#=GENOME_DIFF	1.0
#=AUTHOR	breseq 0.25c 
#=CREATED	22:09:35 05 Mar 2015
#=REFSEQ	/data/savita/refseq/NC_007779.gbk
#=READSEQ	2_D4_GTCCGC_L003_R2_001.fastq
SNP	1	67	NC_007779	66457	A	frequency=1
SNP	2	75	NC_007779	97880	T	frequency=1
SNP	3	88	NC_007779	167632	A	frequency=1
SNP	4	112	NC_007779	274547	G	frequency=1
DEL	5	885,897	NC_007779	274733	97240	frequency=1
SNP	6	150	NC_007779	547694	G	frequency=1
INS	7	151	NC_007779	547831	G	frequency=1	insert_position=1
SNP	8	153	NC_007779	556858	T	frequency=1
SNP	9	154	NC_007779	569996	C	frequency=1
DEL	10	886,902	NC_007779	654214	1199	frequency=1
SNP	11	191	NC_007779	749354	A	frequency=1
SNP	12	195	NC_007779	758440	A	frequency=1
SNP	13	206	NC_007779	887234	A	frequency=1
SNP	14	222	NC_007779	987574	T	frequency=1
SNP	15	241	NC_007779	1093686	C	frequency=1
SNP	16	243	NC_007779	1097580	T	frequency=1.733422e-01
SNP	17	255	NC_007779	1170573	T	frequency=1
DEL	18	907	NC_007779	1298933	3	frequency=9.421961e-02
DEL	19	888,908	NC_007779	1301041	1336	frequency=1
SNP	20	268	NC_007779	1318876	A	frequency=1
DEL	21	889,912	NC_007779	1413639	23060	frequency=1
SNP	22	292	NC_007779	1483588	A	frequency=1
DEL	23	297	NC_007779	1496775	1	frequency=1
SNP	24	311	NC_007779	1615814	A	frequency=1
DEL	25	324	NC_007779	1669599	1	frequency=1
SNP	26	352	NC_007779	1844073	A	frequency=1
SNP	27	363	NC_007779	1918872	A	frequency=1
SNP	28	367	NC_007779	1973476	A	frequency=1
SNP	29	378	NC_007779	2005401	T	frequency=1
SNP	30	391	NC_007779	2170094	A	frequency=1
SNP	31	393	NC_007779	2178210	C	frequency=3.273392e-02
DEL	32	891,920	NC_007779	2320794	1336	frequency=1
SNP	33	434	NC_007779	2406075	T	frequency=1
SNP	34	438	NC_007779	2416102	A	frequency=1
SNP	35	457	NC_007779	2538628	T	frequency=1
INS	36	925	NC_007779	2865274	GCGCTTCGATATTCAGCCCCTGCGTTTGCAGGATTTCGCGCAAACG	frequency=6.640953e-01
SNP	37	507	NC_007779	2866111	G	frequency=1
SNP	38	525	NC_007779	3003330	A	frequency=1
SNP	39	531	NC_007779	3048743	T	frequency=2.111340e-02
SNP	40	532	NC_007779	3049815	T	frequency=1
SNP	41	583	NC_007779	3397813	G	frequency=1
DEL	42	894,933	NC_007779	3742936	1336	frequency=1
DEL	43	726	NC_007779	3750122	1	frequency=1
SNP	44	727	NC_007779	3750123	T	frequency=5.221128e-02
SNP	45	756	NC_007779	3898657	G	frequency=1
DEL	46	895,940	NC_007779	3958123	34	frequency=1
SNP	47	792	NC_007779	4090749	T	frequency=1
SNP	48	800	NC_007779	4165991	C	frequency=1
DEL	49	838,839	NC_007779	4371271	2	frequency=1
SNP	50	852	NC_007779	4514698	G	frequency=1.191235e-02
SNP	51	859	NC_007779	4546535	A	frequency=1
RA	52	.	NC_007779	286	0	A	C	bias_e_value=770.112	bias_p_value=0.000165746	fisher_strand_p_value=1.36058e-05	frequency=4.004765e-02	genotype_quality=960.4	ks_quality_p_value=0.997951	log10_base_likelihood=-5.60097	log10_qual_likelihood_position_model=26.1332	log10_strand_likelihood_position_model=4.96485	new_cov=2/23	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=154/146	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/170
RA	53	.	NC_007779	302	0	T	.	bias_e_value=2630550	bias_p_value=0.566156	fisher_strand_p_value=1	frequency=1.518631e-02	genotype_quality=1265.4	ks_quality_p_value=0.22873	log10_base_likelihood=-13.6012	log10_qual_likelihood_position_model=2.82977	log10_strand_likelihood_position_model=0.482691	new_cov=2/3	polymorphism_quality=8.2	quality=8.2	quality_position_model=2.53779e-12	ref_cov=154/170	reject=INDEL_HOMOPOLYMER	tot_cov=156/173
RA	54	.	NC_007779	11143	0	G	T	bias_e_value=0.000834068	bias_p_value=1.79511e-10	fisher_strand_p_value=6.71661e-12	frequency=5.475044e-02	genotype_quality=1117.4	ks_quality_p_value=1	log10_base_likelihood=-10.614	log10_qual_likelihood_position_model=27.4483	log10_strand_likelihood_position_model=11.1728	new_cov=0/28	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=190/112	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=190/141
RA	55	.	NC_007779	15382	0	A	G	bias_e_value=1.47897e-07	bias_p_value=3.18309e-14	fisher_strand_p_value=8.92819e-16	frequency=6.575394e-02	genotype_quality=754.5	ks_quality_p_value=1	log10_base_likelihood=-10.6557	log10_qual_likelihood_position_model=19.8746	log10_strand_likelihood_position_model=15.0492	new_cov=22/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=36/180	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=58/180
RA	56	.	NC_007779	17050	0	A	C	bias_e_value=5.47532e-14	bias_p_value=1.17842e-20	fisher_strand_p_value=2.319e-22	frequency=1.544218e-01	genotype_quality=431.3	ks_quality_p_value=1	log10_base_likelihood=-25.912	log10_qual_likelihood_position_model=30.9373	log10_strand_likelihood_position_model=21.6347	new_cov=0/36	polymorphism_quality=20.7	quality=20.7	quality_position_model=Inf	ref_cov=119/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=119/59
RA	57	.	NC_007779	29486	0	C	A	bias_e_value=4885.5	bias_p_value=0.00105147	fisher_strand_p_value=0.000103311	frequency=3.441715e-02	genotype_quality=913.8	ks_quality_p_value=1	log10_base_likelihood=-6.76372	log10_qual_likelihood_position_model=11.4873	log10_strand_likelihood_position_model=3.98585	new_cov=0/10	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=139/87	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/97
RA	58	.	NC_007779	29496	0	T	A	bias_e_value=9.88599	bias_p_value=2.1277e-06	fisher_strand_p_value=1.25996e-07	frequency=6.069994e-02	genotype_quality=857.7	ks_quality_p_value=1	log10_base_likelihood=-10.6996	log10_qual_likelihood_position_model=27.2763	log10_strand_likelihood_position_model=6.89964	new_cov=0/18	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=145/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/111
