#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	12:05:05 04 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	4_D2_ACAGTG_L001_R1_001.fastq
SNP	1	60	NC_007779	66457	A	frequency=1
SNP	2	64	NC_007779	97880	T	frequency=1
SNP	3	72	NC_007779	167632	A	frequency=1
SNP	4	85	NC_007779	274547	G	frequency=1
DEL	5	480,495	NC_007779	274733	97240	frequency=1
SNP	6	100	NC_007779	547694	G	frequency=1
INS	7	101	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	103	NC_007779	556858	T	frequency=1
SNP	9	104	NC_007779	569996	C	frequency=1
DEL	10	481,500	NC_007779	654214	1199	frequency=1
SNP	11	119	NC_007779	749354	A	frequency=1
SNP	12	121	NC_007779	758440	A	frequency=1
SNP	13	127	NC_007779	887234	A	frequency=1
SNP	14	136	NC_007779	987574	T	frequency=1
SNP	15	149	NC_007779	1093686	C	frequency=1
SNP	16	151	NC_007779	1097580	T	frequency=2.237210e-01
SNP	17	160	NC_007779	1170573	T	frequency=1
DEL	18	483,505	NC_007779	1301041	1336	frequency=1
SNP	19	170	NC_007779	1318876	A	frequency=1
DEL	20	484,508	NC_007779	1413639	23060	frequency=1
SNP	21	186	NC_007779	1483588	A	frequency=1
DEL	22	188	NC_007779	1496775	1	frequency=1
SNP	23	202	NC_007779	1615814	A	frequency=1
DEL	24	209	NC_007779	1669599	1	frequency=1
SNP	25	227	NC_007779	1844073	A	frequency=1
SNP	26	235	NC_007779	1918872	A	frequency=1
SNP	27	236	NC_007779	1973476	A	frequency=1
SNP	28	240	NC_007779	2005401	T	frequency=1
SNP	29	250	NC_007779	2170094	A	frequency=1
DEL	30	486,515	NC_007779	2320795	1336	frequency=1
SNP	31	274	NC_007779	2406075	T	frequency=1
SNP	32	277	NC_007779	2416102	A	frequency=1
SNP	33	288	NC_007779	2538628	T	frequency=1
INS	34	520	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=6.679156e-01
SNP	35	314	NC_007779	2866111	G	frequency=1
SNP	36	326	NC_007779	3003330	A	frequency=1
SNP	37	330	NC_007779	3049815	T	frequency=1
SNP	38	354	NC_007779	3397813	G	frequency=1
DEL	39	489,528	NC_007779	3742936	1336	frequency=1
DEL	40	490,530	NC_007779	3746911	1199	frequency=1
DEL	41	395	NC_007779	3750122	1	frequency=9.581585e-01
SNP	42	396	NC_007779	3750123	T	frequency=3.771400e-02
DEL	43	491,533	NC_007779	3750591	1199	frequency=1
SNP	44	413	NC_007779	3898657	G	frequency=1
DEL	45	492,535	NC_007779	3958123	34	frequency=1
SNP	46	433	NC_007779	4090749	T	frequency=1
SNP	47	442	NC_007779	4165991	C	frequency=1
DEL	48	493,538	NC_007779	4310363	1199	frequency=1
DEL	49	458,459	NC_007779	4371271	2	frequency=1
SNP	50	468	NC_007779	4546535	A	frequency=1
RA	51	.	NC_007779	301	1	.	T	bias_e_value=4415380	bias_p_value=0.950294	fisher_strand_p_value=1	frequency=9.708405e-03	genotype_quality=976.7	ks_quality_p_value=0.70175	log10_base_likelihood=-8.30232	log10_qual_likelihood_position_model=1.21738	log10_strand_likelihood_position_model=0.300927	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=9.89495e-09	ref_cov=95/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=96/110
RA	52	.	NC_007779	5595	0	G	T	bias_e_value=0.323212	bias_p_value=6.95628e-08	fisher_strand_p_value=3.39305e-09	frequency=8.951330e-02	genotype_quality=708.9	ks_quality_p_value=1	log10_base_likelihood=-14.1382	log10_qual_likelihood_position_model=18.4574	log10_strand_likelihood_position_model=8.48158	new_cov=0/28	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=110/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/123
RA	53	.	NC_007779	11143	0	G	T	bias_e_value=2.39361	bias_p_value=5.1516e-07	fisher_strand_p_value=2.80121e-08	frequency=5.053902e-02	genotype_quality=800.7	ks_quality_p_value=1	log10_base_likelihood=-6.21992	log10_qual_likelihood_position_model=18.2569	log10_strand_likelihood_position_model=7.55265	new_cov=0/20	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=132/85	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/105
RA	54	.	NC_007779	25989	0	T	C	bias_e_value=4306480	bias_p_value=0.926856	fisher_strand_p_value=1	frequency=1.240635e-02	genotype_quality=933.6	ks_quality_p_value=0.642775	log10_base_likelihood=-6.02367	log10_qual_likelihood_position_model=2.12453	log10_strand_likelihood_position_model=0.422357	new_cov=2/1	polymorphism_quality=0.5	quality=0.5	quality_position_model=2.73482e-05	ref_cov=119/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=121/120
RA	55	.	NC_007779	29496	0	T	A	bias_e_value=2359.23	bias_p_value=0.000507761	fisher_strand_p_value=4.62369e-05	frequency=5.234194e-02	genotype_quality=727.4	ks_quality_p_value=1	log10_base_likelihood=-10.5815	log10_qual_likelihood_position_model=17.4494	log10_strand_likelihood_position_model=4.33501	new_cov=0/12	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=116/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/95
RA	56	.	NC_007779	34111	1	.	T	bias_e_value=3481070	bias_p_value=0.749208	fisher_strand_p_value=0.629142	frequency=1.626015e-02	genotype_quality=1176.3	ks_quality_p_value=0.60651	log10_base_likelihood=-17.7115	log10_qual_likelihood_position_model=2.74013	log10_strand_likelihood_position_model=0.524424	new_cov=3/1	polymorphism_quality=12.4	quality=12.4	quality_position_model=1.49614e-16	ref_cov=132/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/111
RA	57	.	NC_007779	34112	0	T	.	bias_e_value=4506760	bias_p_value=0.969961	fisher_strand_p_value=1	frequency=1.611423e-02	genotype_quality=976.5	ks_quality_p_value=0.765125	log10_base_likelihood=-10.8257	log10_qual_likelihood_position_model=4.42662	log10_strand_likelihood_position_model=0.430685	new_cov=2/2	polymorphism_quality=5.4	quality=5.4	quality_position_model=6.8739e-08	ref_cov=134/110	reject=INDEL_HOMOPOLYMER	tot_cov=136/112
RA	58	.	NC_007779	47305	0	G	T	bias_e_value=9.59989e-05	bias_p_value=2.06612e-11	fisher_strand_p_value=7.13219e-13	frequency=1.333756e-01	genotype_quality=697.3	ks_quality_p_value=1	log10_base_likelihood=-23.6734	log10_qual_likelihood_position_model=22.8586	log10_strand_likelihood_position_model=12.2867	new_cov=0/39	polymorphism_quality=18.4	quality=18.4	quality_position_model=Inf	ref_cov=112/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/125
RA	59	.	NC_007779	50358	0	G	T	bias_e_value=7.73222	bias_p_value=1.66416e-06	fisher_strand_p_value=9.70462e-08	frequency=7.841825e-02	genotype_quality=558.1	ks_quality_p_value=1	log10_base_likelihood=-10.2839	log10_qual_likelihood_position_model=13.2028	log10_strand_likelihood_position_model=7.0514	new_cov=0/23	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=94/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/104
RA	60	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1099.6	new_cov=140/133	quality=1099.6	ref_cov=0/0	tot_cov=140/133
RA	61	.	NC_007779	70602	0	G	T	bias_e_value=239.777	bias_p_value=5.16057e-05	fisher_strand_p_value=3.83044e-06	frequency=4.743910e-02	genotype_quality=753.5	ks_quality_p_value=1	log10_base_likelihood=-9.06198	log10_qual_likelihood_position_model=14.4741	log10_strand_likelihood_position_model=5.41675	new_cov=0/16	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=122/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/112
RA	62	.	NC_007779	75074	0	T	G	bias_e_value=3.57247e-19	bias_p_value=7.6888e-26	fisher_strand_p_value=1.22102e-27	frequency=2.126527e-01	genotype_quality=550.3	ks_quality_p_value=1	log10_base_likelihood=-46.9854	log10_qual_likelihood_position_model=36.7063	log10_strand_likelihood_position_model=26.9133	new_cov=51/0	polymorphism_quality=41.9	quality=41.9	quality_position_model=Inf	ref_cov=27/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=78/119
RA	63	.	NC_007779	75079	0	C	T	bias_e_value=6.99313	bias_p_value=1.50509e-06	fisher_strand_p_value=8.72274e-08	frequency=5.296373e-02	genotype_quality=618.1	ks_quality_p_value=1	log10_base_likelihood=-6.69195	log10_qual_likelihood_position_model=14.9741	log10_strand_likelihood_position_model=7.05935	new_cov=11/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=32/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=43/128
RA	64	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=914.3	new_cov=116/108	quality=914.3	ref_cov=0/0	tot_cov=116/108
RA	65	.	NC_007779	101246	0	T	G	bias_e_value=2311.61	bias_p_value=0.000497512	fisher_strand_p_value=4.52113e-05	frequency=3.927040e-02	genotype_quality=492.8	ks_quality_p_value=1	log10_base_likelihood=-12.2355	log10_qual_likelihood_position_model=9.03791	log10_strand_likelihood_position_model=4.34475	new_cov=6/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=21/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=27/105
RA	66	.	NC_007779	107544	1	.	T	bias_e_value=2321070	bias_p_value=0.49955	fisher_strand_p_value=0.213188	frequency=9.852409e-03	genotype_quality=980.9	ks_quality_p_value=0.87441	log10_base_likelihood=-8.07711	log10_qual_likelihood_position_model=1.97736	log10_strand_likelihood_position_model=0.671237	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.49084e-07	ref_cov=109/92	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/94
RA	67	.	NC_007779	107545	0	T	.	bias_e_value=4597050	bias_p_value=0.989393	fisher_strand_p_value=1	frequency=1.441193e-02	genotype_quality=809.5	ks_quality_p_value=0.857927	log10_base_likelihood=-8.11361	log10_qual_likelihood_position_model=1.62135	log10_strand_likelihood_position_model=0.393967	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.04569e-08	ref_cov=110/95	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/96
RA	68	.	NC_007779	119384	0	T	G	bias_e_value=9.55741e-08	bias_p_value=2.05698e-14	fisher_strand_p_value=5.6978e-16	frequency=8.127022e-02	genotype_quality=616.5	ks_quality_p_value=1	log10_base_likelihood=-6.96026	log10_qual_likelihood_position_model=27.4078	log10_strand_likelihood_position_model=15.2443	new_cov=36/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=54/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=91/118
RA	69	.	NC_007779	149550	1	.	T	bias_e_value=4149440	bias_p_value=0.893058	fisher_strand_p_value=1	frequency=7.721901e-03	genotype_quality=1258.2	ks_quality_p_value=0.574749	log10_base_likelihood=-8.34889	log10_qual_likelihood_position_model=1.29549	log10_strand_likelihood_position_model=0.304829	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.07629e-08	ref_cov=143/114	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/115
RA	70	.	NC_007779	150546	0	A	C	bias_e_value=1347300	bias_p_value=0.28997	fisher_strand_p_value=0.0831803	frequency=2.194881e-02	genotype_quality=788.2	ks_quality_p_value=0.999717	log10_base_likelihood=-9.76202	log10_qual_likelihood_position_model=6.9405	log10_strand_likelihood_position_model=1.36087	new_cov=6/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=0.00414502	ref_cov=119/84	reject=POLYMORPHISM_STRAND	tot_cov=125/84
RA	71	.	NC_007779	164597	1	.	C	bias_e_value=1267530	bias_p_value=0.272802	fisher_strand_p_value=0.118031	frequency=2.040863e-02	genotype_quality=416.4	ks_quality_p_value=0.647023	log10_base_likelihood=-8.66958	log10_qual_likelihood_position_model=1.75269	log10_strand_likelihood_position_model=0.928005	new_cov=2/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=6.54663e-08	ref_cov=32/64	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=34/64
RA	72	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=862.4	new_cov=114/102	quality=862.4	ref_cov=0/0	tot_cov=114/102
RA	73	.	NC_007779	170275	0	C	A	bias_e_value=1.11886	bias_p_value=2.40806e-07	fisher_strand_p_value=1.256e-08	frequency=7.691431e-02	genotype_quality=682.3	ks_quality_p_value=0.998882	log10_base_likelihood=-13.3871	log10_qual_likelihood_position_model=15.4971	log10_strand_likelihood_position_model=7.9261	new_cov=26/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=94/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/109
RA	74	.	NC_007779	175694	0	T	G	bias_e_value=8.53148e-09	bias_p_value=1.83618e-15	fisher_strand_p_value=4.75891e-17	frequency=7.008934e-02	genotype_quality=670.0	ks_quality_p_value=1	log10_base_likelihood=-9.60616	log10_qual_likelihood_position_model=28.9312	log10_strand_likelihood_position_model=16.3225	new_cov=40/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=64/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/130
RA	75	.	NC_007779	179256	1	.	A	bias_e_value=3228750	bias_p_value=0.694904	fisher_strand_p_value=0.499819	frequency=8.094788e-03	genotype_quality=1204.8	ks_quality_p_value=0.658517	log10_base_likelihood=-6.88958	log10_qual_likelihood_position_model=2.83915	log10_strand_likelihood_position_model=0.552417	new_cov=0/2	polymorphism_quality=1.4	quality=1.4	quality_position_model=2.5972e-05	ref_cov=116/129	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/131
RA	76	.	NC_007779	193480	0	C	G	bias_e_value=4667.23	bias_p_value=0.0010045	fisher_strand_p_value=9.82064e-05	frequency=3.435707e-02	genotype_quality=762.6	ks_quality_p_value=1	log10_base_likelihood=-5.68302	log10_qual_likelihood_position_model=8.67305	log10_strand_likelihood_position_model=4.00786	new_cov=10/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=77/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=88/125
RA	77	.	NC_007779	193496	0	A	T	bias_e_value=9048.2	bias_p_value=0.00194739	fisher_strand_p_value=0.000205168	frequency=4.001045e-02	genotype_quality=756.7	ks_quality_p_value=1	log10_base_likelihood=-9.41906	log10_qual_likelihood_position_model=12.6493	log10_strand_likelihood_position_model=3.68789	new_cov=9/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=76/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=85/127
RA	78	.	NC_007779	194247	0	G	T	bias_e_value=485.821	bias_p_value=0.00010456	fisher_strand_p_value=8.22792e-06	frequency=4.694223e-02	genotype_quality=606.7	ks_quality_p_value=1	log10_base_likelihood=-6.75522	log10_qual_likelihood_position_model=12.9231	log10_strand_likelihood_position_model=5.08471	new_cov=0/13	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=105/65	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/78
RA	79	.	NC_007779	194839	1	.	T	bias_e_value=4265730	bias_p_value=0.918086	fisher_strand_p_value=1	frequency=1.293087e-02	genotype_quality=1119.0	ks_quality_p_value=0.623586	log10_base_likelihood=-13.1145	log10_qual_likelihood_position_model=2.10209	log10_strand_likelihood_position_model=0.40976	new_cov=2/1	polymorphism_quality=7.7	quality=7.7	quality_position_model=1.21413e-12	ref_cov=118/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/112
RA	80	.	NC_007779	207536	0	G	T	bias_e_value=11.6911	bias_p_value=2.5162e-06	fisher_strand_p_value=1.50592e-07	frequency=7.323837e-02	genotype_quality=603.4	ks_quality_p_value=1	log10_base_likelihood=-10.5292	log10_qual_likelihood_position_model=19.3989	log10_strand_likelihood_position_model=6.83695	new_cov=0/23	polymorphism_quality=5.1	quality=5.1	quality_position_model=Inf	ref_cov=94/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/107
RA	81	.	NC_007779	218828	0	A	.	bias_e_value=3339900	bias_p_value=0.718825	fisher_strand_p_value=0.621898	frequency=1.701260e-02	genotype_quality=943.8	ks_quality_p_value=0.564921	log10_base_likelihood=-11.3729	log10_qual_likelihood_position_model=1.80538	log10_strand_likelihood_position_model=0.590995	new_cov=1/3	polymorphism_quality=6.0	quality=6.0	quality_position_model=5.56015e-11	ref_cov=115/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/119
RA	82	.	NC_007779	229412	0	C	A	bias_e_value=1631.44	bias_p_value=0.000351123	fisher_strand_p_value=3.08359e-05	frequency=3.462982e-02	genotype_quality=835.5	ks_quality_p_value=1	log10_base_likelihood=-7.10233	log10_qual_likelihood_position_model=15.0682	log10_strand_likelihood_position_model=4.51094	new_cov=13/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=101/132	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/132
RA	83	.	NC_007779	231684	1	.	G	bias_e_value=2609970	bias_p_value=0.561726	fisher_strand_p_value=0.230697	frequency=1.047134e-02	genotype_quality=940.9	ks_quality_p_value=0.978516	log10_base_likelihood=-7.9502	log10_qual_likelihood_position_model=2.15155	log10_strand_likelihood_position_model=0.636958	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.71358e-07	ref_cov=90/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=92/99
RA	84	.	NC_007779	253673	0	T	.	bias_e_value=4190740	bias_p_value=0.901945	fisher_strand_p_value=1	frequency=1.361942e-02	genotype_quality=823.8	ks_quality_p_value=0.591219	log10_base_likelihood=-7.85838	log10_qual_likelihood_position_model=3.11932	log10_strand_likelihood_position_model=0.378604	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.22441e-06	ref_cov=122/95	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/96
RA	85	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1007.5	new_cov=119/116	quality=1007.5	ref_cov=0/0	tot_cov=119/116
RA	86	.	NC_007779	290574	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	87	.	NC_007779	290575	0	G	C	deleted=1	frequency=1	genotype_quality=0.0	new_cov=1/0	quality=0.0	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	88	.	NC_007779	379236	1	.	G	bias_e_value=1003510	bias_p_value=0.215978	fisher_strand_p_value=0.18936	frequency=3.999996e-02	genotype_quality=678.5	ks_quality_p_value=0.293106	log10_base_likelihood=-28.681	log10_qual_likelihood_position_model=3.97051	log10_strand_likelihood_position_model=0.848815	new_cov=6/0	polymorphism_quality=23.5	quality=23.5	quality_position_model=4.50518e-26	ref_cov=103/41	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/41
RA	89	.	NC_007779	379237	0	G	.	bias_e_value=1865150	bias_p_value=0.401424	fisher_strand_p_value=1	frequency=4.216194e-02	genotype_quality=664.0	ks_quality_p_value=0.133054	log10_base_likelihood=-23.6512	log10_qual_likelihood_position_model=3.95254	log10_strand_likelihood_position_model=0.489766	new_cov=5/2	polymorphism_quality=18.4	quality=18.4	quality_position_model=2.25258e-21	ref_cov=110/48	reject=INDEL_HOMOPOLYMER	tot_cov=115/51
RA	90	.	NC_007779	379266	0	G	C	bias_e_value=2779.93	bias_p_value=0.000598307	fisher_strand_p_value=5.72379e-05	frequency=8.179569e-02	genotype_quality=494.1	ks_quality_p_value=0.967774	log10_base_likelihood=-14.7234	log10_qual_likelihood_position_model=16.3532	log10_strand_likelihood_position_model=4.27038	new_cov=15/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=71/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/73
RA	91	.	NC_007779	407306	0	C	A	bias_e_value=1.80432	bias_p_value=3.88332e-07	fisher_strand_p_value=2.07782e-08	frequency=7.943392e-02	genotype_quality=562.9	ks_quality_p_value=1	log10_base_likelihood=-9.4316	log10_qual_likelihood_position_model=15.204	log10_strand_likelihood_position_model=7.68239	new_cov=21/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=65/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/100
RA	92	.	NC_007779	440767	0	G	T	bias_e_value=8.25022	bias_p_value=1.77564e-06	fisher_strand_p_value=1.04745e-07	frequency=6.425524e-02	genotype_quality=667.8	ks_quality_p_value=0.992552	log10_base_likelihood=-12.9211	log10_qual_likelihood_position_model=14.1999	log10_strand_likelihood_position_model=6.97987	new_cov=0/17	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=124/70	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/87
RA	93	.	NC_007779	465801	0	C	A	bias_e_value=11675	bias_p_value=0.00251272	fisher_strand_p_value=0.000274771	frequency=4.816914e-02	genotype_quality=579.9	ks_quality_p_value=0.993324	log10_base_likelihood=-6.22992	log10_qual_likelihood_position_model=14.8231	log10_strand_likelihood_position_model=3.56103	new_cov=0/10	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=92/67	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=92/77
RA	94	.	NC_007779	467487	1	.	T	bias_e_value=4255440	bias_p_value=0.915871	fisher_strand_p_value=1	frequency=8.620262e-03	genotype_quality=1121.0	ks_quality_p_value=0.618932	log10_base_likelihood=-7.96192	log10_qual_likelihood_position_model=2.31413	log10_strand_likelihood_position_model=0.299283	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=3.01544e-07	ref_cov=113/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/118
RA	95	.	NC_007779	474686	0	G	T	bias_e_value=245.74	bias_p_value=5.28891e-05	fisher_strand_p_value=3.93345e-06	frequency=5.222607e-02	genotype_quality=616.0	ks_quality_p_value=1	log10_base_likelihood=-7.36712	log10_qual_likelihood_position_model=16.9756	log10_strand_likelihood_position_model=5.55652	new_cov=0/20	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=97/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=97/118
RA	96	.	NC_007779	485599	0	C	.	bias_e_value=3745530	bias_p_value=0.806125	fisher_strand_p_value=1	frequency=9.610176e-03	genotype_quality=884.9	ks_quality_p_value=0.446011	log10_base_likelihood=-5.72183	log10_qual_likelihood_position_model=1.48605	log10_strand_likelihood_position_model=0.29958	new_cov=1/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=8.97538e-06	ref_cov=107/99	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/100
RA	97	.	NC_007779	497102	1	.	A	bias_e_value=1006730	bias_p_value=0.216672	fisher_strand_p_value=0.0557425	frequency=1.675606e-02	genotype_quality=822.9	ks_quality_p_value=1	log10_base_likelihood=-9.73471	log10_qual_likelihood_position_model=3.95191	log10_strand_likelihood_position_model=1.25381	new_cov=0/3	polymorphism_quality=4.3	quality=4.3	quality_position_model=2.1495e-06	ref_cov=110/66	reject=POLYMORPHISM_STRAND	tot_cov=110/69
RA	98	.	NC_007779	513848	0	A	C	bias_e_value=4.95514e-08	bias_p_value=1.06646e-14	fisher_strand_p_value=2.89983e-16	frequency=1.174154e-01	genotype_quality=501.4	ks_quality_p_value=1	log10_base_likelihood=-10.6654	log10_qual_likelihood_position_model=22.6344	log10_strand_likelihood_position_model=15.5376	new_cov=0/31	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=104/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=104/64
RA	99	.	NC_007779	522430	1	.	T	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=2.030277e-02	genotype_quality=945.0	ks_quality_p_value=1	log10_base_likelihood=-16.4776	log10_qual_likelihood_position_model=3.68647	log10_strand_likelihood_position_model=0.446506	new_cov=2/2	polymorphism_quality=11.1	quality=11.1	quality_position_model=2.04364e-14	ref_cov=113/80	reject=INDEL_HOMOPOLYMER	tot_cov=115/82
RA	100	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=929.4	new_cov=102/121	quality=929.4	ref_cov=0/0	tot_cov=102/121
RA	101	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=920.5	new_cov=111/108	quality=920.5	ref_cov=0/0	tot_cov=111/108
RA	102	.	NC_007779	556653	0	A	C	bias_e_value=1.48799e-09	bias_p_value=3.20251e-16	fisher_strand_p_value=7.93179e-18	frequency=9.475946e-02	genotype_quality=501.7	ks_quality_p_value=1	log10_base_likelihood=-7.2337	log10_qual_likelihood_position_model=24.3098	log10_strand_likelihood_position_model=17.1006	new_cov=0/31	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=107/27	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/58
RA	103	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=910.7	new_cov=125/101	quality=910.7	ref_cov=0/0	tot_cov=125/102
RA	104	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=960.5	new_cov=111/110	quality=960.5	ref_cov=0/0	tot_cov=111/110
RA	105	.	NC_007779	589157	0	T	G	bias_e_value=9.50364e-05	bias_p_value=2.04541e-11	fisher_strand_p_value=7.05813e-13	frequency=9.354544e-02	genotype_quality=541.4	ks_quality_p_value=1	log10_base_likelihood=-11.2227	log10_qual_likelihood_position_model=30.6224	log10_strand_likelihood_position_model=12.1513	new_cov=29/0	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=51/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=81/106
RA	106	.	NC_007779	596918	0	G	T	bias_e_value=46.5538	bias_p_value=1.00195e-05	fisher_strand_p_value=6.69513e-07	frequency=4.685831e-02	genotype_quality=774.0	ks_quality_p_value=0.982327	log10_base_likelihood=-5.74391	log10_qual_likelihood_position_model=19.5018	log10_strand_likelihood_position_model=6.17424	new_cov=0/17	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=124/86	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/103
RA	107	.	NC_007779	598799	0	T	G	bias_e_value=1.1435e-10	bias_p_value=2.46109e-17	fisher_strand_p_value=5.72285e-19	frequency=1.471000e-01	genotype_quality=466.9	ks_quality_p_value=1	log10_base_likelihood=-18.0962	log10_qual_likelihood_position_model=27.165	log10_strand_likelihood_position_model=18.2424	new_cov=29/0	polymorphism_quality=12.8	quality=12.8	quality_position_model=Inf	ref_cov=18/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=47/103
RA	108	.	NC_007779	606688	0	T	.	bias_e_value=1938000	bias_p_value=0.417104	fisher_strand_p_value=0.304415	frequency=1.592827e-02	genotype_quality=999.6	ks_quality_p_value=0.462992	log10_base_likelihood=-11.491	log10_qual_likelihood_position_model=2.29544	log10_strand_likelihood_position_model=0.820367	new_cov=1/3	polymorphism_quality=6.1	quality=6.1	quality_position_model=2.29509e-10	ref_cov=150/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/100
RA	109	.	NC_007779	606911	1	.	G	bias_e_value=196954	bias_p_value=0.0423892	fisher_strand_p_value=0.00892171	frequency=2.673817e-02	genotype_quality=905.6	ks_quality_p_value=0.799456	log10_base_likelihood=-23.1387	log10_qual_likelihood_position_model=1.85581	log10_strand_likelihood_position_model=2.04955	new_cov=5/0	polymorphism_quality=17.9	quality=17.9	quality_position_model=2.12795e-21	ref_cov=69/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=74/113
RA	110	.	NC_007779	645484	0	A	C	bias_e_value=0.231347	bias_p_value=4.97914e-08	fisher_strand_p_value=2.38774e-09	frequency=8.094931e-02	genotype_quality=673.3	ks_quality_p_value=1	log10_base_likelihood=-9.18347	log10_qual_likelihood_position_model=24.0921	log10_strand_likelihood_position_model=8.62201	new_cov=0/23	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=116/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/96
