihood_position_model=9.59863	new_cov=39/0	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=108/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/97
RA	223	.	NC_007779	1552377	0	A	C	bias_e_value=6.1016e-06	bias_p_value=1.31321e-12	fisher_strand_p_value=4.12717e-14	frequency=9.548235e-02	genotype_quality=670.0	ks_quality_p_value=1	log10_base_likelihood=-12.9572	log10_qual_likelihood_position_model=26.5568	log10_strand_likelihood_position_model=13.3843	new_cov=0/33	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=127/66	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/100
RA	224	.	NC_007779	1579243	1	.	A	bias_e_value=2389020	bias_p_value=0.514174	fisher_strand_p_value=0.204872	frequency=8.402824e-03	genotype_quality=1166.1	ks_quality_p_value=0.952999	log10_base_likelihood=-8.24475	log10_qual_likelihood_position_model=2.47257	log10_strand_likelihood_position_model=0.688518	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.68144e-07	ref_cov=106/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/130
RA	225	.	NC_007779	1595838	1	.	C	bias_e_value=3673880	bias_p_value=0.790704	fisher_strand_p_value=0.603249	frequency=1.298237e-02	genotype_quality=1117.4	ks_quality_p_value=0.708496	log10_base_likelihood=-11.3152	log10_qual_likelihood_position_model=4.00599	log10_strand_likelihood_position_model=0.450844	new_cov=1/2	polymorphism_quality=5.9	quality=5.9	quality_position_model=8.29521e-09	ref_cov=121/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/109
RA	226	.	NC_007779	1595962	1	.	C	bias_e_value=1940700	bias_p_value=0.417685	fisher_strand_p_value=0.201785	frequency=9.009361e-03	genotype_quality=1071.2	ks_quality_p_value=0.699943	log10_base_likelihood=-8.37759	log10_qual_likelihood_position_model=1.46544	log10_strand_likelihood_position_model=0.69511	new_cov=0/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.80397e-08	ref_cov=122/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/100
RA	227	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=888.9	new_cov=105/130	quality=888.9	ref_cov=0/0	tot_cov=105/130
RA	228	.	NC_007779	1624530	1	.	A	bias_e_value=1356640	bias_p_value=0.291981	fisher_strand_p_value=0.598448	frequency=1.408482e-02	genotype_quality=1002.9	ks_quality_p_value=0.140308	log10_base_likelihood=-13.2958	log10_qual_likelihood_position_model=2.66937	log10_strand_likelihood_position_model=0.458111	new_cov=2/1	polymorphism_quality=7.9	quality=7.9	quality_position_model=3.36768e-12	ref_cov=97/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/114
RA	229	.	NC_007779	1626064	0	T	.	bias_e_value=1558450	bias_p_value=0.335415	fisher_strand_p_value=0.122647	frequency=1.543236e-02	genotype_quality=1022.0	ks_quality_p_value=0.833698	log10_base_likelihood=-11.016	log10_qual_likelihood_position_model=2.67812	log10_strand_likelihood_position_model=1.16745	new_cov=4/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=3.95929e-09	ref_cov=129/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/126
RA	230	.	NC_007779	1628027	0	G	T	bias_e_value=0.000453415	bias_p_value=9.75856e-11	fisher_strand_p_value=6.06584e-12	frequency=1.859426e-01	genotype_quality=417.8	ks_quality_p_value=0.588016	log10_base_likelihood=-47.0007	log10_qual_likelihood_position_model=28.2829	log10_strand_likelihood_position_model=11.2171	new_cov=30/0	polymorphism_quality=41.9	quality=41.9	quality_position_model=1.81162e-09	ref_cov=44/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/80
RA	231	.	NC_007779	1637277	0	T	C	bias_e_value=3468690	bias_p_value=0.746544	fisher_strand_p_value=0.59806	frequency=1.202393e-02	genotype_quality=957.1	ks_quality_p_value=0.633423	log10_base_likelihood=-5.86596	log10_qual_likelihood_position_model=1.81669	log10_strand_likelihood_position_model=0.459508	new_cov=1/2	polymorphism_quality=0.3	quality=0.3	quality_position_model=2.07812e-05	ref_cov=132/113	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=133/116
RA	232	.	NC_007779	1651009	0	T	G	bias_e_value=3.59825e-12	bias_p_value=7.74429e-19	fisher_strand_p_value=1.66392e-20	frequency=1.244245e-01	genotype_quality=627.5	ks_quality_p_value=1	log10_base_likelihood=-18.2897	log10_qual_likelihood_position_model=29.5608	log10_strand_likelihood_position_model=19.7789	new_cov=34/0	polymorphism_quality=13.0	quality=13.0	quality_position_model=Inf	ref_cov=31/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=65/133
RA	233	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=983.0	new_cov=93/104	quality=983.0	ref_cov=0/0	tot_cov=93/104
RA	234	.	NC_007779	1669765	0	C	A	bias_e_value=23949	bias_p_value=0.0051544	fisher_strand_p_value=0.000620426	frequency=4.370499e-02	genotype_quality=963.2	ks_quality_p_value=0.989544	log10_base_likelihood=-11.4637	log10_qual_likelihood_position_model=17.6155	log10_strand_likelihood_position_model=3.24617	new_cov=0/12	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=111/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/134
RA	235	.	NC_007779	1669767	0	T	G	bias_e_value=80435.7	bias_p_value=0.0173117	fisher_strand_p_value=0.00247215	frequency=2.799702e-02	genotype_quality=902.6	ks_quality_p_value=1	log10_base_likelihood=-6.32347	log10_qual_likelihood_position_model=12.6614	log10_strand_likelihood_position_model=2.65579	new_cov=0/10	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=110/125	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=110/135
RA	236	.	NC_007779	1669770	0	T	G	bias_e_value=88739.5	bias_p_value=0.0190988	fisher_strand_p_value=0.00277281	frequency=2.509689e-02	genotype_quality=909.0	ks_quality_p_value=1	log10_base_likelihood=-9.88648	log10_qual_likelihood_position_model=12.1075	log10_strand_likelihood_position_model=2.59301	new_cov=0/10	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=109/128	reject=POLYMORPHISM_STRAND	tot_cov=109/138
RA	237	.	NC_007779	1669772	0	G	A	bias_e_value=463107	bias_p_value=0.0996715	fisher_strand_p_value=0.0203714	frequency=2.132225e-02	genotype_quality=974.1	ks_quality_p_value=0.99977	log10_base_likelihood=-5.684	log10_qual_likelihood_position_model=9.28292	log10_strand_likelihood_position_model=1.74799	new_cov=0/7	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=108/135	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=108/142
RA	238	.	NC_007779	1669773	0	A	G	bias_e_value=497973	bias_p_value=0.107175	fisher_strand_p_value=0.0223706	frequency=2.931023e-02	genotype_quality=901.8	ks_quality_p_value=0.997603	log10_base_likelihood=-9.26397	log10_qual_likelihood_position_model=9.01643	log10_strand_likelihood_position_model=1.93931	new_cov=0/8	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=105/136	reject=POLYMORPHISM_STRAND	tot_cov=105/144
RA	239	.	NC_007779	1669786	0	G	A	bias_e_value=167721	bias_p_value=0.0360976	fisher_strand_p_value=0.00588522	frequency=3.054714e-02	genotype_quality=952.1	ks_quality_p_value=0.999667	log10_base_likelihood=-5.57294	log10_qual_likelihood_position_model=14.8811	log10_strand_likelihood_position_model=2.42436	new_cov=0/10	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=105/135	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=105/145
RA	240	.	NC_007779	1677110	0	G	T	bias_e_value=42.6125	bias_p_value=9.1712e-06	fisher_strand_p_value=8.74389e-07	frequency=5.076981e-02	genotype_quality=733.7	ks_quality_p_value=0.68423	log10_base_likelihood=-6.93246	log10_qual_likelihood_position_model=27.9015	log10_strand_likelihood_position_model=6.09948	new_cov=1/22	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=122/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/121
RA	241	.	NC_007779	1679770	0	A	.	bias_e_value=4645310	bias_p_value=0.99978	fisher_strand_p_value=1	frequency=1.037121e-02	genotype_quality=1165.0	ks_quality_p_value=0.979096	log10_base_likelihood=-7.82491	log10_qual_likelihood_position_model=3.1527	log10_strand_likelihood_position_model=0.397202	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=3.96132e-06	ref_cov=152/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=155/134
RA	242	.	NC_007779	1705209	1	.	T	bias_e_value=2742200	bias_p_value=0.590187	fisher_strand_p_value=0.246073	frequency=1.562023e-02	genotype_quality=913.5	ks_quality_p_value=0.997358	log10_base_likelihood=-9.78392	log10_qual_likelihood_position_model=4.91881	log10_strand_likelihood_position_model=0.909966	new_cov=3/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=8.57349e-06	ref_cov=93/96	reject=POLYMORPHISM_STRAND	tot_cov=96/96
RA	243	.	NC_007779	1705210	0	G	T	bias_e_value=340032	bias_p_value=0.073183	fisher_strand_p_value=0.0139523	frequency=3.363514e-02	genotype_quality=719.5	ks_quality_p_value=0.993714	log10_base_likelihood=-8.22886	log10_qual_likelihood_position_model=10.3753	log10_strand_likelihood_position_model=2.15639	new_cov=7/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=89/96	reject=POLYMORPHISM_STRAND	tot_cov=96/96
RA	244	.	NC_007779	1716032	0	T	.	bias_e_value=4140620	bias_p_value=0.891158	fisher_strand_p_value=0.617915	frequency=1.135254e-02	genotype_quality=1056.8	ks_quality_p_value=0.924622	log10_base_likelihood=-7.83841	log10_qual_likelihood_position_model=2.31688	log10_strand_likelihood_position_model=0.431102	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=5.59016e-07	ref_cov=133/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/130
RA	245	.	NC_007779	1759411	1	.	T	bias_e_value=4183020	bias_p_value=0.900284	fisher_strand_p_value=1	frequency=7.407188e-03	genotype_quality=1314.6	ks_quality_p_value=0.588075	log10_base_likelihood=-8.21297	log10_qual_likelihood_position_model=1.60584	log10_strand_likelihood_position_model=0.310057	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=3.14485e-08	ref_cov=113/155	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/156
RA	246	.	NC_007779	1759412	0	T	.	bias_e_value=276664	bias_p_value=0.0595447	fisher_strand_p_value=0.0300918	frequency=1.453686e-02	genotype_quality=1055.6	ks_quality_p_value=0.357729	log10_base_likelihood=-11.1594	log10_qual_likelihood_position_model=2.47534	log10_strand_likelihood_position_model=1.52155	new_cov=4/0	polymorphism_quality=5.7	quality=5.7	quality_position_model=4.03427e-09	ref_cov=111/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/159
RA	247	.	NC_007779	1763744	0	C	A	bias_e_value=0.00998234	bias_p_value=2.14843e-09	fisher_strand_p_value=8.90634e-11	frequency=5.553055e-02	genotype_quality=818.2	ks_quality_p_value=0.999173	log10_base_likelihood=-7.75742	log10_qual_likelihood_position_model=21.386	log10_strand_likelihood_position_model=10.0503	new_cov=26/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=90/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/148
RA	248	.	NC_007779	1784132	0	G	T	bias_e_value=23304.8	bias_p_value=0.00501574	fisher_strand_p_value=0.000596223	frequency=2.028275e-02	genotype_quality=810.3	ks_quality_p_value=0.998334	log10_base_likelihood=-5.71627	log10_qual_likelihood_position_model=10.8674	log10_strand_likelihood_position_model=3.26789	new_cov=0/12	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=112/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/134
RA	249	.	NC_007779	1820099	0	A	C	bias_e_value=0.0467342	bias_p_value=1.00583e-08	fisher_strand_p_value=4.46446e-10	frequency=5.553532e-02	genotype_quality=833.8	ks_quality_p_value=1	log10_base_likelihood=-9.32076	log10_qual_likelihood_position_model=19.6272	log10_strand_likelihood_position_model=9.35023	new_cov=0/20	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=161/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=161/93
RA	250	.	NC_007779	1823574	0	A	.	bias_e_value=4524500	bias_p_value=0.97378	fisher_strand_p_value=1	frequency=1.090050e-02	genotype_quality=1094.7	ks_quality_p_value=0.779919	log10_base_likelihood=-8.00357	log10_qual_likelihood_position_model=1.57739	log10_strand_likelihood_position_model=0.402451	new_cov=2/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=6.02552e-08	ref_cov=143/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/130
RA	251	.	NC_007779	1840899	0	G	T	bias_e_value=36.2687	bias_p_value=7.80587e-06	fisher_strand_p_value=5.03554e-07	frequency=4.347610e-02	genotype_quality=731.8	ks_quality_p_value=1	log10_base_likelihood=-7.43697	log10_qual_likelihood_position_model=13.5864	log10_strand_likelihood_position_model=6.29795	new_cov=0/17	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=125/84	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/102
RA	252	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=1039.8	new_cov=143/116	quality=1039.8	ref_cov=0/0	tot_cov=143/116
RA	253	.	NC_007779	1846634	0	A	.	bias_e_value=3449930	bias_p_value=0.742507	fisher_strand_p_value=0.622762	frequency=1.580143e-02	genotype_quality=1006.5	ks_quality_p_value=0.601659	log10_base_likelihood=-11.2988	log10_qual_likelihood_position_model=2.58188	log10_strand_likelihood_position_model=0.575051	new_cov=3/1	polymorphism_quality=5.9	quality=5.9	quality_position_model=3.98081e-10	ref_cov=127/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/123
RA	254	.	NC_007779	1861399	0	A	C	bias_e_value=5.8595e-08	bias_p_value=1.2611e-14	fisher_strand_p_value=3.44522e-16	frequency=7.261944e-02	genotype_quality=614.0	ks_quality_p_value=1	log10_base_likelihood=-6.48913	log10_qual_likelihood_position_model=25.6683	log10_strand_likelihood_position_model=15.4628	new_cov=0/27	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=132/35	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/62
RA	255	.	NC_007779	1879404	0	A	C	bias_e_value=4.49177e-16	bias_p_value=9.66735e-23	fisher_strand_p_value=1.73527e-24	frequency=1.141276e-01	genotype_quality=707.1	ks_quality_p_value=1	log10_base_likelihood=-19.9292	log10_qual_likelihood_position_model=32.1642	log10_strand_likelihood_position_model=23.7606	new_cov=0/34	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=156/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/57
RA	256	.	NC_007779	1880187	0	C	T	bias_e_value=4578600	bias_p_value=0.985423	fisher_strand_p_value=1	frequency=1.411343e-02	genotype_quality=1134.6	ks_quality_p_value=0.834183	log10_base_likelihood=-6.81628	log10_qual_likelihood_position_model=2.9029	log10_strand_likelihood_position_model=0.441688	new_cov=2/2	polymorphism_quality=1.3	quality=1.3	quality_position_model=2.76887e-05	ref_cov=159/118	reject=EVALUE	tot_cov=161/120
RA	257	.	NC_007779	1889729	1	.	A	bias_e_value=2259170	bias_p_value=0.486226	fisher_strand_p_value=1	frequency=1.115227e-02	genotype_quality=1308.8	ks_quality_p_value=0.178582	log10_base_likelihood=-12.4308	log10_qual_likelihood_position_model=3.00794	log10_strand_likelihood_position_model=0.378271	new_cov=2/1	polymorphism_quality=7.0	quality=7.0	quality_position_model=4.73641e-11	ref_cov=150/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/117
RA	258	.	NC_007779	1896056	0	A	.	bias_e_value=4134970	bias_p_value=0.889942	fisher_strand_p_value=0.657702	frequency=1.907253e-02	genotype_quality=1048.1	ks_quality_p_value=0.865395	log10_base_likelihood=-14.2282	log10_qual_likelihood_position_model=3.06446	log10_strand_likelihood_position_model=0.567053	new_cov=3/2	polymorphism_quality=8.9	quality=8.9	quality_position_model=1.23126e-12	ref_cov=113/144	reject=INDEL_HOMOPOLYMER	tot_cov=116/146
RA	259	.	NC_007779	1906477	1	.	G	bias_e_value=495979	bias_p_value=0.106746	fisher_strand_p_value=0.0222135	frequency=1.904583e-02	genotype_quality=994.8	ks_quality_p_value=0.999584	log10_base_likelihood=-15.8987	log10_qual_likelihood_position_model=4.94195	log10_strand_likelihood_position_model=1.65338	new_cov=4/0	polymorphism_quality=10.6	quality=10.6	quality_position_model=2.57517e-11	ref_cov=78/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=82/128
RA	260	.	NC_007779	1907281	0	C	A	bias_e_value=4632430	bias_p_value=0.997008	fisher_strand_p_value=1	frequency=7.176399e-03	genotype_quality=2361.3	ks_quality_p_value=0.92365	log10_base_likelihood=-7.17958	log10_qual_likelihood_position_model=3.82785	log10_strand_likelihood_position_model=0.424681	new_cov=2/2	polymorphism_quality=1.7	quality=1.7	quality_position_model=0.000104754	ref_cov=270/280	reject=EVALUE	tot_cov=272/282
RA	261	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=1112.2	new_cov=138/154	quality=1112.2	ref_cov=0/0	tot_cov=138/155
RA	262	.	NC_007779	1920746	0	G	T	bias_e_value=0.0663434	bias_p_value=1.42787e-08	fisher_strand_p_value=6.44259e-10	frequency=7.485294e-02	genotype_quality=824.5	ks_quality_p_value=1	log10_base_likelihood=-18.2015	log10_qual_likelihood_position_model=17.3633	log10_strand_likelihood_position_model=9.19094	new_cov=0/25	polymorphism_quality=12.9	quality=12.9	quality_position_model=Inf	ref_cov=138/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/116
RA	263	.	NC_007779	1971508	0	A	C	bias_e_value=1.3777e-06	bias_p_value=2.96513e-13	fisher_strand_p_value=8.8899e-15	frequency=7.008934e-02	genotype_quality=547.4	ks_quality_p_value=1	log10_base_likelihood=-14.8325	log10_qual_likelihood_position_model=17.7593	log10_strand_likelihood_position_model=14.0511	new_cov=0/15	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=133/10	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/25
RA	264	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=1018.6	new_cov=131/130	quality=1018.6	ref_cov=0/0	tot_cov=131/130
RA	265	.	NC_007779	1993894	0	A	C	bias_e_value=571.549	bias_p_value=0.000123011	fisher_strand_p_value=9.81615e-06	frequency=3.887844e-02	genotype_quality=963.2	ks_quality_p_value=1	log10_base_likelihood=-7.46107	log10_qual_likelihood_position_model=20.161	log10_strand_likelihood_position_model=5.02804	new_cov=0/18	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=133/138	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/158