RA	59	.	NC_007779	29503	0	T	C	bias_e_value=4.65735e-07	bias_p_value=1.00237e-13	fisher_strand_p_value=2.90784e-15	frequency=1.008744e-01	genotype_quality=825.2	ks_quality_p_value=1	log10_base_likelihood=-16.779	log10_qual_likelihood_position_model=28.1689	log10_strand_likelihood_position_model=14.5364	new_cov=0/40	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=158/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/142
RA	60	.	NC_007779	34111	1	.	T	bias_e_value=3821140	bias_p_value=0.822399	fisher_strand_p_value=0.715851	frequency=2.077103e-02	genotype_quality=1585.6	ks_quality_p_value=0.652027	log10_base_likelihood=-30.8775	log10_qual_likelihood_position_model=3.83099	log10_strand_likelihood_position_model=0.57533	new_cov=3/4	polymorphism_quality=25.7	quality=25.7	quality_position_model=1.05208e-28	ref_cov=171/159	reject=INDEL_HOMOPOLYMER	tot_cov=174/163
RA	61	.	NC_007779	36544	0	G	T	bias_e_value=35.7941	bias_p_value=7.70374e-06	fisher_strand_p_value=5.91407e-07	frequency=4.506302e-02	genotype_quality=1045.1	ks_quality_p_value=0.839547	log10_base_likelihood=-7.106	log10_qual_likelihood_position_model=26.5009	log10_strand_likelihood_position_model=6.32059	new_cov=0/25	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=142/167	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/193
RA	62	.	NC_007779	39910	0	G	T	bias_e_value=6986.59	bias_p_value=0.00150368	fisher_strand_p_value=0.000153747	frequency=7.810354e-02	genotype_quality=679.8	ks_quality_p_value=1	log10_base_likelihood=-11.3528	log10_qual_likelihood_position_model=17.8578	log10_strand_likelihood_position_model=3.96566	new_cov=0/28	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=66/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=66/188
RA	63	.	NC_007779	47305	0	G	T	bias_e_value=3.60156e-06	bias_p_value=7.75141e-13	fisher_strand_p_value=2.39516e-14	frequency=7.612133e-02	genotype_quality=1083.6	ks_quality_p_value=1	log10_base_likelihood=-17.6152	log10_qual_likelihood_position_model=26.3829	log10_strand_likelihood_position_model=13.6207	new_cov=0/37	polymorphism_quality=12.3	quality=12.3	quality_position_model=Inf	ref_cov=186/121	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=186/160
RA	64	.	NC_007779	48338	0	T	G	bias_e_value=7.12899e-05	bias_p_value=1.53433e-11	fisher_strand_p_value=5.26375e-13	frequency=7.435417e-02	genotype_quality=469.4	ks_quality_p_value=0.99562	log10_base_likelihood=-19.4431	log10_qual_likelihood_position_model=12.9419	log10_strand_likelihood_position_model=12.2787	new_cov=12/0	polymorphism_quality=14.2	quality=14.2	quality_position_model=Inf	ref_cov=8/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=20/134
RA	65	.	NC_007779	61542	0	C	G	bias_e_value=1.9848	bias_p_value=4.27175e-07	fisher_strand_p_value=2.29984e-08	frequency=5.460215e-02	genotype_quality=626.6	ks_quality_p_value=0.999218	log10_base_likelihood=-9.0155	log10_qual_likelihood_position_model=11.7619	log10_strand_likelihood_position_model=7.64223	new_cov=9/1	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=13/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=22/143
RA	66	.	NC_007779	63419	0	T	.	bias_e_value=2528670	bias_p_value=0.544229	fisher_strand_p_value=1	frequency=1.682568e-02	genotype_quality=1161.5	ks_quality_p_value=0.214187	log10_base_likelihood=-13.9961	log10_qual_likelihood_position_model=2.77691	log10_strand_likelihood_position_model=0.49511	new_cov=2/3	polymorphism_quality=8.6	quality=8.6	quality_position_model=9.12957e-13	ref_cov=144/148	reject=INDEL_HOMOPOLYMER	tot_cov=146/151
RA	67	.	NC_007779	66457	0	C	A	frequency=1	genotype_quality=1389.9	new_cov=193/159	quality=1389.9	ref_cov=1/0	tot_cov=195/159
RA	68	.	NC_007779	70602	0	G	T	bias_e_value=6.16473e-06	bias_p_value=1.32679e-12	fisher_strand_p_value=4.17127e-14	frequency=7.566500e-02	genotype_quality=997.3	ks_quality_p_value=1	log10_base_likelihood=-11.8949	log10_qual_likelihood_position_model=28.2768	log10_strand_likelihood_position_model=13.3797	new_cov=0/38	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=166/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=166/154
RA	69	.	NC_007779	75070	1	.	G	bias_e_value=808525	bias_p_value=0.174014	fisher_strand_p_value=0.0881601	frequency=8.426666e-03	genotype_quality=1731.5	ks_quality_p_value=0.472368	log10_base_likelihood=-12.0542	log10_qual_likelihood_position_model=1.83209	log10_strand_likelihood_position_model=1.05473	new_cov=3/0	polymorphism_quality=6.7	quality=6.7	quality_position_model=3.54694e-11	ref_cov=156/197	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/197
RA	70	.	NC_007779	75074	0	T	G	bias_e_value=5.75671e-45	bias_p_value=1.23898e-51	fisher_strand_p_value=1.00705e-53	frequency=2.045856e-01	genotype_quality=695.2	ks_quality_p_value=1	log10_base_likelihood=-55.2015	log10_qual_likelihood_position_model=67.9944	log10_strand_likelihood_position_model=52.9969	new_cov=83/0	polymorphism_quality=50.1	quality=50.1	quality_position_model=Inf	ref_cov=25/205	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/205