RA	111	.	NC_007779	645970	0	T	G	bias_e_value=2.71773e-12	bias_p_value=5.8492e-19	fisher_strand_p_value=1.24905e-20	frequency=1.446247e-01	genotype_quality=565.8	ks_quality_p_value=1	log10_base_likelihood=-29.9838	log10_qual_likelihood_position_model=29.5481	log10_strand_likelihood_position_model=19.9034	new_cov=28/0	polymorphism_quality=24.8	quality=24.8	quality_position_model=Inf	ref_cov=17/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=45/125
RA	112	.	NC_007779	646440	0	C	A	bias_e_value=0.000187398	bias_p_value=4.03325e-11	fisher_strand_p_value=1.43913e-12	frequency=7.270288e-02	genotype_quality=633.9	ks_quality_p_value=0.991151	log10_base_likelihood=-22.5881	log10_qual_likelihood_position_model=15.0505	log10_strand_likelihood_position_model=11.8419	new_cov=0/12	polymorphism_quality=17.3	quality=17.3	quality_position_model=Inf	ref_cov=140/10	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/22
RA	113	.	NC_007779	667452	0	G	T	bias_e_value=205444	bias_p_value=0.0442165	fisher_strand_p_value=0.00750411	frequency=5.471754e-02	genotype_quality=692.0	ks_quality_p_value=1	log10_base_likelihood=-14.7717	log10_qual_likelihood_position_model=13.6541	log10_strand_likelihood_position_model=2.29658	new_cov=11/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=101/66	reject=POLYMORPHISM_STRAND	tot_cov=112/66
RA	114	.	NC_007779	686495	0	A	C	bias_e_value=2.15317e-08	bias_p_value=4.63413e-15	fisher_strand_p_value=1.23139e-16	frequency=1.259847e-01	genotype_quality=512.5	ks_quality_p_value=1	log10_base_likelihood=-21.4206	log10_qual_likelihood_position_model=24.6034	log10_strand_likelihood_position_model=15.9096	new_cov=0/24	polymorphism_quality=16.1	quality=16.1	quality_position_model=Inf	ref_cov=110/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/43
RA	115	.	NC_007779	687060	0	A	.	bias_e_value=1069290	bias_p_value=0.230136	fisher_strand_p_value=0.080635	frequency=1.448250e-02	genotype_quality=823.2	ks_quality_p_value=0.749969	log10_base_likelihood=-8.20028	log10_qual_likelihood_position_model=2.03195	log10_strand_likelihood_position_model=1.09348	new_cov=0/3	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.8025e-07	ref_cov=117/87	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/90
RA	116	.	NC_007779	687133	0	A	C	bias_e_value=111.658	bias_p_value=2.40314e-05	fisher_strand_p_value=1.68097e-06	frequency=5.924368e-02	genotype_quality=553.8	ks_quality_p_value=1	log10_base_likelihood=-11.9173	log10_qual_likelihood_position_model=14.4379	log10_strand_likelihood_position_model=5.77444	new_cov=0/13	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=103/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/64
RA	117	.	NC_007779	688155	0	T	G	bias_e_value=510.063	bias_p_value=0.000109778	fisher_strand_p_value=8.67456e-06	frequency=5.026150e-02	genotype_quality=688.1	ks_quality_p_value=1	log10_base_likelihood=-9.26597	log10_qual_likelihood_position_model=22.4885	log10_strand_likelihood_position_model=5.19516	new_cov=17/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=94/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/105
RA	118	.	NC_007779	706385	1	.	T	bias_e_value=367951	bias_p_value=0.0791917	fisher_strand_p_value=0.369458	frequency=2.232170e-02	genotype_quality=1051.6	ks_quality_p_value=0.0413726	log10_base_likelihood=-22.8904	log10_qual_likelihood_position_model=3.558	log10_strand_likelihood_position_model=0.798416	new_cov=1/4	polymorphism_quality=17.6	quality=17.6	quality_position_model=1.08439e-20	ref_cov=110/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/113
RA	119	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=789.0	new_cov=79/113	quality=789.0	ref_cov=0/0	tot_cov=79/113
RA	120	.	NC_007779	752693	0	A	C	bias_e_value=0.00456684	bias_p_value=9.82891e-10	fisher_strand_p_value=3.93823e-11	frequency=8.413458e-02	genotype_quality=643.4	ks_quality_p_value=1	log10_base_likelihood=-7.56428	log10_qual_likelihood_position_model=26.9253	log10_strand_likelihood_position_model=10.4047	new_cov=0/29	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=111/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/101
RA	121	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=1023.2	new_cov=116/135	quality=1023.2	ref_cov=0/0	tot_cov=116/135
RA	122	.	NC_007779	759019	0	C	G	bias_e_value=3.45678e-05	bias_p_value=7.4398e-12	fisher_strand_p_value=2.47777e-13	frequency=7.677794e-02	genotype_quality=599.8	ks_quality_p_value=1	log10_base_likelihood=-21.4967	log10_qual_likelihood_position_model=14.4297	log10_strand_likelihood_position_model=12.6059	new_cov=0/12	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=133/7	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/19
RA	123	.	NC_007779	796581	0	G	T	bias_e_value=1.11464	bias_p_value=2.39898e-07	fisher_strand_p_value=1.24961e-08	frequency=6.130886e-02	genotype_quality=626.5	ks_quality_p_value=1	log10_base_likelihood=-6.46877	log10_qual_likelihood_position_model=15.2582	log10_strand_likelihood_position_model=7.90323	new_cov=0/21	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=114/72	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/93
RA	124	.	NC_007779	868836	1	.	C	bias_e_value=4131410	bias_p_value=0.889176	fisher_strand_p_value=1	frequency=9.132385e-03	genotype_quality=1062.8	ks_quality_p_value=0.567816	log10_base_likelihood=-8.36484	log10_qual_likelihood_position_model=1.42266	log10_strand_likelihood_position_model=0.299269	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.38301e-08	ref_cov=111/106	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=112/107
RA	125	.	NC_007779	875961	0	C	.	bias_e_value=4619190	bias_p_value=0.994159	fisher_strand_p_value=1	frequency=9.517670e-03	genotype_quality=890.8	ks_quality_p_value=0.893884	log10_base_likelihood=-5.5696	log10_qual_likelihood_position_model=1.20209	log10_strand_likelihood_position_model=0.311911	new_cov=1/1	polymorphism_quality=0.0	quality=0.0	quality_position_model=6.72554e-06	ref_cov=122/86	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/87
RA	126	.	NC_007779	883947	0	C	A	bias_e_value=1096.76	bias_p_value=0.00023605	fisher_strand_p_value=1.9968e-05	frequency=5.286026e-02	genotype_quality=728.4	ks_quality_p_value=1	log10_base_likelihood=-10.3425	log10_qual_likelihood_position_model=13.7678	log10_strand_likelihood_position_model=4.71697	new_cov=15/1	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=80/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/123
RA	127	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=770.9	new_cov=114/86	quality=770.9	ref_cov=0/0	tot_cov=114/86
RA	128	.	NC_007779	895911	0	C	A	bias_e_value=3.80716	bias_p_value=8.1939e-07	fisher_strand_p_value=4.57773e-08	frequency=5.643606e-02	genotype_quality=743.9	ks_quality_p_value=1	log10_base_likelihood=-8.95116	log10_qual_likelihood_position_model=17.6256	log10_strand_likelihood_position_model=7.33935	new_cov=21/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=92/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/127
RA	129	.	NC_007779	904838	0	C	A	bias_e_value=5.03398e-07	bias_p_value=1.08343e-13	fisher_strand_p_value=4.04866e-15	frequency=1.284194e-01	genotype_quality=743.5	ks_quality_p_value=0.778111	log10_base_likelihood=-27.6982	log10_qual_likelihood_position_model=35.5907	log10_strand_likelihood_position_model=14.3927	new_cov=40/0	polymorphism_quality=22.5	quality=22.5	quality_position_model=Inf	ref_cov=82/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/131
RA	130	.	NC_007779	915697	0	G	T	bias_e_value=36.7107	bias_p_value=7.90101e-06	fisher_strand_p_value=5.10117e-07	frequency=6.502390e-02	genotype_quality=580.0	ks_quality_p_value=1	log10_base_likelihood=-6.57706	log10_qual_likelihood_position_model=13.9205	log10_strand_likelihood_position_model=6.29233	new_cov=0/18	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=98/70	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/88
RA	131	.	NC_007779	917407	0	C	A	bias_e_value=5414.04	bias_p_value=0.00116523	fisher_strand_p_value=0.000120729	frequency=3.577805e-02	genotype_quality=763.3	ks_quality_p_value=0.959048	log10_base_likelihood=-6.04507	log10_qual_likelihood_position_model=14.1572	log10_strand_likelihood_position_model=3.97439	new_cov=14/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=114/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/112
RA	132	.	NC_007779	947970	0	C	A	bias_e_value=37.2323	bias_p_value=8.01328e-06	fisher_strand_p_value=5.1787e-07	frequency=6.861162e-02	genotype_quality=690.1	ks_quality_p_value=1	log10_base_likelihood=-12.7761	log10_qual_likelihood_position_model=13.8963	log10_strand_likelihood_position_model=6.3335	new_cov=21/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=92/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/103
RA	133	.	NC_007779	954820	0	A	C	bias_e_value=0.0473769	bias_p_value=1.01966e-08	fisher_strand_p_value=4.52873e-10	frequency=8.348560e-02	genotype_quality=629.9	ks_quality_p_value=1	log10_base_likelihood=-7.26449	log10_qual_likelihood_position_model=22.041	log10_strand_likelihood_position_model=9.36429	new_cov=0/32	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=97/85	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=97/117
RA	134	.	NC_007779	969494	0	C	A	bias_e_value=16.8391	bias_p_value=3.62416e-06	fisher_strand_p_value=2.22065e-07	frequency=5.789995e-02	genotype_quality=678.6	ks_quality_p_value=1	log10_base_likelihood=-11.01	log10_qual_likelihood_position_model=13.237	log10_strand_likelihood_position_model=6.65352	new_cov=19/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=83/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/115
RA	135	.	NC_007779	987422	1	.	T	bias_e_value=2322580	bias_p_value=0.499875	fisher_strand_p_value=1	frequency=8.658409e-03	genotype_quality=1095.6	ks_quality_p_value=0.186608	log10_base_likelihood=-8.28053	log10_qual_likelihood_position_model=1.64979	log10_strand_likelihood_position_model=0.301504	new_cov=1/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.91337e-08	ref_cov=106/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/124
RA	136	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=863.9	new_cov=109/103	quality=863.9	ref_cov=0/0	tot_cov=109/103
RA	137	.	NC_007779	987916	0	T	G	bias_e_value=1.74004e-05	bias_p_value=3.74499e-12	fisher_strand_p_value=1.21843e-13	frequency=1.030698e-01	genotype_quality=528.8	ks_quality_p_value=1	log10_base_likelihood=-20.3937	log10_qual_likelihood_position_model=20.0727	log10_strand_likelihood_position_model=12.9142	new_cov=17/0	polymorphism_quality=15.1	quality=15.1	quality_position_model=Inf	ref_cov=16/116	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=33/116
RA	138	.	NC_007779	991407	0	G	T	bias_e_value=5.43322	bias_p_value=1.16936e-06	fisher_strand_p_value=1.10922e-07	frequency=5.927658e-02	genotype_quality=723.3	ks_quality_p_value=0.601634	log10_base_likelihood=-6.88983	log10_qual_likelihood_position_model=25.8417	log10_strand_likelihood_position_model=7.03064	new_cov=0/25	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=109/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/132
RA	139	.	NC_007779	999606	0	A	T	bias_e_value=116248	bias_p_value=0.0250194	fisher_strand_p_value=0.00380771	frequency=5.559349e-02	genotype_quality=654.1	ks_quality_p_value=1	log10_base_likelihood=-12.6055	log10_qual_likelihood_position_model=12.3721	log10_strand_likelihood_position_model=2.46984	new_cov=11/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=96/69	reject=POLYMORPHISM_STRAND	tot_cov=107/69
RA	140	.	NC_007779	999607	0	A	C	bias_e_value=190630	bias_p_value=0.041028	fisher_strand_p_value=0.00685822	frequency=4.357338e-02	genotype_quality=638.5	ks_quality_p_value=1	log10_base_likelihood=-11.9011	log10_qual_likelihood_position_model=10.0306	log10_strand_likelihood_position_model=2.2365	new_cov=10/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=97/69	reject=POLYMORPHISM_STRAND	tot_cov=107/69
RA	141	.	NC_007779	999613	0	A	T	bias_e_value=330573	bias_p_value=0.071147	fisher_strand_p_value=0.0133906	frequency=4.853439e-02	genotype_quality=642.4	ks_quality_p_value=1	log10_base_likelihood=-12.2557	log10_qual_likelihood_position_model=10.7529	log10_strand_likelihood_position_model=1.95117	new_cov=9/0	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=97/66	reject=POLYMORPHISM_STRAND	tot_cov=106/66
RA	142	.	NC_007779	999623	0	A	T	bias_e_value=1405220	bias_p_value=0.302437	fisher_strand_p_value=0.0882305	frequency=3.357029e-02	genotype_quality=599.1	ks_quality_p_value=1	log10_base_likelihood=-5.58133	log10_qual_likelihood_position_model=7.8833	log10_strand_likelihood_position_model=1.1874	new_cov=6/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=97/58	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=103/58
RA	143	.	NC_007779	1002640	0	G	.	bias_e_value=2483420	bias_p_value=0.534491	fisher_strand_p_value=0.622927	frequency=1.645565e-02	genotype_quality=1027.1	ks_quality_p_value=0.333791	log10_base_likelihood=-12.1664	log10_qual_likelihood_position_model=2.41673	log10_strand_likelihood_position_model=0.570702	new_cov=3/1	polymorphism_quality=6.8	quality=6.8	quality_position_model=3.45155e-11	ref_cov=123/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/117
RA	144	.	NC_007779	1008243	0	G	T	bias_e_value=1748.42	bias_p_value=0.000376301	fisher_strand_p_value=3.32689e-05	frequency=3.768158e-02	genotype_quality=862.4	ks_quality_p_value=1	log10_base_likelihood=-6.06428	log10_qual_likelihood_position_model=13.4717	log10_strand_likelihood_position_model=4.51357	new_cov=0/16	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=122/125	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/141
RA	145	.	NC_007779	1012726	0	T	.	bias_e_value=3822050	bias_p_value=0.822595	fisher_strand_p_value=0.621788	frequency=1.270294e-02	genotype_quality=931.0	ks_quality_p_value=0.75108	log10_base_likelihood=-8.23778	log10_qual_likelihood_position_model=2.05714	log10_strand_likelihood_position_model=0.425993	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.14385e-07	ref_cov=115/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/118
RA	146	.	NC_007779	1068568	1	.	A	bias_e_value=1412990	bias_p_value=0.304109	fisher_strand_p_value=0.250098	frequency=1.209641e-02	genotype_quality=1206.7	ks_quality_p_value=0.355542	log10_base_likelihood=-12.9081	log10_qual_likelihood_position_model=2.236	log10_strand_likelihood_position_model=0.826295	new_cov=3/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=7.18732e-12	ref_cov=129/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/116
RA	147	.	NC_007779	1070200	0	A	C	bias_e_value=229.881	bias_p_value=4.94757e-05	fisher_strand_p_value=3.66273e-06	frequency=4.083538e-02	genotype_quality=519.6	ks_quality_p_value=0.999248	log10_base_likelihood=-6.95433	log10_qual_likelihood_position_model=9.55532	log10_strand_likelihood_position_model=5.4362	new_cov=0/7	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=114/19	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/26
RA	148	.	NC_007779	1079013	0	C	A	bias_e_value=1.03387	bias_p_value=2.22512e-07	fisher_strand_p_value=1.15933e-08	frequency=7.388783e-02	genotype_quality=670.4	ks_quality_p_value=0.995642	log10_base_likelihood=-11.2306	log10_qual_likelihood_position_model=15.0335	log10_strand_likelihood_position_model=7.93579	new_cov=24/0	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=86/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/112
RA	149	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1176.1	new_cov=140/129	quality=1176.1	ref_cov=0/0	tot_cov=140/129
RA	150	.	NC_007779	1093704	0	G	T	bias_e_value=4495.03	bias_p_value=0.000967436	fisher_strand_p_value=9.41993e-05	frequency=2.482796e-02	genotype_quality=1097.9	ks_quality_p_value=1	log10_base_likelihood=-6.04649	log10_qual_likelihood_position_model=14.7824	log10_strand_likelihood_position_model=4.02595	new_cov=0/11	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=156/112	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/124
RA	151	.	NC_007779	1097580	0	C	T	bias_e_value=87989.3	bias_p_value=0.0189374	fisher_strand_p_value=0.508821	frequency=2.237210e-01	genotype_quality=757.0	ks_quality_p_value=0.00539563	log10_base_likelihood=-218.363	log10_qual_likelihood_position_model=25.0716	log10_strand_likelihood_position_model=1.09528	new_cov=35/40	polymorphism_quality=213.6	quality=213.6	quality_position_model=7.40602e-195	ref_cov=109/151	tot_cov=144/191
RA	152	.	NC_007779	1097729	1	.	G	bias_e_value=1541120	bias_p_value=0.331686	fisher_strand_p_value=0.161615	frequency=3.094673e-03	genotype_quality=2458.9	ks_quality_p_value=0.622596	log10_base_likelihood=-6.23624	log10_qual_likelihood_position_model=2.41028	log10_strand_likelihood_position_model=0.791519	new_cov=2/0	polymorphism_quality=0.7	quality=0.7	quality_position_model=8.05011e-05	ref_cov=258/386	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=260/386
RA	153	.	NC_007779	1116582	0	G	C	bias_e_value=7.19835e-08	bias_p_value=1.54926e-14	fisher_strand_p_value=4.37037e-16	frequency=1.370893e-01	genotype_quality=372.3	ks_quality_p_value=0.974067	log10_base_likelihood=-23.4867	log10_qual_likelihood_position_model=15.7103	log10_strand_likelihood_position_model=15.3595	new_cov=0/16	polymorphism_quality=18.2	quality=18.2	quality_position_model=Inf	ref_cov=93/4	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=93/20
RA	154	.	NC_007779	1120197	0	C	A	bias_e_value=1891.1	bias_p_value=0.000407009	fisher_strand_p_value=3.62598e-05	frequency=4.316998e-02	genotype_quality=646.9	ks_quality_p_value=1	log10_base_likelihood=-6.50605	log10_qual_likelihood_position_model=11.2324	log10_strand_likelihood_position_model=4.65188	new_cov=15/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=90/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/102
RA	155	.	NC_007779	1125354	0	A	C	bias_e_value=463.284	bias_p_value=9.97097e-05	fisher_strand_p_value=7.81453e-06	frequency=4.289818e-02	genotype_quality=672.7	ks_quality_p_value=1	log10_base_likelihood=-5.90159	log10_qual_likelihood_position_model=13.3841	log10_strand_likelihood_position_model=5.1071	new_cov=0/14	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=115/80	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/94
RA	156	.	NC_007779	1148417	0	C	A	bias_e_value=814.886	bias_p_value=0.000175383	fisher_strand_p_value=1.81305e-05	frequency=5.265427e-02	genotype_quality=681.7	ks_quality_p_value=0.796456	log10_base_likelihood=-7.66841	log10_qual_likelihood_position_model=19.5681	log10_strand_likelihood_position_model=4.91294	new_cov=18/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=105/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/100
RA	157	.	NC_007779	1155150	0	T	G	bias_e_value=15.1148	bias_p_value=3.25306e-06	fisher_strand_p_value=1.97931e-07	frequency=3.630638e-02	genotype_quality=558.1	ks_quality_p_value=1	log10_base_likelihood=-7.96558	log10_qual_likelihood_position_model=10.1505	log10_strand_likelihood_position_model=6.70349	new_cov=7/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=12/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=19/128
RA	158	.	NC_007779	1158848	0	T	G	bias_e_value=7.10057e-14	bias_p_value=1.52821e-20	fisher_strand_p_value=3.02313e-22	frequency=1.295052e-01	genotype_quality=654.4	ks_quality_p_value=1	log10_base_likelihood=-17.8056	log10_qual_likelihood_position_model=31.8457	log10_strand_likelihood_position_model=21.5195	new_cov=44/0	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=43/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=88/133
RA	159	.	NC_007779	1164944	0	T	G	bias_e_value=0.00418297	bias_p_value=9.00274e-10	fisher_strand_p_value=3.59403e-11	frequency=7.304144e-02	genotype_quality=468.7	ks_quality_p_value=1	log10_base_likelihood=-7.11759	log10_qual_likelihood_position_model=18.201	log10_strand_likelihood_position_model=10.4444	new_cov=16/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=20/98	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=36/98
RA	160	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=995.5	new_cov=144/99	quality=995.5	ref_cov=0/0	tot_cov=144/99
RA	161	.	NC_007779	1177683	0	A	G	bias_e_value=0.000810898	bias_p_value=1.74524e-10	fisher_strand_p_value=6.52289e-12	frequency=1.140819e-01	genotype_quality=566.9	ks_quality_p_value=1	log10_base_likelihood=-15.0461	log10_qual_likelihood_position_model=21.6966	log10_strand_likelihood_position_model=11.1856	new_cov=26/0	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=55/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=81/115
RA	162	.	NC_007779	1186236	0	C	A	bias_e_value=27545.5	bias_p_value=0.00592844	fisher_strand_p_value=0.00071977	frequency=3.241062e-02	genotype_quality=804.1	ks_quality_p_value=1	log10_base_likelihood=-7.15925	log10_qual_likelihood_position_model=12.0566	log10_strand_likelihood_position_model=3.38608	new_cov=12/1	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=98/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/132
RA	163	.	NC_007779	1200371	0	A	.	bias_e_value=3940530	bias_p_value=0.848095	fisher_strand_p_value=0.621552	frequency=1.368999e-02	genotype_quality=891.4	ks_quality_p_value=0.807981	log10_base_likelihood=-8.35587	log10_qual_likelihood_position_model=1.29799	log10_strand_likelihood_position_model=0.425996	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.41967e-08	ref_cov=107/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/110
RA	164	.	NC_007779	1219648	0	G	T	bias_e_value=229.469	bias_p_value=4.93871e-05	fisher_strand_p_value=3.71536e-06	frequency=3.855324e-02	genotype_quality=898.2	ks_quality_p_value=0.983188	log10_base_likelihood=-6.07152	log10_qual_likelihood_position_model=14.6385	log10_strand_likelihood_position_model=5.43	new_cov=0/15	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=143/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/117
RA	165	.	NC_007779	1262472	0	A	C	bias_e_value=0.00176137	bias_p_value=3.79089e-10	fisher_strand_p_value=1.46088e-11	frequency=5.440187e-02	genotype_quality=653.7	ks_quality_p_value=1	log10_base_likelihood=-6.13071	log10_qual_likelihood_position_model=22.8276	log10_strand_likelihood_position_model=10.8354	new_cov=0/30	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=114/73	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/103
RA	166	.	NC_007779	1273399	0	T	G	bias_e_value=1.97688e-13	bias_p_value=4.25472e-20	fisher_strand_p_value=8.59439e-22	frequency=1.267881e-01	genotype_quality=620.0	ks_quality_p_value=1	log10_base_likelihood=-25.9376	log10_qual_likelihood_position_model=31.0244	log10_strand_likelihood_position_model=21.0658	new_cov=30/0	polymorphism_quality=20.7	quality=20.7	quality_position_model=Inf	ref_cov=20/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=50/138
RA	167	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=48.8	new_cov=9/7	quality=48.8	ref_cov=0/0	tot_cov=9/7
RA	168	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=21.6	new_cov=7/3	quality=21.6	ref_cov=0/0	tot_cov=7/3
RA	169	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=30.2	new_cov=4/9	quality=30.2	ref_cov=0/0	tot_cov=4/9
RA	170	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=944.7	new_cov=110/126	quality=944.7	ref_cov=0/0	tot_cov=110/126
RA	171	.	NC_007779	1324681	1	.	A	bias_e_value=2788840	bias_p_value=0.600223	fisher_strand_p_value=0.509653	frequency=1.041698e-02	genotype_quality=938.0	ks_quality_p_value=0.495715	log10_base_likelihood=-8.30069	log10_qual_likelihood_position_model=1.92088	log10_strand_likelihood_position_model=0.477619	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=8.04792e-08	ref_cov=109/81	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/81
RA	172	.	NC_007779	1325276	0	G	T	bias_e_value=1584.52	bias_p_value=0.000341026	fisher_strand_p_value=2.99834e-05	frequency=3.306484e-02	genotype_quality=833.1	ks_quality_p_value=0.99606	log10_base_likelihood=-5.6718	log10_qual_likelihood_position_model=13.4052	log10_strand_likelihood_position_model=4.52312	new_cov=0/12	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=136/92	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/104
RA	173	.	NC_007779	1337405	0	T	G	bias_e_value=0.00587761	bias_p_value=1.265e-09	fisher_strand_p_value=5.12254e-11	frequency=5.941439e-02	genotype_quality=708.5	ks_quality_p_value=1	log10_base_likelihood=-7.12056	log10_qual_likelihood_position_model=21.6568	log10_strand_likelihood_position_model=10.2905	new_cov=26/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=73/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/128
RA	174	.	NC_007779	1352913	1	.	T	bias_e_value=480947	bias_p_value=0.103511	fisher_strand_p_value=0.0220015	frequency=1.898766e-02	genotype_quality=752.5	ks_quality_p_value=0.97079	log10_base_likelihood=-13.1579	log10_qual_likelihood_position_model=2.31789	log10_strand_likelihood_position_model=1.65755	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=3.42321e-11	ref_cov=42/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=45/113
RA	175	.	NC_007779	1371749	1	.	T	bias_e_value=2123670	bias_p_value=0.457064	fisher_strand_p_value=0.431837	frequency=2.727318e-02	genotype_quality=1021.6	ks_quality_p_value=0.375394	log10_base_likelihood=-27.9486	log10_qual_likelihood_position_model=2.92054	log10_strand_likelihood_position_model=0.662235	new_cov=4/2	polymorphism_quality=22.7	quality=22.7	quality_position_model=1.39669e-26	ref_cov=102/112	reject=INDEL_HOMOPOLYMER	tot_cov=106/114
RA	176	.	NC_007779	1374996	0	A	C	bias_e_value=716.007	bias_p_value=0.000154102	fisher_strand_p_value=1.25425e-05	frequency=2.773762e-02	genotype_quality=728.0	ks_quality_p_value=1	log10_base_likelihood=-7.77293	log10_qual_likelihood_position_model=9.42229	log10_strand_likelihood_position_model=4.90162	new_cov=8/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=43/147	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=51/147