RA	266	.	NC_007779	2004055	0	A	C	bias_e_value=1.5945e-14	bias_p_value=3.43175e-21	fisher_strand_p_value=6.59015e-23	frequency=1.842942e-01	genotype_quality=640.0	ks_quality_p_value=1	log10_base_likelihood=-40.7245	log10_qual_likelihood_position_model=39.9554	log10_strand_likelihood_position_model=22.1978	new_cov=0/62	polymorphism_quality=35.6	quality=35.6	quality_position_model=Inf	ref_cov=127/70	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/134
RA	267	.	NC_007779	2005225	0	A	.	bias_e_value=4039810	bias_p_value=0.869461	fisher_strand_p_value=0.608631	frequency=1.122856e-02	genotype_quality=1079.5	ks_quality_p_value=0.878562	log10_base_likelihood=-8.2391	log10_qual_likelihood_position_model=2.03021	log10_strand_likelihood_position_model=0.443489	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.11492e-07	ref_cov=126/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/139
RA	268	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=1142.2	new_cov=149/134	quality=1142.2	ref_cov=0/0	tot_cov=149/134
RA	269	.	NC_007779	2013225	0	C	A	bias_e_value=125.067	bias_p_value=2.69173e-05	fisher_strand_p_value=1.90043e-06	frequency=4.595566e-02	genotype_quality=799.7	ks_quality_p_value=0.999265	log10_base_likelihood=-6.98697	log10_qual_likelihood_position_model=16.6706	log10_strand_likelihood_position_model=5.87313	new_cov=19/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=102/116	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/116
RA	270	.	NC_007779	2020389	1	.	A	bias_e_value=947934	bias_p_value=0.204018	fisher_strand_p_value=0.0939087	frequency=1.181126e-02	genotype_quality=1227.6	ks_quality_p_value=0.547543	log10_base_likelihood=-13.1345	log10_qual_likelihood_position_model=1.81499	log10_strand_likelihood_position_model=1.02729	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=2.51715e-12	ref_cov=113/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/138
RA	271	.	NC_007779	2032185	0	G	C	bias_e_value=40.5292	bias_p_value=8.72283e-06	fisher_strand_p_value=5.8736e-07	frequency=5.926800e-02	genotype_quality=509.2	ks_quality_p_value=0.965421	log10_base_likelihood=-13.4002	log10_qual_likelihood_position_model=8.97646	log10_strand_likelihood_position_model=6.2311	new_cov=8/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=17/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=25/107
RA	272	.	NC_007779	2036123	1	.	T	bias_e_value=4645950	bias_p_value=0.999918	fisher_strand_p_value=1	frequency=8.064270e-03	genotype_quality=1225.0	ks_quality_p_value=0.987231	log10_base_likelihood=-8.0793	log10_qual_likelihood_position_model=2.06451	log10_strand_likelihood_position_model=0.329206	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.34864e-07	ref_cov=155/91	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/92
RA	273	.	NC_007779	2065611	0	C	A	bias_e_value=72.4374	bias_p_value=1.55902e-05	fisher_strand_p_value=1.05619e-06	frequency=4.232883e-02	genotype_quality=939.7	ks_quality_p_value=1	log10_base_likelihood=-9.64998	log10_qual_likelihood_position_model=19.5891	log10_strand_likelihood_position_model=6.20979	new_cov=22/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=134/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/133
RA	274	.	NC_007779	2156661	0	C	A	bias_e_value=0.943013	bias_p_value=2.02958e-07	fisher_strand_p_value=1.04849e-08	frequency=5.781698e-02	genotype_quality=817.7	ks_quality_p_value=0.999126	log10_base_likelihood=-7.08176	log10_qual_likelihood_position_model=18.901	log10_strand_likelihood_position_model=8.03351	new_cov=32/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=136/119	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/119
RA	275	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1134.5	new_cov=121/156	quality=1134.5	ref_cov=0/0	tot_cov=121/156
RA	276	.	NC_007779	2174678	0	C	G	bias_e_value=10.4165	bias_p_value=2.24187e-06	fisher_strand_p_value=1.3332e-07	frequency=6.723309e-02	genotype_quality=678.8	ks_quality_p_value=0.999064	log10_base_likelihood=-10.479	log10_qual_likelihood_position_model=16.687	log10_strand_likelihood_position_model=6.88474	new_cov=1/15	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=130/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/62
RA	277	.	NC_007779	2200802	0	A	.	bias_e_value=4639100	bias_p_value=0.998443	fisher_strand_p_value=1	frequency=1.097870e-02	genotype_quality=1092.3	ks_quality_p_value=0.944722	log10_base_likelihood=-7.88328	log10_qual_likelihood_position_model=3.14931	log10_strand_likelihood_position_model=0.418076	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.58975e-06	ref_cov=133/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/139
RA	278	.	NC_007779	2213136	0	G	T	bias_e_value=0.390692	bias_p_value=8.40862e-08	fisher_strand_p_value=4.65447e-09	frequency=8.126593e-02	genotype_quality=575.7	ks_quality_p_value=0.88984	log10_base_likelihood=-19.9106	log10_qual_likelihood_position_model=18.172	log10_strand_likelihood_position_model=8.33213	new_cov=15/0	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=37/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=53/116
RA	279	.	NC_007779	2226744	0	T	G	bias_e_value=4.91467	bias_p_value=1.05775e-06	fisher_strand_p_value=6.0001e-08	frequency=4.934168e-02	genotype_quality=842.2	ks_quality_p_value=1	log10_base_likelihood=-6.98087	log10_qual_likelihood_position_model=21.5189	log10_strand_likelihood_position_model=7.22184	new_cov=21/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=106/141	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/141
RA	280	.	NC_007779	2227297	1	.	C	bias_e_value=791038	bias_p_value=0.17025	fisher_strand_p_value=0.237815	frequency=7.575989e-03	genotype_quality=1311.3	ks_quality_p_value=0.170154	log10_base_likelihood=-8.44413	log10_qual_likelihood_position_model=2.13399	log10_strand_likelihood_position_model=0.62376	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.34606e-07	ref_cov=127/135	reject=POLYMORPHISM_STRAND	tot_cov=129/135
RA	281	.	NC_007779	2249963	0	T	G	bias_e_value=0.022354	bias_p_value=4.81111e-09	fisher_strand_p_value=2.06478e-10	frequency=8.175945e-02	genotype_quality=664.2	ks_quality_p_value=1	log10_base_likelihood=-8.67	log10_qual_likelihood_position_model=30.2023	log10_strand_likelihood_position_model=9.92489	new_cov=30/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=84/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/113
RA	282	.	NC_007779	2278635	0	C	A	bias_e_value=1051.5	bias_p_value=0.000226308	fisher_strand_p_value=1.90697e-05	frequency=3.398991e-02	genotype_quality=797.5	ks_quality_p_value=1	log10_base_likelihood=-6.87944	log10_qual_likelihood_position_model=14.5152	log10_strand_likelihood_position_model=4.91964	new_cov=16/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=113/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/125
RA	283	.	NC_007779	2287403	1	.	A	bias_e_value=4617210	bias_p_value=0.993731	fisher_strand_p_value=1	frequency=6.666183e-03	genotype_quality=1486.9	ks_quality_p_value=0.890141	log10_base_likelihood=-8.08698	log10_qual_likelihood_position_model=1.34128	log10_strand_likelihood_position_model=0.299599	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.20693e-08	ref_cov=150/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/149
RA	284	.	NC_007779	2307309	0	T	C	bias_e_value=34.9141	bias_p_value=7.51433e-06	fisher_strand_p_value=4.83477e-07	frequency=4.642439e-02	genotype_quality=628.1	ks_quality_p_value=1	log10_base_likelihood=-6.13953	log10_qual_likelihood_position_model=12.8483	log10_strand_likelihood_position_model=6.31562	new_cov=0/12	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=133/50	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/62
RA	285	.	NC_007779	2317068	0	T	C	bias_e_value=951344	bias_p_value=0.204752	fisher_strand_p_value=0.252264	frequency=1.116371e-02	genotype_quality=973.0	ks_quality_p_value=0.204811	log10_base_likelihood=-6.14869	log10_qual_likelihood_position_model=2.23331	log10_strand_likelihood_position_model=0.804461	new_cov=3/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=6.67575e-05	ref_cov=142/123	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=145/123
RA	286	.	NC_007779	2331120	0	T	G	bias_e_value=5.77383e-13	bias_p_value=1.24267e-19	fisher_strand_p_value=2.56687e-21	frequency=1.256504e-01	genotype_quality=710.1	ks_quality_p_value=1	log10_base_likelihood=-12.7947	log10_qual_likelihood_position_model=32.9973	log10_strand_likelihood_position_model=20.5906	new_cov=54/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=71/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/136
RA	287	.	NC_007779	2332580	0	A	C	bias_e_value=9.34304e-12	bias_p_value=2.01084e-18	fisher_strand_p_value=4.41292e-20	frequency=1.161561e-01	genotype_quality=650.3	ks_quality_p_value=1	log10_base_likelihood=-13.2182	log10_qual_likelihood_position_model=33.4592	log10_strand_likelihood_position_model=19.3553	new_cov=0/44	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=128/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/96
RA	288	.	NC_007779	2342393	0	A	C	bias_e_value=0.00290491	bias_p_value=6.25204e-10	fisher_strand_p_value=2.45864e-11	frequency=7.690573e-02	genotype_quality=711.9	ks_quality_p_value=1	log10_base_likelihood=-9.0391	log10_qual_likelihood_position_model=23.7483	log10_strand_likelihood_position_model=10.6093	new_cov=0/26	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=131/71	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/98
RA	289	.	NC_007779	2353815	0	A	C	bias_e_value=6.98656e-10	bias_p_value=1.50367e-16	fisher_strand_p_value=3.65407e-18	frequency=7.197428e-02	genotype_quality=660.7	ks_quality_p_value=1	log10_base_likelihood=-11.2462	log10_qual_likelihood_position_model=24.7068	log10_strand_likelihood_position_model=17.4372	new_cov=0/25	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=148/25	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/50
RA	290	.	NC_007779	2387487	0	A	.	bias_e_value=1481310	bias_p_value=0.318812	fisher_strand_p_value=1	frequency=1.166439e-02	genotype_quality=1049.2	ks_quality_p_value=0.0950822	log10_base_likelihood=-8.07361	log10_qual_likelihood_position_model=1.982	log10_strand_likelihood_position_model=0.376548	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.25707e-07	ref_cov=110/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/146
RA	291	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=1087.8	new_cov=150/125	quality=1087.8	ref_cov=0/0	tot_cov=150/126
RA	292	.	NC_007779	2410314	1	.	C	bias_e_value=2632670	bias_p_value=0.566614	fisher_strand_p_value=0.229041	frequency=7.427216e-03	genotype_quality=1268.0	ks_quality_p_value=1	log10_base_likelihood=-5.60085	log10_qual_likelihood_position_model=2.049	log10_strand_likelihood_position_model=0.640087	new_cov=0/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.00010876	ref_cov=140/127	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=140/129
RA	293	.	NC_007779	2410316	0	A	C	bias_e_value=0.000134237	bias_p_value=2.88909e-11	fisher_strand_p_value=1.00941e-12	frequency=8.758307e-02	genotype_quality=819.2	ks_quality_p_value=1	log10_base_likelihood=-20.2357	log10_qual_likelihood_position_model=24.3713	log10_strand_likelihood_position_model=11.9959	new_cov=0/34	polymorphism_quality=15.0	quality=15.0	quality_position_model=Inf	ref_cov=144/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/133
RA	294	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=914.4	new_cov=103/131	quality=914.4	ref_cov=0/0	tot_cov=103/131
RA	295	.	NC_007779	2417605	0	C	A	bias_e_value=0.00192501	bias_p_value=4.14307e-10	fisher_strand_p_value=2.08216e-11	frequency=9.328127e-02	genotype_quality=758.1	ks_quality_p_value=0.769537	log10_base_likelihood=-17.9343	log10_qual_likelihood_position_model=30.8926	log10_strand_likelihood_position_model=10.6815	new_cov=32/0	polymorphism_quality=12.6	quality=12.6	quality_position_model=Inf	ref_cov=93/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/126
RA	296	.	NC_007779	2418805	1	.	A	bias_e_value=4138810	bias_p_value=0.89077	fisher_strand_p_value=0.597229	frequency=1.082993e-02	genotype_quality=1357.6	ks_quality_p_value=0.955486	log10_base_likelihood=-11.9538	log10_qual_likelihood_position_model=2.88561	log10_strand_likelihood_position_model=0.4614	new_cov=1/2	polymorphism_quality=6.6	quality=6.6	quality_position_model=1.32907e-10	ref_cov=148/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/128
RA	297	.	NC_007779	2465370	0	C	A	bias_e_value=62.9355	bias_p_value=1.35452e-05	fisher_strand_p_value=9.57122e-07	frequency=6.271172e-02	genotype_quality=518.7	ks_quality_p_value=0.94906	log10_base_likelihood=-11.9399	log10_qual_likelihood_position_model=12.1521	log10_strand_likelihood_position_model=6.01903	new_cov=0/10	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=103/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/39
RA	298	.	NC_007779	2468326	1	.	C	bias_e_value=509875	bias_p_value=0.109737	fisher_strand_p_value=0.202013	frequency=8.584023e-03	genotype_quality=1107.0	ks_quality_p_value=0.113822	log10_base_likelihood=-8.88981	log10_qual_likelihood_position_model=1.82651	log10_strand_likelihood_position_model=0.694621	new_cov=2/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=2.65264e-08	ref_cov=103/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/128
RA	299	.	NC_007779	2468327	0	C	.	bias_e_value=865433	bias_p_value=0.186262	fisher_strand_p_value=0.09112	frequency=2.541447e-02	genotype_quality=958.5	ks_quality_p_value=0.499927	log10_base_likelihood=-18.1026	log10_qual_likelihood_position_model=6.13064	log10_strand_likelihood_position_model=1.25025	new_cov=5/1	polymorphism_quality=12.8	quality=12.8	quality_position_model=9.18062e-13	ref_cov=100/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/131
RA	300	.	NC_007779	2476279	0	C	G	bias_e_value=894738	bias_p_value=0.192569	fisher_strand_p_value=0.0484182	frequency=1.770210e-02	genotype_quality=888.1	ks_quality_p_value=0.983306	log10_base_likelihood=-8.19028	log10_qual_likelihood_position_model=3.61566	log10_strand_likelihood_position_model=1.31499	new_cov=0/4	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.64185e-05	ref_cov=116/100	reject=POLYMORPHISM_STRAND	tot_cov=116/104
RA	301	.	NC_007779	2489982	0	A	.	bias_e_value=2905150	bias_p_value=0.625256	fisher_strand_p_value=1	frequency=1.218796e-02	genotype_quality=994.6	ks_quality_p_value=0.271328	log10_base_likelihood=-8.37265	log10_qual_likelihood_position_model=1.80264	log10_strand_likelihood_position_model=0.385104	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=4.10613e-08	ref_cov=109/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/136
RA	302	.	NC_007779	2504972	0	A	.	bias_e_value=4632960	bias_p_value=0.997121	fisher_strand_p_value=1	frequency=1.156998e-02	genotype_quality=1038.3	ks_quality_p_value=0.925091	log10_base_likelihood=-7.59536	log10_qual_likelihood_position_model=3.62165	log10_strand_likelihood_position_model=0.406871	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=2.19709e-05	ref_cov=133/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/124
RA	303	.	NC_007779	2509304	0	C	.	bias_e_value=1064810	bias_p_value=0.229171	fisher_strand_p_value=0.601262	frequency=1.051903e-02	genotype_quality=1159.5	ks_quality_p_value=0.100007	log10_base_likelihood=-8.17408	log10_qual_likelihood_position_model=2.31696	log10_strand_likelihood_position_model=0.45483	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.65186e-07	ref_cov=150/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/133
RA	304	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=999.8	new_cov=136/113	quality=999.8	ref_cov=0/0	tot_cov=136/113
RA	305	.	NC_007779	2541409	1	.	A	bias_e_value=2586220	bias_p_value=0.556616	fisher_strand_p_value=0.236226	frequency=7.434845e-03	genotype_quality=1312.0	ks_quality_p_value=0.941153	log10_base_likelihood=-7.99627	log10_qual_likelihood_position_model=3.35274	log10_strand_likelihood_position_model=0.626672	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=7.3854e-06	ref_cov=129/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/138
RA	306	.	NC_007779	2556426	0	G	T	bias_e_value=0.0312749	bias_p_value=6.73109e-09	fisher_strand_p_value=3.82005e-10	frequency=4.871607e-02	genotype_quality=964.7	ks_quality_p_value=0.767779	log10_base_likelihood=-9.19611	log10_qual_likelihood_position_model=27.1172	log10_strand_likelihood_position_model=9.41793	new_cov=0/27	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=166/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/148
RA	307	.	NC_007779	2601998	0	A	C	bias_e_value=1.40551	bias_p_value=3.02498e-07	fisher_strand_p_value=1.59706e-08	frequency=3.497982e-02	genotype_quality=627.9	ks_quality_p_value=0.999358	log10_base_likelihood=-6.25519	log10_qual_likelihood_position_model=12.7863	log10_strand_likelihood_position_model=7.79668	new_cov=0/9	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=145/18	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/27
RA	308	.	NC_007779	2602394	0	G	T	bias_e_value=56533.4	bias_p_value=0.0121673	fisher_strand_p_value=0.00164208	frequency=2.212238e-02	genotype_quality=886.4	ks_quality_p_value=0.999672	log10_base_likelihood=-6.78035	log10_qual_likelihood_position_model=9.74979	log10_strand_likelihood_position_model=3.01997	new_cov=0/10	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=124/118	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=124/129