RA	71	.	NC_007779	75079	0	C	T	bias_e_value=4.54015e-06	bias_p_value=9.77146e-13	fisher_strand_p_value=3.04182e-14	frequency=5.767584e-02	genotype_quality=952.0	ks_quality_p_value=1	log10_base_likelihood=-14.8823	log10_qual_likelihood_position_model=21.6273	log10_strand_likelihood_position_model=13.5169	new_cov=17/0	polymorphism_quality=9.5	quality=9.5	quality_position_model=Inf	ref_cov=32/213	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/213
RA	72	.	NC_007779	81760	0	G	T	bias_e_value=17520.3	bias_p_value=0.00377078	fisher_strand_p_value=0.000437331	frequency=2.742863e-02	genotype_quality=967.4	ks_quality_p_value=0.985461	log10_base_likelihood=-8.85874	log10_qual_likelihood_position_model=10.817	log10_strand_likelihood_position_model=3.35919	new_cov=9/0	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=114/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/162
RA	73	.	NC_007779	84005	1	.	T	bias_e_value=4621700	bias_p_value=0.9947	fisher_strand_p_value=1	frequency=1.075268e-02	genotype_quality=1356.4	ks_quality_p_value=0.898822	log10_base_likelihood=-12.5915	log10_qual_likelihood_position_model=2.1486	log10_strand_likelihood_position_model=0.352921	new_cov=1/2	polymorphism_quality=7.2	quality=7.2	quality_position_model=4.04841e-12	ref_cov=101/175	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=102/177
RA	74	.	NC_007779	89555	0	G	T	bias_e_value=0.000611879	bias_p_value=1.31691e-10	fisher_strand_p_value=5.00441e-12	frequency=5.274963e-02	genotype_quality=1181.2	ks_quality_p_value=0.972892	log10_base_likelihood=-14.5948	log10_qual_likelihood_position_model=26.0752	log10_strand_likelihood_position_model=11.3006	new_cov=23/0	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=94/222	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/222
RA	75	.	NC_007779	97880	0	C	T	frequency=1	genotype_quality=1171.6	new_cov=168/125	quality=1171.6	ref_cov=0/0	tot_cov=168/125
RA	76	.	NC_007779	101246	0	T	G	bias_e_value=92004.6	bias_p_value=0.0198016	fisher_strand_p_value=0.00290204	frequency=1.885891e-02	genotype_quality=550.2	ks_quality_p_value=0.996745	log10_base_likelihood=-5.92622	log10_qual_likelihood_position_model=5.67429	log10_strand_likelihood_position_model=2.5373	new_cov=4/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=35/124	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=39/124
RA	77	.	NC_007779	107544	1	.	T	bias_e_value=1849330	bias_p_value=0.39802	fisher_strand_p_value=0.273194	frequency=2.341175e-02	genotype_quality=1394.7	ks_quality_p_value=0.480874	log10_base_likelihood=-30.6481	log10_qual_likelihood_position_model=4.42675	log10_strand_likelihood_position_model=0.818511	new_cov=5/2	polymorphism_quality=25.5	quality=25.5	quality_position_model=1.25655e-27	ref_cov=141/151	reject=INDEL_HOMOPOLYMER	tot_cov=146/153
RA	78	.	NC_007779	107545	0	T	.	bias_e_value=2983000	bias_p_value=0.642012	fisher_strand_p_value=0.623174	frequency=1.314735e-02	genotype_quality=1186.2	ks_quality_p_value=0.456392	log10_base_likelihood=-10.6532	log10_qual_likelihood_position_model=2.60041	log10_strand_likelihood_position_model=0.576783	new_cov=1/3	polymorphism_quality=5.2	quality=5.2	quality_position_model=1.92068e-09	ref_cov=146/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/157
RA	79	.	NC_007779	116855	0	G	T	bias_e_value=120.008	bias_p_value=2.58286e-05	fisher_strand_p_value=1.81654e-06	frequency=3.466511e-02	genotype_quality=1006.8	ks_quality_p_value=1	log10_base_likelihood=-6.01324	log10_qual_likelihood_position_model=16.4511	log10_strand_likelihood_position_model=5.74076	new_cov=0/18	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=150/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/147
RA	80	.	NC_007779	119384	0	T	G	bias_e_value=1.54028e-32	bias_p_value=3.31504e-39	fisher_strand_p_value=3.52112e-41	frequency=1.888418e-01	genotype_quality=560.1	ks_quality_p_value=1	log10_base_likelihood=-35.8427	log10_qual_likelihood_position_model=52.4718	log10_strand_likelihood_position_model=40.4533	new_cov=67/0	polymorphism_quality=30.7	quality=30.7	quality_position_model=Inf	ref_cov=25/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=94/165
RA	81	.	NC_007779	119389	0	C	A	bias_e_value=0.0427635	bias_p_value=9.20371e-09	fisher_strand_p_value=4.06837e-10	frequency=4.874134e-02	genotype_quality=912.6	ks_quality_p_value=1	log10_base_likelihood=-8.12173	log10_qual_likelihood_position_model=15.0509	log10_strand_likelihood_position_model=9.39058	new_cov=20/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=76/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=96/168
RA	82	.	NC_007779	134366	0	G	T	bias_e_value=7.09225	bias_p_value=1.52642e-06	fisher_strand_p_value=8.85403e-08	frequency=3.549767e-02	genotype_quality=1106.6	ks_quality_p_value=1	log10_base_likelihood=-5.8531	log10_qual_likelihood_position_model=18.0102	log10_strand_likelihood_position_model=7.05286	new_cov=0/20	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=177/131	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=177/151
RA	83	.	NC_007779	137009	0	G	T	bias_e_value=6.37304e-09	bias_p_value=1.37163e-15	fisher_strand_p_value=4.06054e-17	frequency=8.724070e-02	genotype_quality=972.0	ks_quality_p_value=0.868737	log10_base_likelihood=-24.7072	log10_qual_likelihood_position_model=36.6659	log10_strand_likelihood_position_model=16.3914	new_cov=32/0	polymorphism_quality=19.5	quality=19.5	quality_position_model=Inf	ref_cov=76/207	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=108/207