RA	177	.	NC_007779	1375289	0	G	T	bias_e_value=0.926334	bias_p_value=1.99369e-07	fisher_strand_p_value=1.02804e-08	frequency=8.145428e-02	genotype_quality=666.1	ks_quality_p_value=1	log10_base_likelihood=-13.3551	log10_qual_likelihood_position_model=17.6849	log10_strand_likelihood_position_model=8.03006	new_cov=0/26	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=111/94	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/120
RA	178	.	NC_007779	1378219	0	A	C	bias_e_value=0.000538306	bias_p_value=1.15856e-10	fisher_strand_p_value=4.26236e-12	frequency=7.535934e-02	genotype_quality=587.5	ks_quality_p_value=1	log10_base_likelihood=-9.14479	log10_qual_likelihood_position_model=32.0773	log10_strand_likelihood_position_model=11.3703	new_cov=0/27	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=107/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=107/79
RA	179	.	NC_007779	1378854	0	A	C	bias_e_value=1.60829e-10	bias_p_value=3.46143e-17	fisher_strand_p_value=8.11485e-19	frequency=1.323462e-01	genotype_quality=641.2	ks_quality_p_value=1	log10_base_likelihood=-16.4188	log10_qual_likelihood_position_model=32.5405	log10_strand_likelihood_position_model=18.0907	new_cov=0/47	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=119/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/108
RA	180	.	NC_007779	1405508	0	G	T	bias_e_value=0.021604	bias_p_value=4.6497e-09	fisher_strand_p_value=1.99559e-10	frequency=7.858801e-02	genotype_quality=452.1	ks_quality_p_value=0.998432	log10_base_likelihood=-18.1068	log10_qual_likelihood_position_model=11.8304	log10_strand_likelihood_position_model=9.69993	new_cov=10/0	polymorphism_quality=12.8	quality=12.8	quality_position_model=Inf	ref_cov=7/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=17/101
RA	181	.	NC_007779	1409137	0	G	T	bias_e_value=6.91305e-14	bias_p_value=1.48785e-20	fisher_strand_p_value=2.9417e-22	frequency=2.521472e-01	genotype_quality=484.4	ks_quality_p_value=1	log10_base_likelihood=-83.1788	log10_qual_likelihood_position_model=28.4137	log10_strand_likelihood_position_model=21.5737	new_cov=0/58	polymorphism_quality=78.2	quality=78.2	quality_position_model=1.79231e-35	ref_cov=107/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/110
RA	182	.	NC_007779	1412694	0	C	A	bias_e_value=0.000285185	bias_p_value=6.13786e-11	fisher_strand_p_value=2.20465e-12	frequency=1.157603e-01	genotype_quality=571.0	ks_quality_p_value=1	log10_base_likelihood=-16.8953	log10_qual_likelihood_position_model=20.8027	log10_strand_likelihood_position_model=11.6567	new_cov=31/0	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=61/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=92/105
RA	183	.	NC_007779	1437447	0	G	C	bias_e_value=1.99804e-05	bias_p_value=4.30024e-12	fisher_strand_p_value=1.40562e-13	frequency=9.809589e-02	genotype_quality=684.7	ks_quality_p_value=1	log10_base_likelihood=-18.7726	log10_qual_likelihood_position_model=18.8293	log10_strand_likelihood_position_model=12.8521	new_cov=0/26	polymorphism_quality=13.5	quality=13.5	quality_position_model=Inf	ref_cov=142/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/80
RA	184	.	NC_007779	1438937	0	T	.	bias_e_value=446443	bias_p_value=0.0960849	fisher_strand_p_value=0.251177	frequency=1.529694e-02	genotype_quality=780.8	ks_quality_p_value=0.0774391	log10_base_likelihood=-8.36054	log10_qual_likelihood_position_model=1.71741	log10_strand_likelihood_position_model=0.806564	new_cov=3/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=9.40988e-08	ref_cov=103/90	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/90
RA	185	.	NC_007779	1476017	0	T	.	bias_e_value=4520950	bias_p_value=0.973016	fisher_strand_p_value=1	frequency=1.693916e-02	genotype_quality=646.8	ks_quality_p_value=0.776869	log10_base_likelihood=-8.44304	log10_qual_likelihood_position_model=1.49735	log10_strand_likelihood_position_model=0.390923	new_cov=1/2	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.70493e-08	ref_cov=80/94	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=81/96
RA	186	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=617.6	new_cov=113/44	quality=617.6	ref_cov=0/0	tot_cov=113/44
RA	187	.	NC_007779	1493621	0	T	C	bias_e_value=190.634	bias_p_value=4.10289e-05	fisher_strand_p_value=2.99042e-06	frequency=4.071999e-02	genotype_quality=779.6	ks_quality_p_value=1	log10_base_likelihood=-6.21099	log10_qual_likelihood_position_model=13.1847	log10_strand_likelihood_position_model=5.52427	new_cov=0/12	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=146/71	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/83
RA	188	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1108.6	new_cov=100/125	quality=1108.6	ref_cov=0/0	tot_cov=100/125
RA	189	.	NC_007779	1504851	0	C	A	bias_e_value=230667	bias_p_value=0.049645	fisher_strand_p_value=0.00878497	frequency=7.039595e-02	genotype_quality=532.9	ks_quality_p_value=0.982379	log10_base_likelihood=-8.76627	log10_qual_likelihood_position_model=13.7272	log10_strand_likelihood_position_model=2.34997	new_cov=19/1	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=120/60	reject=POLYMORPHISM_STRAND	tot_cov=139/61
RA	190	.	NC_007779	1515709	0	A	G	bias_e_value=0.167885	bias_p_value=3.61328e-08	fisher_strand_p_value=1.70522e-09	frequency=1.205182e-01	genotype_quality=506.0	ks_quality_p_value=1	log10_base_likelihood=-15.1107	log10_qual_likelihood_position_model=27.5737	log10_strand_likelihood_position_model=8.78651	new_cov=28/0	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=71/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/90
RA	191	.	NC_007779	1526885	0	G	T	bias_e_value=1911.31	bias_p_value=0.000411359	fisher_strand_p_value=3.66855e-05	frequency=4.182625e-02	genotype_quality=700.9	ks_quality_p_value=1	log10_base_likelihood=-6.77879	log10_qual_likelihood_position_model=10.3959	log10_strand_likelihood_position_model=4.43551	new_cov=0/12	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=120/83	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/95
RA	192	.	NC_007779	1527474	0	G	A	bias_e_value=0.466691	bias_p_value=1.00443e-07	fisher_strand_p_value=4.99339e-09	frequency=8.002138e-02	genotype_quality=769.3	ks_quality_p_value=1	log10_base_likelihood=-13.6902	log10_qual_likelihood_position_model=23.4072	log10_strand_likelihood_position_model=8.3016	new_cov=0/22	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=129/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/104
RA	193	.	NC_007779	1530864	0	C	A	bias_e_value=268.168	bias_p_value=5.77161e-05	fisher_strand_p_value=4.32278e-06	frequency=8.832073e-02	genotype_quality=332.9	ks_quality_p_value=1	log10_base_likelihood=-7.68459	log10_qual_likelihood_position_model=10.2476	log10_strand_likelihood_position_model=5.36424	new_cov=15/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=40/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=55/61
RA	194	.	NC_007779	1533124	0	C	A	bias_e_value=84610.3	bias_p_value=0.0182101	fisher_strand_p_value=0.00262816	frequency=4.195976e-02	genotype_quality=816.5	ks_quality_p_value=0.997875	log10_base_likelihood=-12.0039	log10_qual_likelihood_position_model=12.2006	log10_strand_likelihood_position_model=2.61681	new_cov=0/10	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=88/101	reject=POLYMORPHISM_STRAND	tot_cov=88/111
RA	195	.	NC_007779	1533140	0	C	A	bias_e_value=710979	bias_p_value=0.153019	fisher_strand_p_value=0.0352046	frequency=3.563404e-02	genotype_quality=866.1	ks_quality_p_value=1	log10_base_likelihood=-11.8766	log10_qual_likelihood_position_model=13.093	log10_strand_likelihood_position_model=1.76817	new_cov=1/8	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=104/99	reject=POLYMORPHISM_STRAND	tot_cov=105/107
RA	196	.	NC_007779	1537499	0	A	G	bias_e_value=0.0587583	bias_p_value=1.26462e-08	fisher_strand_p_value=5.67346e-10	frequency=8.109474e-02	genotype_quality=640.1	ks_quality_p_value=1	log10_base_likelihood=-8.41692	log10_qual_likelihood_position_model=17.8612	log10_strand_likelihood_position_model=9.24615	new_cov=25/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=76/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/119
RA	197	.	NC_007779	1552377	0	A	C	bias_e_value=8.70856e-10	bias_p_value=1.87429e-16	fisher_strand_p_value=4.57982e-18	frequency=1.467047e-01	genotype_quality=578.6	ks_quality_p_value=1	log10_base_likelihood=-21.9032	log10_qual_likelihood_position_model=31.0495	log10_strand_likelihood_position_model=17.3392	new_cov=0/37	polymorphism_quality=16.6	quality=16.6	quality_position_model=Inf	ref_cov=112/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/77
RA	198	.	NC_007779	1558141	0	G	.	bias_e_value=4369610	bias_p_value=0.940443	fisher_strand_p_value=1	frequency=7.995605e-03	genotype_quality=1076.5	ks_quality_p_value=0.675355	log10_base_likelihood=-5.57992	log10_qual_likelihood_position_model=1.32935	log10_strand_likelihood_position_model=0.302666	new_cov=1/1	polymorphism_quality=0.0	quality=0.0	quality_position_model=8.72497e-06	ref_cov=113/135	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/136
RA	199	.	NC_007779	1564550	0	G	T	bias_e_value=35222.7	bias_p_value=0.00758075	fisher_strand_p_value=0.000957015	frequency=2.990246e-02	genotype_quality=618.0	ks_quality_p_value=0.995622	log10_base_likelihood=-6.13244	log10_qual_likelihood_position_model=9.17811	log10_strand_likelihood_position_model=3.01908	new_cov=7/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=59/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=66/107
RA	200	.	NC_007779	1567404	0	A	.	bias_e_value=4640380	bias_p_value=0.998719	fisher_strand_p_value=1	frequency=1.243401e-02	genotype_quality=933.6	ks_quality_p_value=0.949817	log10_base_likelihood=-7.78105	log10_qual_likelihood_position_model=2.00278	log10_strand_likelihood_position_model=0.373742	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.6377e-07	ref_cov=135/101	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/104
RA	201	.	NC_007779	1581577	1	.	T	bias_e_value=2321660	bias_p_value=0.499675	fisher_strand_p_value=0.228901	frequency=8.196831e-03	genotype_quality=1195.8	ks_quality_p_value=0.814714	log10_base_likelihood=-8.27958	log10_qual_likelihood_position_model=1.6747	log10_strand_likelihood_position_model=0.640352	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.93753e-08	ref_cov=127/115	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/117
RA	202	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=859.4	new_cov=112/111	quality=859.4	ref_cov=0/0	tot_cov=112/111
RA	203	.	NC_007779	1628027	0	G	T	bias_e_value=481.633	bias_p_value=0.000103659	fisher_strand_p_value=9.70809e-06	frequency=1.459727e-01	genotype_quality=330.2	ks_quality_p_value=0.839604	log10_base_likelihood=-28.7511	log10_qual_likelihood_position_model=16.1078	log10_strand_likelihood_position_model=5.12512	new_cov=18/0	polymorphism_quality=23.5	quality=23.5	quality_position_model=1.73816e-09	ref_cov=47/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=65/52
RA	204	.	NC_007779	1647535	0	C	A	bias_e_value=2.33671	bias_p_value=5.02915e-07	fisher_strand_p_value=3.04342e-08	frequency=6.221581e-02	genotype_quality=789.7	ks_quality_p_value=0.897296	log10_base_likelihood=-11.461	log10_qual_likelihood_position_model=17.2599	log10_strand_likelihood_position_model=7.51664	new_cov=23/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=105/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/131
RA	205	.	NC_007779	1648465	1	.	G	bias_e_value=2410990	bias_p_value=0.518902	fisher_strand_p_value=0.198165	frequency=8.579254e-03	genotype_quality=1144.1	ks_quality_p_value=0.999926	log10_base_likelihood=-5.60826	log10_qual_likelihood_position_model=4.43181	log10_strand_likelihood_position_model=0.702973	new_cov=2/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.0653885	ref_cov=102/129	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=104/129
RA	206	.	NC_007779	1651009	0	T	G	bias_e_value=6.44999e-09	bias_p_value=1.38819e-15	fisher_strand_p_value=3.57127e-17	frequency=1.636319e-01	genotype_quality=474.7	ks_quality_p_value=1	log10_base_likelihood=-21.3783	log10_qual_likelihood_position_model=25.7013	log10_strand_likelihood_position_model=16.4472	new_cov=29/0	polymorphism_quality=16.1	quality=16.1	quality_position_model=Inf	ref_cov=23/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=53/99
RA	207	.	NC_007779	1660545	0	G	T	bias_e_value=29.2522	bias_p_value=6.29577e-06	fisher_strand_p_value=4.00207e-07	frequency=5.918694e-02	genotype_quality=641.4	ks_quality_p_value=1	log10_base_likelihood=-6.94793	log10_qual_likelihood_position_model=12.9999	log10_strand_likelihood_position_model=6.39772	new_cov=0/17	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=110/71	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/88
RA	208	.	NC_007779	1660637	0	G	T	bias_e_value=1539.88	bias_p_value=0.000331419	fisher_strand_p_value=2.89446e-05	frequency=4.407787e-02	genotype_quality=680.6	ks_quality_p_value=1	log10_base_likelihood=-5.90925	log10_qual_likelihood_position_model=13.6962	log10_strand_likelihood_position_model=4.57667	new_cov=0/16	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=101/100	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/116
RA	209	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=879.0	new_cov=78/98	quality=879.0	ref_cov=0/0	tot_cov=78/98
RA	210	.	NC_007779	1677110	0	G	T	bias_e_value=0.0614251	bias_p_value=1.32201e-08	fisher_strand_p_value=1.10706e-09	frequency=1.012344e-01	genotype_quality=592.0	ks_quality_p_value=0.536859	log10_base_likelihood=-13.9501	log10_qual_likelihood_position_model=28.753	log10_strand_likelihood_position_model=9.23605	new_cov=0/30	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=100/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/112
RA	211	.	NC_007779	1681402	0	T	G	bias_e_value=0.00419275	bias_p_value=9.02378e-10	fisher_strand_p_value=3.60278e-11	frequency=4.371834e-02	genotype_quality=706.3	ks_quality_p_value=1	log10_base_likelihood=-6.01031	log10_qual_likelihood_position_model=22.3559	log10_strand_likelihood_position_model=10.4434	new_cov=20/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=50/140	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=70/140
RA	212	.	NC_007779	1698552	0	G	T	bias_e_value=58.9292	bias_p_value=1.26829e-05	fisher_strand_p_value=8.46539e-07	frequency=5.210304e-02	genotype_quality=738.5	ks_quality_p_value=1	log10_base_likelihood=-9.43654	log10_qual_likelihood_position_model=15.3244	log10_strand_likelihood_position_model=6.07235	new_cov=0/17	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=121/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/103
RA	213	.	NC_007779	1703335	0	G	C	bias_e_value=1155.38	bias_p_value=0.000248666	fisher_strand_p_value=2.1137e-05	frequency=5.439568e-02	genotype_quality=455.3	ks_quality_p_value=1	log10_base_likelihood=-10.8585	log10_qual_likelihood_position_model=10.1463	log10_strand_likelihood_position_model=4.67496	new_cov=7/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=21/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=28/91
RA	214	.	NC_007779	1705204	0	A	C	bias_e_value=28818.7	bias_p_value=0.00620245	fisher_strand_p_value=0.000757771	frequency=4.345512e-02	genotype_quality=554.4	ks_quality_p_value=1	log10_base_likelihood=-9.20318	log10_qual_likelihood_position_model=12.6702	log10_strand_likelihood_position_model=3.12046	new_cov=9/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=63/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=72/83
RA	215	.	NC_007779	1705209	1	.	T	bias_e_value=2188110	bias_p_value=0.470933	fisher_strand_p_value=0.195232	frequency=1.324463e-02	genotype_quality=712.9	ks_quality_p_value=0.869894	log10_base_likelihood=-8.27648	log10_qual_likelihood_position_model=2.60688	log10_strand_likelihood_position_model=0.709449	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=7.63704e-07	ref_cov=65/84	reject=POLYMORPHISM_STRAND	tot_cov=67/84
RA	216	.	NC_007779	1705210	0	G	T	bias_e_value=41612.1	bias_p_value=0.0089559	fisher_strand_p_value=0.00117492	frequency=4.906082e-02	genotype_quality=567.1	ks_quality_p_value=0.981646	log10_base_likelihood=-10.7756	log10_qual_likelihood_position_model=11.0632	log10_strand_likelihood_position_model=2.92999	new_cov=8/0	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=59/84	reject=POLYMORPHISM_STRAND	tot_cov=67/84
RA	217	.	NC_007779	1705224	0	G	T	bias_e_value=4162.31	bias_p_value=0.000895826	fisher_strand_p_value=8.65093e-05	frequency=5.276108e-02	genotype_quality=651.9	ks_quality_p_value=1	log10_base_likelihood=-8.35613	log10_qual_likelihood_position_model=14.006	log10_strand_likelihood_position_model=4.06294	new_cov=12/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=69/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=81/89
RA	218	.	NC_007779	1713510	0	A	C	bias_e_value=2.61487	bias_p_value=5.62781e-07	fisher_strand_p_value=3.07579e-08	frequency=7.412052e-02	genotype_quality=598.5	ks_quality_p_value=1	log10_base_likelihood=-6.93359	log10_qual_likelihood_position_model=24.5963	log10_strand_likelihood_position_model=7.61153	new_cov=0/24	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=98/79	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/104
RA	219	.	NC_007779	1716031	1	.	T	bias_e_value=3007590	bias_p_value=0.647305	fisher_strand_p_value=0.498062	frequency=8.264542e-03	genotype_quality=1167.9	ks_quality_p_value=0.579538	log10_base_likelihood=-7.87284	log10_qual_likelihood_position_model=2.48253	log10_strand_likelihood_position_model=0.589567	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.11919e-06	ref_cov=119/121	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=119/123
RA	220	.	NC_007779	1722510	0	G	T	bias_e_value=287752	bias_p_value=0.061931	fisher_strand_p_value=0.0112941	frequency=2.588749e-02	genotype_quality=788.0	ks_quality_p_value=1	log10_base_likelihood=-6.7487	log10_qual_likelihood_position_model=9.04535	log10_strand_likelihood_position_model=2.17902	new_cov=0/9	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=94/121	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=94/130
RA	221	.	NC_007779	1759411	1	.	T	bias_e_value=2792830	bias_p_value=0.601083	fisher_strand_p_value=0.510389	frequency=1.117325e-02	genotype_quality=865.0	ks_quality_p_value=0.496227	log10_base_likelihood=-8.68223	log10_qual_likelihood_position_model=1.32718	log10_strand_likelihood_position_model=0.473402	new_cov=0/2	polymorphism_quality=3.2	quality=3.2	quality_position_model=7.84961e-09	ref_cov=75/102	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=75/104
RA	222	.	NC_007779	1763744	0	C	A	bias_e_value=0.852086	bias_p_value=1.83389e-07	fisher_strand_p_value=9.41368e-09	frequency=6.528807e-02	genotype_quality=731.4	ks_quality_p_value=1	log10_base_likelihood=-13.5011	log10_qual_likelihood_position_model=18.2272	log10_strand_likelihood_position_model=8.02624	new_cov=21/0	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=80/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/128
RA	223	.	NC_007779	1766507	0	A	C	bias_e_value=4.2343e-06	bias_p_value=9.11321e-13	fisher_strand_p_value=2.83057e-14	frequency=1.057324e-01	genotype_quality=532.2	ks_quality_p_value=1	log10_base_likelihood=-13.4638	log10_qual_likelihood_position_model=21.778	log10_strand_likelihood_position_model=13.5481	new_cov=0/27	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=107/36	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/63
RA	224	.	NC_007779	1781198	0	T	.	bias_e_value=3933200	bias_p_value=0.846517	fisher_strand_p_value=0.596028	frequency=1.244068e-02	genotype_quality=967.3	ks_quality_p_value=0.83875	log10_base_likelihood=-8.35397	log10_qual_likelihood_position_model=1.66985	log10_strand_likelihood_position_model=0.462846	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.76588e-08	ref_cov=109/129	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/130
RA	225	.	NC_007779	1786232	0	T	.	bias_e_value=4617070	bias_p_value=0.993702	fisher_strand_p_value=1	frequency=1.297951e-02	genotype_quality=930.3	ks_quality_p_value=0.889892	log10_base_likelihood=-8.3294	log10_qual_likelihood_position_model=1.42713	log10_strand_likelihood_position_model=0.386846	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.87186e-08	ref_cov=103/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/127
RA	226	.	NC_007779	1832491	0	G	T	bias_e_value=0.388833	bias_p_value=8.3686e-08	fisher_strand_p_value=4.12606e-09	frequency=8.635092e-02	genotype_quality=643.2	ks_quality_p_value=0.998777	log10_base_likelihood=-16.4961	log10_qual_likelihood_position_model=16.0806	log10_strand_likelihood_position_model=8.38446	new_cov=0/25	polymorphism_quality=11.2	quality=11.2	quality_position_model=Inf	ref_cov=109/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/107
RA	227	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=809.2	new_cov=108/93	quality=809.2	ref_cov=0/0	tot_cov=108/93
RA	228	.	NC_007779	1844628	0	A	G	bias_e_value=13.4158	bias_p_value=2.8874e-06	fisher_strand_p_value=1.74336e-07	frequency=6.231070e-02	genotype_quality=439.0	ks_quality_p_value=1	log10_base_likelihood=-7.28939	log10_qual_likelihood_position_model=12.6926	log10_strand_likelihood_position_model=6.7636	new_cov=9/1	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=12/103	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=21/104
RA	229	.	NC_007779	1861399	0	A	C	bias_e_value=8.40367e-13	bias_p_value=1.80867e-19	fisher_strand_p_value=3.76584e-21	frequency=1.271591e-01	genotype_quality=494.7	ks_quality_p_value=1	log10_base_likelihood=-11.9124	log10_qual_likelihood_position_model=28.9861	log10_strand_likelihood_position_model=20.4241	new_cov=0/34	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=107/20	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/54
RA	230	.	NC_007779	1879404	0	A	C	bias_e_value=1.75839e-08	bias_p_value=3.78446e-15	fisher_strand_p_value=1.00009e-16	frequency=7.242584e-02	genotype_quality=703.9	ks_quality_p_value=1	log10_base_likelihood=-11.5913	log10_qual_likelihood_position_model=26.5951	log10_strand_likelihood_position_model=16	new_cov=0/25	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=149/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/57
RA	231	.	NC_007779	1889730	0	A	.	bias_e_value=2323160	bias_p_value=0.5	fisher_strand_p_value=1	frequency=1.242828e-02	genotype_quality=960.6	ks_quality_p_value=0.186682	log10_base_likelihood=-7.68076	log10_qual_likelihood_position_model=3.31248	log10_strand_likelihood_position_model=0.388233	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=8.07263e-06	ref_cov=130/108	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/109
RA	232	.	NC_007779	1891709	0	A	C	bias_e_value=16.6679	bias_p_value=3.58732e-06	fisher_strand_p_value=2.19829e-07	frequency=5.037308e-02	genotype_quality=647.5	ks_quality_p_value=0.999236	log10_base_likelihood=-6.72357	log10_qual_likelihood_position_model=17.7535	log10_strand_likelihood_position_model=6.65792	new_cov=0/13	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=128/50	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/63
RA	233	.	NC_007779	1906477	1	.	G	bias_e_value=404690	bias_p_value=0.0870989	fisher_strand_p_value=0.0173408	frequency=2.072048e-02	genotype_quality=901.6	ks_quality_p_value=0.992136	log10_base_likelihood=-13.5262	log10_qual_likelihood_position_model=5.54431	log10_strand_likelihood_position_model=1.76093	new_cov=4/0	polymorphism_quality=8.2	quality=8.2	quality_position_model=3.76875e-08	ref_cov=67/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=71/122
RA	234	.	NC_007779	1906488	0	G	T	bias_e_value=3893.2	bias_p_value=0.000837908	fisher_strand_p_value=8.03424e-05	frequency=4.317570e-02	genotype_quality=665.1	ks_quality_p_value=1	log10_base_likelihood=-6.23664	log10_qual_likelihood_position_model=10.2997	log10_strand_likelihood_position_model=4.11125	new_cov=10/1	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=51/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/122
RA	235	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=944.0	new_cov=121/122	quality=944.0	ref_cov=0/1	tot_cov=121/123
RA	236	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=951.7	new_cov=109/130	quality=951.7	ref_cov=0/0	tot_cov=109/130
RA	237	.	NC_007779	1993891	0	A	C	bias_e_value=256.998	bias_p_value=5.5312e-05	fisher_strand_p_value=4.12851e-06	frequency=5.142689e-02	genotype_quality=676.3	ks_quality_p_value=1	log10_base_likelihood=-7.21863	log10_qual_likelihood_position_model=16.4714	log10_strand_likelihood_position_model=5.48604	new_cov=0/18	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=100/89	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/107
RA	238	.	NC_007779	1993894	0	A	C	bias_e_value=111.174	bias_p_value=2.39272e-05	fisher_strand_p_value=1.67313e-06	frequency=5.658960e-02	genotype_quality=710.6	ks_quality_p_value=1	log10_base_likelihood=-8.10472	log10_qual_likelihood_position_model=20.4443	log10_strand_likelihood_position_model=5.9704	new_cov=0/19	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=107/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=107/113
RA	239	.	NC_007779	2004055	0	A	C	bias_e_value=1.32344e-16	bias_p_value=2.84835e-23	fisher_strand_p_value=5.00106e-25	frequency=1.868138e-01	genotype_quality=610.6	ks_quality_p_value=1	log10_base_likelihood=-30.3739	log10_qual_likelihood_position_model=40.6639	log10_strand_likelihood_position_model=24.3009	new_cov=0/52	polymorphism_quality=25.2	quality=25.2	quality_position_model=Inf	ref_cov=124/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/92