RA	309	.	NC_007779	2623159	0	T	G	bias_e_value=1.32936e-21	bias_p_value=2.86109e-28	fisher_strand_p_value=4.16764e-30	frequency=1.986914e-01	genotype_quality=635.0	ks_quality_p_value=1	log10_base_likelihood=-40.4433	log10_qual_likelihood_position_model=41.1286	log10_strand_likelihood_position_model=29.3801	new_cov=56/0	polymorphism_quality=35.3	quality=35.3	quality_position_model=Inf	ref_cov=34/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/140
RA	310	.	NC_007779	2641345	0	T	G	bias_e_value=16.9537	bias_p_value=3.64885e-06	fisher_strand_p_value=2.23676e-07	frequency=4.362869e-02	genotype_quality=455.3	ks_quality_p_value=1	log10_base_likelihood=-6.3109	log10_qual_likelihood_position_model=11.7276	log10_strand_likelihood_position_model=6.65038	new_cov=10/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=22/99	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=32/100
RA	311	.	NC_007779	2643620	1	.	T	bias_e_value=2059430	bias_p_value=0.443238	fisher_strand_p_value=0.223041	frequency=7.633209e-03	genotype_quality=1300.4	ks_quality_p_value=0.693176	log10_base_likelihood=-8.1631	log10_qual_likelihood_position_model=1.62436	log10_strand_likelihood_position_model=0.651615	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=8.34187e-08	ref_cov=122/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/138
RA	312	.	NC_007779	2648595	0	A	C	bias_e_value=9.61553e-09	bias_p_value=2.06949e-15	fisher_strand_p_value=5.38073e-17	frequency=9.767771e-02	genotype_quality=563.9	ks_quality_p_value=1	log10_base_likelihood=-16.8755	log10_qual_likelihood_position_model=23.3396	log10_strand_likelihood_position_model=16.2692	new_cov=0/19	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=131/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/32
RA	313	.	NC_007779	2672817	0	A	C	bias_e_value=1.76252e-06	bias_p_value=3.79335e-13	fisher_strand_p_value=1.14603e-14	frequency=1.074562e-01	genotype_quality=611.9	ks_quality_p_value=1	log10_base_likelihood=-21.5908	log10_qual_likelihood_position_model=22.8211	log10_strand_likelihood_position_model=13.9408	new_cov=0/33	polymorphism_quality=16.3	quality=16.3	quality_position_model=Inf	ref_cov=122/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/91
RA	314	.	NC_007779	2704797	0	C	A	bias_e_value=1187970	bias_p_value=0.25568	fisher_strand_p_value=0.607439	frequency=1.309967e-02	genotype_quality=954.2	ks_quality_p_value=0.114948	log10_base_likelihood=-5.86044	log10_qual_likelihood_position_model=3.45741	log10_strand_likelihood_position_model=0.444551	new_cov=1/2	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.00116185	ref_cov=118/107	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=119/109
RA	315	.	NC_007779	2715028	0	T	.	bias_e_value=2700800	bias_p_value=0.581275	fisher_strand_p_value=0.250802	frequency=9.163857e-03	genotype_quality=1309.7	ks_quality_p_value=0.953489	log10_base_likelihood=-7.56676	log10_qual_likelihood_position_model=2.46483	log10_strand_likelihood_position_model=0.825525	new_cov=3/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=3.94806e-06	ref_cov=171/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=174/153
RA	316	.	NC_007779	2757983	1	.	A	bias_e_value=2865210	bias_p_value=0.616661	fisher_strand_p_value=0.624846	frequency=1.142883e-02	genotype_quality=1716.9	ks_quality_p_value=0.423785	log10_base_likelihood=-16.7951	log10_qual_likelihood_position_model=2.6084	log10_strand_likelihood_position_model=0.559294	new_cov=3/1	polymorphism_quality=11.5	quality=11.5	quality_position_model=1.01583e-15	ref_cov=181/165	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=184/166
RA	317	.	NC_007779	2791635	0	C	T	bias_e_value=2.23391e-07	bias_p_value=4.80791e-14	fisher_strand_p_value=1.36481e-15	frequency=1.018038e-01	genotype_quality=602.1	ks_quality_p_value=1	log10_base_likelihood=-7.75239	log10_qual_likelihood_position_model=24.2375	log10_strand_likelihood_position_model=14.8649	new_cov=0/29	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=129/43	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/72
RA	318	.	NC_007779	2803750	0	A	.	bias_e_value=2945060	bias_p_value=0.633846	fisher_strand_p_value=1	frequency=1.090145e-02	genotype_quality=1082.0	ks_quality_p_value=0.277975	log10_base_likelihood=-8.15657	log10_qual_likelihood_position_model=1.64187	log10_strand_likelihood_position_model=0.407926	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.94485e-08	ref_cov=131/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/143
RA	319	.	NC_007779	2816615	0	G	C	bias_e_value=0.00448937	bias_p_value=9.66219e-10	fisher_strand_p_value=4.37137e-11	frequency=7.586145e-02	genotype_quality=753.6	ks_quality_p_value=0.885	log10_base_likelihood=-16.9725	log10_qual_likelihood_position_model=24.474	log10_strand_likelihood_position_model=10.3594	new_cov=22/0	polymorphism_quality=11.7	quality=11.7	quality_position_model=Inf	ref_cov=66/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=88/151
RA	320	.	NC_007779	2817030	0	G	C	bias_e_value=6.57953e-10	bias_p_value=1.41607e-16	fisher_strand_p_value=4.25098e-18	frequency=1.152859e-01	genotype_quality=771.0	ks_quality_p_value=0.808294	log10_base_likelihood=-31.0983	log10_qual_likelihood_position_model=35.501	log10_strand_likelihood_position_model=17.3715	new_cov=32/0	polymorphism_quality=25.9	quality=25.9	quality_position_model=Inf	ref_cov=49/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=81/161
RA	321	.	NC_007779	2833989	0	A	C	bias_e_value=3.8175e-14	bias_p_value=8.21615e-21	fisher_strand_p_value=1.60523e-22	frequency=1.363821e-01	genotype_quality=724.7	ks_quality_p_value=1	log10_base_likelihood=-27.623	log10_qual_likelihood_position_model=37.3661	log10_strand_likelihood_position_model=21.7945	new_cov=0/40	polymorphism_quality=22.4	quality=22.4	quality_position_model=Inf	ref_cov=148/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/80
RA	322	.	NC_007779	2839296	0	A	G	bias_e_value=8.49299e-05	bias_p_value=1.82789e-11	fisher_strand_p_value=6.2823e-13	frequency=7.066345e-02	genotype_quality=677.9	ks_quality_p_value=1	log10_base_likelihood=-9.39303	log10_qual_likelihood_position_model=19.9801	log10_strand_likelihood_position_model=12.2019	new_cov=20/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=40/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=60/154
RA	323	.	NC_007779	2847445	0	G	T	bias_e_value=5.94403e-05	bias_p_value=1.27929e-11	fisher_strand_p_value=4.34169e-13	frequency=7.749987e-02	genotype_quality=900.6	ks_quality_p_value=1	log10_base_likelihood=-9.89586	log10_qual_likelihood_position_model=27.1085	log10_strand_likelihood_position_model=12.3623	new_cov=0/37	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=151/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/149
RA	324	.	NC_007779	2850262	0	C	.	bias_e_value=2750350	bias_p_value=0.591939	fisher_strand_p_value=0.249885	frequency=9.858131e-03	genotype_quality=1267.5	ks_quality_p_value=0.987146	log10_base_likelihood=-7.79098	log10_qual_likelihood_position_model=2.59072	log10_strand_likelihood_position_model=0.835842	new_cov=3/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=3.19378e-06	ref_cov=157/143	reject=POLYMORPHISM_STRAND	tot_cov=161/143
RA	325	.	NC_007779	2859840	0	T	.	bias_e_value=2427260	bias_p_value=0.522403	fisher_strand_p_value=0.268775	frequency=1.184177e-02	genotype_quality=1013.4	ks_quality_p_value=0.74531	log10_base_likelihood=-7.53952	log10_qual_likelihood_position_model=2.99694	log10_strand_likelihood_position_model=0.702263	new_cov=3/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.13191e-05	ref_cov=145/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/105
RA	326	.	NC_007779	2862783	1	.	T	bias_e_value=4045070	bias_p_value=0.870595	fisher_strand_p_value=0.5367	frequency=8.693695e-03	genotype_quality=1128.9	ks_quality_p_value=0.999695	log10_base_likelihood=-6.93498	log10_qual_likelihood_position_model=3.27441	log10_strand_likelihood_position_model=0.389893	new_cov=0/2	polymorphism_quality=1.4	quality=1.4	quality_position_model=4.51838e-05	ref_cov=83/145	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=83/147
RA	327	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1313.5	new_cov=135/172	quality=1313.5	ref_cov=0/0	tot_cov=136/172
RA	328	.	NC_007779	2895131	0	A	C	bias_e_value=6.14356e-08	bias_p_value=1.32224e-14	fisher_strand_p_value=3.61705e-16	frequency=7.798243e-02	genotype_quality=638.5	ks_quality_p_value=1	log10_base_likelihood=-6.14788	log10_qual_likelihood_position_model=34.0901	log10_strand_likelihood_position_model=15.4416	new_cov=0/31	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=127/44	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/75
RA	329	.	NC_007779	2898837	0	G	T	bias_e_value=0.0287978	bias_p_value=6.19797e-09	fisher_strand_p_value=2.69055e-10	frequency=5.032492e-02	genotype_quality=1074.9	ks_quality_p_value=1	log10_base_likelihood=-13.0192	log10_qual_likelihood_position_model=22.7945	log10_strand_likelihood_position_model=9.57016	new_cov=0/26	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=175/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/144
RA	330	.	NC_007779	2898953	1	.	A	bias_e_value=3690390	bias_p_value=0.794258	fisher_strand_p_value=0.590171	frequency=1.098919e-02	genotype_quality=1314.0	ks_quality_p_value=0.731322	log10_base_likelihood=-12.4299	log10_qual_likelihood_position_model=1.7129	log10_strand_likelihood_position_model=0.474223	new_cov=2/1	polymorphism_quality=7.0	quality=7.0	quality_position_model=2.8272e-12	ref_cov=121/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/150
RA	331	.	NC_007779	2898954	0	A	.	bias_e_value=622722	bias_p_value=0.134024	fisher_strand_p_value=0.0488011	frequency=2.544594e-02	genotype_quality=1082.0	ks_quality_p_value=0.6079	log10_base_likelihood=-21.4079	log10_qual_likelihood_position_model=3.76642	log10_strand_likelihood_position_model=1.50231	new_cov=6/1	polymorphism_quality=16.1	quality=16.1	quality_position_model=2.87962e-18	ref_cov=118/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/151
RA	332	.	NC_007779	2905341	0	T	.	bias_e_value=451035	bias_p_value=0.0970734	fisher_strand_p_value=0.112505	frequency=1.030064e-02	genotype_quality=1155.2	ks_quality_p_value=0.175123	log10_base_likelihood=-7.92284	log10_qual_likelihood_position_model=2.21987	log10_strand_likelihood_position_model=0.948827	new_cov=3/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.25159e-06	ref_cov=138/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/150
RA	333	.	NC_007779	2926157	0	T	G	bias_e_value=5.04141e-10	bias_p_value=1.08503e-16	fisher_strand_p_value=2.61547e-18	frequency=7.091475e-02	genotype_quality=693.6	ks_quality_p_value=1	log10_base_likelihood=-9.76957	log10_qual_likelihood_position_model=29.2947	log10_strand_likelihood_position_model=17.5848	new_cov=26/1	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=23/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/155
RA	334	.	NC_007779	2953753	0	C	.	bias_e_value=4437440	bias_p_value=0.955041	fisher_strand_p_value=1	frequency=1.502895e-02	genotype_quality=1067.3	ks_quality_p_value=0.715531	log10_base_likelihood=-11.2865	log10_qual_likelihood_position_model=1.97406	log10_strand_likelihood_position_model=0.423477	new_cov=2/2	polymorphism_quality=5.9	quality=5.9	quality_position_model=6.83412e-11	ref_cov=135/127	reject=INDEL_HOMOPOLYMER	tot_cov=137/129
RA	335	.	NC_007779	2974959	1	.	A	bias_e_value=2846420	bias_p_value=0.612618	fisher_strand_p_value=0.336043	frequency=1.492500e-02	genotype_quality=1289.1	ks_quality_p_value=0.778977	log10_base_likelihood=-16.9322	log10_qual_likelihood_position_model=3.25271	log10_strand_likelihood_position_model=0.680295	new_cov=1/3	polymorphism_quality=11.6	quality=11.6	quality_position_model=4.41544e-15	ref_cov=144/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/123
RA	336	.	NC_007779	2987535	0	A	C	bias_e_value=4.91253e-07	bias_p_value=1.05729e-13	fisher_strand_p_value=3.07206e-15	frequency=1.195993e-01	genotype_quality=736.1	ks_quality_p_value=1	log10_base_likelihood=-17.978	log10_qual_likelihood_position_model=39.1554	log10_strand_likelihood_position_model=14.5126	new_cov=0/41	polymorphism_quality=12.7	quality=12.7	quality_position_model=Inf	ref_cov=131/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/125
RA	337	.	NC_007779	2994664	0	T	.	bias_e_value=584067	bias_p_value=0.125705	fisher_strand_p_value=1	frequency=1.148701e-02	genotype_quality=1054.2	ks_quality_p_value=0.0273281	log10_base_likelihood=-8.28579	log10_qual_likelihood_position_model=1.93248	log10_strand_likelihood_position_model=0.422634	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.52003e-08	ref_cov=129/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/130
RA	338	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=1112.6	new_cov=135/139	quality=1112.6	ref_cov=0/0	tot_cov=135/139
RA	339	.	NC_007779	3029385	0	C	A	bias_e_value=0.0540403	bias_p_value=1.16307e-08	fisher_strand_p_value=5.30139e-10	frequency=4.912806e-02	genotype_quality=822.3	ks_quality_p_value=0.980399	log10_base_likelihood=-15.5695	log10_qual_likelihood_position_model=16.793	log10_strand_likelihood_position_model=9.27561	new_cov=0/12	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=174/29	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=174/41
RA	340	.	NC_007779	3034413	0	A	C	bias_e_value=2.22125e-18	bias_p_value=4.78064e-25	fisher_strand_p_value=7.82266e-27	frequency=1.394963e-01	genotype_quality=696.1	ks_quality_p_value=1	log10_base_likelihood=-28.4263	log10_qual_likelihood_position_model=37.3603	log10_strand_likelihood_position_model=26.1066	new_cov=0/47	polymorphism_quality=23.2	quality=23.2	quality_position_model=Inf	ref_cov=153/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/84
RA	341	.	NC_007779	3035390	0	T	C	bias_e_value=6.77256e-06	bias_p_value=1.45761e-12	fisher_strand_p_value=4.59658e-14	frequency=1.470366e-01	genotype_quality=474.9	ks_quality_p_value=1	log10_base_likelihood=-29.3953	log10_qual_likelihood_position_model=21.5172	log10_strand_likelihood_position_model=13.346	new_cov=2/29	polymorphism_quality=24.2	quality=24.2	quality_position_model=Inf	ref_cov=126/37	reject=FISHER_STRAND_P_VALUE	tot_cov=129/66
RA	342	.	NC_007779	3044707	1	.	C	bias_e_value=500168	bias_p_value=0.107648	fisher_strand_p_value=0.0232359	frequency=1.030922e-02	genotype_quality=908.0	ks_quality_p_value=0.965805	log10_base_likelihood=-7.47568	log10_qual_likelihood_position_model=3.49418	log10_strand_likelihood_position_model=1.63384	new_cov=2/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=0.000438328	ref_cov=28/164	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=30/164
RA	343	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=1026.9	new_cov=119/140	quality=1026.9	ref_cov=0/0	tot_cov=119/140
RA	344	.	NC_007779	3074129	0	G	T	bias_e_value=117.176	bias_p_value=2.52191e-05	fisher_strand_p_value=1.77047e-06	frequency=4.739189e-02	genotype_quality=892.7	ks_quality_p_value=1	log10_base_likelihood=-6.51507	log10_qual_likelihood_position_model=19.1868	log10_strand_likelihood_position_model=6.04866	new_cov=1/26	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=127/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/157
RA	345	.	NC_007779	3136660	0	G	A	deleted=1	frequency=1	genotype_quality=4.0	new_cov=1/0	quality=4.0	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	346	.	NC_007779	3152854	1	.	A	bias_e_value=2254690	bias_p_value=0.485263	fisher_strand_p_value=1	frequency=1.111126e-02	genotype_quality=1314.8	ks_quality_p_value=0.178023	log10_base_likelihood=-12.7639	log10_qual_likelihood_position_model=2.50764	log10_strand_likelihood_position_model=0.381514	new_cov=2/1	polymorphism_quality=7.4	quality=7.4	quality_position_model=6.71456e-12	ref_cov=149/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/119
RA	347	.	NC_007779	3152855	0	A	.	bias_e_value=4388080	bias_p_value=0.944419	fisher_strand_p_value=0.70253	frequency=2.515793e-02	genotype_quality=1085.3	ks_quality_p_value=0.976021	log10_base_likelihood=-20.0396	log10_qual_likelihood_position_model=4.88467	log10_strand_likelihood_position_model=0.632767	new_cov=5/2	polymorphism_quality=14.8	quality=14.8	quality_position_model=1.25504e-16	ref_cov=153/118	reject=INDEL_HOMOPOLYMER	tot_cov=158/120
RA	348	.	NC_007779	3160153	0	G	C	bias_e_value=47.9856	bias_p_value=1.03276e-05	fisher_strand_p_value=6.79693e-07	frequency=3.742123e-02	genotype_quality=684.2	ks_quality_p_value=0.999501	log10_base_likelihood=-6.77718	log10_qual_likelihood_position_model=10.2172	log10_strand_likelihood_position_model=6.16769	new_cov=8/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=26/149	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/149
RA	349	.	NC_007779	3195962	0	G	T	bias_e_value=213.652	bias_p_value=4.59829e-05	fisher_strand_p_value=3.38182e-06	frequency=6.024694e-02	genotype_quality=675.2	ks_quality_p_value=1	log10_base_likelihood=-7.87736	log10_qual_likelihood_position_model=15.8587	log10_strand_likelihood_position_model=5.72901	new_cov=0/25	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=95/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/149
RA	350	.	NC_007779	3223274	0	G	T	bias_e_value=9.31509	bias_p_value=2.00483e-06	fisher_strand_p_value=1.18277e-07	frequency=7.177925e-02	genotype_quality=651.5	ks_quality_p_value=1	log10_base_likelihood=-12.6078	log10_qual_likelihood_position_model=12.9159	log10_strand_likelihood_position_model=6.9271	new_cov=0/21	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=110/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/108