RA	84	.	NC_007779	138970	0	A	C	bias_e_value=0.0390257	bias_p_value=8.39924e-09	fisher_strand_p_value=3.69713e-10	frequency=6.711149e-02	genotype_quality=704.8	ks_quality_p_value=1	log10_base_likelihood=-11.0384	log10_qual_likelihood_position_model=23.6156	log10_strand_likelihood_position_model=9.43214	new_cov=0/28	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=129/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/124
RA	85	.	NC_007779	146288	0	T	G	bias_e_value=1.32008	bias_p_value=2.84113e-07	fisher_strand_p_value=1.49381e-08	frequency=6.998014e-02	genotype_quality=542.6	ks_quality_p_value=1	log10_base_likelihood=-9.98428	log10_qual_likelihood_position_model=18.1358	log10_strand_likelihood_position_model=7.8257	new_cov=19/0	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=63/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=82/115
RA	86	.	NC_007779	151656	0	T	G	bias_e_value=7.35987e-12	bias_p_value=1.58402e-18	fisher_strand_p_value=3.45772e-20	frequency=1.371765e-01	genotype_quality=767.2	ks_quality_p_value=1	log10_base_likelihood=-30.9208	log10_qual_likelihood_position_model=40.4456	log10_strand_likelihood_position_model=19.4612	new_cov=53/0	polymorphism_quality=25.7	quality=25.7	quality_position_model=Inf	ref_cov=97/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=150/163
RA	87	.	NC_007779	160649	0	A	.	bias_e_value=2280350	bias_p_value=0.490785	fisher_strand_p_value=0.587759	frequency=8.759499e-03	genotype_quality=1342.8	ks_quality_p_value=0.308357	log10_base_likelihood=-7.33828	log10_qual_likelihood_position_model=2.87706	log10_strand_likelihood_position_model=0.480029	new_cov=2/1	polymorphism_quality=1.8	quality=1.8	quality_position_model=8.05034e-06	ref_cov=150/188	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=153/189
RA	88	.	NC_007779	167632	0	C	A	frequency=1	genotype_quality=1146.0	new_cov=146/142	quality=1146.0	ref_cov=0/0	tot_cov=146/142
RA	89	.	NC_007779	175694	0	T	G	bias_e_value=1.28723e-19	bias_p_value=2.77042e-26	fisher_strand_p_value=4.3283e-28	frequency=1.461940e-01	genotype_quality=618.4	ks_quality_p_value=1	log10_base_likelihood=-24.732	log10_qual_likelihood_position_model=43.0779	log10_strand_likelihood_position_model=27.3637	new_cov=63/0	polymorphism_quality=19.5	quality=19.5	quality_position_model=Inf	ref_cov=59/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=128/152
RA	90	.	NC_007779	179256	1	.	A	bias_e_value=3225280	bias_p_value=0.694157	fisher_strand_p_value=0.499148	frequency=5.916595e-03	genotype_quality=1649.8	ks_quality_p_value=0.658058	log10_base_likelihood=-7.88248	log10_qual_likelihood_position_model=1.03511	log10_strand_likelihood_position_model=0.572959	new_cov=0/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.3189e-08	ref_cov=163/173	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=163/175
RA	91	.	NC_007779	193477	1	.	G	bias_e_value=1401610	bias_p_value=0.30166	fisher_strand_p_value=0.0984983	frequency=1.140690e-02	genotype_quality=1283.6	ks_quality_p_value=0.89251	log10_base_likelihood=-11.8307	log10_qual_likelihood_position_model=2.13879	log10_strand_likelihood_position_model=1.00657	new_cov=3/0	polymorphism_quality=6.4	quality=6.4	quality_position_model=1.10437e-10	ref_cov=119/141	reject=POLYMORPHISM_STRAND	tot_cov=122/141
RA	92	.	NC_007779	193480	0	C	G	bias_e_value=5.67398e-17	bias_p_value=1.22117e-23	fisher_strand_p_value=2.11214e-25	frequency=1.960959e-01	genotype_quality=639.3	ks_quality_p_value=1	log10_base_likelihood=-57.9651	log10_qual_likelihood_position_model=31.6718	log10_strand_likelihood_position_model=24.6753	new_cov=47/0	polymorphism_quality=52.9	quality=52.9	quality_position_model=0.00276204	ref_cov=38/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=86/141
RA	93	.	NC_007779	193483	0	C	G	bias_e_value=2.70946e-06	bias_p_value=5.8314e-13	fisher_strand_p_value=1.78568e-14	frequency=9.758615e-02	genotype_quality=674.0	ks_quality_p_value=1	log10_base_likelihood=-11.3489	log10_qual_likelihood_position_model=24.6327	log10_strand_likelihood_position_model=13.753	new_cov=29/1	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=47/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=76/142
RA	94	.	NC_007779	193489	0	G	T	bias_e_value=0.403603	bias_p_value=8.68648e-08	fisher_strand_p_value=4.28582e-09	frequency=6.785727e-02	genotype_quality=787.1	ks_quality_p_value=1	log10_base_likelihood=-13.5213	log10_qual_likelihood_position_model=15.8017	log10_strand_likelihood_position_model=8.36797	new_cov=20/0	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=78/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/143
RA	95	.	NC_007779	193496	0	A	T	bias_e_value=1.20864e-08	bias_p_value=2.60127e-15	fisher_strand_p_value=6.80493e-17	frequency=1.432223e-01	genotype_quality=749.3	ks_quality_p_value=1	log10_base_likelihood=-51.289	log10_qual_likelihood_position_model=37.8089	log10_strand_likelihood_position_model=16.1672	new_cov=32/0	polymorphism_quality=46.2	quality=46.2	quality_position_model=Inf	ref_cov=48/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/140
RA	96	.	NC_007779	201737	1	.	G	bias_e_value=1682010	bias_p_value=0.362007	fisher_strand_p_value=0.156446	frequency=8.096695e-03	genotype_quality=1191.5	ks_quality_p_value=0.730009	log10_base_likelihood=-7.3851	log10_qual_likelihood_position_model=2.16038	log10_strand_likelihood_position_model=0.805634	new_cov=2/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=2.79999e-06	ref_cov=96/149	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=98/149