RA	240	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=1049.4	new_cov=132/125	quality=1049.4	ref_cov=0/0	tot_cov=132/125
RA	241	.	NC_007779	2020389	1	.	A	bias_e_value=4646150	bias_p_value=0.99996	fisher_strand_p_value=1	frequency=9.433746e-03	genotype_quality=1035.3	ks_quality_p_value=0.991056	log10_base_likelihood=-7.88793	log10_qual_likelihood_position_model=2.87247	log10_strand_likelihood_position_model=0.299131	new_cov=1/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.37049e-06	ref_cov=103/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/108
RA	242	.	NC_007779	2023811	0	C	A	bias_e_value=134.664	bias_p_value=2.89829e-05	fisher_strand_p_value=2.05631e-06	frequency=4.892254e-02	genotype_quality=710.0	ks_quality_p_value=1	log10_base_likelihood=-7.77304	log10_qual_likelihood_position_model=18.9597	log10_strand_likelihood_position_model=5.81355	new_cov=21/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=107/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/105
RA	243	.	NC_007779	2027359	0	T	A	bias_e_value=268155	bias_p_value=0.0577133	fisher_strand_p_value=0.0103622	frequency=2.447033e-02	genotype_quality=847.0	ks_quality_p_value=1	log10_base_likelihood=-6.58652	log10_qual_likelihood_position_model=9.38502	log10_strand_likelihood_position_model=1.98455	new_cov=0/6	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=117/99	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=117/105
RA	244	.	NC_007779	2034810	0	C	A	bias_e_value=28400.2	bias_p_value=0.0061124	fisher_strand_p_value=0.000745252	frequency=3.766346e-02	genotype_quality=687.4	ks_quality_p_value=1	log10_base_likelihood=-6.72824	log10_qual_likelihood_position_model=11.2737	log10_strand_likelihood_position_model=3.38353	new_cov=11/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=95/104	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=107/104
RA	245	.	NC_007779	2046875	0	G	T	bias_e_value=0.0418814	bias_p_value=9.01386e-09	fisher_strand_p_value=3.98061e-10	frequency=5.645132e-02	genotype_quality=890.2	ks_quality_p_value=1	log10_base_likelihood=-10.4498	log10_qual_likelihood_position_model=20.324	log10_strand_likelihood_position_model=9.40005	new_cov=0/24	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=154/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/117
RA	246	.	NC_007779	2082880	1	.	A	bias_e_value=2101590	bias_p_value=0.452311	fisher_strand_p_value=0.16826	frequency=8.840561e-03	genotype_quality=1109.3	ks_quality_p_value=0.947988	log10_base_likelihood=-6.58456	log10_qual_likelihood_position_model=3.36387	log10_strand_likelihood_position_model=0.77402	new_cov=2/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=0.000342719	ref_cov=91/133	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=93/133
RA	247	.	NC_007779	2107010	1	.	A	bias_e_value=1411540	bias_p_value=0.303797	fisher_strand_p_value=0.142558	frequency=9.132385e-03	genotype_quality=1064.7	ks_quality_p_value=0.622847	log10_base_likelihood=-8.41801	log10_qual_likelihood_position_model=1.24337	log10_strand_likelihood_position_model=0.846009	new_cov=0/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.91757e-08	ref_cov=136/81	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/83
RA	248	.	NC_007779	2107011	0	A	.	bias_e_value=533930	bias_p_value=0.114914	fisher_strand_p_value=0.639354	frequency=1.645279e-02	genotype_quality=975.8	ks_quality_p_value=0.0381269	log10_base_likelihood=-11.4342	log10_qual_likelihood_position_model=2.63905	log10_strand_likelihood_position_model=0.487731	new_cov=3/1	polymorphism_quality=6.0	quality=6.0	quality_position_model=2.69315e-10	ref_cov=137/102	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/103
RA	249	.	NC_007779	2161945	1	.	A	bias_e_value=3930550	bias_p_value=0.845948	fisher_strand_p_value=0.499803	frequency=9.340286e-03	genotype_quality=1048.3	ks_quality_p_value=0.99859	log10_base_likelihood=-6.30069	log10_qual_likelihood_position_model=4.35776	log10_strand_likelihood_position_model=0.54881	new_cov=2/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=0.00492813	ref_cov=112/100	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=114/100
RA	250	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=870.4	new_cov=104/108	quality=870.4	ref_cov=0/0	tot_cov=104/108
RA	251	.	NC_007779	2173942	1	.	G	bias_e_value=3420590	bias_p_value=0.736192	fisher_strand_p_value=0.540529	frequency=1.282024e-02	genotype_quality=730.3	ks_quality_p_value=0.681393	log10_base_likelihood=-7.73948	log10_qual_likelihood_position_model=2.53836	log10_strand_likelihood_position_model=0.379135	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.06358e-06	ref_cov=99/55	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=101/55
RA	252	.	NC_007779	2200802	0	A	.	bias_e_value=3334460	bias_p_value=0.717654	fisher_strand_p_value=1	frequency=1.194477e-02	genotype_quality=1011.4	ks_quality_p_value=0.350206	log10_base_likelihood=-8.25906	log10_qual_likelihood_position_model=1.25573	log10_strand_likelihood_position_model=0.412532	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.56511e-08	ref_cov=121/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/129
RA	253	.	NC_007779	2203780	1	.	A	bias_e_value=2578540	bias_p_value=0.554963	fisher_strand_p_value=0.501223	frequency=8.657455e-03	genotype_quality=1139.4	ks_quality_p_value=0.441375	log10_base_likelihood=-8.14604	log10_qual_likelihood_position_model=1.46862	log10_strand_likelihood_position_model=0.535008	new_cov=0/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=4.54292e-08	ref_cov=106/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=106/125
RA	254	.	NC_007779	2213136	0	G	T	bias_e_value=7.92911	bias_p_value=1.70653e-06	fisher_strand_p_value=1.05391e-07	frequency=7.742167e-02	genotype_quality=580.4	ks_quality_p_value=0.94574	log10_base_likelihood=-18.2522	log10_qual_likelihood_position_model=19.064	log10_strand_likelihood_position_model=6.9772	new_cov=15/0	polymorphism_quality=12.9	quality=12.9	quality_position_model=Inf	ref_cov=48/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=63/107
RA	255	.	NC_007779	2226024	0	C	A	bias_e_value=0.0225596	bias_p_value=4.85536e-09	fisher_strand_p_value=2.08463e-10	frequency=6.909084e-02	genotype_quality=821.6	ks_quality_p_value=1	log10_base_likelihood=-9.70456	log10_qual_likelihood_position_model=20.0897	log10_strand_likelihood_position_model=9.68097	new_cov=26/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=93/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/144
RA	256	.	NC_007779	2229341	0	G	T	bias_e_value=59.6263	bias_p_value=1.2833e-05	fisher_strand_p_value=8.57275e-07	frequency=6.088018e-02	genotype_quality=716.3	ks_quality_p_value=1	log10_base_likelihood=-8.445	log10_qual_likelihood_position_model=18.0499	log10_strand_likelihood_position_model=6.36059	new_cov=0/22	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=109/104	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/128
RA	257	.	NC_007779	2231556	0	T	G	bias_e_value=1.83397	bias_p_value=3.94714e-07	fisher_strand_p_value=2.11392e-08	frequency=5.115461e-02	genotype_quality=706.0	ks_quality_p_value=1	log10_base_likelihood=-6.86068	log10_qual_likelihood_position_model=17.8932	log10_strand_likelihood_position_model=7.67491	new_cov=19/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=73/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=92/127
RA	258	.	NC_007779	2251513	0	C	A	bias_e_value=4137.47	bias_p_value=0.000890482	fisher_strand_p_value=8.59382e-05	frequency=3.252506e-02	genotype_quality=843.2	ks_quality_p_value=1	log10_base_likelihood=-7.34887	log10_qual_likelihood_position_model=11.835	log10_strand_likelihood_position_model=4.2781	new_cov=14/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=116/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/126
RA	259	.	NC_007779	2254201	0	G	T	bias_e_value=131.274	bias_p_value=2.82533e-05	fisher_strand_p_value=2.00065e-06	frequency=6.470537e-02	genotype_quality=713.9	ks_quality_p_value=1	log10_base_likelihood=-11.6385	log10_qual_likelihood_position_model=17.1172	log10_strand_likelihood_position_model=5.80451	new_cov=0/19	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=109/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/116
RA	260	.	NC_007779	2266892	0	G	T	bias_e_value=0.417227	bias_p_value=8.97971e-08	fisher_strand_p_value=4.43815e-09	frequency=7.599640e-02	genotype_quality=850.5	ks_quality_p_value=1	log10_base_likelihood=-15.1395	log10_qual_likelihood_position_model=18.642	log10_strand_likelihood_position_model=8.53153	new_cov=0/31	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=127/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/159
RA	261	.	NC_007779	2271592	0	G	T	bias_e_value=4341.35	bias_p_value=0.00093436	fisher_strand_p_value=9.06386e-05	frequency=3.240871e-02	genotype_quality=852.6	ks_quality_p_value=1	log10_base_likelihood=-8.61427	log10_qual_likelihood_position_model=11.9223	log10_strand_likelihood_position_model=4.04269	new_cov=0/11	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=125/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/99
RA	262	.	NC_007779	2277624	0	G	T	bias_e_value=98847.8	bias_p_value=0.0212744	fisher_strand_p_value=0.00336517	frequency=2.946854e-02	genotype_quality=840.9	ks_quality_p_value=0.93499	log10_base_likelihood=-5.60288	log10_qual_likelihood_position_model=7.51287	log10_strand_likelihood_position_model=2.77402	new_cov=0/9	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=125/116	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=125/126
RA	263	.	NC_007779	2286490	0	T	.	bias_e_value=4594350	bias_p_value=0.988813	fisher_strand_p_value=1	frequency=1.098156e-02	genotype_quality=1089.1	ks_quality_p_value=0.854199	log10_base_likelihood=-8.13087	log10_qual_likelihood_position_model=2.44323	log10_strand_likelihood_position_model=0.38971	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=3.40294e-07	ref_cov=123/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/149
RA	264	.	NC_007779	2295451	0	C	A	bias_e_value=0.723965	bias_p_value=1.55814e-07	fisher_strand_p_value=7.92834e-09	frequency=6.427479e-02	genotype_quality=851.0	ks_quality_p_value=1	log10_base_likelihood=-11.846	log10_qual_likelihood_position_model=18.7578	log10_strand_likelihood_position_model=8.11136	new_cov=24/1	polymorphism_quality=6.4	quality=6.4	quality_position_model=Inf	ref_cov=94/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/153
RA	265	.	NC_007779	2296303	0	C	A	bias_e_value=1650.48	bias_p_value=0.000355222	fisher_strand_p_value=3.2038e-05	frequency=3.347969e-02	genotype_quality=853.3	ks_quality_p_value=0.974802	log10_base_likelihood=-7.57072	log10_qual_likelihood_position_model=17.3971	log10_strand_likelihood_position_model=4.53212	new_cov=16/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=121/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/119
RA	266	.	NC_007779	2331120	0	T	G	bias_e_value=1.24736e-08	bias_p_value=2.6846e-15	fisher_strand_p_value=7.02888e-17	frequency=9.096527e-02	genotype_quality=678.3	ks_quality_p_value=1	log10_base_likelihood=-10.301	log10_qual_likelihood_position_model=26.7114	log10_strand_likelihood_position_model=16.1531	new_cov=38/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=61/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/132
RA	267	.	NC_007779	2332580	0	A	C	bias_e_value=6.33789e-10	bias_p_value=1.36406e-16	fisher_strand_p_value=3.30677e-18	frequency=8.770418e-02	genotype_quality=632.6	ks_quality_p_value=1	log10_base_likelihood=-7.68018	log10_qual_likelihood_position_model=27.6125	log10_strand_likelihood_position_model=17.4806	new_cov=0/41	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=123/54	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/95
RA	268	.	NC_007779	2334630	0	C	A	bias_e_value=2630.94	bias_p_value=0.000566241	fisher_strand_p_value=5.21317e-05	frequency=4.157257e-02	genotype_quality=795.4	ks_quality_p_value=1	log10_base_likelihood=-5.58724	log10_qual_likelihood_position_model=13.0087	log10_strand_likelihood_position_model=4.35627	new_cov=15/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=114/116	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/116
RA	269	.	NC_007779	2342393	0	A	C	bias_e_value=0.000139283	bias_p_value=2.99769e-11	fisher_strand_p_value=1.04875e-12	frequency=7.885838e-02	genotype_quality=689.4	ks_quality_p_value=1	log10_base_likelihood=-9.64816	log10_qual_likelihood_position_model=25.041	log10_strand_likelihood_position_model=11.9793	new_cov=0/24	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=138/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/76
RA	270	.	NC_007779	2353815	0	A	C	bias_e_value=8.2162e-07	bias_p_value=1.76832e-13	fisher_strand_p_value=5.21834e-15	frequency=1.112189e-01	genotype_quality=517.0	ks_quality_p_value=1	log10_base_likelihood=-12.5064	log10_qual_likelihood_position_model=23.5264	log10_strand_likelihood_position_model=14.2825	new_cov=0/27	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=105/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/58
RA	271	.	NC_007779	2373239	0	A	C	bias_e_value=0.000433414	bias_p_value=9.32809e-11	fisher_strand_p_value=3.40364e-12	frequency=6.096697e-02	genotype_quality=608.3	ks_quality_p_value=1	log10_base_likelihood=-6.08157	log10_qual_likelihood_position_model=23.0714	log10_strand_likelihood_position_model=11.4681	new_cov=0/25	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=119/51	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/76
RA	272	.	NC_007779	2385358	1	.	A	bias_e_value=4622940	bias_p_value=0.994966	fisher_strand_p_value=1	frequency=9.433746e-03	genotype_quality=1043.1	ks_quality_p_value=0.901348	log10_base_likelihood=-8.54975	log10_qual_likelihood_position_model=1.18168	log10_strand_likelihood_position_model=0.299944	new_cov=1/1	polymorphism_quality=3.1	quality=3.1	quality_position_model=5.04519e-09	ref_cov=110/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/101
RA	273	.	NC_007779	2387486	1	.	A	bias_e_value=4621700	bias_p_value=0.9947	fisher_strand_p_value=1	frequency=1.255226e-02	genotype_quality=1167.9	ks_quality_p_value=0.898821	log10_base_likelihood=-12.8499	log10_qual_likelihood_position_model=2.44502	log10_strand_likelihood_position_model=0.39341	new_cov=1/2	polymorphism_quality=7.5	quality=7.5	quality_position_model=4.86886e-12	ref_cov=109/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/129
RA	274	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=908.7	new_cov=121/108	quality=908.7	ref_cov=0/0	tot_cov=121/108
RA	275	.	NC_007779	2409404	0	A	C	bias_e_value=0.00178629	bias_p_value=3.84452e-10	fisher_strand_p_value=1.48238e-11	frequency=8.975220e-02	genotype_quality=592.4	ks_quality_p_value=1	log10_base_likelihood=-15.9341	log10_qual_likelihood_position_model=20.3835	log10_strand_likelihood_position_model=10.829	new_cov=0/22	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=118/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/67
RA	276	.	NC_007779	2410316	0	A	C	bias_e_value=0.000258168	bias_p_value=5.55637e-11	fisher_strand_p_value=1.98842e-12	frequency=9.458113e-02	genotype_quality=603.5	ks_quality_p_value=1	log10_base_likelihood=-18.6522	log10_qual_likelihood_position_model=24.5645	log10_strand_likelihood_position_model=11.7015	new_cov=0/28	polymorphism_quality=13.4	quality=13.4	quality_position_model=Inf	ref_cov=113/56	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/85
RA	277	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=805.9	new_cov=84/121	quality=805.9	ref_cov=0/0	tot_cov=84/121
RA	278	.	NC_007779	2417605	0	C	A	bias_e_value=94.8924	bias_p_value=2.04231e-05	fisher_strand_p_value=1.87821e-06	frequency=5.517244e-02	genotype_quality=719.4	ks_quality_p_value=0.751414	log10_base_likelihood=-7.12837	log10_qual_likelihood_position_model=22.6749	log10_strand_likelihood_position_model=5.74423	new_cov=20/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=106/109	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/109
RA	279	.	NC_007779	2418806	0	A	.	bias_e_value=1310740	bias_p_value=0.282103	fisher_strand_p_value=0.0932257	frequency=1.208687e-02	genotype_quality=1014.2	ks_quality_p_value=0.858322	log10_base_likelihood=-7.92774	log10_qual_likelihood_position_model=2.02409	log10_strand_likelihood_position_model=1.03046	new_cov=0/3	polymorphism_quality=2.4	quality=2.4	quality_position_model=9.40686e-07	ref_cov=135/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/113
RA	280	.	NC_007779	2459733	1	.	T	bias_e_value=4645200	bias_p_value=0.999756	fisher_strand_p_value=1	frequency=9.900093e-03	genotype_quality=991.5	ks_quality_p_value=0.977969	log10_base_likelihood=-7.65533	log10_qual_likelihood_position_model=2.96509	log10_strand_likelihood_position_model=0.300966	new_cov=1/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=3.0083e-06	ref_cov=107/93	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/94
RA	281	.	NC_007779	2468327	0	C	.	bias_e_value=1998470	bias_p_value=0.430117	fisher_strand_p_value=0.151854	frequency=2.126694e-02	genotype_quality=768.3	ks_quality_p_value=0.972405	log10_base_likelihood=-11.7045	log10_qual_likelihood_position_model=1.84	log10_strand_likelihood_position_model=0.893672	new_cov=0/4	polymorphism_quality=6.3	quality=6.3	quality_position_model=5.63527e-11	ref_cov=75/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=75/113
RA	282	.	NC_007779	2475172	0	T	.	bias_e_value=1725030	bias_p_value=0.371267	fisher_strand_p_value=0.15277	frequency=2.365589e-02	genotype_quality=682.3	ks_quality_p_value=0.775756	log10_base_likelihood=-11.5698	log10_qual_likelihood_position_model=2.89738	log10_strand_likelihood_position_model=0.874859	new_cov=1/3	polymorphism_quality=6.2	quality=6.2	quality_position_model=8.97876e-10	ref_cov=104/61	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=105/64
RA	283	.	NC_007779	2478675	0	C	A	bias_e_value=959.12	bias_p_value=0.000206425	fisher_strand_p_value=1.72484e-05	frequency=4.300594e-02	genotype_quality=706.9	ks_quality_p_value=1	log10_base_likelihood=-5.63686	log10_qual_likelihood_position_model=10.5169	log10_strand_likelihood_position_model=5.06428	new_cov=16/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=97/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/113
RA	284	.	NC_007779	2495058	1	.	T	bias_e_value=4645950	bias_p_value=0.999919	fisher_strand_p_value=1	frequency=9.389877e-03	genotype_quality=1050.0	ks_quality_p_value=0.987266	log10_base_likelihood=-7.98361	log10_qual_likelihood_position_model=2.2745	log10_strand_likelihood_position_model=0.300146	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.60992e-07	ref_cov=100/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=101/112
RA	285	.	NC_007779	2501740	0	A	.	bias_e_value=4061550	bias_p_value=0.874141	fisher_strand_p_value=1	frequency=1.189709e-02	genotype_quality=991.1	ks_quality_p_value=0.542281	log10_base_likelihood=-8.22167	log10_qual_likelihood_position_model=1.90077	log10_strand_likelihood_position_model=0.420809	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=8.08829e-08	ref_cov=125/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/125
RA	286	.	NC_007779	2517218	0	A	C	bias_e_value=4.38947e-06	bias_p_value=9.44716e-13	fisher_strand_p_value=2.93768e-14	frequency=6.799078e-02	genotype_quality=527.2	ks_quality_p_value=1	log10_base_likelihood=-5.88597	log10_qual_likelihood_position_model=27.826	log10_strand_likelihood_position_model=13.532	new_cov=0/23	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=113/28	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/51
RA	287	.	NC_007779	2536601	0	T	G	bias_e_value=418.526	bias_p_value=9.00766e-05	fisher_strand_p_value=6.99911e-06	frequency=6.071711e-02	genotype_quality=657.5	ks_quality_p_value=1	log10_base_likelihood=-6.72326	log10_qual_likelihood_position_model=19.9696	log10_strand_likelihood_position_model=5.17058	new_cov=16/1	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=71/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=87/114
RA	288	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=923.5	new_cov=104/125	quality=923.5	ref_cov=0/0	tot_cov=104/125
RA	289	.	NC_007779	2547822	0	T	C	bias_e_value=4365960	bias_p_value=0.939658	fisher_strand_p_value=1	frequency=1.231098e-02	genotype_quality=922.4	ks_quality_p_value=0.673361	log10_base_likelihood=-6.29549	log10_qual_likelihood_position_model=1.74911	log10_strand_likelihood_position_model=0.418871	new_cov=2/1	polymorphism_quality=0.8	quality=0.8	quality_position_model=5.65365e-06	ref_cov=121/119	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=123/120
RA	290	.	NC_007779	2556426	0	G	T	bias_e_value=18.4444	bias_p_value=3.96967e-06	fisher_strand_p_value=3.13503e-07	frequency=6.725979e-02	genotype_quality=697.9	ks_quality_p_value=0.780503	log10_base_likelihood=-11.6583	log10_qual_likelihood_position_model=24.6061	log10_strand_likelihood_position_model=6.53837	new_cov=0/24	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=104/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=104/131
RA	291	.	NC_007779	2598509	1	.	T	bias_e_value=3642290	bias_p_value=0.783907	fisher_strand_p_value=1	frequency=9.661674e-03	genotype_quality=1013.8	ks_quality_p_value=0.419489	log10_base_likelihood=-8.37646	log10_qual_likelihood_position_model=1.42301	log10_strand_likelihood_position_model=0.299749	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.34803e-08	ref_cov=107/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=108/99
RA	292	.	NC_007779	2601998	0	A	C	bias_e_value=0.0536884	bias_p_value=1.1555e-08	fisher_strand_p_value=5.16205e-10	frequency=5.844975e-02	genotype_quality=530.6	ks_quality_p_value=1	log10_base_likelihood=-12.8061	log10_qual_likelihood_position_model=15.3342	log10_strand_likelihood_position_model=9.28718	new_cov=0/11	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=118/14	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/25
RA	293	.	NC_007779	2614764	1	.	A	bias_e_value=1939720	bias_p_value=0.417473	fisher_strand_p_value=0.221053	frequency=9.523392e-03	genotype_quality=1028.2	ks_quality_p_value=0.638446	log10_base_likelihood=-8.45229	log10_qual_likelihood_position_model=1.65114	log10_strand_likelihood_position_model=0.655504	new_cov=2/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=4.50808e-08	ref_cov=97/111	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/111
RA	294	.	NC_007779	2618856	1	.	A	bias_e_value=4427640	bias_p_value=0.952933	fisher_strand_p_value=1	frequency=9.259224e-03	genotype_quality=1057.9	ks_quality_p_value=0.709313	log10_base_likelihood=-8.46704	log10_qual_likelihood_position_model=0.988374	log10_strand_likelihood_position_model=0.305353	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.93236e-09	ref_cov=94/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/121
RA	295	.	NC_007779	2623159	0	T	G	bias_e_value=9.54186e-18	bias_p_value=2.05363e-24	fisher_strand_p_value=3.44393e-26	frequency=2.028027e-01	genotype_quality=556.3	ks_quality_p_value=1	log10_base_likelihood=-33.021	log10_qual_likelihood_position_model=37.6304	log10_strand_likelihood_position_model=25.4629	new_cov=53/0	polymorphism_quality=27.8	quality=27.8	quality_position_model=Inf	ref_cov=34/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=87/118
RA	296	.	NC_007779	2623173	0	G	T	bias_e_value=33.7687	bias_p_value=7.26781e-06	fisher_strand_p_value=4.66546e-07	frequency=6.774998e-02	genotype_quality=644.9	ks_quality_p_value=1	log10_base_likelihood=-9.64106	log10_qual_likelihood_position_model=12.6857	log10_strand_likelihood_position_model=6.33111	new_cov=16/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=65/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=81/109
RA	297	.	NC_007779	2648595	0	A	C	bias_e_value=0.00470303	bias_p_value=1.0122e-09	fisher_strand_p_value=4.06066e-11	frequency=6.295252e-02	genotype_quality=446.8	ks_quality_p_value=1	log10_base_likelihood=-7.38594	log10_qual_likelihood_position_model=14.9468	log10_strand_likelihood_position_model=10.3914	new_cov=0/12	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=102/10	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/22
RA	298	.	NC_007779	2676695	0	T	G	bias_e_value=0.00689894	bias_p_value=1.48481e-09	fisher_strand_p_value=6.0536e-11	frequency=1.063328e-01	genotype_quality=499.1	ks_quality_p_value=1	log10_base_likelihood=-6.87498	log10_qual_likelihood_position_model=32.2874	log10_strand_likelihood_position_model=10.244	new_cov=31/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=55/80	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/80
RA	299	.	NC_007779	2680638	0	G	T	bias_e_value=14.0681	bias_p_value=3.02779e-06	fisher_strand_p_value=1.8361e-07	frequency=6.717253e-02	genotype_quality=730.4	ks_quality_p_value=0.9987	log10_base_likelihood=-12.3081	log10_qual_likelihood_position_model=21.435	log10_strand_likelihood_position_model=6.86957	new_cov=0/22	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=116/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/121
RA	300	.	NC_007779	2756310	1	.	T	bias_e_value=1132020	bias_p_value=0.243638	fisher_strand_p_value=0.498224	frequency=7.843018e-03	genotype_quality=1255.4	ks_quality_p_value=0.131176	log10_base_likelihood=-8.19508	log10_qual_likelihood_position_model=1.07882	log10_strand_likelihood_position_model=0.586841	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.81068e-08	ref_cov=128/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/125