RA	351	.	NC_007779	3231302	0	C	G	bias_e_value=24.4311	bias_p_value=5.25816e-06	fisher_strand_p_value=3.32141e-07	frequency=4.633617e-02	genotype_quality=774.1	ks_quality_p_value=0.994196	log10_base_likelihood=-7.5121	log10_qual_likelihood_position_model=18.8656	log10_strand_likelihood_position_model=6.47868	new_cov=0/15	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=136/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/87
RA	352	.	NC_007779	3231832	1	.	G	bias_e_value=248384	bias_p_value=0.0534581	fisher_strand_p_value=0.0136312	frequency=1.666641e-02	genotype_quality=1163.5	ks_quality_p_value=0.692551	log10_base_likelihood=-17.9826	log10_qual_likelihood_position_model=3.62566	log10_strand_likelihood_position_model=1.86547	new_cov=4/0	polymorphism_quality=12.7	quality=12.7	quality_position_model=1.44903e-14	ref_cov=79/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=83/157
RA	353	.	NC_007779	3238315	1	.	T	bias_e_value=3955970	bias_p_value=0.851417	fisher_strand_p_value=0.512272	frequency=1.117229e-02	genotype_quality=811.5	ks_quality_p_value=0.989826	log10_base_likelihood=-7.81453	log10_qual_likelihood_position_model=2.57899	log10_strand_likelihood_position_model=0.46505	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.20345e-06	ref_cov=103/74	reject=POLYMORPHISM_STRAND	tot_cov=105/74
RA	354	.	NC_007779	3238322	0	T	C	bias_e_value=15629.8	bias_p_value=0.0033639	fisher_strand_p_value=0.000378891	frequency=4.586029e-02	genotype_quality=508.7	ks_quality_p_value=1	log10_base_likelihood=-7.63861	log10_qual_likelihood_position_model=11.976	log10_strand_likelihood_position_model=3.42149	new_cov=10/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=68/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=78/88
RA	355	.	NC_007779	3247115	1	.	T	bias_e_value=4074600	bias_p_value=0.876951	fisher_strand_p_value=0.546904	frequency=7.242203e-03	genotype_quality=1355.5	ks_quality_p_value=1	log10_base_likelihood=-6.08455	log10_qual_likelihood_position_model=3.97715	log10_strand_likelihood_position_model=0.367291	new_cov=2/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.00202113	ref_cov=179/95	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=181/95
RA	356	.	NC_007779	3267102	0	A	.	bias_e_value=1582040	bias_p_value=0.340492	fisher_strand_p_value=0.107816	frequency=1.434612e-02	genotype_quality=855.9	ks_quality_p_value=0.969131	log10_base_likelihood=-8.52885	log10_qual_likelihood_position_model=1.52137	log10_strand_likelihood_position_model=0.967319	new_cov=0/3	polymorphism_quality=3.1	quality=3.1	quality_position_model=5.79438e-08	ref_cov=109/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/100
RA	357	.	NC_007779	3280326	0	A	C	bias_e_value=8.48002e-12	bias_p_value=1.8251e-18	fisher_strand_p_value=3.99661e-20	frequency=9.036064e-02	genotype_quality=787.3	ks_quality_p_value=1	log10_base_likelihood=-12.7144	log10_qual_likelihood_position_model=32.0487	log10_strand_likelihood_position_model=19.3983	new_cov=0/42	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=158/63	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/105
RA	358	.	NC_007779	3287872	1	.	G	bias_e_value=3655560	bias_p_value=0.786763	fisher_strand_p_value=0.497653	frequency=9.346008e-03	genotype_quality=1041.3	ks_quality_p_value=0.849572	log10_base_likelihood=-8.69578	log10_qual_likelihood_position_model=2.95982	log10_strand_likelihood_position_model=0.604104	new_cov=2/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=5.06248e-07	ref_cov=105/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/107
RA	359	.	NC_007779	3300073	0	T	G	bias_e_value=1.93724e-07	bias_p_value=4.1694e-14	fisher_strand_p_value=1.17865e-15	frequency=1.073637e-01	genotype_quality=619.6	ks_quality_p_value=1	log10_base_likelihood=-10.2665	log10_qual_likelihood_position_model=39.9609	log10_strand_likelihood_position_model=14.9286	new_cov=41/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=67/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/114
RA	360	.	NC_007779	3305552	0	A	C	bias_e_value=535.175	bias_p_value=0.000115182	fisher_strand_p_value=9.13932e-06	frequency=2.881908e-02	genotype_quality=970.8	ks_quality_p_value=1	log10_base_likelihood=-5.70878	log10_qual_likelihood_position_model=22.0294	log10_strand_likelihood_position_model=5.03909	new_cov=0/16	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=141/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/140
RA	361	.	NC_007779	3362866	1	.	A	bias_e_value=3906640	bias_p_value=0.840801	fisher_strand_p_value=0.498113	frequency=7.518768e-03	genotype_quality=1312.8	ks_quality_p_value=0.987266	log10_base_likelihood=-8.04168	log10_qual_likelihood_position_model=2.04467	log10_strand_likelihood_position_model=0.603702	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.70935e-07	ref_cov=133/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/133
RA	362	.	NC_007779	3385700	1	.	T	bias_e_value=3655540	bias_p_value=0.786758	fisher_strand_p_value=1	frequency=6.849289e-03	genotype_quality=1407.3	ks_quality_p_value=0.422786	log10_base_likelihood=-8.16028	log10_qual_likelihood_position_model=1.57363	log10_strand_likelihood_position_model=0.299866	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=3.22272e-08	ref_cov=141/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/150
RA	363	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1193.3	new_cov=137/142	quality=1193.3	ref_cov=0/0	tot_cov=137/142
RA	364	.	NC_007779	3412772	0	A	C	bias_e_value=4.21608e-06	bias_p_value=9.07399e-13	fisher_strand_p_value=2.81799e-14	frequency=4.878139e-02	genotype_quality=739.6	ks_quality_p_value=1	log10_base_likelihood=-7.50172	log10_qual_likelihood_position_model=23.9956	log10_strand_likelihood_position_model=13.5501	new_cov=0/21	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=159/36	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/57
RA	365	.	NC_007779	3431259	0	T	G	bias_e_value=286893	bias_p_value=0.0617461	fisher_strand_p_value=0.0112529	frequency=2.453613e-02	genotype_quality=839.2	ks_quality_p_value=1	log10_base_likelihood=-5.77608	log10_qual_likelihood_position_model=10.8406	log10_strand_likelihood_position_model=2.21855	new_cov=0/9	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=97/122	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=97/131
RA	366	.	NC_007779	3439587	0	A	C	bias_e_value=187557	bias_p_value=0.0403667	fisher_strand_p_value=0.00672828	frequency=3.126144e-02	genotype_quality=923.8	ks_quality_p_value=0.999625	log10_base_likelihood=-9.33038	log10_qual_likelihood_position_model=12.0905	log10_strand_likelihood_position_model=2.29207	new_cov=11/1	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=128/119	reject=POLYMORPHISM_STRAND	tot_cov=139/120
RA	367	.	NC_007779	3439592	0	G	.	bias_e_value=53444	bias_p_value=0.0115024	fisher_strand_p_value=0.00155556	frequency=3.535748e-02	genotype_quality=919.7	ks_quality_p_value=0.988947	log10_base_likelihood=-21.3537	log10_qual_likelihood_position_model=14.0882	log10_strand_likelihood_position_model=2.80811	new_cov=9/0	polymorphism_quality=16.1	quality=16.1	quality_position_model=2.55329e-06	ref_cov=113/124	reject=POLYMORPHISM_STRAND	tot_cov=130/124
RA	368	.	NC_007779	3439597	1	.	G	bias_e_value=2780030	bias_p_value=0.598328	fisher_strand_p_value=0.252024	frequency=1.332188e-02	genotype_quality=1068.6	ks_quality_p_value=0.997002	log10_base_likelihood=-7.90607	log10_qual_likelihood_position_model=3.85098	log10_strand_likelihood_position_model=0.802409	new_cov=3/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.72129e-05	ref_cov=119/103	reject=POLYMORPHISM_STRAND	tot_cov=122/103
RA	369	.	NC_007779	3439598	1	.	T	bias_e_value=614656	bias_p_value=0.132288	fisher_strand_p_value=0.0328586	frequency=2.678585e-02	genotype_quality=1032.3	ks_quality_p_value=0.887862	log10_base_likelihood=-24.9195	log10_qual_likelihood_position_model=8.27832	log10_strand_likelihood_position_model=1.60822	new_cov=6/0	polymorphism_quality=19.7	quality=19.7	quality_position_model=3.8068e-17	ref_cov=116/102	reject=POLYMORPHISM_STRAND	tot_cov=122/102
RA	370	.	NC_007779	3439601	0	G	T	bias_e_value=3849.43	bias_p_value=0.000828488	fisher_strand_p_value=7.9344e-05	frequency=6.347561e-02	genotype_quality=844.9	ks_quality_p_value=1	log10_base_likelihood=-19.6586	log10_qual_likelihood_position_model=16.9365	log10_strand_likelihood_position_model=4.36587	new_cov=16/0	polymorphism_quality=14.4	quality=14.4	quality_position_model=Inf	ref_cov=114/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/108
RA	371	.	NC_007779	3439605	0	T	C	bias_e_value=2009.67	bias_p_value=0.000432529	fisher_strand_p_value=3.8764e-05	frequency=5.734110e-02	genotype_quality=808.3	ks_quality_p_value=1	log10_base_likelihood=-16.1395	log10_qual_likelihood_position_model=15.9993	log10_strand_likelihood_position_model=4.62925	new_cov=17/0	polymorphism_quality=10.8	quality=10.8	quality_position_model=Inf	ref_cov=115/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/108
RA	372	.	NC_007779	3439607	0	G	T	bias_e_value=521.151	bias_p_value=0.000112164	fisher_strand_p_value=8.87952e-06	frequency=6.455421e-02	genotype_quality=896.9	ks_quality_p_value=1	log10_base_likelihood=-18.6742	log10_qual_likelihood_position_model=20.0825	log10_strand_likelihood_position_model=5.23798	new_cov=19/0	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=112/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/108
RA	373	.	NC_007779	3447067	1	.	C	bias_e_value=2547060	bias_p_value=0.548187	fisher_strand_p_value=0.226012	frequency=7.268906e-03	genotype_quality=1293.2	ks_quality_p_value=0.959089	log10_base_likelihood=-5.82492	log10_qual_likelihood_position_model=3.62181	log10_strand_likelihood_position_model=0.645869	new_cov=0/2	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.00322908	ref_cov=144/129	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/131
RA	374	.	NC_007779	3475527	0	T	G	bias_e_value=9.3896e-08	bias_p_value=2.02086e-14	fisher_strand_p_value=5.59494e-16	frequency=9.995699e-02	genotype_quality=738.8	ks_quality_p_value=1	log10_base_likelihood=-11.6888	log10_qual_likelihood_position_model=34.2087	log10_strand_likelihood_position_model=15.2522	new_cov=43/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=82/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/130
RA	375	.	NC_007779	3475533	0	C	T	bias_e_value=0.00953284	bias_p_value=2.05169e-09	fisher_strand_p_value=8.48137e-11	frequency=9.320593e-02	genotype_quality=826.8	ks_quality_p_value=1	log10_base_likelihood=-19.3906	log10_qual_likelihood_position_model=36.4454	log10_strand_likelihood_position_model=10.0715	new_cov=29/0	polymorphism_quality=14.1	quality=14.1	quality_position_model=Inf	ref_cov=103/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=132/144
RA	376	.	NC_007779	3499066	0	A	C	bias_e_value=0.0242944	bias_p_value=5.22872e-09	fisher_strand_p_value=2.25241e-10	frequency=6.212425e-02	genotype_quality=703.5	ks_quality_p_value=1	log10_base_likelihood=-8.98116	log10_qual_likelihood_position_model=20.7875	log10_strand_likelihood_position_model=9.64735	new_cov=0/17	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=142/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/61
RA	377	.	NC_007779	3519465	1	.	A	bias_e_value=2155250	bias_p_value=0.46386	fisher_strand_p_value=1	frequency=6.993294e-03	genotype_quality=1412.7	ks_quality_p_value=0.165868	log10_base_likelihood=-8.07688	log10_qual_likelihood_position_model=1.6859	log10_strand_likelihood_position_model=0.304314	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.18728e-08	ref_cov=157/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=158/128
RA	378	.	NC_007779	3523734	0	G	T	bias_e_value=18.9828	bias_p_value=4.08555e-06	fisher_strand_p_value=2.5231e-07	frequency=5.237341e-02	genotype_quality=930.5	ks_quality_p_value=1	log10_base_likelihood=-7.88411	log10_qual_likelihood_position_model=22.3884	log10_strand_likelihood_position_model=6.73818	new_cov=0/24	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=132/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/157
RA	379	.	NC_007779	3523811	1	.	T	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=6.492615e-03	genotype_quality=1524.5	ks_quality_p_value=0.99983	log10_base_likelihood=-7.38037	log10_qual_likelihood_position_model=2.5883	log10_strand_likelihood_position_model=0.300076	new_cov=1/1	polymorphism_quality=1.9	quality=1.9	quality_position_model=2.34949e-06	ref_cov=148/158	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/159
RA	380	.	NC_007779	3523812	0	T	.	bias_e_value=1948940	bias_p_value=0.419458	fisher_strand_p_value=0.623702	frequency=1.261044e-02	genotype_quality=1253.1	ks_quality_p_value=0.227906	log10_base_likelihood=-11.0008	log10_qual_likelihood_position_model=2.02759	log10_strand_likelihood_position_model=0.570022	new_cov=1/3	polymorphism_quality=5.6	quality=5.6	quality_position_model=2.14839e-10	ref_cov=151/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/165
RA	381	.	NC_007779	3543542	0	G	T	bias_e_value=2585.3	bias_p_value=0.000556417	fisher_strand_p_value=5.73059e-05	frequency=2.677059e-02	genotype_quality=853.6	ks_quality_p_value=0.892342	log10_base_likelihood=-5.77392	log10_qual_likelihood_position_model=13.221	log10_strand_likelihood_position_model=4.2418	new_cov=0/12	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=135/101	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=135/113
RA	382	.	NC_007779	3543547	0	A	C	bias_e_value=2.00445e-13	bias_p_value=4.31406e-20	fisher_strand_p_value=8.71674e-22	frequency=1.617432e-01	genotype_quality=743.3	ks_quality_p_value=1	log10_base_likelihood=-26.713	log10_qual_likelihood_position_model=56.3518	log10_strand_likelihood_position_model=21.1865	new_cov=0/64	polymorphism_quality=21.5	quality=21.5	quality_position_model=Inf	ref_cov=133/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/152
RA	383	.	NC_007779	3589932	1	.	A	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=5.648613e-03	genotype_quality=1772.3	ks_quality_p_value=1	log10_base_likelihood=-7.03211	log10_qual_likelihood_position_model=3.2906	log10_strand_likelihood_position_model=0.305958	new_cov=1/1	polymorphism_quality=1.5	quality=1.5	quality_position_model=3.0234e-05	ref_cov=197/155	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=198/156
RA	384	.	NC_007779	3627545	0	T	.	bias_e_value=2129570	bias_p_value=0.458333	fisher_strand_p_value=0.362529	frequency=1.350021e-02	genotype_quality=1144.9	ks_quality_p_value=0.449088	log10_base_likelihood=-10.5746	log10_qual_likelihood_position_model=3.12044	log10_strand_likelihood_position_model=0.620225	new_cov=3/1	polymorphism_quality=5.2	quality=5.2	quality_position_model=8.78986e-09	ref_cov=142/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/151
RA	385	.	NC_007779	3633797	1	.	T	bias_e_value=4556550	bias_p_value=0.980676	fisher_strand_p_value=1	frequency=9.049416e-03	genotype_quality=1088.4	ks_quality_p_value=0.809961	log10_base_likelihood=-8.2469	log10_qual_likelihood_position_model=2.00557	log10_strand_likelihood_position_model=0.328956	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.85511e-08	ref_cov=138/81	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/82
RA	386	.	NC_007779	3651641	0	G	C	bias_e_value=5862.89	bias_p_value=0.00126183	fisher_strand_p_value=0.000126821	frequency=3.773117e-02	genotype_quality=1130.6	ks_quality_p_value=0.997431	log10_base_likelihood=-15.1439	log10_qual_likelihood_position_model=14.7655	log10_strand_likelihood_position_model=3.89681	new_cov=11/0	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=117/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/155
RA	387	.	NC_007779	3653996	1	.	G	bias_e_value=3340560	bias_p_value=0.718968	fisher_strand_p_value=1	frequency=1.132107e-02	genotype_quality=1272.2	ks_quality_p_value=0.351461	log10_base_likelihood=-13.1863	log10_qual_likelihood_position_model=2.2869	log10_strand_likelihood_position_model=0.354457	new_cov=2/1	polymorphism_quality=7.8	quality=7.8	quality_position_model=1.39031e-12	ref_cov=164/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/99
RA	388	.	NC_007779	3671123	1	.	A	bias_e_value=4644220	bias_p_value=0.999545	fisher_strand_p_value=1	frequency=7.905006e-03	genotype_quality=1246.4	ks_quality_p_value=0.969973	log10_base_likelihood=-8.27862	log10_qual_likelihood_position_model=2.27818	log10_strand_likelihood_position_model=0.300458	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.30311e-07	ref_cov=119/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/133
RA	389	.	NC_007779	3671124	0	A	.	bias_e_value=2546120	bias_p_value=0.547984	fisher_strand_p_value=1	frequency=1.161671e-02	genotype_quality=1034.3	ks_quality_p_value=0.216633	log10_base_likelihood=-7.77662	log10_qual_likelihood_position_model=2.91508	log10_strand_likelihood_position_model=0.403794	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.55126e-06	ref_cov=121/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/136
RA	390	.	NC_007779	3677212	0	C	G	bias_e_value=11.0603	bias_p_value=2.38045e-06	fisher_strand_p_value=1.41966e-07	frequency=3.846455e-02	genotype_quality=593.9	ks_quality_p_value=1	log10_base_likelihood=-6.4282	log10_qual_likelihood_position_model=10.1188	log10_strand_likelihood_position_model=6.84781	new_cov=0/7	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=135/12	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/19