RA	97	.	NC_007779	204470	0	C	A	bias_e_value=1450.64	bias_p_value=0.000312211	fisher_strand_p_value=2.81571e-05	frequency=3.015137e-02	genotype_quality=848.3	ks_quality_p_value=0.962892	log10_base_likelihood=-6.75311	log10_qual_likelihood_position_model=18.3401	log10_strand_likelihood_position_model=4.55041	new_cov=0/12	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=147/99	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/111
RA	98	.	NC_007779	205208	1	.	A	bias_e_value=880949	bias_p_value=0.189601	fisher_strand_p_value=1	frequency=6.369591e-03	genotype_quality=1526.9	ks_quality_p_value=0.0466386	log10_base_likelihood=-7.75474	log10_qual_likelihood_position_model=2.09047	log10_strand_likelihood_position_model=0.299715	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.90203e-07	ref_cov=158/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/155
RA	99	.	NC_007779	212548	0	T	G	bias_e_value=1.28599e-07	bias_p_value=2.76775e-14	fisher_strand_p_value=7.73202e-16	frequency=9.599733e-02	genotype_quality=697.3	ks_quality_p_value=1	log10_base_likelihood=-16.3376	log10_qual_likelihood_position_model=36.52	log10_strand_likelihood_position_model=15.1168	new_cov=38/1	polymorphism_quality=11.0	quality=11.0	quality_position_model=Inf	ref_cov=73/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=111/158
RA	100	.	NC_007779	218828	0	A	.	bias_e_value=3499300	bias_p_value=0.753132	fisher_strand_p_value=1	frequency=1.131248e-02	genotype_quality=1054.0	ks_quality_p_value=0.385676	log10_base_likelihood=-8.08825	log10_qual_likelihood_position_model=1.85541	log10_strand_likelihood_position_model=0.377709	new_cov=1/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.00273e-08	ref_cov=114/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/150
RA	101	.	NC_007779	221544	0	A	.	bias_e_value=4109180	bias_p_value=0.884392	fisher_strand_p_value=1	frequency=1.193905e-02	genotype_quality=992.7	ks_quality_p_value=0.559472	log10_base_likelihood=-7.68458	log10_qual_likelihood_position_model=3.02499	log10_strand_likelihood_position_model=0.406147	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=4.17264e-06	ref_cov=128/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=131/120
RA	102	.	NC_007779	223974	0	G	T	frequency=1	genotype_quality=1.3	new_cov=1/0	quality=1.3	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	103	.	NC_007779	227967	0	G	T	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	104	.	NC_007779	227998	0	T	G	frequency=1	genotype_quality=-0.1	new_cov=1/0	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	105	.	NC_007779	228001	0	T	G	frequency=1	genotype_quality=-0.2	new_cov=1/0	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	106	.	NC_007779	233118	0	T	C	bias_e_value=0.0209027	bias_p_value=4.49875e-09	fisher_strand_p_value=1.92493e-10	frequency=6.568718e-02	genotype_quality=549.3	ks_quality_p_value=1	log10_base_likelihood=-10.3347	log10_qual_likelihood_position_model=16.7495	log10_strand_likelihood_position_model=9.71558	new_cov=0/12	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=132/18	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/30
RA	107	.	NC_007779	249538	0	T	G	bias_e_value=4.93053e-06	bias_p_value=1.06117e-12	fisher_strand_p_value=3.31215e-14	frequency=6.982803e-02	genotype_quality=661.3	ks_quality_p_value=1	log10_base_likelihood=-8.74411	log10_qual_likelihood_position_model=34.7133	log10_strand_likelihood_position_model=13.4799	new_cov=33/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=74/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=107/141
RA	108	.	NC_007779	252970	0	A	C	bias_e_value=1.19996e-15	bias_p_value=2.58259e-22	fisher_strand_p_value=4.7205e-24	frequency=6.812525e-02	genotype_quality=782.1	ks_quality_p_value=1	log10_base_likelihood=-6.3501	log10_qual_likelihood_position_model=40.8014	log10_strand_likelihood_position_model=23.326	new_cov=0/51	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=182/73	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=182/124
RA	109	.	NC_007779	261239	0	T	G	bias_e_value=877.58	bias_p_value=0.000188876	fisher_strand_p_value=1.58273e-05	frequency=2.659702e-02	genotype_quality=618.3	ks_quality_p_value=0.989129	log10_base_likelihood=-6.44738	log10_qual_likelihood_position_model=7.66481	log10_strand_likelihood_position_model=4.80059	new_cov=5/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=17/162	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=22/162
RA	110	.	NC_007779	265564	0	T	G	bias_e_value=3.87218e-10	bias_p_value=8.33383e-17	fisher_strand_p_value=1.99587e-18	frequency=6.124926e-02	genotype_quality=742.4	ks_quality_p_value=1	log10_base_likelihood=-5.6679	log10_qual_likelihood_position_model=32.7427	log10_strand_likelihood_position_model=17.6999	new_cov=39/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=71/166	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=111/166
RA	111	.	NC_007779	265582	0	T	G	bias_e_value=0.000614172	bias_p_value=1.32184e-10	fisher_strand_p_value=4.8877e-12	frequency=5.954838e-02	genotype_quality=792.7	ks_quality_p_value=1	log10_base_likelihood=-6.30881	log10_qual_likelihood_position_model=24.2984	log10_strand_likelihood_position_model=11.3109	new_cov=29/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=92/155	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/155