RA	301	.	NC_007779	2757983	1	.	A	bias_e_value=4637000	bias_p_value=0.997992	fisher_strand_p_value=1	frequency=8.883476e-03	genotype_quality=1111.9	ks_quality_p_value=0.937299	log10_base_likelihood=-6.61915	log10_qual_likelihood_position_model=2.8332	log10_strand_likelihood_position_model=0.301582	new_cov=1/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=2.68482e-05	ref_cov=120/103	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=121/104
RA	302	.	NC_007779	2783729	0	A	.	bias_e_value=1377550	bias_p_value=0.296482	fisher_strand_p_value=0.497784	frequency=1.098251e-02	genotype_quality=744.1	ks_quality_p_value=0.172348	log10_base_likelihood=-5.58487	log10_qual_likelihood_position_model=0.940028	log10_strand_likelihood_position_model=0.576139	new_cov=2/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=6.51609e-06	ref_cov=92/88	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=94/88
RA	303	.	NC_007779	2791635	0	C	T	bias_e_value=0.0401818	bias_p_value=8.64806e-09	fisher_strand_p_value=3.81735e-10	frequency=8.054066e-02	genotype_quality=552.6	ks_quality_p_value=0.998539	log10_base_likelihood=-5.75426	log10_qual_likelihood_position_model=18.8493	log10_strand_likelihood_position_model=9.41824	new_cov=0/19	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=110/42	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/63
RA	304	.	NC_007779	2797644	0	C	A	bias_e_value=81629.1	bias_p_value=0.0175685	fisher_strand_p_value=0.00251603	frequency=3.918552e-02	genotype_quality=783.5	ks_quality_p_value=0.99959	log10_base_likelihood=-8.34533	log10_qual_likelihood_position_model=9.75938	log10_strand_likelihood_position_model=2.62794	new_cov=1/9	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=128/88	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=129/97
RA	305	.	NC_007779	2816615	0	G	C	bias_e_value=63.0789	bias_p_value=1.35761e-05	fisher_strand_p_value=9.2143e-07	frequency=4.893589e-02	genotype_quality=610.0	ks_quality_p_value=0.988228	log10_base_likelihood=-6.45593	log10_qual_likelihood_position_model=14.0166	log10_strand_likelihood_position_model=6.03554	new_cov=11/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=43/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=54/124
RA	306	.	NC_007779	2817030	0	G	C	bias_e_value=0.245344	bias_p_value=5.28038e-08	fisher_strand_p_value=4.47333e-09	frequency=8.789825e-02	genotype_quality=580.7	ks_quality_p_value=0.567746	log10_base_likelihood=-19.2244	log10_qual_likelihood_position_model=22.1046	log10_strand_likelihood_position_model=8.34937	new_cov=19/0	polymorphism_quality=13.9	quality=13.9	quality_position_model=Inf	ref_cov=56/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=75/115
RA	307	.	NC_007779	2833989	0	A	C	bias_e_value=4.7943e-07	bias_p_value=1.03185e-13	fisher_strand_p_value=2.99594e-15	frequency=1.051841e-01	genotype_quality=533.3	ks_quality_p_value=1	log10_base_likelihood=-15.2765	log10_qual_likelihood_position_model=21.8643	log10_strand_likelihood_position_model=14.5235	new_cov=0/22	polymorphism_quality=9.9	quality=9.9	quality_position_model=Inf	ref_cov=117/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/44
RA	308	.	NC_007779	2847445	0	G	T	bias_e_value=11.4303	bias_p_value=2.46008e-06	fisher_strand_p_value=1.47022e-07	frequency=8.030605e-02	genotype_quality=628.4	ks_quality_p_value=1	log10_base_likelihood=-14.2924	log10_qual_likelihood_position_model=15.1079	log10_strand_likelihood_position_model=7.00694	new_cov=0/22	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=103/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/106
RA	309	.	NC_007779	2862768	0	C	A	bias_e_value=775677	bias_p_value=0.166944	fisher_strand_p_value=0.0394508	frequency=2.740002e-02	genotype_quality=807.8	ks_quality_p_value=0.999691	log10_base_likelihood=-6.97658	log10_qual_likelihood_position_model=9.71185	log10_strand_likelihood_position_model=1.46669	new_cov=0/6	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=85/109	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=85/115
RA	310	.	NC_007779	2862772	0	A	.	bias_e_value=1875310	bias_p_value=0.403611	fisher_strand_p_value=0.134423	frequency=2.125168e-02	genotype_quality=736.8	ks_quality_p_value=0.997898	log10_base_likelihood=-10.2337	log10_qual_likelihood_position_model=5.91498	log10_strand_likelihood_position_model=0.996978	new_cov=0/4	polymorphism_quality=4.8	quality=4.8	quality_position_model=3.98934e-05	ref_cov=81/102	reject=POLYMORPHISM_STRAND	tot_cov=82/106
RA	311	.	NC_007779	2862781	0	C	G	bias_e_value=1222520	bias_p_value=0.263115	fisher_strand_p_value=0.142014	frequency=2.081203e-02	genotype_quality=780.0	ks_quality_p_value=0.511486	log10_base_likelihood=-9.93176	log10_qual_likelihood_position_model=3.91197	log10_strand_likelihood_position_model=0.94619	new_cov=0/4	polymorphism_quality=4.5	quality=4.5	quality_position_model=5.81993e-07	ref_cov=80/108	reject=POLYMORPHISM_STRAND	tot_cov=80/112
RA	312	.	NC_007779	2862783	1	.	T	bias_e_value=1934160	bias_p_value=0.416277	fisher_strand_p_value=0.140553	frequency=2.149773e-02	genotype_quality=894.1	ks_quality_p_value=0.999764	log10_base_likelihood=-12.6878	log10_qual_likelihood_position_model=7.68374	log10_strand_likelihood_position_model=0.954651	new_cov=0/4	polymorphism_quality=7.3	quality=7.3	quality_position_model=6.82695e-06	ref_cov=78/104	reject=POLYMORPHISM_STRAND	tot_cov=78/108
RA	313	.	NC_007779	2864518	0	T	G	bias_e_value=0.00028017	bias_p_value=6.02991e-11	fisher_strand_p_value=2.16445e-12	frequency=7.195711e-02	genotype_quality=535.7	ks_quality_p_value=1	log10_base_likelihood=-5.91012	log10_qual_likelihood_position_model=22.2754	log10_strand_likelihood_position_model=11.6647	new_cov=24/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=40/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=65/107
RA	314	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1106.4	new_cov=127/127	quality=1106.4	ref_cov=0/0	tot_cov=127/127
RA	315	.	NC_007779	2895131	0	A	C	bias_e_value=9.67945e-05	bias_p_value=2.08324e-11	fisher_strand_p_value=7.19342e-13	frequency=8.020306e-02	genotype_quality=536.3	ks_quality_p_value=1	log10_base_likelihood=-6.44915	log10_qual_likelihood_position_model=25.2573	log10_strand_likelihood_position_model=12.1431	new_cov=0/22	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=110/32	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/54
RA	316	.	NC_007779	2898837	0	G	T	bias_e_value=0.0382968	bias_p_value=8.24237e-09	fisher_strand_p_value=3.62493e-10	frequency=5.691910e-02	genotype_quality=824.5	ks_quality_p_value=1	log10_base_likelihood=-8.95698	log10_qual_likelihood_position_model=17.4634	log10_strand_likelihood_position_model=9.4407	new_cov=0/22	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=147/76	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/99
RA	317	.	NC_007779	2898953	1	.	A	bias_e_value=4488720	bias_p_value=0.966079	fisher_strand_p_value=1	frequency=8.193970e-03	genotype_quality=1194.7	ks_quality_p_value=0.751106	log10_base_likelihood=-6.93723	log10_qual_likelihood_position_model=2.71609	log10_strand_likelihood_position_model=0.299276	new_cov=1/1	polymorphism_quality=1.4	quality=1.4	quality_position_model=9.2921e-06	ref_cov=122/120	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/121
RA	318	.	NC_007779	2911644	0	G	T	bias_e_value=88.5508	bias_p_value=1.90582e-05	fisher_strand_p_value=1.56171e-06	frequency=7.020807e-02	genotype_quality=613.1	ks_quality_p_value=0.838995	log10_base_likelihood=-12.7166	log10_qual_likelihood_position_model=18.4201	log10_strand_likelihood_position_model=5.99254	new_cov=0/19	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=99/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=99/102
RA	319	.	NC_007779	2926157	0	T	G	bias_e_value=3.62958e-09	bias_p_value=7.81172e-16	fisher_strand_p_value=1.9796e-17	frequency=1.003222e-01	genotype_quality=485.4	ks_quality_p_value=1	log10_base_likelihood=-10.0004	log10_qual_likelihood_position_model=23.969	log10_strand_likelihood_position_model=16.7034	new_cov=21/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=11/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=32/110
RA	320	.	NC_007779	2953752	1	.	C	bias_e_value=2512930	bias_p_value=0.540841	fisher_strand_p_value=1	frequency=9.049416e-03	genotype_quality=1053.1	ks_quality_p_value=0.211996	log10_base_likelihood=-8.20278	log10_qual_likelihood_position_model=1.84172	log10_strand_likelihood_position_model=0.300566	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=5.52058e-08	ref_cov=103/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/117
RA	321	.	NC_007779	2953753	0	C	.	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=1.331615e-02	genotype_quality=900.4	ks_quality_p_value=0.99952	log10_base_likelihood=-7.72847	log10_qual_likelihood_position_model=2.75883	log10_strand_likelihood_position_model=0.404162	new_cov=1/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.96901e-06	ref_cov=106/116	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/118
RA	322	.	NC_007779	2980838	0	T	.	bias_e_value=3829980	bias_p_value=0.824302	fisher_strand_p_value=0.600662	frequency=1.208878e-02	genotype_quality=990.4	ks_quality_p_value=0.78124	log10_base_likelihood=-8.26854	log10_qual_likelihood_position_model=1.29192	log10_strand_likelihood_position_model=0.455233	new_cov=2/1	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.84553e-08	ref_cov=114/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/132
RA	323	.	NC_007779	2987535	0	A	C	bias_e_value=0.000383187	bias_p_value=8.24708e-11	fisher_strand_p_value=2.99524e-12	frequency=9.349775e-02	genotype_quality=740.3	ks_quality_p_value=1	log10_base_likelihood=-16.0099	log10_qual_likelihood_position_model=35.2527	log10_strand_likelihood_position_model=11.5236	new_cov=0/32	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=129/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/116
RA	324	.	NC_007779	2994664	0	T	.	bias_e_value=133578	bias_p_value=0.0287491	fisher_strand_p_value=0.0976635	frequency=1.309395e-02	genotype_quality=926.4	ks_quality_p_value=0.0459489	log10_base_likelihood=-8.60755	log10_qual_likelihood_position_model=1.63516	log10_strand_likelihood_position_model=1.01027	new_cov=0/3	polymorphism_quality=3.1	quality=3.1	quality_position_model=6.97739e-08	ref_cov=123/103	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/106
RA	325	.	NC_007779	3002577	0	T	G	bias_e_value=0.570732	bias_p_value=1.22835e-07	fisher_strand_p_value=6.17159e-09	frequency=4.022121e-02	genotype_quality=678.8	ks_quality_p_value=1	log10_base_likelihood=-5.70961	log10_qual_likelihood_position_model=21.5329	log10_strand_likelihood_position_model=8.2096	new_cov=23/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=77/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/113
RA	326	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=855.2	new_cov=111/100	quality=855.2	ref_cov=0/0	tot_cov=111/100
RA	327	.	NC_007779	3029385	0	C	A	bias_e_value=1221.22	bias_p_value=0.000262836	fisher_strand_p_value=2.24571e-05	frequency=3.902435e-02	genotype_quality=593.1	ks_quality_p_value=1	log10_base_likelihood=-7.14861	log10_qual_likelihood_position_model=10.2692	log10_strand_likelihood_position_model=4.64865	new_cov=0/7	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=119/29	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/36
RA	328	.	NC_007779	3034413	0	A	C	bias_e_value=7.45162e-07	bias_p_value=1.60376e-13	fisher_strand_p_value=4.71873e-15	frequency=8.696079e-02	genotype_quality=527.1	ks_quality_p_value=1	log10_base_likelihood=-7.39254	log10_qual_likelihood_position_model=25.7472	log10_strand_likelihood_position_model=14.3262	new_cov=0/27	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=108/32	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/59
RA	329	.	NC_007779	3035390	0	T	C	bias_e_value=1.32803e-05	bias_p_value=2.85824e-12	fisher_strand_p_value=9.21558e-14	frequency=1.397538e-01	genotype_quality=433.6	ks_quality_p_value=1	log10_base_likelihood=-28.3498	log10_qual_likelihood_position_model=19.5184	log10_strand_likelihood_position_model=13.04	new_cov=1/26	polymorphism_quality=23.1	quality=23.1	quality_position_model=Inf	ref_cov=119/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/60
RA	330	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=985.0	new_cov=115/128	quality=985.0	ref_cov=0/0	tot_cov=115/128
RA	331	.	NC_007779	3074129	0	G	T	bias_e_value=63.3228	bias_p_value=1.36285e-05	fisher_strand_p_value=9.14358e-07	frequency=5.336142e-02	genotype_quality=770.4	ks_quality_p_value=1	log10_base_likelihood=-6.65128	log10_qual_likelihood_position_model=16.2635	log10_strand_likelihood_position_model=6.25418	new_cov=0/22	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=113/111	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/133
RA	332	.	NC_007779	3088549	0	G	T	bias_e_value=30.0836	bias_p_value=6.47469e-06	fisher_strand_p_value=4.13814e-07	frequency=7.168293e-02	genotype_quality=747.8	ks_quality_p_value=0.996498	log10_base_likelihood=-10.4459	log10_qual_likelihood_position_model=18.6488	log10_strand_likelihood_position_model=6.43305	new_cov=0/27	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=105/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/157
RA	333	.	NC_007779	3110532	0	C	A	bias_e_value=19712.1	bias_p_value=0.00424251	fisher_strand_p_value=0.000502902	frequency=3.682423e-02	genotype_quality=543.3	ks_quality_p_value=0.979087	log10_base_likelihood=-8.28429	log10_qual_likelihood_position_model=9.08359	log10_strand_likelihood_position_model=3.29852	new_cov=0/6	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=103/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/43
RA	334	.	NC_007779	3124070	0	G	.	bias_e_value=2830600	bias_p_value=0.609212	fisher_strand_p_value=0.603066	frequency=1.522160e-02	genotype_quality=813.9	ks_quality_p_value=0.429867	log10_base_likelihood=-8.76161	log10_qual_likelihood_position_model=2.389	log10_strand_likelihood_position_model=0.450332	new_cov=2/1	polymorphism_quality=3.3	quality=3.3	quality_position_model=7.67183e-08	ref_cov=91/103	reject=POLYMORPHISM_STRAND	tot_cov=93/104
RA	335	.	NC_007779	3124071	0	C	.	bias_e_value=3071800	bias_p_value=0.661124	fisher_strand_p_value=0.602852	frequency=1.537704e-02	genotype_quality=808.6	ks_quality_p_value=0.497541	log10_base_likelihood=-8.73521	log10_qual_likelihood_position_model=1.75784	log10_strand_likelihood_position_model=0.450606	new_cov=2/1	polymorphism_quality=3.3	quality=3.3	quality_position_model=1.82215e-08	ref_cov=90/102	reject=POLYMORPHISM_STRAND	tot_cov=92/103
RA	336	.	NC_007779	3147621	0	G	T	bias_e_value=9.43701	bias_p_value=2.03107e-06	fisher_strand_p_value=1.20078e-07	frequency=6.733274e-02	genotype_quality=515.9	ks_quality_p_value=0.99871	log10_base_likelihood=-7.04531	log10_qual_likelihood_position_model=13.7826	log10_strand_likelihood_position_model=6.92054	new_cov=0/17	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=99/55	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/73
RA	337	.	NC_007779	3162929	0	G	C	bias_e_value=55197.2	bias_p_value=0.0118797	fisher_strand_p_value=0.00164275	frequency=2.959061e-02	genotype_quality=666.8	ks_quality_p_value=0.972021	log10_base_likelihood=-6.29156	log10_qual_likelihood_position_model=10.0401	log10_strand_likelihood_position_model=2.78443	new_cov=8/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=81/105	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=89/105
RA	338	.	NC_007779	3188902	1	.	A	bias_e_value=2146610	bias_p_value=0.462001	fisher_strand_p_value=0.240118	frequency=8.849144e-03	genotype_quality=1107.9	ks_quality_p_value=0.686475	log10_base_likelihood=-8.41683	log10_qual_likelihood_position_model=1.09905	log10_strand_likelihood_position_model=0.619575	new_cov=0/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.21291e-08	ref_cov=115/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/111
RA	339	.	NC_007779	3195962	0	G	T	bias_e_value=13.6243	bias_p_value=2.93227e-06	fisher_strand_p_value=1.77221e-07	frequency=9.255219e-02	genotype_quality=570.4	ks_quality_p_value=1	log10_base_likelihood=-12.7951	log10_qual_likelihood_position_model=16.6725	log10_strand_likelihood_position_model=6.83127	new_cov=0/24	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=89/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=89/110
RA	340	.	NC_007779	3216602	0	C	A	bias_e_value=264822	bias_p_value=0.056996	fisher_strand_p_value=0.0299304	frequency=2.611542e-02	genotype_quality=919.7	ks_quality_p_value=0.340975	log10_base_likelihood=-11.7052	log10_qual_likelihood_position_model=7.26954	log10_strand_likelihood_position_model=1.73266	new_cov=0/6	polymorphism_quality=6.3	quality=6.3	quality_position_model=0.000181787	ref_cov=110/113	reject=POLYMORPHISM_STRAND	tot_cov=110/119
RA	341	.	NC_007779	3216614	0	C	T	bias_e_value=471927	bias_p_value=0.10157	fisher_strand_p_value=0.0296398	frequency=2.629566e-02	genotype_quality=923.0	ks_quality_p_value=0.703637	log10_base_likelihood=-11.5068	log10_qual_likelihood_position_model=4.65849	log10_strand_likelihood_position_model=1.75468	new_cov=0/6	polymorphism_quality=6.1	quality=6.1	quality_position_model=5.54751e-07	ref_cov=110/111	reject=POLYMORPHISM_STRAND	tot_cov=110/117
RA	342	.	NC_007779	3216644	0	A	G	bias_e_value=148263	bias_p_value=0.0319098	fisher_strand_p_value=0.00943082	frequency=2.582073e-02	genotype_quality=890.9	ks_quality_p_value=0.538559	log10_base_likelihood=-13.8974	log10_qual_likelihood_position_model=4.64984	log10_strand_likelihood_position_model=2.02545	new_cov=0/6	polymorphism_quality=8.5	quality=8.5	quality_position_model=3.50321e-09	ref_cov=124/102	reject=POLYMORPHISM_STRAND	tot_cov=124/108
RA	343	.	NC_007779	3216647	0	C	A	bias_e_value=234576	bias_p_value=0.0504862	fisher_strand_p_value=0.00890688	frequency=2.578735e-02	genotype_quality=976.8	ks_quality_p_value=0.988848	log10_base_likelihood=-12.6222	log10_qual_likelihood_position_model=5.55123	log10_strand_likelihood_position_model=2.05027	new_cov=0/6	polymorphism_quality=7.2	quality=7.2	quality_position_model=6.60602e-07	ref_cov=125/101	reject=POLYMORPHISM_STRAND	tot_cov=125/107
RA	344	.	NC_007779	3223274	0	G	T	bias_e_value=3758.65	bias_p_value=0.00080895	fisher_strand_p_value=7.72775e-05	frequency=3.782272e-02	genotype_quality=623.3	ks_quality_p_value=1	log10_base_likelihood=-5.8127	log10_qual_likelihood_position_model=11.1151	log10_strand_likelihood_position_model=4.13239	new_cov=0/15	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=92/96	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=93/111
RA	345	.	NC_007779	3231832	1	.	G	bias_e_value=1497600	bias_p_value=0.322319	fisher_strand_p_value=0.111105	frequency=1.063824e-02	genotype_quality=928.6	ks_quality_p_value=0.869247	log10_base_likelihood=-8.18338	log10_qual_likelihood_position_model=0.887416	log10_strand_likelihood_position_model=0.954267	new_cov=2/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.82833e-08	ref_cov=61/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=63/125
RA	346	.	NC_007779	3239641	0	T	G	bias_e_value=2.86473	bias_p_value=6.16558e-07	fisher_strand_p_value=3.38758e-08	frequency=4.651260e-02	genotype_quality=637.7	ks_quality_p_value=1	log10_base_likelihood=-5.67666	log10_qual_likelihood_position_model=13.786	log10_strand_likelihood_position_model=7.47011	new_cov=16/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=57/126	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/126
RA	347	.	NC_007779	3243783	1	.	T	bias_e_value=2561640	bias_p_value=0.551326	fisher_strand_p_value=0.500507	frequency=1.058197e-02	genotype_quality=889.7	ks_quality_p_value=0.437207	log10_base_likelihood=-8.0839	log10_qual_likelihood_position_model=2.59638	log10_strand_likelihood_position_model=0.537698	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=7.82834e-07	ref_cov=87/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=87/102
RA	348	.	NC_007779	3280326	0	A	C	bias_e_value=0.000875333	bias_p_value=1.88392e-10	fisher_strand_p_value=7.06216e-12	frequency=6.662893e-02	genotype_quality=583.0	ks_quality_p_value=1	log10_base_likelihood=-8.3676	log10_qual_likelihood_position_model=20.0562	log10_strand_likelihood_position_model=11.1511	new_cov=0/23	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=116/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/68
RA	349	.	NC_007779	3300073	0	T	G	bias_e_value=2.35876e-05	bias_p_value=5.07661e-12	fisher_strand_p_value=1.66876e-13	frequency=1.612487e-01	genotype_quality=455.0	ks_quality_p_value=1	log10_base_likelihood=-25.784	log10_qual_likelihood_position_model=30.2631	log10_strand_likelihood_position_model=12.8218	new_cov=37/0	polymorphism_quality=20.6	quality=20.6	quality_position_model=Inf	ref_cov=51/84	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=89/84
RA	350	.	NC_007779	3305552	1	.	C	bias_e_value=2149990	bias_p_value=0.462729	fisher_strand_p_value=0.220321	frequency=9.049416e-03	genotype_quality=1046.7	ks_quality_p_value=0.749993	log10_base_likelihood=-8.10225	log10_qual_likelihood_position_model=2.57287	log10_strand_likelihood_position_model=0.656944	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.42391e-07	ref_cov=117/102	reject=POLYMORPHISM_STRAND	tot_cov=117/104
RA	351	.	NC_007779	3362667	0	A	.	bias_e_value=4123180	bias_p_value=0.887405	fisher_strand_p_value=0.61444	frequency=1.218700e-02	genotype_quality=994.6	ks_quality_p_value=0.919052	log10_base_likelihood=-8.25624	log10_qual_likelihood_position_model=2.22415	log10_strand_likelihood_position_model=0.435271	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.66668e-07	ref_cov=125/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/120
RA	352	.	NC_007779	3385700	1	.	T	bias_e_value=852523	bias_p_value=0.183483	fisher_strand_p_value=0.119832	frequency=1.388931e-02	genotype_quality=1025.6	ks_quality_p_value=0.37266	log10_base_likelihood=-13.5439	log10_qual_likelihood_position_model=1.64143	log10_strand_likelihood_position_model=0.921427	new_cov=0/3	polymorphism_quality=8.2	quality=8.2	quality_position_model=4.99505e-13	ref_cov=109/104	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=109/107
RA	353	.	NC_007779	3389914	0	A	C	bias_e_value=1.94116e-11	bias_p_value=4.17783e-18	fisher_strand_p_value=9.32149e-20	frequency=1.418743e-01	genotype_quality=631.4	ks_quality_p_value=1	log10_base_likelihood=-15.638	log10_qual_likelihood_position_model=34.2392	log10_strand_likelihood_position_model=19.0305	new_cov=0/49	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=116/57	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/107
RA	354	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=995.4	new_cov=124/108	quality=995.4	ref_cov=0/0	tot_cov=124/108
RA	355	.	NC_007779	3404070	0	T	G	bias_e_value=2.62727	bias_p_value=5.65451e-07	fisher_strand_p_value=3.09123e-08	frequency=7.479620e-02	genotype_quality=633.3	ks_quality_p_value=1	log10_base_likelihood=-9.71336	log10_qual_likelihood_position_model=20.5853	log10_strand_likelihood_position_model=7.76581	new_cov=26/0	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=87/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=114/99
RA	356	.	NC_007779	3412753	0	C	T	bias_e_value=2.56073	bias_p_value=5.51129e-07	fisher_strand_p_value=3.00847e-08	frequency=5.395222e-02	genotype_quality=765.1	ks_quality_p_value=1	log10_base_likelihood=-8.02737	log10_qual_likelihood_position_model=18.3798	log10_strand_likelihood_position_model=7.52165	new_cov=0/15	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=143/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/73
RA	357	.	NC_007779	3412772	0	A	C	bias_e_value=0.000324321	bias_p_value=6.98016e-11	fisher_strand_p_value=2.51927e-12	frequency=4.354382e-02	genotype_quality=680.6	ks_quality_p_value=1	log10_base_likelihood=-5.59038	log10_qual_likelihood_position_model=20.6933	log10_strand_likelihood_position_model=11.5987	new_cov=0/18	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=147/34	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/52
RA	358	.	NC_007779	3431259	0	T	G	bias_e_value=388549	bias_p_value=0.0836248	fisher_strand_p_value=0.0163545	frequency=2.779388e-02	genotype_quality=736.4	ks_quality_p_value=1	log10_base_likelihood=-7.92282	log10_qual_likelihood_position_model=9.45469	log10_strand_likelihood_position_model=1.89578	new_cov=0/7	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=90/100	reject=POLYMORPHISM_STRAND	tot_cov=90/107
RA	359	.	NC_007779	3439587	0	A	C	bias_e_value=94092.9	bias_p_value=0.020251	fisher_strand_p_value=0.00296966	frequency=3.753376e-02	genotype_quality=800.7	ks_quality_p_value=1	log10_base_likelihood=-7.86505	log10_qual_likelihood_position_model=13.6781	log10_strand_likelihood_position_model=2.68016	new_cov=11/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=115/91	reject=POLYMORPHISM_STRAND	tot_cov=126/91
RA	360	.	NC_007779	3439598	1	.	T	bias_e_value=2860090	bias_p_value=0.615558	fisher_strand_p_value=0.264142	frequency=1.546288e-02	genotype_quality=920.3	ks_quality_p_value=0.999353	log10_base_likelihood=-11.2008	log10_qual_likelihood_position_model=3.64715	log10_strand_likelihood_position_model=0.720727	new_cov=3/0	polymorphism_quality=5.8	quality=5.8	quality_position_model=8.81096e-09	ref_cov=109/82	reject=POLYMORPHISM_STRAND	tot_cov=112/82
RA	361	.	NC_007779	3439601	0	G	T	bias_e_value=496175	bias_p_value=0.106788	fisher_strand_p_value=0.0222239	frequency=3.582859e-02	genotype_quality=790.1	ks_quality_p_value=0.999615	log10_base_likelihood=-8.98051	log10_qual_likelihood_position_model=10.4273	log10_strand_likelihood_position_model=1.86702	new_cov=8/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=115/85	reject=POLYMORPHISM_STRAND	tot_cov=123/85