RA	391	.	NC_007779	3677217	0	T	G	bias_e_value=126.227	bias_p_value=2.7167e-05	fisher_strand_p_value=1.92042e-06	frequency=6.196117e-02	genotype_quality=446.4	ks_quality_p_value=0.998741	log10_base_likelihood=-9.02923	log10_qual_likelihood_position_model=12.4358	log10_strand_likelihood_position_model=5.7394	new_cov=4/11	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=127/20	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=131/31
RA	392	.	NC_007779	3686205	0	A	.	bias_e_value=2491180	bias_p_value=0.53616	fisher_strand_p_value=0.303899	frequency=1.618576e-02	genotype_quality=968.2	ks_quality_p_value=0.6877	log10_base_likelihood=-11.3165	log10_qual_likelihood_position_model=2.21779	log10_strand_likelihood_position_model=0.824673	new_cov=1/3	polymorphism_quality=5.9	quality=5.9	quality_position_model=2.91391e-10	ref_cov=148/95	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/98
RA	393	.	NC_007779	3688858	0	A	C	bias_e_value=1.6244e-08	bias_p_value=3.4961e-15	fisher_strand_p_value=9.21901e-17	frequency=1.151333e-01	genotype_quality=572.1	ks_quality_p_value=1	log10_base_likelihood=-10.9399	log10_qual_likelihood_position_model=30.3995	log10_strand_likelihood_position_model=16.0353	new_cov=0/39	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=110/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/90
RA	394	.	NC_007779	3689613	1	.	A	bias_e_value=3027620	bias_p_value=0.651614	fisher_strand_p_value=0.498618	frequency=7.143021e-03	genotype_quality=1381.4	ks_quality_p_value=0.585883	log10_base_likelihood=-7.85763	log10_qual_likelihood_position_model=1.7332	log10_strand_likelihood_position_model=0.579064	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.88438e-07	ref_cov=136/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/144
RA	395	.	NC_007779	3700228	0	A	G	bias_e_value=2097850	bias_p_value=0.451506	fisher_strand_p_value=0.248971	frequency=1.127625e-02	genotype_quality=1026.7	ks_quality_p_value=0.638911	log10_base_likelihood=-5.78382	log10_qual_likelihood_position_model=1.33168	log10_strand_likelihood_position_model=0.845191	new_cov=3/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=1.99319e-05	ref_cov=136/126	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=139/126
RA	396	.	NC_007779	3701118	0	G	T	bias_e_value=0.0691586	bias_p_value=1.48846e-08	fisher_strand_p_value=6.72919e-10	frequency=7.203197e-02	genotype_quality=828.2	ks_quality_p_value=1	log10_base_likelihood=-11.0454	log10_qual_likelihood_position_model=20.4424	log10_strand_likelihood_position_model=9.17204	new_cov=0/26	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=138/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/123
RA	397	.	NC_007779	3728146	1	.	T	bias_e_value=297414	bias_p_value=0.0640105	fisher_strand_p_value=0.0128332	frequency=1.886749e-02	genotype_quality=757.9	ks_quality_p_value=0.91638	log10_base_likelihood=-12.6278	log10_qual_likelihood_position_model=3.32925	log10_strand_likelihood_position_model=1.89167	new_cov=3/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=2.26199e-09	ref_cov=35/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=38/121
RA	398	.	NC_007779	3731041	1	.	T	bias_e_value=4103100	bias_p_value=0.883084	fisher_strand_p_value=1	frequency=7.326126e-03	genotype_quality=1333.0	ks_quality_p_value=0.557227	log10_base_likelihood=-8.20334	log10_qual_likelihood_position_model=1.23204	log10_strand_likelihood_position_model=0.299489	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.29132e-08	ref_cov=134/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/138
RA	399	.	NC_007779	3732310	0	G	T	bias_e_value=0.0106571	bias_p_value=2.29367e-09	fisher_strand_p_value=9.52746e-11	frequency=7.090425e-02	genotype_quality=844.3	ks_quality_p_value=1	log10_base_likelihood=-16.4509	log10_qual_likelihood_position_model=22.5039	log10_strand_likelihood_position_model=10.021	new_cov=0/30	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=139/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/136
RA	400	.	NC_007779	3734126	0	G	T	bias_e_value=2.08287	bias_p_value=4.48283e-07	fisher_strand_p_value=2.41823e-08	frequency=3.781033e-02	genotype_quality=1096.5	ks_quality_p_value=1	log10_base_likelihood=-5.7087	log10_qual_likelihood_position_model=25.2402	log10_strand_likelihood_position_model=7.7755	new_cov=0/25	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=163/143	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/168
RA	401	.	NC_007779	3734364	1	.	A	bias_e_value=4628710	bias_p_value=0.996207	fisher_strand_p_value=1	frequency=1.379299e-02	genotype_quality=1403.3	ks_quality_p_value=0.91418	log10_base_likelihood=-17.446	log10_qual_likelihood_position_model=2.59747	log10_strand_likelihood_position_model=0.423	new_cov=2/2	polymorphism_quality=12.1	quality=12.1	quality_position_model=1.57289e-16	ref_cov=142/144	reject=INDEL_HOMOPOLYMER	tot_cov=144/146
RA	402	.	NC_007779	3750122	0	C	.	bias_e_value=8812.42	bias_p_value=0.00189664	fisher_strand_p_value=0.0533298	frequency=9.461536e-01	genotype_quality=1157.7	ks_quality_p_value=0.00373528	log10_base_likelihood=-70.6917	log10_qual_likelihood_position_model=11.1798	log10_strand_likelihood_position_model=1.56162	new_cov=122/124	polymorphism_quality=65.7	quality=65.7	quality_position_model=2.36985e-60	ref_cov=3/11	tot_cov=125/135
RA	403	.	NC_007779	3750123	0	C	T	bias_e_value=890192	bias_p_value=0.19159	fisher_strand_p_value=0.0533298	frequency=5.369616e-02	genotype_quality=969.9	ks_quality_p_value=0.886727	log10_base_likelihood=-30.5495	log10_qual_likelihood_position_model=10.961	log10_strand_likelihood_position_model=1.56162	new_cov=3/11	polymorphism_quality=25.4	quality=25.4	quality_position_model=3.53325e-20	ref_cov=122/124	tot_cov=125/135
RA	404	.	NC_007779	3788380	0	G	T	bias_e_value=3.58779	bias_p_value=7.72176e-07	fisher_strand_p_value=4.29886e-08	frequency=5.535698e-02	genotype_quality=886.3	ks_quality_p_value=1	log10_base_likelihood=-9.70137	log10_qual_likelihood_position_model=19.6333	log10_strand_likelihood_position_model=7.67765	new_cov=0/28	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=126/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/158
RA	405	.	NC_007779	3813810	0	T	G	bias_e_value=9.69566e-08	bias_p_value=2.08673e-14	fisher_strand_p_value=5.78259e-16	frequency=9.643745e-02	genotype_quality=628.4	ks_quality_p_value=1	log10_base_likelihood=-10.0312	log10_qual_likelihood_position_model=26.0874	log10_strand_likelihood_position_model=15.242	new_cov=32/1	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=42/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/133
RA	406	.	NC_007779	3840146	1	.	A	bias_e_value=4198910	bias_p_value=0.903704	fisher_strand_p_value=1	frequency=8.546829e-03	genotype_quality=1148.0	ks_quality_p_value=0.594584	log10_base_likelihood=-8.47114	log10_qual_likelihood_position_model=0.987609	log10_strand_likelihood_position_model=0.299297	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.83195e-09	ref_cov=118/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/115
RA	407	.	NC_007779	3841755	1	.	A	bias_e_value=2387910	bias_p_value=0.513935	fisher_strand_p_value=0.498212	frequency=7.905006e-03	genotype_quality=1250.1	ks_quality_p_value=0.391594	log10_base_likelihood=-8.08035	log10_qual_likelihood_position_model=1.99161	log10_strand_likelihood_position_model=0.586721	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.08983e-07	ref_cov=127/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/124
RA	408	.	NC_007779	3841756	0	A	.	bias_e_value=3350230	bias_p_value=0.721048	fisher_strand_p_value=0.681397	frequency=1.944733e-02	genotype_quality=1041.5	ks_quality_p_value=0.518721	log10_base_likelihood=-14.8948	log10_qual_likelihood_position_model=1.86765	log10_strand_likelihood_position_model=0.50705	new_cov=2/3	polymorphism_quality=9.5	quality=9.5	quality_position_model=1.35507e-14	ref_cov=128/124	reject=INDEL_HOMOPOLYMER	tot_cov=130/127
RA	409	.	NC_007779	3845596	0	G	T	bias_e_value=9.52569	bias_p_value=2.05015e-06	fisher_strand_p_value=1.21121e-07	frequency=4.989576e-02	genotype_quality=923.8	ks_quality_p_value=1	log10_base_likelihood=-13.2172	log10_qual_likelihood_position_model=15.0428	log10_strand_likelihood_position_model=7.00263	new_cov=0/23	polymorphism_quality=7.8	quality=7.8	quality_position_model=Inf	ref_cov=143/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/152
RA	410	.	NC_007779	3846240	0	G	C	bias_e_value=1037.01	bias_p_value=0.000223188	fisher_strand_p_value=1.89279e-05	frequency=3.500938e-02	genotype_quality=650.6	ks_quality_p_value=0.992334	log10_base_likelihood=-5.63925	log10_qual_likelihood_position_model=9.30649	log10_strand_likelihood_position_model=4.7229	new_cov=0/9	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=136/53	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=136/62
RA	411	.	NC_007779	3859254	1	.	T	bias_e_value=578050	bias_p_value=0.12441	fisher_strand_p_value=0.0413215	frequency=1.587296e-02	genotype_quality=909.3	ks_quality_p_value=0.652663	log10_base_likelihood=-13.0067	log10_qual_likelihood_position_model=2.73724	log10_strand_likelihood_position_model=1.38382	new_cov=3/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=6.88797e-11	ref_cov=63/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=66/123
RA	412	.	NC_007779	3859270	0	G	C	bias_e_value=587.06	bias_p_value=0.000126349	fisher_strand_p_value=1.0106e-05	frequency=3.916073e-02	genotype_quality=632.0	ks_quality_p_value=1	log10_base_likelihood=-9.1447	log10_qual_likelihood_position_model=8.32065	log10_strand_likelihood_position_model=4.99542	new_cov=7/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=27/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=34/129
RA	413	.	NC_007779	3866109	0	G	T	bias_e_value=5.65661	bias_p_value=1.21744e-06	fisher_strand_p_value=6.98911e-08	frequency=5.700350e-02	genotype_quality=693.2	ks_quality_p_value=0.996523	log10_base_likelihood=-7.71361	log10_qual_likelihood_position_model=19.5847	log10_strand_likelihood_position_model=7.32047	new_cov=0/29	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=114/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/159
RA	414	.	NC_007779	3874863	0	G	T	frequency=1	genotype_quality=1.0	new_cov=0/1	quality=1.0	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	415	.	NC_007779	3891907	0	T	.	bias_e_value=2707230	bias_p_value=0.582659	fisher_strand_p_value=0.603148	frequency=1.078224e-02	genotype_quality=1100.1	ks_quality_p_value=0.398088	log10_base_likelihood=-7.9822	log10_qual_likelihood_position_model=2.05975	log10_strand_likelihood_position_model=0.45178	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.25224e-07	ref_cov=146/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/131
RA	416	.	NC_007779	3893880	0	G	T	bias_e_value=2.9415	bias_p_value=6.33079e-07	fisher_strand_p_value=3.48642e-08	frequency=6.938314e-02	genotype_quality=769.2	ks_quality_p_value=0.999222	log10_base_likelihood=-16.4033	log10_qual_likelihood_position_model=18.3566	log10_strand_likelihood_position_model=7.45762	new_cov=0/21	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=130/92	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/114
RA	417	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1109.7	new_cov=131/130	quality=1109.7	ref_cov=1/0	tot_cov=132/130
RA	418	.	NC_007779	3900676	1	.	G	bias_e_value=112352	bias_p_value=0.0241808	fisher_strand_p_value=0.00459785	frequency=2.214050e-02	genotype_quality=1302.9	ks_quality_p_value=0.795524	log10_base_likelihood=-27.656	log10_qual_likelihood_position_model=2.98255	log10_strand_likelihood_position_model=2.33745	new_cov=6/0	polymorphism_quality=22.4	quality=22.4	quality_position_model=1.56124e-24	ref_cov=106/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/159
RA	419	.	NC_007779	3900680	0	T	G	bias_e_value=8.16804e-11	bias_p_value=1.75795e-17	fisher_strand_p_value=4.05534e-19	frequency=6.380606e-02	genotype_quality=707.0	ks_quality_p_value=1	log10_base_likelihood=-9.77663	log10_qual_likelihood_position_model=24.4608	log10_strand_likelihood_position_model=18.392	new_cov=18/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=9/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/168
RA	420	.	NC_007779	3910746	0	C	A	bias_e_value=2.0549	bias_p_value=4.42264e-07	fisher_strand_p_value=2.38392e-08	frequency=5.742931e-02	genotype_quality=988.6	ks_quality_p_value=1	log10_base_likelihood=-10.4129	log10_qual_likelihood_position_model=24.409	log10_strand_likelihood_position_model=7.90829	new_cov=29/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=149/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/143
RA	421	.	NC_007779	3952095	1	.	G	bias_e_value=642288	bias_p_value=0.138235	fisher_strand_p_value=0.0546416	frequency=1.530647e-02	genotype_quality=953.5	ks_quality_p_value=0.564957	log10_base_likelihood=-13.105	log10_qual_likelihood_position_model=1.63341	log10_strand_likelihood_position_model=1.26248	new_cov=3/0	polymorphism_quality=7.7	quality=7.7	quality_position_model=3.05986e-12	ref_cov=72/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=75/121
RA	422	.	NC_007779	3962968	0	A	C	bias_e_value=0.000953729	bias_p_value=2.05265e-10	fisher_strand_p_value=7.72046e-12	frequency=4.584122e-02	genotype_quality=897.7	ks_quality_p_value=1	log10_base_likelihood=-7.40055	log10_qual_likelihood_position_model=20.5507	log10_strand_likelihood_position_model=11.1124	new_cov=0/30	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=163/106	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/137
RA	423	.	NC_007779	3976304	0	A	.	bias_e_value=198264	bias_p_value=0.0426711	fisher_strand_p_value=0.0603487	frequency=1.383209e-02	genotype_quality=1169.2	ks_quality_p_value=0.119134	log10_base_likelihood=-11.1381	log10_qual_likelihood_position_model=2.38765	log10_strand_likelihood_position_model=1.21933	new_cov=0/4	polymorphism_quality=5.7	quality=5.7	quality_position_model=1.68588e-09	ref_cov=145/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/144
RA	424	.	NC_007779	3989388	0	T	.	bias_e_value=3782320	bias_p_value=0.814044	fisher_strand_p_value=1	frequency=1.900291e-02	genotype_quality=1055.2	ks_quality_p_value=0.455954	log10_base_likelihood=-14.5104	log10_qual_likelihood_position_model=2.93354	log10_strand_likelihood_position_model=0.493841	new_cov=3/2	polymorphism_quality=9.2	quality=9.2	quality_position_model=3.93209e-13	ref_cov=131/127	reject=INDEL_HOMOPOLYMER	tot_cov=134/129
RA	425	.	NC_007779	4017854	0	G	C	frequency=1	genotype_quality=0.6	new_cov=1/0	quality=0.6	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	426	.	NC_007779	4029633	0	T	G	bias_e_value=8.70402e-07	bias_p_value=1.87331e-13	fisher_strand_p_value=5.53789e-15	frequency=8.121395e-02	genotype_quality=704.0	ks_quality_p_value=1	log10_base_likelihood=-12.2969	log10_qual_likelihood_position_model=27.8209	log10_strand_likelihood_position_model=14.2567	new_cov=23/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=35/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=58/147
RA	427	.	NC_007779	4031691	1	.	T	bias_e_value=102484	bias_p_value=0.0220569	fisher_strand_p_value=0.00552776	frequency=2.061844e-02	genotype_quality=927.0	ks_quality_p_value=0.593863	log10_base_likelihood=-17.6923	log10_qual_likelihood_position_model=3.17752	log10_strand_likelihood_position_model=2.25745	new_cov=4/0	polymorphism_quality=12.4	quality=12.4	quality_position_model=2.50721e-14	ref_cov=50/140	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=54/140
RA	428	.	NC_007779	4031696	0	C	T	bias_e_value=36.0608	bias_p_value=7.76113e-06	fisher_strand_p_value=5.00469e-07	frequency=3.413486e-02	genotype_quality=690.2	ks_quality_p_value=1	log10_base_likelihood=-7.11199	log10_qual_likelihood_position_model=9.19177	log10_strand_likelihood_position_model=6.30062	new_cov=8/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=26/156	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/156
RA	429	.	NC_007779	4036507	0	G	T	bias_e_value=1105.28	bias_p_value=0.000237883	fisher_strand_p_value=2.1165e-05	frequency=3.150940e-02	genotype_quality=976.1	ks_quality_p_value=0.951455	log10_base_likelihood=-9.67779	log10_qual_likelihood_position_model=17.228	log10_strand_likelihood_position_model=4.89891	new_cov=0/18	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=138/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/167
RA	430	.	NC_007779	4043703	0	C	A	bias_e_value=60.1466	bias_p_value=1.2945e-05	fisher_strand_p_value=8.65294e-07	frequency=4.557610e-02	genotype_quality=818.8	ks_quality_p_value=1	log10_base_likelihood=-7.71745	log10_qual_likelihood_position_model=13.1494	log10_strand_likelihood_position_model=6.08712	new_cov=21/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=123/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/127
RA	431	.	NC_007779	4052978	0	G	T	bias_e_value=2.71222	bias_p_value=5.83733e-07	fisher_strand_p_value=3.19706e-08	frequency=3.940105e-02	genotype_quality=974.2	ks_quality_p_value=1	log10_base_likelihood=-8.83621	log10_qual_likelihood_position_model=14.9353	log10_strand_likelihood_position_model=7.49525	new_cov=0/21	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=168/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/142
RA	432	.	NC_007779	4055100	0	G	T	bias_e_value=1.12832	bias_p_value=2.42841e-07	fisher_strand_p_value=1.26911e-08	frequency=5.535126e-02	genotype_quality=875.7	ks_quality_p_value=0.997385	log10_base_likelihood=-8.25406	log10_qual_likelihood_position_model=28.6145	log10_strand_likelihood_position_model=7.8965	new_cov=21/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=96/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/147