RA	112	.	NC_007779	274547	0	A	G	frequency=1	genotype_quality=1404.4	new_cov=176/157	quality=1404.4	ref_cov=1/1	tot_cov=177/158
RA	113	.	NC_007779	296038	0	C	T	deleted=1	frequency=1	genotype_quality=0.9	new_cov=0/1	quality=0.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	114	.	NC_007779	374799	0	T	G	bias_e_value=9.25926e-15	bias_p_value=1.99281e-21	fisher_strand_p_value=3.7866e-23	frequency=8.062410e-02	genotype_quality=628.5	ks_quality_p_value=1	log10_base_likelihood=-14.5219	log10_qual_likelihood_position_model=31.1726	log10_strand_likelihood_position_model=22.4218	new_cov=28/0	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=19/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=47/172
RA	115	.	NC_007779	379236	1	.	G	bias_e_value=2466490	bias_p_value=0.530847	fisher_strand_p_value=0.50057	frequency=4.255390e-02	genotype_quality=1035.2	ks_quality_p_value=0.410763	log10_base_likelihood=-47.1637	log10_qual_likelihood_position_model=5.27729	log10_strand_likelihood_position_model=0.754139	new_cov=8/2	polymorphism_quality=42.1	quality=42.1	quality_position_model=1.84705e-43	ref_cov=145/80	reject=INDEL_HOMOPOLYMER	tot_cov=153/82
RA	116	.	NC_007779	379237	0	G	.	bias_e_value=3900180	bias_p_value=0.83941	fisher_strand_p_value=0.688912	frequency=2.272034e-02	genotype_quality=1057.5	ks_quality_p_value=0.710998	log10_base_likelihood=-18.3819	log10_qual_likelihood_position_model=2.7452	log10_strand_likelihood_position_model=0.54851	new_cov=3/3	polymorphism_quality=13.1	quality=13.1	quality_position_model=3.34621e-17	ref_cov=154/104	reject=INDEL_HOMOPOLYMER	tot_cov=157/107
RA	117	.	NC_007779	382878	1	.	T	bias_e_value=2536280	bias_p_value=0.545867	fisher_strand_p_value=0.510691	frequency=6.389618e-03	genotype_quality=1512.5	ks_quality_p_value=0.421492	log10_base_likelihood=-7.8662	log10_qual_likelihood_position_model=1.67837	log10_strand_likelihood_position_model=0.476748	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.26906e-07	ref_cov=179/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=181/132
RA	118	.	NC_007779	387560	0	A	C	bias_e_value=4.93499e-06	bias_p_value=1.06213e-12	fisher_strand_p_value=3.31524e-14	frequency=4.488754e-02	genotype_quality=832.8	ks_quality_p_value=1	log10_base_likelihood=-6.1062	log10_qual_likelihood_position_model=24.9526	log10_strand_likelihood_position_model=13.4795	new_cov=0/36	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=164/102	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/138
RA	119	.	NC_007779	387917	0	T	G	bias_e_value=0.869866	bias_p_value=1.87216e-07	fisher_strand_p_value=9.84367e-09	frequency=6.081152e-02	genotype_quality=490.6	ks_quality_p_value=0.977366	log10_base_likelihood=-14.7865	log10_qual_likelihood_position_model=11.1239	log10_strand_likelihood_position_model=8.01337	new_cov=2/10	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=144/12	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/22
RA	120	.	NC_007779	387919	0	A	G	bias_e_value=3.8771e-10	bias_p_value=8.34444e-17	fisher_strand_p_value=2.00094e-18	frequency=9.139919e-02	genotype_quality=490.9	ks_quality_p_value=0.998763	log10_base_likelihood=-26.9441	log10_qual_likelihood_position_model=14.1887	log10_strand_likelihood_position_model=17.6988	new_cov=0/16	polymorphism_quality=21.7	quality=21.7	quality_position_model=Inf	ref_cov=148/5	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=148/21
RA	121	.	NC_007779	401660	0	A	.	bias_e_value=4583850	bias_p_value=0.986553	fisher_strand_p_value=1	frequency=9.572983e-03	genotype_quality=1207.7	ks_quality_p_value=0.84055	log10_base_likelihood=-7.44876	log10_qual_likelihood_position_model=1.7969	log10_strand_likelihood_position_model=0.376611	new_cov=2/1	polymorphism_quality=1.9	quality=1.9	quality_position_model=3.59251e-07	ref_cov=176/134	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=178/135
RA	122	.	NC_007779	407306	0	C	A	bias_e_value=2.47376	bias_p_value=5.32412e-07	fisher_strand_p_value=2.90051e-08	frequency=4.958296e-02	genotype_quality=1005.0	ks_quality_p_value=1	log10_base_likelihood=-10.4682	log10_qual_likelihood_position_model=15.783	log10_strand_likelihood_position_model=7.53753	new_cov=23/0	polymorphism_quality=5.0	quality=5.0	quality_position_model=Inf	ref_cov=132/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/162
RA	123	.	NC_007779	414911	0	T	G	bias_e_value=9.45561e-12	bias_p_value=2.03507e-18	fisher_strand_p_value=4.46729e-20	frequency=5.709076e-02	genotype_quality=816.0	ks_quality_p_value=1	log10_base_likelihood=-7.64897	log10_qual_likelihood_position_model=33.0836	log10_strand_likelihood_position_model=19.35	new_cov=47/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=86/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=133/172
RA	124	.	NC_007779	416015	0	C	G	bias_e_value=182.032	bias_p_value=3.91775e-05	fisher_strand_p_value=2.91931e-06	frequency=3.987408e-02	genotype_quality=927.0	ks_quality_p_value=0.974598	log10_base_likelihood=-8.15215	log10_qual_likelihood_position_model=16.9182	log10_strand_likelihood_position_model=5.53472	new_cov=0/14	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=158/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/113