RA	362	.	NC_007779	3439605	0	T	C	bias_e_value=105588	bias_p_value=0.0227251	fisher_strand_p_value=0.00339992	frequency=3.864670e-02	genotype_quality=747.4	ks_quality_p_value=1	log10_base_likelihood=-7.97314	log10_qual_likelihood_position_model=15.0203	log10_strand_likelihood_position_model=2.55255	new_cov=11/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=113/84	reject=POLYMORPHISM_STRAND	tot_cov=124/84
RA	363	.	NC_007779	3439607	0	G	T	bias_e_value=105588	bias_p_value=0.0227251	fisher_strand_p_value=0.00339992	frequency=4.100895e-02	genotype_quality=813.6	ks_quality_p_value=1	log10_base_likelihood=-10.3845	log10_qual_likelihood_position_model=12.8328	log10_strand_likelihood_position_model=2.55255	new_cov=11/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=113/84	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=124/84
RA	364	.	NC_007779	3440270	0	C	A	bias_e_value=3.08846	bias_p_value=6.64708e-07	fisher_strand_p_value=3.66817e-08	frequency=6.695700e-02	genotype_quality=677.3	ks_quality_p_value=1	log10_base_likelihood=-11.5701	log10_qual_likelihood_position_model=15.2514	log10_strand_likelihood_position_model=7.43555	new_cov=19/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=73/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=94/121
RA	365	.	NC_007779	3440600	0	A	C	bias_e_value=0.0769588	bias_p_value=1.65634e-08	fisher_strand_p_value=7.52625e-10	frequency=6.278563e-02	genotype_quality=616.0	ks_quality_p_value=1	log10_base_likelihood=-8.81255	log10_qual_likelihood_position_model=18.2192	log10_strand_likelihood_position_model=9.12342	new_cov=0/21	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=118/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/80
RA	366	.	NC_007779	3441442	0	C	A	bias_e_value=74.5465	bias_p_value=1.60442e-05	fisher_strand_p_value=1.08921e-06	frequency=6.419134e-02	genotype_quality=646.6	ks_quality_p_value=1	log10_base_likelihood=-9.23838	log10_qual_likelihood_position_model=18.552	log10_strand_likelihood_position_model=6.00972	new_cov=20/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=87/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/97
RA	367	.	NC_007779	3475527	0	T	G	bias_e_value=1.68211e-06	bias_p_value=3.6203e-13	fisher_strand_p_value=1.09216e-14	frequency=1.242371e-01	genotype_quality=608.2	ks_quality_p_value=1	log10_base_likelihood=-21.5901	log10_qual_likelihood_position_model=27.0459	log10_strand_likelihood_position_model=13.9617	new_cov=38/0	polymorphism_quality=16.3	quality=16.3	quality_position_model=Inf	ref_cov=62/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/107
RA	368	.	NC_007779	3475533	0	C	T	bias_e_value=0.0917888	bias_p_value=1.97551e-08	fisher_strand_p_value=9.05251e-10	frequency=1.121802e-01	genotype_quality=627.8	ks_quality_p_value=1	log10_base_likelihood=-24.5275	log10_qual_likelihood_position_model=26.998	log10_strand_likelihood_position_model=9.04323	new_cov=26/0	polymorphism_quality=19.3	quality=19.3	quality_position_model=Inf	ref_cov=79/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=105/114
RA	369	.	NC_007779	3475539	0	G	T	bias_e_value=135437	bias_p_value=0.0291493	fisher_strand_p_value=0.00475724	frequency=3.123665e-02	genotype_quality=690.6	ks_quality_p_value=0.958888	log10_base_likelihood=-7.50804	log10_qual_likelihood_position_model=7.25609	log10_strand_likelihood_position_model=2.32264	new_cov=6/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=73/110	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=79/110
RA	370	.	NC_007779	3487963	0	C	A	bias_e_value=12833.5	bias_p_value=0.00276206	fisher_strand_p_value=0.000303521	frequency=2.721691e-02	genotype_quality=851.1	ks_quality_p_value=1	log10_base_likelihood=-7.09445	log10_qual_likelihood_position_model=11.8261	log10_strand_likelihood_position_model=3.51781	new_cov=11/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=108/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/124
RA	371	.	NC_007779	3499066	0	A	C	bias_e_value=0.0010838	bias_p_value=2.33259e-10	fisher_strand_p_value=8.81745e-12	frequency=7.497311e-02	genotype_quality=699.7	ks_quality_p_value=1	log10_base_likelihood=-15.0882	log10_qual_likelihood_position_model=22.2698	log10_strand_likelihood_position_model=11.0547	new_cov=0/17	polymorphism_quality=9.7	quality=9.7	quality_position_model=Inf	ref_cov=148/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=148/51
RA	372	.	NC_007779	3523734	0	G	T	bias_e_value=2.61719	bias_p_value=5.63281e-07	fisher_strand_p_value=3.07868e-08	frequency=7.442856e-02	genotype_quality=760.9	ks_quality_p_value=1	log10_base_likelihood=-15.5322	log10_qual_likelihood_position_model=18.7091	log10_strand_likelihood_position_model=7.54076	new_cov=0/25	polymorphism_quality=10.2	quality=10.2	quality_position_model=Inf	ref_cov=119/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/131
RA	373	.	NC_007779	3523812	0	T	.	bias_e_value=3999740	bias_p_value=0.860839	fisher_strand_p_value=0.616162	frequency=1.184940e-02	genotype_quality=1013.1	ks_quality_p_value=0.845915	log10_base_likelihood=-8.2245	log10_qual_likelihood_position_model=2.0704	log10_strand_likelihood_position_model=0.433157	new_cov=2/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.23957e-07	ref_cov=122/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/129
RA	374	.	NC_007779	3543547	0	A	C	bias_e_value=4.9439e-08	bias_p_value=1.06404e-14	fisher_strand_p_value=2.89307e-16	frequency=1.705990e-01	genotype_quality=652.0	ks_quality_p_value=1	log10_base_likelihood=-37.6773	log10_qual_likelihood_position_model=44.6643	log10_strand_likelihood_position_model=15.8071	new_cov=0/53	polymorphism_quality=32.5	quality=32.5	quality_position_model=Inf	ref_cov=110/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/139
RA	375	.	NC_007779	3560478	0	G	T	bias_e_value=843.729	bias_p_value=0.00018159	fisher_strand_p_value=1.49981e-05	frequency=5.933619e-02	genotype_quality=741.7	ks_quality_p_value=1	log10_base_likelihood=-11.5083	log10_qual_likelihood_position_model=13.1108	log10_strand_likelihood_position_model=4.85567	new_cov=0/19	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=100/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/134
RA	376	.	NC_007779	3573438	0	C	A	bias_e_value=116.414	bias_p_value=2.5055e-05	fisher_strand_p_value=1.93267e-06	frequency=4.262161e-02	genotype_quality=835.7	ks_quality_p_value=0.909666	log10_base_likelihood=-6.8744	log10_qual_likelihood_position_model=20.9737	log10_strand_likelihood_position_model=5.71384	new_cov=17/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=105/133	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/133
RA	377	.	NC_007779	3576400	1	.	A	bias_e_value=539046	bias_p_value=0.116015	fisher_strand_p_value=0.497817	frequency=8.849144e-03	genotype_quality=1102.2	ks_quality_p_value=0.0495633	log10_base_likelihood=-8.32183	log10_qual_likelihood_position_model=1.73781	log10_strand_likelihood_position_model=0.596308	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=6.56492e-08	ref_cov=112/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/112
RA	378	.	NC_007779	3576401	0	A	.	bias_e_value=476335	bias_p_value=0.102518	fisher_strand_p_value=0.246754	frequency=1.315117e-02	genotype_quality=920.0	ks_quality_p_value=0.0855149	log10_base_likelihood=-8.50878	log10_qual_likelihood_position_model=2.05388	log10_strand_likelihood_position_model=0.897388	new_cov=3/0	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.83058e-07	ref_cov=112/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/113
RA	379	.	NC_007779	3580297	0	G	T	bias_e_value=0.130356	bias_p_value=2.80557e-08	fisher_strand_p_value=1.30765e-09	frequency=8.944654e-02	genotype_quality=782.5	ks_quality_p_value=1	log10_base_likelihood=-17.4863	log10_qual_likelihood_position_model=19.1123	log10_strand_likelihood_position_model=8.92262	new_cov=0/31	polymorphism_quality=12.2	quality=12.2	quality_position_model=Inf	ref_cov=118/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/141
RA	380	.	NC_007779	3580566	0	T	G	bias_e_value=0.0884051	bias_p_value=1.90269e-08	fisher_strand_p_value=8.7031e-10	frequency=8.693409e-02	genotype_quality=700.0	ks_quality_p_value=1	log10_base_likelihood=-9.40026	log10_qual_likelihood_position_model=28.31	log10_strand_likelihood_position_model=9.10399	new_cov=29/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=93/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/114
RA	381	.	NC_007779	3609448	0	A	T	bias_e_value=5.64773	bias_p_value=1.21552e-06	fisher_strand_p_value=6.95321e-08	frequency=6.091976e-02	genotype_quality=723.4	ks_quality_p_value=1	log10_base_likelihood=-14.9802	log10_qual_likelihood_position_model=18.5949	log10_strand_likelihood_position_model=7.15781	new_cov=13/0	polymorphism_quality=9.6	quality=9.6	quality_position_model=Inf	ref_cov=48/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=61/140
RA	382	.	NC_007779	3651641	0	G	C	bias_e_value=379560	bias_p_value=0.0816902	fisher_strand_p_value=0.0158858	frequency=2.384090e-02	genotype_quality=1079.2	ks_quality_p_value=1	log10_base_likelihood=-10.0759	log10_qual_likelihood_position_model=8.9069	log10_strand_likelihood_position_model=1.93756	new_cov=7/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=134/123	reject=POLYMORPHISM_STRAND	tot_cov=141/123
RA	383	.	NC_007779	3654011	1	.	C	bias_e_value=1538770	bias_p_value=0.33118	fisher_strand_p_value=0.110145	frequency=8.652687e-03	genotype_quality=1090.2	ks_quality_p_value=0.911531	log10_base_likelihood=-5.81145	log10_qual_likelihood_position_model=3.42431	log10_strand_likelihood_position_model=0.958035	new_cov=0/2	polymorphism_quality=0.3	quality=0.3	quality_position_model=0.00449895	ref_cov=154/75	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/77
RA	384	.	NC_007779	3659516	0	C	A	bias_e_value=2252.83	bias_p_value=0.000484863	fisher_strand_p_value=4.39487e-05	frequency=3.883266e-02	genotype_quality=852.5	ks_quality_p_value=1	log10_base_likelihood=-6.59934	log10_qual_likelihood_position_model=13.3351	log10_strand_likelihood_position_model=4.49192	new_cov=15/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=115/122	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/122
RA	385	.	NC_007779	3662675	0	A	.	bias_e_value=2752050	bias_p_value=0.592306	fisher_strand_p_value=1	frequency=1.118565e-02	genotype_quality=1065.7	ks_quality_p_value=0.246935	log10_base_likelihood=-8.12752	log10_qual_likelihood_position_model=1.65105	log10_strand_likelihood_position_model=0.414876	new_cov=2/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.50617e-08	ref_cov=135/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/131
RA	386	.	NC_007779	3673380	0	G	T	bias_e_value=65.5996	bias_p_value=1.41186e-05	fisher_strand_p_value=1.35407e-06	frequency=6.311750e-02	genotype_quality=687.3	ks_quality_p_value=0.701327	log10_base_likelihood=-11.3639	log10_qual_likelihood_position_model=22.8723	log10_strand_likelihood_position_model=5.91181	new_cov=0/22	polymorphism_quality=6.0	quality=6.0	quality_position_model=Inf	ref_cov=103/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/132
RA	387	.	NC_007779	3686205	0	A	.	bias_e_value=74807.1	bias_p_value=0.0161003	fisher_strand_p_value=0.246312	frequency=1.537800e-02	genotype_quality=774.1	ks_quality_p_value=0.00922297	log10_base_likelihood=-8.81836	log10_qual_likelihood_position_model=2.77903	log10_strand_likelihood_position_model=0.889761	new_cov=3/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=4.85236e-07	ref_cov=96/96	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/96
RA	388	.	NC_007779	3688858	0	A	C	bias_e_value=2.33345e-11	bias_p_value=5.02214e-18	fisher_strand_p_value=1.12526e-19	frequency=9.190130e-02	genotype_quality=674.9	ks_quality_p_value=1	log10_base_likelihood=-10.7689	log10_qual_likelihood_position_model=29.6821	log10_strand_likelihood_position_model=18.9487	new_cov=0/36	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=140/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=140/78
RA	389	.	NC_007779	3701118	0	G	T	bias_e_value=2.18174e-05	bias_p_value=4.69562e-12	fisher_strand_p_value=1.53944e-13	frequency=1.005344e-01	genotype_quality=840.0	ks_quality_p_value=1	log10_base_likelihood=-19.9975	log10_qual_likelihood_position_model=25.2557	log10_strand_likelihood_position_model=12.8126	new_cov=0/35	polymorphism_quality=14.7	quality=14.7	quality_position_model=Inf	ref_cov=142/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/125
RA	390	.	NC_007779	3711109	0	C	A	bias_e_value=0.0131865	bias_p_value=2.83804e-09	fisher_strand_p_value=1.18985e-10	frequency=1.072469e-01	genotype_quality=672.7	ks_quality_p_value=1	log10_base_likelihood=-14.7076	log10_qual_likelihood_position_model=20.068	log10_strand_likelihood_position_model=10.1716	new_cov=33/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=92/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/112
RA	391	.	NC_007779	3731041	1	.	T	bias_e_value=3727080	bias_p_value=0.802154	fisher_strand_p_value=1	frequency=1.606464e-02	genotype_quality=1194.1	ks_quality_p_value=0.441126	log10_base_likelihood=-17.9181	log10_qual_likelihood_position_model=2.36461	log10_strand_likelihood_position_model=0.423152	new_cov=2/2	polymorphism_quality=12.6	quality=12.6	quality_position_model=3.03258e-17	ref_cov=119/126	reject=INDEL_HOMOPOLYMER	tot_cov=121/128
RA	392	.	NC_007779	3732310	0	G	T	bias_e_value=0.00167209	bias_p_value=3.59872e-10	fisher_strand_p_value=1.38394e-11	frequency=8.991241e-02	genotype_quality=785.9	ks_quality_p_value=1	log10_base_likelihood=-16.7111	log10_qual_likelihood_position_model=20.1172	log10_strand_likelihood_position_model=10.8589	new_cov=0/30	polymorphism_quality=11.4	quality=11.4	quality_position_model=Inf	ref_cov=134/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/118
RA	393	.	NC_007779	3741455	0	T	G	bias_e_value=0.0685693	bias_p_value=1.47577e-08	fisher_strand_p_value=6.66914e-10	frequency=4.820108e-02	genotype_quality=790.1	ks_quality_p_value=1	log10_base_likelihood=-5.65406	log10_qual_likelihood_position_model=21.7591	log10_strand_likelihood_position_model=9.17593	new_cov=25/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=89/135	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/135
RA	394	.	NC_007779	3741461	0	A	T	bias_e_value=1888.4	bias_p_value=0.000406429	fisher_strand_p_value=3.62031e-05	frequency=4.523087e-02	genotype_quality=826.2	ks_quality_p_value=1	log10_base_likelihood=-9.54143	log10_qual_likelihood_position_model=18.5465	log10_strand_likelihood_position_model=4.44125	new_cov=12/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=91/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=103/131
RA	395	.	NC_007779	3750122	0	C	.	bias_e_value=1100950	bias_p_value=0.23695	fisher_strand_p_value=1	frequency=9.581585e-01	genotype_quality=1097.1	ks_quality_p_value=0.06292	log10_base_likelihood=-48.3951	log10_qual_likelihood_position_model=5.6828	log10_strand_likelihood_position_model=0.609078	new_cov=102/127	polymorphism_quality=43.3	quality=43.3	quality_position_model=1.95212e-44	ref_cov=4/6	tot_cov=106/133
RA	396	.	NC_007779	3750123	0	C	T	bias_e_value=4641240	bias_p_value=0.998904	fisher_strand_p_value=1	frequency=3.771400e-02	genotype_quality=917.0	ks_quality_p_value=0.953555	log10_base_likelihood=-17.7152	log10_qual_likelihood_position_model=7.81208	log10_strand_likelihood_position_model=0.57638	new_cov=4/5	polymorphism_quality=12.4	quality=12.4	quality_position_model=2.43731e-11	ref_cov=102/127	tot_cov=106/133
RA	397	.	NC_007779	3758414	0	G	T	bias_e_value=10.8602	bias_p_value=2.33737e-06	fisher_strand_p_value=1.39236e-07	frequency=6.079817e-02	genotype_quality=807.7	ks_quality_p_value=1	log10_base_likelihood=-11.7451	log10_qual_likelihood_position_model=20.2876	log10_strand_likelihood_position_model=6.89359	new_cov=0/23	polymorphism_quality=6.3	quality=6.3	quality_position_model=Inf	ref_cov=120/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/132
RA	398	.	NC_007779	3780902	0	T	G	bias_e_value=3.4235	bias_p_value=7.36817e-07	fisher_strand_p_value=4.09071e-08	frequency=4.558945e-02	genotype_quality=522.5	ks_quality_p_value=1	log10_base_likelihood=-7.65132	log10_qual_likelihood_position_model=10.762	log10_strand_likelihood_position_model=7.3882	new_cov=9/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=16/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=25/117
RA	399	.	NC_007779	3788380	0	G	T	bias_e_value=15.3785	bias_p_value=3.30982e-06	fisher_strand_p_value=2.0161e-07	frequency=1.156783e-01	genotype_quality=638.6	ks_quality_p_value=1	log10_base_likelihood=-31.8978	log10_qual_likelihood_position_model=18.4933	log10_strand_likelihood_position_model=6.74708	new_cov=0/29	polymorphism_quality=26.7	quality=26.7	quality_position_model=1.33632e-08	ref_cov=84/104	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/134
RA	400	.	NC_007779	3803769	0	T	.	bias_e_value=3727990	bias_p_value=0.802351	fisher_strand_p_value=0.563389	frequency=1.374817e-02	genotype_quality=857.0	ks_quality_p_value=0.783414	log10_base_likelihood=-7.82245	log10_qual_likelihood_position_model=2.80978	log10_strand_likelihood_position_model=0.547757	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.50763e-06	ref_cov=131/84	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/86
RA	401	.	NC_007779	3812429	0	G	T	bias_e_value=4.43908	bias_p_value=9.55394e-07	fisher_strand_p_value=5.38652e-08	frequency=5.450487e-02	genotype_quality=769.0	ks_quality_p_value=1	log10_base_likelihood=-6.16609	log10_qual_likelihood_position_model=16.3857	log10_strand_likelihood_position_model=7.26869	new_cov=0/20	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=126/86	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/106
RA	402	.	NC_007779	3813810	0	T	G	bias_e_value=7.26056e-07	bias_p_value=1.56264e-13	fisher_strand_p_value=4.59412e-15	frequency=8.998442e-02	genotype_quality=580.7	ks_quality_p_value=1	log10_base_likelihood=-7.23455	log10_qual_likelihood_position_model=26.8268	log10_strand_likelihood_position_model=14.3378	new_cov=32/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=47/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/113
RA	403	.	NC_007779	3835358	1	.	A	bias_e_value=3832650	bias_p_value=0.824876	fisher_strand_p_value=0.48326	frequency=1.273918e-02	genotype_quality=768.8	ks_quality_p_value=0.972603	log10_base_likelihood=-8.89684	log10_qual_likelihood_position_model=1.24166	log10_strand_likelihood_position_model=0.391463	new_cov=1/1	polymorphism_quality=3.4	quality=3.4	quality_position_model=3.17447e-09	ref_cov=43/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=44/113
RA	404	.	NC_007779	3843373	1	.	A	bias_e_value=2071110	bias_p_value=0.445752	fisher_strand_p_value=1	frequency=1.111126e-02	genotype_quality=885.7	ks_quality_p_value=0.155957	log10_base_likelihood=-8.50976	log10_qual_likelihood_position_model=0.988823	log10_strand_likelihood_position_model=0.299953	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=3.51253e-09	ref_cov=94/84	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/85
RA	405	.	NC_007779	3845596	0	G	T	bias_e_value=6.98213	bias_p_value=1.50272e-06	fisher_strand_p_value=8.70817e-08	frequency=4.935265e-02	genotype_quality=858.9	ks_quality_p_value=1	log10_base_likelihood=-6.69365	log10_qual_likelihood_position_model=18.208	log10_strand_likelihood_position_model=7.28779	new_cov=0/23	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=134/113	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/136
RA	406	.	NC_007779	3859254	1	.	T	bias_e_value=115194	bias_p_value=0.0247924	fisher_strand_p_value=0.00812456	frequency=2.312183e-02	genotype_quality=813.3	ks_quality_p_value=0.463655	log10_base_likelihood=-18.7474	log10_qual_likelihood_position_model=1.44859	log10_strand_likelihood_position_model=2.0902	new_cov=4/0	polymorphism_quality=13.4	quality=13.4	quality_position_model=2.52612e-17	ref_cov=49/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=53/120
RA	407	.	NC_007779	3859263	0	T	C	bias_e_value=0.0043746	bias_p_value=9.41516e-10	fisher_strand_p_value=3.76569e-11	frequency=7.738590e-02	genotype_quality=456.8	ks_quality_p_value=1	log10_base_likelihood=-11.9493	log10_qual_likelihood_position_model=15.3551	log10_strand_likelihood_position_model=10.4242	new_cov=14/0	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=19/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=33/119
RA	408	.	NC_007779	3859270	0	G	C	bias_e_value=596.145	bias_p_value=0.000128304	fisher_strand_p_value=1.02761e-05	frequency=4.906511e-02	genotype_quality=526.9	ks_quality_p_value=1	log10_base_likelihood=-8.99189	log10_qual_likelihood_position_model=10.115	log10_strand_likelihood_position_model=4.99559	new_cov=7/1	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=16/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=23/116
RA	409	.	NC_007779	3866109	0	G	T	bias_e_value=50.2984	bias_p_value=1.08254e-05	fisher_strand_p_value=7.15419e-07	frequency=8.287334e-02	genotype_quality=515.7	ks_quality_p_value=0.998668	log10_base_likelihood=-13.0333	log10_qual_likelihood_position_model=12.5037	log10_strand_likelihood_position_model=6.30412	new_cov=0/22	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=88/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=88/105
RA	410	.	NC_007779	3873374	1	.	T	bias_e_value=3016460	bias_p_value=0.649212	fisher_strand_p_value=0.623483	frequency=1.913834e-02	genotype_quality=1000.4	ks_quality_p_value=0.465425	log10_base_likelihood=-17.6838	log10_qual_likelihood_position_model=3.22816	log10_strand_likelihood_position_model=0.558109	new_cov=1/3	polymorphism_quality=12.4	quality=12.4	quality_position_model=5.40207e-16	ref_cov=98/107	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/110
RA	411	.	NC_007779	3873375	0	T	.	bias_e_value=4622280	bias_p_value=0.994824	fisher_strand_p_value=1	frequency=2.368259e-02	genotype_quality=827.9	ks_quality_p_value=0.9	log10_base_likelihood=-14.3082	log10_qual_likelihood_position_model=4.07893	log10_strand_likelihood_position_model=0.480904	new_cov=2/3	polymorphism_quality=8.9	quality=8.9	quality_position_model=9.03829e-12	ref_cov=98/108	reject=INDEL_HOMOPOLYMER	tot_cov=100/111
RA	412	.	NC_007779	3893880	0	G	T	bias_e_value=0.000814709	bias_p_value=1.75345e-10	fisher_strand_p_value=6.56423e-12	frequency=1.043415e-01	genotype_quality=660.3	ks_quality_p_value=0.998553	log10_base_likelihood=-17.5474	log10_qual_likelihood_position_model=22.9889	log10_strand_likelihood_position_model=11.1828	new_cov=0/31	polymorphism_quality=12.2	quality=12.2	quality_position_model=Inf	ref_cov=117/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/107
RA	413	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1065.0	new_cov=115/133	quality=1065.0	ref_cov=0/0	tot_cov=115/133
RA	414	.	NC_007779	3900680	0	T	G	bias_e_value=3.22017e-06	bias_p_value=6.93056e-13	fisher_strand_p_value=2.13669e-14	frequency=6.705618e-02	genotype_quality=595.2	ks_quality_p_value=0.998699	log10_base_likelihood=-9.68528	log10_qual_likelihood_position_model=20.9878	log10_strand_likelihood_position_model=13.6703	new_cov=16/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=14/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=30/135
RA	415	.	NC_007779	3900687	0	G	T	bias_e_value=8.44559	bias_p_value=1.81769e-06	fisher_strand_p_value=1.06582e-07	frequency=4.493332e-02	genotype_quality=655.0	ks_quality_p_value=1	log10_base_likelihood=-7.83295	log10_qual_likelihood_position_model=11.7785	log10_strand_likelihood_position_model=6.97232	new_cov=9/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=Inf	ref_cov=22/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=31/133
RA	416	.	NC_007779	3910746	0	C	A	bias_e_value=0.000511805	bias_p_value=1.10153e-10	fisher_strand_p_value=4.05146e-12	frequency=1.294398e-01	genotype_quality=671.7	ks_quality_p_value=0.998339	log10_base_likelihood=-22.7787	log10_qual_likelihood_position_model=28.7526	log10_strand_likelihood_position_model=11.4975	new_cov=39/0	polymorphism_quality=17.5	quality=17.5	quality_position_model=Inf	ref_cov=91/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/107
RA	417	.	NC_007779	3926062	0	A	G	bias_e_value=1765290	bias_p_value=0.379932	fisher_strand_p_value=0.122627	frequency=1.454353e-02	genotype_quality=884.9	ks_quality_p_value=0.999843	log10_base_likelihood=-5.71759	log10_qual_likelihood_position_model=3.9173	log10_strand_likelihood_position_model=1.15503	new_cov=0/4	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.0384561	ref_cov=110/114	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=110/118
RA	418	.	NC_007779	3930443	0	T	G	bias_e_value=2.63627e-07	bias_p_value=5.67387e-14	fisher_strand_p_value=1.61846e-15	frequency=9.987211e-02	genotype_quality=514.3	ks_quality_p_value=1	log10_base_likelihood=-5.67027	log10_qual_likelihood_position_model=25.7512	log10_strand_likelihood_position_model=14.7909	new_cov=33/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=40/101	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/101
RA	419	.	NC_007779	3946445	1	.	T	bias_e_value=3941020	bias_p_value=0.848201	fisher_strand_p_value=0.505309	frequency=9.523392e-03	genotype_quality=1024.9	ks_quality_p_value=0.994156	log10_base_likelihood=-7.21299	log10_qual_likelihood_position_model=3.19521	log10_strand_likelihood_position_model=0.502298	new_cov=0/2	polymorphism_quality=1.7	quality=1.7	quality_position_model=2.48918e-05	ref_cov=92/116	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=92/118
RA	420	.	NC_007779	3952095	1	.	G	bias_e_value=363089	bias_p_value=0.0781453	fisher_strand_p_value=0.0160757	frequency=2.259922e-02	genotype_quality=846.8	ks_quality_p_value=0.935305	log10_base_likelihood=-17.3537	log10_qual_likelihood_position_model=2.44949	log10_strand_likelihood_position_model=1.79383	new_cov=4/0	polymorphism_quality=12.0	quality=12.0	quality_position_model=3.4041e-15	ref_cov=60/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=64/113