RA	433	.	NC_007779	4055172	0	A	G	bias_e_value=324095	bias_p_value=0.0697529	fisher_strand_p_value=1	frequency=9.595871e-03	genotype_quality=1219.7	ks_quality_p_value=0.0130683	log10_base_likelihood=-6.61714	log10_qual_likelihood_position_model=2.46218	log10_strand_likelihood_position_model=0.421799	new_cov=1/2	polymorphism_quality=1.1	quality=1.1	quality_position_model=1.46744e-05	ref_cov=154/155	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=155/157
RA	434	.	NC_007779	4055329	0	T	G	bias_e_value=1.74826e-16	bias_p_value=3.76266e-23	fisher_strand_p_value=6.63942e-25	frequency=1.275373e-01	genotype_quality=633.4	ks_quality_p_value=1	log10_base_likelihood=-17.5888	log10_qual_likelihood_position_model=33.3655	log10_strand_likelihood_position_model=24.1779	new_cov=35/0	polymorphism_quality=12.3	quality=12.3	quality_position_model=Inf	ref_cov=22/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=58/150
RA	435	.	NC_007779	4059484	1	.	T	bias_e_value=1447280	bias_p_value=0.311488	fisher_strand_p_value=0.498054	frequency=7.751465e-03	genotype_quality=1253.5	ks_quality_p_value=0.184702	log10_base_likelihood=-8.04027	log10_qual_likelihood_position_model=1.81809	log10_strand_likelihood_position_model=0.603753	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.58293e-07	ref_cov=127/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/129
RA	436	.	NC_007779	4059485	0	T	.	bias_e_value=2924300	bias_p_value=0.629378	fisher_strand_p_value=1	frequency=2.271938e-02	genotype_quality=1029.9	ks_quality_p_value=0.274502	log10_base_likelihood=-17.966	log10_qual_likelihood_position_model=3.00767	log10_strand_likelihood_position_model=0.50032	new_cov=3/3	polymorphism_quality=12.7	quality=12.7	quality_position_model=1.45797e-16	ref_cov=130/127	reject=INDEL_HOMOPOLYMER	tot_cov=134/130
RA	437	.	NC_007779	4062114	0	T	G	bias_e_value=3.61432e-14	bias_p_value=7.77886e-21	fisher_strand_p_value=1.51814e-22	frequency=8.289862e-02	genotype_quality=704.0	ks_quality_p_value=1	log10_base_likelihood=-8.06814	log10_qual_likelihood_position_model=34.4017	log10_strand_likelihood_position_model=21.8187	new_cov=37/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=35/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=72/152
RA	438	.	NC_007779	4064463	0	G	T	bias_e_value=0.590853	bias_p_value=1.27165e-07	fisher_strand_p_value=6.40089e-09	frequency=6.240940e-02	genotype_quality=829.5	ks_quality_p_value=1	log10_base_likelihood=-8.35694	log10_qual_likelihood_position_model=17.4983	log10_strand_likelihood_position_model=8.19376	new_cov=0/25	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=136/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/133
RA	439	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=999.9	new_cov=129/128	quality=999.9	ref_cov=0/0	tot_cov=129/128
RA	440	.	NC_007779	4098730	0	G	T	bias_e_value=88.1881	bias_p_value=1.89802e-05	fisher_strand_p_value=1.30451e-06	frequency=4.238701e-02	genotype_quality=687.6	ks_quality_p_value=1	log10_base_likelihood=-7.01984	log10_qual_likelihood_position_model=14.2279	log10_strand_likelihood_position_model=5.88455	new_cov=0/18	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=116/94	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/113
RA	441	.	NC_007779	4124974	0	G	T	bias_e_value=0.00331209	bias_p_value=7.1284e-10	fisher_strand_p_value=2.81841e-11	frequency=6.574488e-02	genotype_quality=946.6	ks_quality_p_value=1	log10_base_likelihood=-11.898	log10_qual_likelihood_position_model=19.9975	log10_strand_likelihood_position_model=10.55	new_cov=0/30	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=156/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/140
RA	442	.	NC_007779	4148399	0	A	C	bias_e_value=7.15308e-05	bias_p_value=1.53951e-11	fisher_strand_p_value=5.25903e-13	frequency=9.311295e-02	genotype_quality=673.2	ks_quality_p_value=1	log10_base_likelihood=-16.7415	log10_qual_likelihood_position_model=25.0997	log10_strand_likelihood_position_model=12.285	new_cov=1/29	polymorphism_quality=11.4	quality=11.4	quality_position_model=Inf	ref_cov=134/55	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/85
RA	443	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1148.1	new_cov=152/117	quality=1148.1	ref_cov=1/0	tot_cov=153/117
RA	444	.	NC_007779	4174730	0	T	.	bias_e_value=4296760	bias_p_value=0.924763	fisher_strand_p_value=1	frequency=1.199245e-02	genotype_quality=978.5	ks_quality_p_value=0.638077	log10_base_likelihood=-8.2615	log10_qual_likelihood_position_model=1.57386	log10_strand_likelihood_position_model=0.396055	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=3.18614e-08	ref_cov=115/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/134
RA	445	.	NC_007779	4176563	1	.	A	bias_e_value=3854450	bias_p_value=0.829568	fisher_strand_p_value=0.498566	frequency=6.872177e-03	genotype_quality=1437.6	ks_quality_p_value=0.955321	log10_base_likelihood=-7.87579	log10_qual_likelihood_position_model=1.83568	log10_strand_likelihood_position_model=0.582843	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.32552e-07	ref_cov=142/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=142/149
RA	446	.	NC_007779	4194164	0	T	G	bias_e_value=4824.27	bias_p_value=0.0010383	fisher_strand_p_value=0.000112858	frequency=2.411366e-02	genotype_quality=470.5	ks_quality_p_value=0.902693	log10_base_likelihood=-5.82887	log10_qual_likelihood_position_model=4.01441	log10_strand_likelihood_position_model=3.94747	new_cov=3/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=4/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=7/118
RA	447	.	NC_007779	4197139	0	T	G	bias_e_value=1.56203e-11	bias_p_value=3.36185e-18	fisher_strand_p_value=7.46388e-20	frequency=1.178942e-01	genotype_quality=586.8	ks_quality_p_value=1	log10_base_likelihood=-24.008	log10_qual_likelihood_position_model=26.4161	log10_strand_likelihood_position_model=19.127	new_cov=26/0	polymorphism_quality=18.8	quality=18.8	quality_position_model=Inf	ref_cov=18/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=44/135
RA	448	.	NC_007779	4212653	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	449	.	NC_007779	4212760	0	C	A	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	450	.	NC_007779	4212762	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	451	.	NC_007779	4213438	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	452	.	NC_007779	4213439	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	453	.	NC_007779	4213441	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	454	.	NC_007779	4213442	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	455	.	NC_007779	4213443	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	456	.	NC_007779	4213444	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	457	.	NC_007779	4213445	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	458	.	NC_007779	4213446	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	459	.	NC_007779	4213448	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	460	.	NC_007779	4213450	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	461	.	NC_007779	4213451	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	462	.	NC_007779	4213452	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	463	.	NC_007779	4213453	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	464	.	NC_007779	4213454	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	465	.	NC_007779	4213456	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	466	.	NC_007779	4213457	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	467	.	NC_007779	4213459	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	468	.	NC_007779	4213460	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	469	.	NC_007779	4213461	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	470	.	NC_007779	4213462	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	471	.	NC_007779	4213463	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	472	.	NC_007779	4213464	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	473	.	NC_007779	4213465	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	474	.	NC_007779	4213467	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	4213468	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	476	.	NC_007779	4213469	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	4213471	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	478	.	NC_007779	4213472	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	479	.	NC_007779	4213476	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	480	.	NC_007779	4213483	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	481	.	NC_007779	4213917	0	G	A	frequency=1	genotype_quality=1.3	new_cov=1/0	quality=1.3	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	482	.	NC_007779	4213940	0	G	A	frequency=1	genotype_quality=1.2	new_cov=1/0	quality=1.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	483	.	NC_007779	4214914	0	T	G	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	484	.	NC_007779	4218761	0	C	G	bias_e_value=289446	bias_p_value=0.0622956	fisher_strand_p_value=0.0113755	frequency=2.671623e-02	genotype_quality=979.8	ks_quality_p_value=1	log10_base_likelihood=-8.39546	log10_qual_likelihood_position_model=12.0972	log10_strand_likelihood_position_model=2.22806	new_cov=0/9	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=106/133	reject=POLYMORPHISM_STRAND	tot_cov=106/143
RA	485	.	NC_007779	4218769	0	T	G	bias_e_value=55903.8	bias_p_value=0.0120318	fisher_strand_p_value=0.00162043	frequency=2.515411e-02	genotype_quality=940.4	ks_quality_p_value=1	log10_base_likelihood=-5.8808	log10_qual_likelihood_position_model=13.5615	log10_strand_likelihood_position_model=2.90972	new_cov=0/12	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=108/138	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=108/150
RA	486	.	NC_007779	4218770	0	C	A	bias_e_value=500331	bias_p_value=0.107683	fisher_strand_p_value=0.0224506	frequency=2.119446e-02	genotype_quality=1007.9	ks_quality_p_value=1	log10_base_likelihood=-6.24189	log10_qual_likelihood_position_model=10.6954	log10_strand_likelihood_position_model=1.94289	new_cov=0/8	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=109/141	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=109/149
RA	487	.	NC_007779	4227183	0	T	G	bias_e_value=2.15785e-09	bias_p_value=4.6442e-16	fisher_strand_p_value=1.16121e-17	frequency=6.196594e-02	genotype_quality=963.8	ks_quality_p_value=1	log10_base_likelihood=-9.13191	log10_qual_likelihood_position_model=34.4751	log10_strand_likelihood_position_model=16.9351	new_cov=36/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=81/193	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/193
RA	488	.	NC_007779	4318994	0	A	G	bias_e_value=208.091	bias_p_value=4.47861e-05	fisher_strand_p_value=3.28692e-06	frequency=2.332783e-02	genotype_quality=633.2	ks_quality_p_value=1	log10_base_likelihood=-5.85434	log10_qual_likelihood_position_model=5.49459	log10_strand_likelihood_position_model=5.48321	new_cov=0/5	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=160/11	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=160/16
RA	489	.	NC_007779	4321435	0	G	C	bias_e_value=40.9739	bias_p_value=8.81855e-06	fisher_strand_p_value=5.80921e-07	frequency=4.690027e-02	genotype_quality=502.3	ks_quality_p_value=0.987583	log10_base_likelihood=-10.3621	log10_qual_likelihood_position_model=8.0322	log10_strand_likelihood_position_model=6.23588	new_cov=6/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=8/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=14/113
RA	490	.	NC_007779	4337469	0	A	C	bias_e_value=2.49241e-07	bias_p_value=5.36426e-14	fisher_strand_p_value=1.52762e-15	frequency=1.167741e-01	genotype_quality=602.6	ks_quality_p_value=1	log10_base_likelihood=-13.7966	log10_qual_likelihood_position_model=28.7811	log10_strand_likelihood_position_model=14.8205	new_cov=1/34	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=122/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=123/79
RA	491	.	NC_007779	4348529	0	T	G	bias_e_value=0.00805521	bias_p_value=1.73367e-09	fisher_strand_p_value=7.11505e-11	frequency=5.581999e-02	genotype_quality=635.3	ks_quality_p_value=1	log10_base_likelihood=-5.87531	log10_qual_likelihood_position_model=27.2661	log10_strand_likelihood_position_model=10.1478	new_cov=24/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=62/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/122
RA	492	.	NC_007779	4361106	1	.	A	bias_e_value=1595840	bias_p_value=0.343462	fisher_strand_p_value=0.222944	frequency=7.168770e-03	genotype_quality=1338.1	ks_quality_p_value=0.474586	log10_base_likelihood=-8.43917	log10_qual_likelihood_position_model=2.08076	log10_strand_likelihood_position_model=0.651804	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.28269e-07	ref_cov=130/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/147
RA	493	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=1121.9	new_cov=121/102	quality=1121.9	ref_cov=0/0	tot_cov=121/102
RA	494	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=1121.9	new_cov=121/102	quality=1121.9	ref_cov=0/0	tot_cov=121/102
RA	495	.	NC_007779	4393985	0	G	T	bias_e_value=596292	bias_p_value=0.128336	fisher_strand_p_value=0.0280818	frequency=1.844215e-02	genotype_quality=942.5	ks_quality_p_value=0.999285	log10_base_likelihood=-6.78604	log10_qual_likelihood_position_model=5.93072	log10_strand_likelihood_position_model=1.55157	new_cov=5/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=113/121	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=118/121
RA	496	.	NC_007779	4396933	1	.	A	bias_e_value=1068210	bias_p_value=0.229905	fisher_strand_p_value=0.189855	frequency=6.666183e-03	genotype_quality=1474.1	ks_quality_p_value=0.318092	log10_base_likelihood=-7.79508	log10_qual_likelihood_position_model=2.28627	log10_strand_likelihood_position_model=0.721578	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.15607e-06	ref_cov=129/169	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/169
RA	497	.	NC_007779	4414724	1	.	T	bias_e_value=2851960	bias_p_value=0.613808	fisher_strand_p_value=0.540037	frequency=8.130074e-03	genotype_quality=1214.8	ks_quality_p_value=0.486374	log10_base_likelihood=-7.90217	log10_qual_likelihood_position_model=2.25376	log10_strand_likelihood_position_model=0.358728	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.4707e-07	ref_cov=78/166	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=79/167
RA	498	.	NC_007779	4414725	0	T	.	bias_e_value=4623010	bias_p_value=0.99498	fisher_strand_p_value=1	frequency=1.991272e-02	genotype_quality=960.8	ks_quality_p_value=0.901486	log10_base_likelihood=-14.7825	log10_qual_likelihood_position_model=2.70958	log10_strand_likelihood_position_model=0.472032	new_cov=1/4	polymorphism_quality=9.4	quality=9.4	quality_position_model=1.16732e-13	ref_cov=80/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=81/170
RA	499	.	NC_007779	4419586	0	T	G	bias_e_value=76.9515	bias_p_value=1.65618e-05	fisher_strand_p_value=1.12696e-06	frequency=4.351425e-02	genotype_quality=820.3	ks_quality_p_value=1	log10_base_likelihood=-6.18495	log10_qual_likelihood_position_model=18.3905	log10_strand_likelihood_position_model=5.94809	new_cov=17/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=101/136	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/136
RA	500	.	NC_007779	4429120	0	G	T	bias_e_value=0.0895057	bias_p_value=1.92637e-08	fisher_strand_p_value=1.4085e-09	frequency=3.375626e-02	genotype_quality=968.0	ks_quality_p_value=0.625963	log10_base_likelihood=-8.11235	log10_qual_likelihood_position_model=27.2888	log10_strand_likelihood_position_model=8.85124	new_cov=0/23	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=175/111	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/134
RA	501	.	NC_007779	4479209	0	G	T	bias_e_value=597.661	bias_p_value=0.000128631	fisher_strand_p_value=1.03045e-05	frequency=1.960945e-02	genotype_quality=973.3	ks_quality_p_value=1	log10_base_likelihood=-5.99335	log10_qual_likelihood_position_model=13.8596	log10_strand_likelihood_position_model=4.98697	new_cov=0/15	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=154/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/142
RA	502	.	NC_007779	4493252	1	.	C	bias_e_value=3813590	bias_p_value=0.820775	fisher_strand_p_value=1	frequency=8.000374e-03	genotype_quality=1201.5	ks_quality_p_value=0.464629	log10_base_likelihood=-8.71385	log10_qual_likelihood_position_model=1.31847	log10_strand_likelihood_position_model=0.30839	new_cov=1/1	polymorphism_quality=3.2	quality=3.2	quality_position_model=4.82462e-09	ref_cov=142/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=143/107
RA	503	.	NC_007779	4510865	1	.	A	bias_e_value=4369920	bias_p_value=0.94051	fisher_strand_p_value=1	frequency=1.418400e-02	genotype_quality=1367.8	ks_quality_p_value=0.675525	log10_base_likelihood=-17.6736	log10_qual_likelihood_position_model=2.24587	log10_strand_likelihood_position_model=0.427284	new_cov=2/2	polymorphism_quality=12.4	quality=12.4	quality_position_model=4.10704e-17	ref_cov=129/149	reject=INDEL_HOMOPOLYMER	tot_cov=131/151
RA	504	.	NC_007779	4540870	0	T	G	bias_e_value=1.20845e-15	bias_p_value=2.60086e-22	fisher_strand_p_value=4.75452e-24	frequency=7.212067e-02	genotype_quality=819.6	ks_quality_p_value=1	log10_base_likelihood=-6.16254	log10_qual_likelihood_position_model=37.0142	log10_strand_likelihood_position_model=23.3229	new_cov=43/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=49/173	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=93/173