RA	125	.	NC_007779	432858	0	T	G	bias_e_value=1.24616e-11	bias_p_value=2.68203e-18	fisher_strand_p_value=5.92418e-20	frequency=1.406922e-01	genotype_quality=573.6	ks_quality_p_value=1	log10_base_likelihood=-24.3658	log10_qual_likelihood_position_model=39.0625	log10_strand_likelihood_position_model=19.3497	new_cov=59/0	polymorphism_quality=19.1	quality=19.1	quality_position_model=Inf	ref_cov=81/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/123
RA	126	.	NC_007779	440767	0	G	T	bias_e_value=0.934467	bias_p_value=2.01119e-07	fisher_strand_p_value=1.03756e-08	frequency=5.817318e-02	genotype_quality=833.5	ks_quality_p_value=1	log10_base_likelihood=-9.88085	log10_qual_likelihood_position_model=16.5444	log10_strand_likelihood_position_model=7.98399	new_cov=0/22	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=144/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/121
RA	127	.	NC_007779	450484	0	G	T	bias_e_value=0.0226807	bias_p_value=4.88142e-09	fisher_strand_p_value=2.21369e-10	frequency=7.095861e-02	genotype_quality=748.7	ks_quality_p_value=0.946979	log10_base_likelihood=-11.621	log10_qual_likelihood_position_model=22.3339	log10_strand_likelihood_position_model=9.65488	new_cov=19/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=56/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=75/146
RA	128	.	NC_007779	455713	1	.	T	bias_e_value=3324540	bias_p_value=0.715519	fisher_strand_p_value=0.49951	frequency=7.575989e-03	genotype_quality=1285.3	ks_quality_p_value=0.697036	log10_base_likelihood=-7.97874	log10_qual_likelihood_position_model=1.39627	log10_strand_likelihood_position_model=0.558666	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=6.02438e-08	ref_cov=137/125	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/125
RA	129	.	NC_007779	465801	0	C	A	bias_e_value=3.01839e-07	bias_p_value=6.49628e-14	fisher_strand_p_value=1.93926e-15	frequency=1.276798e-01	genotype_quality=602.7	ks_quality_p_value=0.959356	log10_base_likelihood=-25.7922	log10_qual_likelihood_position_model=31.871	log10_strand_likelihood_position_model=14.7124	new_cov=0/29	polymorphism_quality=20.6	quality=20.6	quality_position_model=Inf	ref_cov=129/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=129/73
RA	130	.	NC_007779	468787	1	.	A	bias_e_value=3775960	bias_p_value=0.812676	fisher_strand_p_value=0.499322	frequency=7.662773e-03	genotype_quality=1259.6	ks_quality_p_value=0.909668	log10_base_likelihood=-7.81408	log10_qual_likelihood_position_model=1.53232	log10_strand_likelihood_position_model=0.561354	new_cov=0/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.24117e-07	ref_cov=124/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/137
RA	131	.	NC_007779	480444	1	.	C	bias_e_value=3858050	bias_p_value=0.830343	fisher_strand_p_value=0.498319	frequency=7.379532e-03	genotype_quality=1317.6	ks_quality_p_value=0.957894	log10_base_likelihood=-7.55558	log10_qual_likelihood_position_model=2.51409	log10_strand_likelihood_position_model=0.587733	new_cov=2/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=2.57582e-06	ref_cov=136/133	reject=POLYMORPHISM_STRAND	tot_cov=138/133
RA	132	.	NC_007779	487626	0	A	C	bias_e_value=0.0149913	bias_p_value=3.22648e-09	fisher_strand_p_value=1.36034e-10	frequency=4.033852e-02	genotype_quality=982.7	ks_quality_p_value=1	log10_base_likelihood=-5.58431	log10_qual_likelihood_position_model=28.3474	log10_strand_likelihood_position_model=9.86635	new_cov=0/24	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=188/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=188/131
RA	133	.	NC_007779	494814	1	.	G	bias_e_value=2147290	bias_p_value=0.462147	fisher_strand_p_value=0.186633	frequency=6.872177e-03	genotype_quality=1426.2	ks_quality_p_value=0.883635	log10_base_likelihood=-7.63459	log10_qual_likelihood_position_model=2.25605	log10_strand_likelihood_position_model=0.72901	new_cov=2/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.60891e-06	ref_cov=124/165	reject=POLYMORPHISM_STRAND	tot_cov=126/165
RA	134	.	NC_007779	494823	0	T	G	bias_e_value=5.21802e-07	bias_p_value=1.12304e-13	fisher_strand_p_value=3.269e-15	frequency=5.800915e-02	genotype_quality=708.2	ks_quality_p_value=1	log10_base_likelihood=-10.9223	log10_qual_likelihood_position_model=26.0598	log10_strand_likelihood_position_model=14.4856	new_cov=23/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=40/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=63/168
RA	135	.	NC_007779	497098	0	A	G	bias_e_value=3.15938	bias_p_value=6.79972e-07	fisher_strand_p_value=3.75739e-08	frequency=3.958988e-02	genotype_quality=878.7	ks_quality_p_value=1	log10_base_likelihood=-8.69747	log10_qual_likelihood_position_model=16.543	log10_strand_likelihood_position_model=7.42511	new_cov=0/14	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=185/70	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=185/84
RA	136	.	NC_007779	497102	1	.	A	bias_e_value=1870650	bias_p_value=0.402607	fisher_strand_p_value=0.135301	frequency=7.375717e-03	genotype_quality=1272.0	ks_quality_p_value=0.98773	log10_base_likelihood=-5.58244	log10_qual_likelihood_position_model=4.5633	log10_strand_likelihood_position_model=0.868698	new_cov=0/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.22564	ref_cov=171/98	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=171/100