RA	421	.	NC_007779	3977186	0	T	.	bias_e_value=1835870	bias_p_value=0.395123	fisher_strand_p_value=0.248161	frequency=1.270390e-02	genotype_quality=906.5	ks_quality_p_value=0.523645	log10_base_likelihood=-8.36214	log10_qual_likelihood_position_model=2.20587	log10_strand_likelihood_position_model=0.854145	new_cov=0/3	polymorphism_quality=2.9	quality=2.9	quality_position_model=3.36898e-07	ref_cov=113/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/123
RA	422	.	NC_007779	3981332	1	.	A	bias_e_value=2063150	bias_p_value=0.444039	fisher_strand_p_value=0.244626	frequency=8.620262e-03	genotype_quality=1135.6	ks_quality_p_value=0.633768	log10_base_likelihood=-8.39397	log10_qual_likelihood_position_model=1.10792	log10_strand_likelihood_position_model=0.611497	new_cov=0/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.28295e-08	ref_cov=117/113	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/115
RA	423	.	NC_007779	3986830	0	T	.	bias_e_value=3421890	bias_p_value=0.73647	fisher_strand_p_value=1	frequency=1.400280e-02	genotype_quality=858.0	ks_quality_p_value=0.368592	log10_base_likelihood=-7.88275	log10_qual_likelihood_position_model=3.01946	log10_strand_likelihood_position_model=0.423935	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.66665e-06	ref_cov=106/105	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=107/107
RA	424	.	NC_007779	4023064	1	.	G	bias_e_value=967204	bias_p_value=0.208165	fisher_strand_p_value=0.0618133	frequency=2.808952e-02	genotype_quality=844.7	ks_quality_p_value=0.854556	log10_base_likelihood=-22.7177	log10_qual_likelihood_position_model=1.85974	log10_strand_likelihood_position_model=1.38533	new_cov=5/0	polymorphism_quality=17.5	quality=17.5	quality_position_model=1.2191e-21	ref_cov=90/83	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=95/83
RA	425	.	NC_007779	4029633	0	T	G	bias_e_value=0.00318783	bias_p_value=6.86095e-10	fisher_strand_p_value=2.7084e-11	frequency=9.683847e-02	genotype_quality=534.4	ks_quality_p_value=1	log10_base_likelihood=-17.829	log10_qual_likelihood_position_model=20.5916	log10_strand_likelihood_position_model=10.5673	new_cov=18/0	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=29/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=47/110
RA	426	.	NC_007779	4031691	1	.	T	bias_e_value=5288.95	bias_p_value=0.00113831	fisher_strand_p_value=0.00011296	frequency=6.422043e-02	genotype_quality=466.8	ks_quality_p_value=0.998742	log10_base_likelihood=-34.4464	log10_qual_likelihood_position_model=4.46947	log10_strand_likelihood_position_model=3.94707	new_cov=7/0	polymorphism_quality=29.3	quality=29.3	quality_position_model=2.93061e-28	ref_cov=25/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=32/77
RA	427	.	NC_007779	4031696	0	C	T	bias_e_value=5.60255	bias_p_value=1.2058e-06	fisher_strand_p_value=6.89423e-08	frequency=6.697798e-02	genotype_quality=378.9	ks_quality_p_value=1	log10_base_likelihood=-7.21336	log10_qual_likelihood_position_model=10.4537	log10_strand_likelihood_position_model=7.16151	new_cov=9/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=12/88	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=21/88
RA	428	.	NC_007779	4036507	0	G	T	bias_e_value=10.2324	bias_p_value=2.20225e-06	fisher_strand_p_value=1.43404e-07	frequency=5.117559e-02	genotype_quality=840.2	ks_quality_p_value=0.911373	log10_base_likelihood=-7.70381	log10_qual_likelihood_position_model=23.2978	log10_strand_likelihood_position_model=6.84344	new_cov=0/21	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=135/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/131
RA	429	.	NC_007779	4055100	0	G	T	bias_e_value=6.43551	bias_p_value=1.38507e-06	fisher_strand_p_value=8.05368e-08	frequency=7.917881e-02	genotype_quality=716.6	ks_quality_p_value=0.991644	log10_base_likelihood=-20.5845	log10_qual_likelihood_position_model=24.7411	log10_strand_likelihood_position_model=7.09401	new_cov=21/0	polymorphism_quality=15.3	quality=15.3	quality_position_model=Inf	ref_cov=87/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/115
RA	430	.	NC_007779	4055329	0	T	G	bias_e_value=1.05062e-05	bias_p_value=2.26117e-12	fisher_strand_p_value=7.23404e-14	frequency=8.219242e-02	genotype_quality=539.7	ks_quality_p_value=1	log10_base_likelihood=-9.03971	log10_qual_likelihood_position_model=20.3829	log10_strand_likelihood_position_model=13.1406	new_cov=20/0	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=24/120	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=45/120
RA	431	.	NC_007779	4062114	0	T	G	bias_e_value=1.92053e-07	bias_p_value=4.13343e-14	fisher_strand_p_value=1.16819e-15	frequency=9.881020e-02	genotype_quality=519.2	ks_quality_p_value=1	log10_base_likelihood=-12.6788	log10_qual_likelihood_position_model=24.5828	log10_strand_likelihood_position_model=14.9325	new_cov=26/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=27/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=53/109
RA	432	.	NC_007779	4087369	0	T	.	bias_e_value=4147040	bias_p_value=0.892541	fisher_strand_p_value=0.593114	frequency=1.381683e-02	genotype_quality=879.3	ks_quality_p_value=0.967465	log10_base_likelihood=-8.42347	log10_qual_likelihood_position_model=2.45464	log10_strand_likelihood_position_model=0.467487	new_cov=1/2	polymorphism_quality=2.9	quality=2.9	quality_position_model=2.09323e-07	ref_cov=117/97	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/99
RA	433	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1012.2	new_cov=140/112	quality=1012.2	ref_cov=0/0	tot_cov=140/112
RA	434	.	NC_007779	4098730	0	G	T	bias_e_value=1.03297	bias_p_value=2.22319e-07	fisher_strand_p_value=1.15322e-08	frequency=7.014847e-02	genotype_quality=685.7	ks_quality_p_value=1	log10_base_likelihood=-12.9435	log10_qual_likelihood_position_model=16.0975	log10_strand_likelihood_position_model=7.93809	new_cov=0/22	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=122/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/105
RA	435	.	NC_007779	4114782	0	G	T	bias_e_value=24194.4	bias_p_value=0.00520719	fisher_strand_p_value=0.000621084	frequency=4.590797e-02	genotype_quality=759.5	ks_quality_p_value=1	log10_base_likelihood=-7.00034	log10_qual_likelihood_position_model=17.4407	log10_strand_likelihood_position_model=3.35038	new_cov=1/16	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=105/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/133
RA	436	.	NC_007779	4115400	0	T	C	bias_e_value=46.8228	bias_p_value=1.00774e-05	fisher_strand_p_value=6.61749e-07	frequency=6.612730e-02	genotype_quality=514.3	ks_quality_p_value=1	log10_base_likelihood=-7.13305	log10_qual_likelihood_position_model=12.0059	log10_strand_likelihood_position_model=6.17931	new_cov=0/13	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=103/45	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=103/58
RA	437	.	NC_007779	4115400	1	.	C	bias_e_value=898018	bias_p_value=0.193275	fisher_strand_p_value=0.047842	frequency=1.896000e-02	genotype_quality=726.4	ks_quality_p_value=1	log10_base_likelihood=-7.26185	log10_qual_likelihood_position_model=3.53307	log10_strand_likelihood_position_model=1.32019	new_cov=0/3	polymorphism_quality=1.8	quality=1.8	quality_position_model=0.000376706	ref_cov=100/55	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=100/58
RA	438	.	NC_007779	4121300	0	T	C	bias_e_value=4512220	bias_p_value=0.971137	fisher_strand_p_value=1	frequency=1.223850e-02	genotype_quality=959.9	ks_quality_p_value=0.769563	log10_base_likelihood=-5.78642	log10_qual_likelihood_position_model=2.60928	log10_strand_likelihood_position_model=0.424185	new_cov=2/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.000160728	ref_cov=120/121	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=122/122
RA	439	.	NC_007779	4124974	0	G	T	bias_e_value=0.359727	bias_p_value=7.74217e-08	fisher_strand_p_value=3.79723e-09	frequency=7.273054e-02	genotype_quality=764.9	ks_quality_p_value=1	log10_base_likelihood=-15.147	log10_qual_likelihood_position_model=18.7399	log10_strand_likelihood_position_model=8.42053	new_cov=0/24	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=127/90	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/115
RA	440	.	NC_007779	4148399	0	A	C	bias_e_value=0.000160598	bias_p_value=3.45645e-11	fisher_strand_p_value=1.21553e-12	frequency=9.818459e-02	genotype_quality=577.6	ks_quality_p_value=1	log10_base_likelihood=-10.8188	log10_qual_likelihood_position_model=24.5126	log10_strand_likelihood_position_model=11.9152	new_cov=0/29	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=106/53	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/83
RA	441	.	NC_007779	4148399	1	.	C	bias_e_value=1356150	bias_p_value=0.291875	fisher_strand_p_value=0.083924	frequency=1.610184e-02	genotype_quality=837.4	ks_quality_p_value=1	log10_base_likelihood=-7.04776	log10_qual_likelihood_position_model=3.37014	log10_strand_likelihood_position_model=1.07611	new_cov=0/3	polymorphism_quality=1.5	quality=1.5	quality_position_model=0.000233555	ref_cov=104/79	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=104/82
RA	442	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1003.9	new_cov=118/116	quality=1003.9	ref_cov=0/0	tot_cov=118/116
RA	443	.	NC_007779	4197139	0	T	G	bias_e_value=7.15429e-10	bias_p_value=1.53977e-16	fisher_strand_p_value=3.744e-18	frequency=1.391120e-01	genotype_quality=476.7	ks_quality_p_value=1	log10_base_likelihood=-24.9196	log10_qual_likelihood_position_model=25.2689	log10_strand_likelihood_position_model=17.4267	new_cov=23/0	polymorphism_quality=19.7	quality=19.7	quality_position_model=Inf	ref_cov=12/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/108
RA	444	.	NC_007779	4200494	0	T	G	bias_e_value=90.4877	bias_p_value=1.94751e-05	fisher_strand_p_value=1.34107e-06	frequency=5.196905e-02	genotype_quality=661.6	ks_quality_p_value=1	log10_base_likelihood=-8.07412	log10_qual_likelihood_position_model=18.9187	log10_strand_likelihood_position_model=5.87255	new_cov=16/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=76/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=92/112
RA	445	.	NC_007779	4200831	1	.	G	bias_e_value=3861450	bias_p_value=0.831075	fisher_strand_p_value=0.501868	frequency=9.090424e-03	genotype_quality=1088.5	ks_quality_p_value=0.953096	log10_base_likelihood=-7.98968	log10_qual_likelihood_position_model=1.28842	log10_strand_likelihood_position_model=0.528139	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.2228e-08	ref_cov=118/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=120/100
RA	446	.	NC_007779	4207565	0	C	A	bias_e_value=0.645455	bias_p_value=1.38917e-07	fisher_strand_p_value=7.02533e-09	frequency=6.777954e-02	genotype_quality=714.6	ks_quality_p_value=1	log10_base_likelihood=-9.32972	log10_qual_likelihood_position_model=19.3752	log10_strand_likelihood_position_model=8.15333	new_cov=23/0	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=85/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/122
RA	447	.	NC_007779	4211222	0	C	A	bias_e_value=357.206	bias_p_value=7.68791e-05	fisher_strand_p_value=5.95239e-06	frequency=4.480171e-02	genotype_quality=828.6	ks_quality_p_value=0.990359	log10_base_likelihood=-6.66113	log10_qual_likelihood_position_model=17.6419	log10_strand_likelihood_position_model=5.28101	new_cov=18/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=115/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/120
RA	448	.	NC_007779	4218853	1	.	G	bias_e_value=1675740	bias_p_value=0.360658	fisher_strand_p_value=0.240372	frequency=8.620262e-03	genotype_quality=1151.7	ks_quality_p_value=0.472544	log10_base_likelihood=-8.31	log10_qual_likelihood_position_model=2.55301	log10_strand_likelihood_position_model=0.619117	new_cov=2/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=4.99005e-07	ref_cov=112/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=114/118
RA	449	.	NC_007779	4218867	0	A	T	bias_e_value=6904.86	bias_p_value=0.00148609	fisher_strand_p_value=0.000151745	frequency=4.059792e-02	genotype_quality=953.2	ks_quality_p_value=1	log10_base_likelihood=-7.88882	log10_qual_likelihood_position_model=19.4189	log10_strand_likelihood_position_model=3.81888	new_cov=12/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=112/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/128
RA	450	.	NC_007779	4220019	0	A	C	bias_e_value=0.00135215	bias_p_value=2.91014e-10	fisher_strand_p_value=1.10971e-11	frequency=6.913757e-02	genotype_quality=728.0	ks_quality_p_value=1	log10_base_likelihood=-7.91935	log10_qual_likelihood_position_model=39.7358	log10_strand_likelihood_position_model=11.1907	new_cov=0/36	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=119/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/132
RA	451	.	NC_007779	4226513	0	C	A	bias_e_value=1.6306	bias_p_value=3.50945e-07	fisher_strand_p_value=1.86709e-08	frequency=6.520033e-02	genotype_quality=774.4	ks_quality_p_value=1	log10_base_likelihood=-10.349	log10_qual_likelihood_position_model=21.536	log10_strand_likelihood_position_model=7.82718	new_cov=25/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=100/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=125/119
RA	452	.	NC_007779	4227183	0	T	G	bias_e_value=2.63791e-11	bias_p_value=5.67741e-18	fisher_strand_p_value=1.27566e-19	frequency=1.272073e-01	genotype_quality=649.9	ks_quality_p_value=1	log10_base_likelihood=-21.2216	log10_qual_likelihood_position_model=31.8043	log10_strand_likelihood_position_model=18.8943	new_cov=43/0	polymorphism_quality=15.9	quality=15.9	quality_position_model=Inf	ref_cov=52/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=96/127
RA	453	.	NC_007779	4241272	0	G	T	bias_e_value=223.573	bias_p_value=4.81182e-05	fisher_strand_p_value=3.55166e-06	frequency=2.668381e-02	genotype_quality=914.1	ks_quality_p_value=1	log10_base_likelihood=-5.85602	log10_qual_likelihood_position_model=14.157	log10_strand_likelihood_position_model=5.44957	new_cov=0/15	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=149/106	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/121
RA	454	.	NC_007779	4254117	0	T	.	bias_e_value=2249150	bias_p_value=0.484069	fisher_strand_p_value=1	frequency=1.332474e-02	genotype_quality=911.4	ks_quality_p_value=0.177332	log10_base_likelihood=-8.20403	log10_qual_likelihood_position_model=2.31259	log10_strand_likelihood_position_model=0.418308	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=2.23906e-07	ref_cov=110/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/114
RA	455	.	NC_007779	4312218	0	T	G	bias_e_value=0.641349	bias_p_value=1.38033e-07	fisher_strand_p_value=6.97827e-09	frequency=3.629684e-02	genotype_quality=700.5	ks_quality_p_value=1	log10_base_likelihood=-6.78053	log10_qual_likelihood_position_model=23.1504	log10_strand_likelihood_position_model=8.15625	new_cov=18/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=62/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=81/131
RA	456	.	NC_007779	4337469	0	A	C	bias_e_value=5.61546e-09	bias_p_value=1.20858e-15	fisher_strand_p_value=3.09787e-17	frequency=1.078124e-01	genotype_quality=544.5	ks_quality_p_value=1	log10_base_likelihood=-9.97911	log10_qual_likelihood_position_model=31.8661	log10_strand_likelihood_position_model=16.5089	new_cov=0/33	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=110/35	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=110/68
RA	457	.	NC_007779	4348529	0	T	G	bias_e_value=0.0105946	bias_p_value=2.28021e-09	fisher_strand_p_value=9.46917e-11	frequency=6.679201e-02	genotype_quality=599.2	ks_quality_p_value=1	log10_base_likelihood=-7.48406	log10_qual_likelihood_position_model=26.3605	log10_strand_likelihood_position_model=10.0237	new_cov=22/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=52/117	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=74/117
RA	458	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=785.3	new_cov=79/77	quality=785.3	ref_cov=0/0	tot_cov=79/77
RA	459	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=785.3	new_cov=79/77	quality=785.3	ref_cov=0/0	tot_cov=79/77
RA	460	.	NC_007779	4395097	1	.	A	bias_e_value=762918	bias_p_value=0.164198	fisher_strand_p_value=0.510311	frequency=8.510590e-03	genotype_quality=1153.0	ks_quality_p_value=0.0756246	log10_base_likelihood=-8.24005	log10_qual_likelihood_position_model=1.69731	log10_strand_likelihood_position_model=0.476411	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=5.44455e-08	ref_cov=99/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=99/136
RA	461	.	NC_007779	4429120	0	G	T	bias_e_value=0.0360382	bias_p_value=7.75627e-09	fisher_strand_p_value=5.88748e-10	frequency=6.569624e-02	genotype_quality=770.6	ks_quality_p_value=0.577775	log10_base_likelihood=-9.64428	log10_qual_likelihood_position_model=28.7618	log10_strand_likelihood_position_model=9.23007	new_cov=0/27	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=130/95	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/122
RA	462	.	NC_007779	4429129	1	.	A	bias_e_value=4636430	bias_p_value=0.99787	fisher_strand_p_value=1	frequency=8.298874e-03	genotype_quality=1179.7	ks_quality_p_value=0.935441	log10_base_likelihood=-7.97751	log10_qual_likelihood_position_model=2.05466	log10_strand_likelihood_position_model=0.30013	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.56678e-07	ref_cov=114/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/126
RA	463	.	NC_007779	4429130	0	A	.	bias_e_value=4646280	bias_p_value=0.999988	fisher_strand_p_value=1	frequency=1.223183e-02	genotype_quality=992.2	ks_quality_p_value=0.995054	log10_base_likelihood=-7.71972	log10_qual_likelihood_position_model=3.70823	log10_strand_likelihood_position_model=0.405841	new_cov=1/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.99949e-05	ref_cov=116/126	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/128
RA	464	.	NC_007779	4477099	0	A	.	bias_e_value=4644480	bias_p_value=0.9996	fisher_strand_p_value=1	frequency=1.208591e-02	genotype_quality=999.0	ks_quality_p_value=0.971865	log10_base_likelihood=-7.91204	log10_qual_likelihood_position_model=2.30735	log10_strand_likelihood_position_model=0.361879	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.88229e-07	ref_cov=147/98	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=149/99
RA	465	.	NC_007779	4479209	0	G	T	bias_e_value=6.89332	bias_p_value=1.4836e-06	fisher_strand_p_value=8.59064e-08	frequency=7.091570e-02	genotype_quality=684.5	ks_quality_p_value=1	log10_base_likelihood=-9.6196	log10_qual_likelihood_position_model=16.384	log10_strand_likelihood_position_model=7.06597	new_cov=0/21	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=112/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/106
RA	466	.	NC_007779	4540870	0	T	G	bias_e_value=9.58272e-15	bias_p_value=2.06243e-21	fisher_strand_p_value=3.92149e-23	frequency=1.328793e-01	genotype_quality=632.9	ks_quality_p_value=1	log10_base_likelihood=-17.6146	log10_qual_likelihood_position_model=32.845	log10_strand_likelihood_position_model=22.4065	new_cov=47/0	polymorphism_quality=12.3	quality=12.3	quality_position_model=Inf	ref_cov=42/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=90/128
RA	467	.	NC_007779	4540877	0	A	T	bias_e_value=5.70096e-05	bias_p_value=1.22698e-11	fisher_strand_p_value=4.15805e-13	frequency=1.157436e-01	genotype_quality=694.0	ks_quality_p_value=1	log10_base_likelihood=-24.5793	log10_qual_likelihood_position_model=19.7701	log10_strand_likelihood_position_model=12.3811	new_cov=27/0	polymorphism_quality=19.3	quality=19.3	quality_position_model=Inf	ref_cov=57/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/132
RA	468	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=740.8	new_cov=94/89	quality=740.8	ref_cov=0/0	tot_cov=94/89
RA	469	.	NC_007779	4554532	0	T	C	bias_e_value=24.7674	bias_p_value=5.33052e-06	fisher_strand_p_value=3.35065e-07	frequency=6.052637e-02	genotype_quality=450.0	ks_quality_p_value=1	log10_base_likelihood=-9.21643	log10_qual_likelihood_position_model=11.26	log10_strand_likelihood_position_model=6.47487	new_cov=11/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=31/106	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=42/106
RA	470	.	NC_007779	4554534	0	A	C	bias_e_value=31112.9	bias_p_value=0.00669623	fisher_strand_p_value=0.000827516	frequency=3.792381e-02	genotype_quality=437.4	ks_quality_p_value=0.999279	log10_base_likelihood=-6.59309	log10_qual_likelihood_position_model=8.53247	log10_strand_likelihood_position_model=3.10092	new_cov=7/1	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=38/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=45/108
RA	471	.	NC_007779	4561440	1	.	T	bias_e_value=2346400	bias_p_value=0.505001	fisher_strand_p_value=0.289934	frequency=1.648331e-02	genotype_quality=867.8	ks_quality_p_value=0.654204	log10_base_likelihood=-13.1515	log10_qual_likelihood_position_model=1.97368	log10_strand_likelihood_position_model=0.625403	new_cov=3/0	polymorphism_quality=7.8	quality=7.8	quality_position_model=1.36613e-12	ref_cov=110/69	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=113/69
RA	472	.	NC_007779	4573184	0	T	G	bias_e_value=7.56849e-05	bias_p_value=1.62892e-11	fisher_strand_p_value=5.57558e-13	frequency=6.877232e-02	genotype_quality=718.7	ks_quality_p_value=1	log10_base_likelihood=-7.08424	log10_qual_likelihood_position_model=28.6554	log10_strand_likelihood_position_model=12.2766	new_cov=38/0	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=90/120	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/120
RA	473	.	NC_007779	4584556	0	C	A	bias_e_value=2.85709	bias_p_value=6.14912e-07	fisher_strand_p_value=3.47241e-08	frequency=8.066750e-02	genotype_quality=687.1	ks_quality_p_value=0.972814	log10_base_likelihood=-14.1474	log10_qual_likelihood_position_model=24.4504	log10_strand_likelihood_position_model=7.57188	new_cov=24/0	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=89/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=113/109
RA	474	.	NC_007779	4610781	0	A	C	bias_e_value=0.00105524	bias_p_value=2.27112e-10	fisher_strand_p_value=8.57608e-12	frequency=8.836031e-02	genotype_quality=654.4	ks_quality_p_value=1	log10_base_likelihood=-13.8488	log10_qual_likelihood_position_model=24.9354	log10_strand_likelihood_position_model=11.0667	new_cov=0/27	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=120/63	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/90
RA	475	.	NC_007779	4613456	0	C	A	bias_e_value=110934	bias_p_value=0.0238756	fisher_strand_p_value=0.00360557	frequency=3.730392e-02	genotype_quality=621.7	ks_quality_p_value=0.999393	log10_base_likelihood=-6.32243	log10_qual_likelihood_position_model=8.19088	log10_strand_likelihood_position_model=2.50872	new_cov=11/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=107/78	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=118/78
RA	476	.	NC_007779	4622730	0	G	T	bias_e_value=11.1057	bias_p_value=2.39022e-06	fisher_strand_p_value=1.50329e-07	frequency=5.528069e-02	genotype_quality=761.7	ks_quality_p_value=0.948494	log10_base_likelihood=-13.4507	log10_qual_likelihood_position_model=17.5505	log10_strand_likelihood_position_model=6.82296	new_cov=0/18	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=137/89	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/107
RA	477	.	NC_007779	4635770	0	G	T	bias_e_value=986.49	bias_p_value=0.000212316	fisher_strand_p_value=1.77862e-05	frequency=5.394411e-02	genotype_quality=669.9	ks_quality_p_value=1	log10_base_likelihood=-9.0929	log10_qual_likelihood_position_model=12.4133	log10_strand_likelihood_position_model=5.03184	new_cov=0/18	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=106/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=106/126
RA	478	.	NC_007779	4636470	0	C	G	bias_e_value=19.8662	bias_p_value=4.27568e-06	fisher_strand_p_value=2.6508e-07	frequency=5.430603e-02	genotype_quality=590.9	ks_quality_p_value=0.999112	log10_base_likelihood=-7.66176	log10_qual_likelihood_position_model=14.9811	log10_strand_likelihood_position_model=6.57662	new_cov=11/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=34/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=45/118
RA	479	.	NC_007779	4642414	1	.	A	bias_e_value=524901	bias_p_value=0.112971	fisher_strand_p_value=1	frequency=1.630402e-02	genotype_quality=875.9	ks_quality_p_value=0.0238549	log10_base_likelihood=-13.2107	log10_qual_likelihood_position_model=2.79647	log10_strand_likelihood_position_model=0.423602	new_cov=2/1	polymorphism_quality=7.8	quality=7.8	quality_position_model=5.1133e-12	ref_cov=90/91	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=92/92
MC	480	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=203	right_inside_cov=0	right_outside_cov=206
MC	481	.	NC_007779	654214	655412	1193	0	left_inside_cov=0	left_outside_cov=229	right_inside_cov=0	right_outside_cov=229
MC	482	.	NC_007779	1288311	1288522	99	63	left_inside_cov=167	left_outside_cov=169	right_inside_cov=166	right_outside_cov=171
MC	483	.	NC_007779	1301041	1302376	1326	0	left_inside_cov=0	left_outside_cov=244	right_inside_cov=0	right_outside_cov=244
MC	484	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=245	right_inside_cov=0	right_outside_cov=249
MC	485	.	NC_007779	2176983	2178208	1194	0	left_inside_cov=0	left_outside_cov=291	right_inside_cov=0	right_outside_cov=230
MC	486	.	NC_007779	2320795	2322130	1327	0	left_inside_cov=0	left_outside_cov=233	right_inside_cov=0	right_outside_cov=235