RA	505	.	NC_007779	4540877	0	A	T	bias_e_value=1.89469e-07	bias_p_value=4.07781e-14	fisher_strand_p_value=1.15201e-15	frequency=1.069226e-01	genotype_quality=796.7	ks_quality_p_value=1	log10_base_likelihood=-22.5031	log10_qual_likelihood_position_model=22.6281	log10_strand_likelihood_position_model=14.9385	new_cov=29/0	polymorphism_quality=17.2	quality=17.2	quality_position_model=Inf	ref_cov=56/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=85/160
RA	506	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=908.2	new_cov=127/95	quality=908.2	ref_cov=0/1	tot_cov=127/96
RA	507	.	NC_007779	4556225	0	C	A	bias_e_value=364.622	bias_p_value=7.84752e-05	fisher_strand_p_value=6.02768e-06	frequency=3.194427e-02	genotype_quality=895.7	ks_quality_p_value=1	log10_base_likelihood=-8.49606	log10_qual_likelihood_position_model=14.079	log10_strand_likelihood_position_model=5.21985	new_cov=16/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=114/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/137
RA	508	.	NC_007779	4561440	1	.	T	bias_e_value=4629440	bias_p_value=0.996364	fisher_strand_p_value=1	frequency=9.216309e-03	genotype_quality=1061.4	ks_quality_p_value=0.91595	log10_base_likelihood=-8.41251	log10_qual_likelihood_position_model=2.4061	log10_strand_likelihood_position_model=0.310472	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.31571e-07	ref_cov=125/90	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/91
RA	509	.	NC_007779	4573184	0	T	G	bias_e_value=2.22763e-06	bias_p_value=4.79438e-13	fisher_strand_p_value=1.45911e-14	frequency=5.409098e-02	genotype_quality=893.2	ks_quality_p_value=1	log10_base_likelihood=-6.05544	log10_qual_likelihood_position_model=33.532	log10_strand_likelihood_position_model=13.9039	new_cov=49/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=130/142	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/142
RA	510	.	NC_007779	4583431	0	T	.	bias_e_value=1126770	bias_p_value=0.242506	fisher_strand_p_value=1	frequency=1.249027e-02	genotype_quality=939.1	ks_quality_p_value=0.0649406	log10_base_likelihood=-8.02762	log10_qual_likelihood_position_model=3.4997	log10_strand_likelihood_position_model=0.397833	new_cov=1/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.61863e-06	ref_cov=111/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/128
RA	511	.	NC_007779	4584556	0	C	A	bias_e_value=226.557	bias_p_value=4.87604e-05	fisher_strand_p_value=3.63717e-06	frequency=4.788685e-02	genotype_quality=828.4	ks_quality_p_value=0.99057	log10_base_likelihood=-7.77654	log10_qual_likelihood_position_model=18.764	log10_strand_likelihood_position_model=5.46899	new_cov=19/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=121/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/123
RA	512	.	NC_007779	4599760	0	C	A	bias_e_value=0.449578	bias_p_value=9.67598e-08	fisher_strand_p_value=4.80091e-09	frequency=6.520033e-02	genotype_quality=929.3	ks_quality_p_value=1	log10_base_likelihood=-10.7363	log10_qual_likelihood_position_model=18.8414	log10_strand_likelihood_position_model=8.43349	new_cov=27/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=125/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/146
RA	513	.	NC_007779	4611002	1	.	G	bias_e_value=4312950	bias_p_value=0.928248	fisher_strand_p_value=1	frequency=8.333206e-03	genotype_quality=1171.4	ks_quality_p_value=0.645942	log10_base_likelihood=-8.42845	log10_qual_likelihood_position_model=2.46635	log10_strand_likelihood_position_model=0.299971	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.42622e-07	ref_cov=124/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=125/115
RA	514	.	NC_007779	4636470	0	C	G	bias_e_value=5.7165e-06	bias_p_value=1.23033e-12	fisher_strand_p_value=3.85853e-14	frequency=8.214521e-02	genotype_quality=703.4	ks_quality_p_value=1	log10_base_likelihood=-10.8956	log10_qual_likelihood_position_model=21.1421	log10_strand_likelihood_position_model=13.4136	new_cov=19/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=27/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=46/149
RA	515	.	NC_007779	4638468	0	A	.	bias_e_value=3281070	bias_p_value=0.706164	fisher_strand_p_value=0.357305	frequency=1.272869e-02	genotype_quality=1250.7	ks_quality_p_value=0.949931	log10_base_likelihood=-10.6443	log10_qual_likelihood_position_model=3.29614	log10_strand_likelihood_position_model=0.630902	new_cov=1/3	polymorphism_quality=5.2	quality=5.2	quality_position_model=1.15929e-08	ref_cov=161/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/152
RA	516	.	NC_007779	4642414	1	.	A	bias_e_value=1334830	bias_p_value=0.287288	fisher_strand_p_value=0.251012	frequency=1.229477e-02	genotype_quality=1176.0	ks_quality_p_value=0.327001	log10_base_likelihood=-12.8176	log10_qual_likelihood_position_model=1.92804	log10_strand_likelihood_position_model=0.815007	new_cov=0/3	polymorphism_quality=7.4	quality=7.4	quality_position_model=4.19792e-12	ref_cov=113/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/131
RA	517	.	NC_007779	4644244	1	.	T	bias_e_value=4150260	bias_p_value=0.893235	fisher_strand_p_value=0.588032	frequency=1.136303e-02	genotype_quality=1271.4	ks_quality_p_value=0.977955	log10_base_likelihood=-12.265	log10_qual_likelihood_position_model=2.23227	log10_strand_likelihood_position_model=0.478319	new_cov=1/2	polymorphism_quality=6.9	quality=6.9	quality_position_model=1.42633e-11	ref_cov=145/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/118
RA	518	.	NC_007779	4644245	0	T	.	bias_e_value=1987460	bias_p_value=0.427748	fisher_strand_p_value=0.178345	frequency=1.878548e-02	genotype_quality=1016.9	ks_quality_p_value=0.821036	log10_base_likelihood=-13.9395	log10_qual_likelihood_position_model=3.78951	log10_strand_likelihood_position_model=0.94987	new_cov=1/4	polymorphism_quality=8.6	quality=8.6	quality_position_model=3.28378e-11	ref_cov=145/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/120
MC	519	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=262	right_inside_cov=0	right_outside_cov=265
MC	520	.	NC_007779	654214	655412	1194	0	left_inside_cov=0	left_outside_cov=261	right_inside_cov=1	right_outside_cov=262
MC	521	.	NC_007779	1288311	1288511	89	52	left_inside_cov=196	left_outside_cov=200	right_inside_cov=196	right_outside_cov=198
MC	522	.	NC_007779	1301041	1302376	1326	0	left_inside_cov=1	left_outside_cov=277	right_inside_cov=0	right_outside_cov=278
MC	523	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=308	right_inside_cov=0	right_outside_cov=309
MC	524	.	NC_007779	2176983	2178208	0	0	left_inside_cov=0	left_outside_cov=315	right_inside_cov=0	right_outside_cov=268
MC	525	.	NC_007779	2320795	2322130	1327	0	left_inside_cov=0	left_outside_cov=305	right_inside_cov=0	right_outside_cov=306
MC	526	.	NC_007779	3128833	3147473	1164	0	left_inside_cov=196	left_outside_cov=199	right_inside_cov=0	right_outside_cov=469
MC	527	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=316	right_inside_cov=0	right_outside_cov=324
MC	528	.	NC_007779	3742934	3744269	0	0	left_inside_cov=0	left_outside_cov=322	right_inside_cov=1	right_outside_cov=322
MC	529	.	NC_007779	3746911	3748109	0	1197	left_inside_cov=0	left_outside_cov=313	right_inside_cov=0	right_outside_cov=316
MC	530	.	NC_007779	3750591	3751789	1195	0	left_inside_cov=0	left_outside_cov=356	right_inside_cov=0	right_outside_cov=351
MC	531	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=299	right_inside_cov=1	right_outside_cov=298
MC	532	.	NC_007779	4310363	4311561	0	1197	left_inside_cov=0	left_outside_cov=305	right_inside_cov=1	right_outside_cov=305
JC	533	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=135	coverage_plus=151	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=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=48	max_min_right=50	max_min_right_minus=48	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=1.000000e+00	new_junction_read_count=286	pos_hash_score=146	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=286
JC	534	.	NC_007779	273179	1	NC_007779	657843	1	0	alignment_overlap=0	coverage_minus=64	coverage_plus=53	flanking_left=101	flanking_right=101	frequency=4.680000e-01	junction_possible_overlap_registers=90	key=NC_007779__273179__1__NC_007779__657843__1__0____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=88	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=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.45	new_junction_frequency=4.680000e-01	new_junction_read_count=117	pos_hash_score=78	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=0.52	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=133	side_2_redundant=0	total_non_overlap_reads=117
JC	535	.	NC_007779	274373	-1	NC_007779	663499	1	0	alignment_overlap=0	coverage_minus=159	coverage_plus=166	flanking_left=101	flanking_right=101	frequency=5.504132e-01	junction_possible_overlap_registers=90	key=NC_007779__274373__-1__NC_007779__663499__1__0____101__101__1__0	max_left=94	max_left_minus=92	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=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=1.29	new_junction_frequency=5.504132e-01	new_junction_read_count=333	pos_hash_score=151	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=1.05	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=272	side_2_redundant=0	total_non_overlap_reads=325
JC	536	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=10	coverage_minus=90	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__371963__1__10____101__101__0__0	max_left=85	max_left_minus=85	max_left_plus=85	max_min_left=45	max_min_left_minus=45	max_min_left_plus=44	max_min_right=45	max_min_right_minus=45	max_min_right_plus=44	max_pos_hash_score=160	max_right=85	max_right_minus=85	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=1.000000e+00	new_junction_read_count=198	pos_hash_score=106	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=10	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=80	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=198
JC	537	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=106	coverage_plus=111	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=57	key=NC_007779__289856__1__NC_007779__2176982__-1__-33__CTATTGCAATACCGCATTGTGAGGCGATTCATG__101__101__1__0	max_left=62	max_left_minus=62	max_left_plus=62	max_min_left=33	max_min_left_minus=33	max_min_left_plus=33	max_min_right=34	max_min_right_minus=34	max_min_right_plus=34	max_pos_hash_score=114	max_right=62	max_right_minus=62	max_right_plus=62	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.33	new_junction_frequency=1.000000e+00	new_junction_read_count=218	pos_hash_score=96	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=217	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	538	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=159	coverage_plus=99	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=89	max_left_plus=90	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=NA	new_junction_read_count=260	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=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	539	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=79	coverage_plus=133	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=86	max_left_plus=93	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=48	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=0.85	new_junction_frequency=NA	new_junction_read_count=214	pos_hash_score=119	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=212
JC	540	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=92	coverage_plus=122	flanking_left=101	flanking_right=101	frequency=9.737319e-01	junction_possible_overlap_registers=87	key=NC_007779__608573__-1__NC_007779__1305025__1__3____101__101__1__0	max_left=92	max_left_minus=92	max_left_plus=92	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=49	max_min_right_minus=47	max_min_right_plus=49	max_pos_hash_score=174	max_right=92	max_right_minus=91	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=9.737319e-01	new_junction_read_count=215	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=0.02	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=6	side_2_redundant=0	total_non_overlap_reads=214
JC	541	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=112	coverage_plus=112	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=86	max_left_plus=90	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=48	max_min_right_minus=48	max_min_right_plus=47	max_pos_hash_score=170	max_right=90	max_right_minus=89	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=224	pos_hash_score=117	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=224
JC	542	.	NC_007779	654213	1	NC_007779	657846	-1	0	alignment_overlap=0	coverage_minus=58	coverage_plus=36	flanking_left=101	flanking_right=101	frequency=4.120172e-01	junction_possible_overlap_registers=90	key=NC_007779__654213__1__NC_007779__657846__-1__0____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=88	max_min_left=49	max_min_left_minus=49	max_min_left_plus=46	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.37	new_junction_frequency=4.120172e-01	new_junction_read_count=96	pos_hash_score=70	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=0.53	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=137	side_2_redundant=0	total_non_overlap_reads=94
JC	543	.	NC_007779	678974	1	NC_007779	689467	-1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=9.652510e-03	junction_possible_overlap_registers=90	key=NC_007779__678974__1__NC_007779__689467__-1__0____101__101__0__1	max_left=72	max_left_minus=72	max_left_plus=61	max_min_left=40	max_min_left_minus=40	max_min_left_plus=18	max_min_right=47	max_min_right_minus=47	max_min_right_plus=40	max_pos_hash_score=180	max_right=83	max_right_minus=61	max_right_plus=83	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=9.652510e-03	new_junction_read_count=5	pos_hash_score=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.99	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=513	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=5
JC	544	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=48	coverage_plus=62	flanking_left=101	flanking_right=101	frequency=5.130554e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=79	max_left_minus=79	max_left_plus=79	max_min_left=40	max_min_left_minus=40	max_min_left_plus=40	max_min_right=42	max_min_right_minus=41	max_min_right_plus=42	max_pos_hash_score=148	max_right=79	max_right_minus=79	max_right_plus=79	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.53	new_junction_frequency=5.130554e-01	new_junction_read_count=112	pos_hash_score=75	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.49	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=126	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.51	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=109	side_2_redundant=0	total_non_overlap_reads=110
JC	545	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=47	coverage_plus=40	flanking_left=101	flanking_right=101	frequency=4.520002e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=79	max_left_minus=79	max_left_plus=69	max_min_left=42	max_min_left_minus=41	max_min_left_plus=42	max_min_right=42	max_min_right_minus=42	max_min_right_plus=42	max_pos_hash_score=148	max_right=79	max_right_minus=79	max_right_plus=79	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.41	new_junction_frequency=4.520002e-01	new_junction_read_count=87	pos_hash_score=69	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.48	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=124	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.51	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=109	side_2_redundant=0	total_non_overlap_reads=87
JC	546	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=96	coverage_plus=111	flanking_left=101	flanking_right=101	frequency=9.814561e-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=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=87	max_right_minus=86	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=9.814561e-01	new_junction_read_count=207	pos_hash_score=117	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=4	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=207
JC	547	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=131	coverage_plus=119	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1221495__-1__NC_007779__1302369__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=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=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=254	pos_hash_score=137	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=250
JC	548	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=107	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=9.980333e-01	junction_possible_overlap_registers=83	key=NC_007779__1301040__-1__NC_007779__1302370__1__7____101__101__0__0	max_left=88	max_left_minus=87	max_left_plus=88	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=46	max_min_right_minus=44	max_min_right_plus=46	max_pos_hash_score=166	max_right=88	max_right_minus=88	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=9.980333e-01	new_junction_read_count=234	pos_hash_score=122	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=1	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=83	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=231
JC	549	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=121	coverage_plus=150	flanking_left=101	flanking_right=101	frequency=9.504608e-01	junction_possible_overlap_registers=86	key=NC_007779__1305037__-1__NC_007779__2519719__1__4____101__101__0__1	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=47	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.11	new_junction_frequency=9.504608e-01	new_junction_read_count=275	pos_hash_score=138	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.06	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=15	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=271
JC	550	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=114	coverage_plus=123	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=92	max_left_minus=92	max_left_plus=85	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=1.000000e+00	new_junction_read_count=241	pos_hash_score=125	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=237
JC	551	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=80	coverage_plus=105	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=64	key=NC_007779__1413638__-1__NC_007779__1436673__1__26____101__101__0__0	max_left=69	max_left_minus=69	max_left_plus=69	max_min_left=37	max_min_left_minus=37	max_min_left_plus=35	max_min_right=36	max_min_right_minus=36	max_min_right_plus=34	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=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=187	pos_hash_score=91	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=185
JC	552	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=102	coverage_plus=138	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=94	max_left_minus=94	max_left_plus=94	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=88	max_right_minus=88	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=1.000000e+00	new_junction_read_count=240	pos_hash_score=127	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=240
JC	553	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=153	coverage_plus=126	flanking_left=101	flanking_right=101	frequency=9.587629e-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=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=9.587629e-01	new_junction_read_count=279	pos_hash_score=140	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.05	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=12	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=279
JC	554	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=98	coverage_plus=127	flanking_left=101	flanking_right=101	frequency=9.336100e-01	junction_possible_overlap_registers=90	key=NC_007779__1907288__-1__NC_007779__2411458__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=48	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.87	new_junction_frequency=9.336100e-01	new_junction_read_count=225	pos_hash_score=121	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.06	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=16	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=225
JC	555	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=125	coverage_plus=42	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=47	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=40	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=0.65	new_junction_frequency=1.000000e+00	new_junction_read_count=167	pos_hash_score=87	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=167
JC	556	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=129	coverage_plus=113	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=91	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	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=0.95	new_junction_frequency=1.000000e+00	new_junction_read_count=242	pos_hash_score=127	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=242
JC	557	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=120	coverage_plus=134	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=89	max_right_minus=89	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.99	new_junction_frequency=1.000000e+00	new_junction_read_count=255	pos_hash_score=122	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=254
JC	558	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=116	coverage_plus=139	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=84	key=NC_007779__2320794__-1__NC_007779__2322125__1__6____101__101__0__0	max_left=89	max_left_minus=89	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.06	new_junction_frequency=1.000000e+00	new_junction_read_count=255	pos_hash_score=137	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=255
JC	559	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=70	coverage_plus=169	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=84	max_left_minus=84	max_left_plus=84	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=92	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.93	new_junction_frequency=1.000000e+00	new_junction_read_count=239	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=239
JC	560	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=124	coverage_plus=183	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2322124__-1__NC_007779__2589830__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.19	new_junction_frequency=1.000000e+00	new_junction_read_count=308	pos_hash_score=142	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=307
JC	561	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=127	flanking_left=101	flanking_right=101	frequency=9.581749e-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=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=9.581749e-01	new_junction_read_count=252	pos_hash_score=136	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.04	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=249
JC	562	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=101	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=9.194915e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=88	max_left_minus=88	max_left_plus=87	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.84	new_junction_frequency=9.194915e-01	new_junction_read_count=217	pos_hash_score=117	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.07	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=19	side_2_redundant=0	total_non_overlap_reads=214
JC	563	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=76	coverage_plus=91	flanking_left=101	flanking_right=101	frequency=4.831288e-01	junction_possible_overlap_registers=86	key=NC_007779__2865229__1__NC_007779__2865278__-1__4____101__101__0__0	max_left=91	max_left_minus=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=47	max_min_right_minus=45	max_min_right_plus=47	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.68	new_junction_frequency=4.831288e-01	new_junction_read_count=168	pos_hash_score=113	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.74	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=192	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.71	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=176	side_2_redundant=0	total_non_overlap_reads=167
JC	564	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=140	coverage_plus=163	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3147474__1__NC_007779__3262328__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.18	new_junction_frequency=1.000000e+00	new_junction_read_count=304	pos_hash_score=147	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=303
JC	565	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=133	coverage_plus=109	flanking_left=101	flanking_right=101	frequency=9.840473e-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=93	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=9.840473e-01	new_junction_read_count=244	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=0.02	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=4	side_2_redundant=0	total_non_overlap_reads=242
JC	566	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=162	coverage_plus=114	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=46	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=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=280	pos_hash_score=138	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=276	unique_read_sequence=CTTTGC
JC	567	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=113	coverage_plus=107	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=87	max_left_minus=85	max_left_plus=87	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=93	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=1.000000e+00	new_junction_read_count=223	pos_hash_score=117	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=220
JC	568	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=146	coverage_plus=120	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3261134__1__NC_007779__3262338__1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=267	pos_hash_score=134	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=266
JC	569	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=156	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=9.963504e-01	junction_possible_overlap_registers=90	key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.06	new_junction_frequency=9.963504e-01	new_junction_read_count=273	pos_hash_score=132	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=271
JC	570	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=97	coverage_plus=144	flanking_left=101	flanking_right=101	frequency=9.879387e-01	junction_possible_overlap_registers=89	key=NC_007779__3512759__-1__NC_007779__3744263__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=90	max_right_minus=90	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=9.879387e-01	new_junction_read_count=243	pos_hash_score=119	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=241
JC	571	.	NC_007779	3742933	-1	NC_007779	3744270	1	0	alignment_overlap=6	coverage_minus=131	coverage_plus=110	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=84	key=NC_007779__3742933__-1__NC_007779__3744264__1__6____101__101__0__0	max_left=89	max_left_minus=89	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=46	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=164	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=242	pos_hash_score=122	side_1_annotate_key=gene	side_1_continuation=2	side_1_coverage=0.00	side_1_overlap=6	side_1_possible_overlap_registers=88	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=241
JC	572	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=155	coverage_plus=103	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3744263__-1__NC_007779__3903274__1__0____101__101__1__0	max_left=90	max_left_minus=88	max_left_plus=90	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=260	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=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=258
JC	573	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=126	coverage_plus=139	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3746910__-1__NC_007779__3748106__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=90	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=267	pos_hash_score=127	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=265
JC	574	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=117	coverage_plus=117	flanking_left=101	flanking_right=101	frequency=9.961240e-01	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=1.00	new_junction_frequency=9.961240e-01	new_junction_read_count=257	pos_hash_score=127	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=1	side_2_redundant=0	total_non_overlap_reads=234
JC	575	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=141	coverage_plus=136	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=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=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=280	pos_hash_score=146	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=277
JC	576	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=144	coverage_plus=170	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3750590__-1__NC_007779__3751786__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.28	new_junction_frequency=1.000000e+00	new_junction_read_count=315	pos_hash_score=150	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=314
JC	577	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=135	coverage_plus=123	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=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	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	578	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=136	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=88	key=NC_007779__3958122__-1__NC_007779__3958155__1__2____101__101__0__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=48	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=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=253	pos_hash_score=132	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=251
JC	579	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=128	coverage_plus=143	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.07	new_junction_frequency=1.000000e+00	new_junction_read_count=272	pos_hash_score=137	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=271
JC	580	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=147	coverage_plus=145	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3988379__-1__NC_007779__4009199__1__0____101__101__1__0	max_left=95	max_left_minus=93	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=295	pos_hash_score=139	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=292
JC	581	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=134	coverage_plus=123	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=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=90	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=260	pos_hash_score=132	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=257
JC	582	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=125	coverage_plus=120	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4310363__1__NC_007779__4353540__1__0____101__101__1__0	max_left=94	max_left_minus=93	max_left_plus=94	max_min_left=50	max_min_left_minus=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=0.97	new_junction_frequency=1.000000e+00	new_junction_read_count=250	pos_hash_score=132	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=245
JC	583	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=114	coverage_plus=152	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4311557__-1__NC_007779__4353543__-1__0____101__101__1__0	max_left=93	max_left_minus=92	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.09	new_junction_frequency=1.000000e+00	new_junction_read_count=282	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=266
JC	584	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=120	coverage_plus=160	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4355060__1__NC_007779__4502861__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.08	new_junction_frequency=1.000000e+00	new_junction_read_count=280	pos_hash_score=139	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=280
JC	585	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=104	coverage_plus=123	flanking_left=101	flanking_right=101	frequency=9.830623e-01	junction_possible_overlap_registers=88	key=NC_007779__4355066__-1__NC_007779__4504191__-1__2____101__101__0__1	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=9.830623e-01	new_junction_read_count=227	pos_hash_score=118	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=4	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=227
JC	586	.	NC_007779	4547362	1	NC_007779	4547676	1	0	alignment_overlap=9	coverage_minus=15	coverage_plus=8	flanking_left=101	flanking_right=101	frequency=9.952402e-02	junction_possible_overlap_registers=81	key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0	max_left=78	max_left_minus=72	max_left_plus=78	max_min_left=43	max_min_left_minus=43	max_min_left_plus=39	max_min_right=44	max_min_right_minus=44	max_min_right_plus=43	max_pos_hash_score=162	max_right=85	max_right_minus=85	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.10	new_junction_frequency=9.952402e-02	new_junction_read_count=23	pos_hash_score=23	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.84	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=218	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.95	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=220	side_2_redundant=0	total_non_overlap_reads=23
JC	587	.	NC_007779	4547370	-1	NC_007779	4547666	-1	0	alignment_overlap=9	coverage_minus=14	coverage_plus=4	flanking_left=101	flanking_right=101	frequency=7.945266e-02	junction_possible_overlap_registers=81	key=NC_007779__4547370__-1__NC_007779__4547675__-1__9____101__101__0__0	max_left=77	max_left_minus=77	max_left_plus=63	max_min_left=39	max_min_left_minus=39	max_min_left_plus=39	max_min_right=41	max_min_right_minus=41	max_min_right_plus=29	max_pos_hash_score=162	max_right=85	max_right_minus=84	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.08	new_junction_frequency=7.945266e-02	new_junction_read_count=18	pos_hash_score=17	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.85	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=219	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.95	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=220	side_2_redundant=0	total_non_overlap_reads=18
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UN	716	.	NC_007779	4502953	4504094
UN	717	.	NC_007779	4512231	4513265