MC	487	.	NC_007779	3128821	3147473	1181	0	left_inside_cov=168	left_outside_cov=171	right_inside_cov=1	right_outside_cov=222
MC	488	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=0	left_outside_cov=257	right_inside_cov=0	right_outside_cov=187
MC	489	.	NC_007779	3742936	3744271	1325	0	left_inside_cov=0	left_outside_cov=273	right_inside_cov=1	right_outside_cov=275
MC	490	.	NC_007779	3746911	3748109	1194	0	left_inside_cov=0	left_outside_cov=242	right_inside_cov=1	right_outside_cov=247
MC	491	.	NC_007779	3750591	3751789	1194	0	left_inside_cov=0	left_outside_cov=281	right_inside_cov=0	right_outside_cov=281
MC	492	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=269	right_inside_cov=0	right_outside_cov=270
MC	493	.	NC_007779	4310363	4311561	1194	0	left_inside_cov=0	left_outside_cov=272	right_inside_cov=0	right_outside_cov=272
JC	494	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=115	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1__1__NC_007779__4646332__-1__0____101__101__0__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=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=1.13	new_junction_frequency=1.000000e+00	new_junction_read_count=247	pos_hash_score=128	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=247
JC	495	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=10	coverage_minus=78	coverage_plus=84	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371963__1__10____101__101__0__0	max_left=85	max_left_minus=85	max_left_plus=85	max_min_left=45	max_min_left_minus=45	max_min_left_plus=45	max_min_right=45	max_min_right_minus=45	max_min_right_plus=45	max_pos_hash_score=160	max_right=85	max_right_minus=85	max_right_plus=85	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.83	new_junction_frequency=1.000000e+00	new_junction_read_count=162	pos_hash_score=98	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=162
JC	496	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=92	coverage_plus=80	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=61	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=33	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=1.24	new_junction_frequency=1.000000e+00	new_junction_read_count=172	pos_hash_score=94	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=172	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	497	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=121	coverage_plus=100	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=95	max_left_minus=95	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=NA	new_junction_read_count=221	pos_hash_score=124	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=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=221
JC	498	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=95	coverage_plus=109	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=88	key=NC_007779__381401__1__NC_007779__381814__-1__2____101__101__1__1	max_left=93	max_left_minus=92	max_left_plus=93	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=49	max_min_right_minus=47	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.95	new_junction_frequency=NA	new_junction_read_count=204	pos_hash_score=115	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=2	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=204
JC	499	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=124	coverage_plus=134	flanking_left=101	flanking_right=101	frequency=9.710072e-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=49	max_min_right_plus=48	max_pos_hash_score=174	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.22	new_junction_frequency=9.710072e-01	new_junction_read_count=259	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=3	side_2_possible_overlap_registers=90	side_2_read_count=8	side_2_redundant=0	total_non_overlap_reads=258
JC	500	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=104	coverage_plus=84	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=88	max_left_plus=90	max_min_left=47	max_min_left_minus=47	max_min_left_plus=47	max_min_right=48	max_min_right_minus=48	max_min_right_plus=44	max_pos_hash_score=170	max_right=90	max_right_minus=90	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=188	pos_hash_score=114	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=188
JC	501	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=42	coverage_plus=39	flanking_left=101	flanking_right=101	frequency=4.089532e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=77	max_left_minus=77	max_left_plus=74	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=77	max_right_plus=79	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.45	new_junction_frequency=4.089532e-01	new_junction_read_count=81	pos_hash_score=61	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.56	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=123	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.74	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=133	side_2_redundant=0	total_non_overlap_reads=81
JC	502	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=36	coverage_plus=36	flanking_left=101	flanking_right=101	frequency=3.850039e-01	junction_possible_overlap_registers=74	key=NC_007779__1209382__-1__NC_007779__1211195__-1__16____101__101__0__0	max_left=78	max_left_minus=76	max_left_plus=78	max_min_left=41	max_min_left_minus=40	max_min_left_plus=41	max_min_right=40	max_min_right_minus=38	max_min_right_plus=40	max_pos_hash_score=148	max_right=79	max_right_minus=79	max_right_plus=77	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.40	new_junction_frequency=3.850039e-01	new_junction_read_count=72	pos_hash_score=55	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.54	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=118	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.74	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=133	side_2_redundant=0	total_non_overlap_reads=72
JC	503	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=81	coverage_plus=101	flanking_left=101	flanking_right=101	frequency=9.789625e-01	junction_possible_overlap_registers=88	key=NC_007779__1221489__1__NC_007779__1301039__1__2____101__101__0__1	max_left=93	max_left_minus=92	max_left_plus=93	max_min_left=49	max_min_left_minus=47	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=86	max_right_minus=85	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.85	new_junction_frequency=9.789625e-01	new_junction_read_count=182	pos_hash_score=108	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=182
JC	504	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=106	coverage_plus=75	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1221495__-1__NC_007779__1302369__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=88	max_right_minus=88	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.83	new_junction_frequency=1.000000e+00	new_junction_read_count=182	pos_hash_score=111	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=181
JC	505	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=97	coverage_plus=97	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=83	key=NC_007779__1301040__-1__NC_007779__1302370__1__7____101__101__0__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=47	max_min_right_minus=47	max_min_right_plus=44	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=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=195	pos_hash_score=114	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=7	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=83	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=194
JC	506	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=127	coverage_plus=117	flanking_left=101	flanking_right=101	frequency=9.733180e-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=1.17	new_junction_frequency=9.733180e-01	new_junction_read_count=244	pos_hash_score=130	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.03	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=7	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=244
JC	507	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=94	coverage_plus=102	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1397758__1__NC_007779__1672777__1__0____101__101__1__0	max_left=87	max_left_minus=87	max_left_plus=87	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=196	pos_hash_score=119	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=196
JC	508	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=76	coverage_plus=82	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=37	max_min_right=37	max_min_right_minus=37	max_min_right_plus=37	max_pos_hash_score=128	max_right=69	max_right_minus=69	max_right_plus=69	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=1.000000e+00	new_junction_read_count=159	pos_hash_score=96	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=26	side_1_possible_overlap_registers=90	side_1_read_count=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=158
JC	509	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=97	coverage_plus=114	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=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=87	max_right_minus=86	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=1.000000e+00	new_junction_read_count=211	pos_hash_score=115	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=211
JC	510	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=96	coverage_plus=101	flanking_left=101	flanking_right=101	frequency=9.248826e-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=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=90	max_right_minus=88	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=9.248826e-01	new_junction_read_count=197	pos_hash_score=122	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.07	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=197
JC	511	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=90	coverage_plus=101	flanking_left=101	flanking_right=101	frequency=9.414634e-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=48	max_min_left_minus=47	max_min_left_plus=48	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.88	new_junction_frequency=9.414634e-01	new_junction_read_count=193	pos_hash_score=111	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=191
JC	512	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=112	coverage_plus=39	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=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=6	max_min_right=50	max_min_right_minus=50	max_min_right_plus=40	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=0.69	new_junction_frequency=1.000000e+00	new_junction_read_count=151	pos_hash_score=90	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=151
JC	513	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=102	coverage_plus=114	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__1980095__-1__NC_007779__2176983__1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=92	max_right_minus=92	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=216	pos_hash_score=125	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=216
JC	514	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=106	coverage_plus=106	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2178209__1__NC_007779__2412225__-1__0____101__101__0__1	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=87	max_right_minus=87	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=214	pos_hash_score=112	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=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=212
JC	515	.	NC_007779	2320794	-1	NC_007779	2322131	1	0	alignment_overlap=6	coverage_minus=86	coverage_plus=97	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=46	max_min_left_plus=47	max_min_right=46	max_min_right_minus=46	max_min_right_plus=45	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=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=183	pos_hash_score=115	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=6	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=84	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=183
JC	516	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=86	coverage_plus=128	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=95	max_left_minus=95	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=214	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=214
JC	517	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=124	coverage_plus=120	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2322124__-1__NC_007779__2589830__1__0____101__101__1__0	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=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=1.11	new_junction_frequency=1.000000e+00	new_junction_read_count=244	pos_hash_score=129	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=244
JC	518	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=122	coverage_plus=123	flanking_left=101	flanking_right=101	frequency=9.570312e-01	junction_possible_overlap_registers=90	key=NC_007779__2411458__1__NC_007779__2985055__-1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.12	new_junction_frequency=9.570312e-01	new_junction_read_count=245	pos_hash_score=136	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.05	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=245
JC	519	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=102	coverage_plus=117	flanking_left=101	flanking_right=101	frequency=9.521739e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.00	new_junction_frequency=9.521739e-01	new_junction_read_count=219	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=0.05	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=219
JC	520	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=100	coverage_plus=106	flanking_left=101	flanking_right=101	frequency=6.679156e-01	junction_possible_overlap_registers=86	key=NC_007779__2865229__1__NC_007779__2865278__-1__4____101__101__0__0	max_left=91	max_left_minus=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=6.679156e-01	new_junction_read_count=206	pos_hash_score=117	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.53	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=116	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.45	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=94	side_2_redundant=0	total_non_overlap_reads=206
JC	521	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=102	coverage_plus=105	flanking_left=101	flanking_right=101	frequency=9.951923e-01	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=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=46	max_min_right_plus=50	max_pos_hash_score=180	max_right=92	max_right_minus=92	max_right_plus=84	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.94	new_junction_frequency=9.951923e-01	new_junction_read_count=207	pos_hash_score=112	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=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=207
JC	522	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=91	coverage_plus=105	flanking_left=101	flanking_right=101	frequency=9.850896e-01	junction_possible_overlap_registers=89	key=NC_007779__3186082__-1__NC_007779__3512753__1__1____101__101__1__0	max_left=84	max_left_minus=82	max_left_plus=84	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=9.850896e-01	new_junction_read_count=196	pos_hash_score=115	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.01	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=3	side_2_redundant=0	total_non_overlap_reads=196
JC	523	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=120	coverage_plus=104	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=88	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=43	max_min_right=47	max_min_right_minus=47	max_min_right_plus=46	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=224	pos_hash_score=117	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=224	unique_read_sequence=CTTTGC
JC	524	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=109	coverage_plus=119	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=229	pos_hash_score=130	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=228
JC	525	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=77	coverage_plus=97	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3261134__1__NC_007779__3262338__1__1____101__101__1__0	max_left=84	max_left_minus=84	max_left_plus=84	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.80	new_junction_frequency=1.000000e+00	new_junction_read_count=174	pos_hash_score=101	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=174
JC	526	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=132	coverage_plus=94	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=227	pos_hash_score=123	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=226
JC	527	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=101	coverage_plus=93	flanking_left=101	flanking_right=101	frequency=9.949285e-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=48	max_min_left_minus=46	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=178	max_right=85	max_right_minus=85	max_right_plus=82	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=9.949285e-01	new_junction_read_count=194	pos_hash_score=105	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=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=194
JC	528	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=117	coverage_plus=116	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=82	key=NC_007779__3742935__-1__NC_007779__3744264__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=87	max_min_left=46	max_min_left_minus=45	max_min_left_plus=46	max_min_right=46	max_min_right_minus=46	max_min_right_plus=44	max_pos_hash_score=164	max_right=87	max_right_minus=87	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=233	pos_hash_score=123	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=82	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=233
JC	529	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=117	coverage_plus=73	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=89	max_left_minus=89	max_left_plus=85	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.87	new_junction_frequency=1.000000e+00	new_junction_read_count=190	pos_hash_score=112	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=190
JC	530	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=103	coverage_plus=109	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=90	max_left_minus=90	max_left_plus=90	max_min_left=48	max_min_left_minus=46	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=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=212	pos_hash_score=117	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=212
JC	531	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=113	coverage_plus=92	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3746911__1__NC_007779__3748646__-1__0____101__101__1__0	max_left=92	max_left_minus=91	max_left_plus=92	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=222	pos_hash_score=123	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=205
JC	532	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=108	coverage_plus=124	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=94	max_left_minus=94	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=48	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.06	new_junction_frequency=1.000000e+00	new_junction_read_count=233	pos_hash_score=121	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=232
JC	533	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=122	coverage_plus=119	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=47	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=90	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=242	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=241
JC	534	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=98	coverage_plus=115	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3903279__-1__NC_007779__4504191__-1__1____101__101__0__1	max_left=94	max_left_minus=93	max_left_plus=94	max_min_left=48	max_min_left_minus=47	max_min_left_plus=48	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=92	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=213	pos_hash_score=120	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=213
JC	535	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=115	coverage_plus=107	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=92	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=92	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=224	pos_hash_score=118	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=88	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=222
JC	536	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=115	coverage_plus=127	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.12	new_junction_frequency=1.000000e+00	new_junction_read_count=243	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=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=242
JC	537	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=105	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3988379__-1__NC_007779__4009199__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=93	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.05	new_junction_frequency=1.000000e+00	new_junction_read_count=230	pos_hash_score=130	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=229
JC	538	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=127	coverage_plus=102	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=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=48	max_min_right_minus=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=1.09	new_junction_frequency=1.000000e+00	new_junction_read_count=229	pos_hash_score=121	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=229
JC	539	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=114	coverage_plus=122	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=91	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.09	new_junction_frequency=1.000000e+00	new_junction_read_count=239	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=236
JC	540	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=108	coverage_plus=133	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4311557__-1__NC_007779__4353543__-1__0____101__101__1__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=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=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.24	new_junction_frequency=1.000000e+00	new_junction_read_count=271	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=0	side_2_redundant=0	total_non_overlap_reads=241
JC	541	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=116	coverage_plus=139	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=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=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=255	pos_hash_score=130	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=255
JC	542	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=92	coverage_plus=106	flanking_left=101	flanking_right=101	frequency=9.806295e-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=92	max_left_plus=93	max_min_left=48	max_min_left_minus=47	max_min_left_plus=48	max_min_right=49	max_min_right_minus=45	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=9.806295e-01	new_junction_read_count=198	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=198
JC	543	.	NC_007779	4547362	1	NC_007779	4547676	1	0	alignment_overlap=9	coverage_minus=22	coverage_plus=19	flanking_left=101	flanking_right=101	frequency=2.160169e-01	junction_possible_overlap_registers=81	key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0	max_left=80	max_left_minus=78	max_left_plus=80	max_min_left=43	max_min_left_minus=43	max_min_left_plus=41	max_min_right=44	max_min_right_minus=44	max_min_right_plus=34	max_pos_hash_score=162	max_right=86	max_right_minus=86	max_right_plus=78	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.21	new_junction_frequency=2.160169e-01	new_junction_read_count=41	pos_hash_score=35	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.79	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=174	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=81	side_2_read_count=141	side_2_redundant=0	total_non_overlap_reads=41
JC	544	.	NC_007779	4547370	-1	NC_007779	4547666	-1	0	alignment_overlap=9	coverage_minus=14	coverage_plus=22	flanking_left=101	flanking_right=101	frequency=1.920000e-01	junction_possible_overlap_registers=81	key=NC_007779__4547370__-1__NC_007779__4547675__-1__9____101__101__0__0	max_left=82	max_left_minus=82	max_left_plus=82	max_min_left=45	max_min_left_minus=36	max_min_left_plus=45	max_min_right=45	max_min_right_minus=45	max_min_right_plus=41	max_pos_hash_score=162	max_right=79	max_right_minus=78	max_right_plus=79	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.18	new_junction_frequency=1.920000e-01	new_junction_read_count=36	pos_hash_score=27	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.82	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=180	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=81	side_2_read_count=141	side_2_redundant=0	total_non_overlap_reads=36
UN	545	.	NC_007779	15485	16635
UN	546	.	NC_007779	19892	20466
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UN	666	.	NC_007779	4215987	4216658
UN	667	.	NC_007779	4299521	4299550
UN	668	.	NC_007779	4299747	4299777
UN	669	.	NC_007779	4310363	4311561
UN	670	.	NC_007779	4502953	4504100
UN	671	.	NC_007779	4512231	4513265