RA	137	.	NC_007779	500788	0	A	C	bias_e_value=3.91954e-11	bias_p_value=8.43576e-18	fisher_strand_p_value=1.91285e-19	frequency=5.823421e-02	genotype_quality=863.8	ks_quality_p_value=1	log10_base_likelihood=-9.74288	log10_qual_likelihood_position_model=34.8895	log10_strand_likelihood_position_model=18.7183	new_cov=0/36	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=191/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=191/101
RA	138	.	NC_007779	500799	0	A	C	bias_e_value=3.77045e-16	bias_p_value=8.11489e-23	fisher_strand_p_value=1.45196e-24	frequency=6.204128e-02	genotype_quality=753.5	ks_quality_p_value=1	log10_base_likelihood=-6.36603	log10_qual_likelihood_position_model=43.1187	log10_strand_likelihood_position_model=23.838	new_cov=0/40	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=186/44	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=186/84
RA	139	.	NC_007779	503058	0	T	C	bias_e_value=4.84337e-07	bias_p_value=1.04241e-13	fisher_strand_p_value=3.02752e-15	frequency=8.273220e-02	genotype_quality=798.3	ks_quality_p_value=1	log10_base_likelihood=-11.5861	log10_qual_likelihood_position_model=30.0735	log10_strand_likelihood_position_model=14.5189	new_cov=0/29	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=159/59	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/89
RA	140	.	NC_007779	506363	1	.	A	bias_e_value=2245850	bias_p_value=0.483359	fisher_strand_p_value=0.601288	frequency=1.003361e-02	genotype_quality=1451.9	ks_quality_p_value=0.294238	log10_base_likelihood=-12.1561	log10_qual_likelihood_position_model=2.92268	log10_strand_likelihood_position_model=0.454983	new_cov=2/1	polymorphism_quality=6.8	quality=6.8	quality_position_model=8.86768e-11	ref_cov=138/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/159
RA	141	.	NC_007779	511742	0	A	.	bias_e_value=2402450	bias_p_value=0.517063	fisher_strand_p_value=1	frequency=9.700775e-03	genotype_quality=1216.9	ks_quality_p_value=0.197016	log10_base_likelihood=-7.93262	log10_qual_likelihood_position_model=1.66396	log10_strand_likelihood_position_model=0.412381	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=8.97797e-08	ref_cov=149/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/159
RA	142	.	NC_007779	513848	0	A	C	bias_e_value=1.15287e-19	bias_p_value=2.48124e-26	fisher_strand_p_value=3.86974e-28	frequency=1.118307e-01	genotype_quality=629.8	ks_quality_p_value=1	log10_base_likelihood=-23.3841	log10_qual_likelihood_position_model=34.6286	log10_strand_likelihood_position_model=27.4123	new_cov=0/37	polymorphism_quality=18.1	quality=18.1	quality_position_model=Inf	ref_cov=177/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=177/59
RA	143	.	NC_007779	522430	1	.	T	bias_e_value=4335740	bias_p_value=0.933152	fisher_strand_p_value=0.691603	frequency=1.840496e-02	genotype_quality=1552.9	ks_quality_p_value=0.950537	log10_base_likelihood=-26.4165	log10_qual_likelihood_position_model=3.07552	log10_strand_likelihood_position_model=0.562597	new_cov=4/2	polymorphism_quality=21.2	quality=21.2	quality_position_model=5.58354e-25	ref_cov=173/147	reject=INDEL_HOMOPOLYMER	tot_cov=177/149
RA	144	.	NC_007779	524490	0	T	G	bias_e_value=1.79362e-13	bias_p_value=3.8603e-20	fisher_strand_p_value=7.78207e-22	frequency=1.123018e-01	genotype_quality=740.4	ks_quality_p_value=1	log10_base_likelihood=-25.1343	log10_qual_likelihood_position_model=35.5487	log10_strand_likelihood_position_model=21.1089	new_cov=37/0	polymorphism_quality=19.9	quality=19.9	quality_position_model=Inf	ref_cov=49/182	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=86/182
RA	145	.	NC_007779	527270	0	A	C	bias_e_value=4.29288e-10	bias_p_value=9.2393e-17	fisher_strand_p_value=2.21833e-18	frequency=9.031534e-02	genotype_quality=800.0	ks_quality_p_value=1	log10_base_likelihood=-17.3588	log10_qual_likelihood_position_model=33.7127	log10_strand_likelihood_position_model=17.654	new_cov=0/35	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=187/68	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=187/103
RA	146	.	NC_007779	527931	0	T	.	bias_e_value=1127570	bias_p_value=0.242679	fisher_strand_p_value=0.254839	frequency=8.789062e-03	genotype_quality=1374.1	ks_quality_p_value=0.255078	log10_base_likelihood=-7.78547	log10_qual_likelihood_position_model=1.19173	log10_strand_likelihood_position_model=0.785907	new_cov=3/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.00767e-07	ref_cov=184/154	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=187/154
RA	147	.	NC_007779	528271	1	.	T	bias_e_value=3946040	bias_p_value=0.84928	fisher_strand_p_value=0.504891	frequency=5.449295e-03	genotype_quality=1814.4	ks_quality_p_value=0.998091	log10_base_likelihood=-7.49255	log10_qual_likelihood_position_model=2.95206	log10_strand_likelihood_position_model=0.511021	new_cov=2/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=7.16373e-06	ref_cov=202/163	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=204/163
RA	148	.	NC_007779	535125	0	T	G	bias_e_value=5.19596e-17	bias_p_value=1.11829e-23	fisher_strand_p_value=1.93121e-25	frequency=1.210093e-01	genotype_quality=656.5	ks_quality_p_value=1	log10_base_likelihood=-19.7758	log10_qual_likelihood_position_model=39.5002	log10_strand_likelihood_position_model=24.7142	new_cov=60/0	polymorphism_quality=14.5	quality=14.5	quality_position_model=Inf	ref_cov=69/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/154
RA	149	.	NC_007779	535142	0	A	G	bias_e_value=5.07313e-09	bias_p_value=1.09186e-15	fisher_strand_p_value=2.79123e-17	frequency=1.001611e-01	genotype_quality=787.8	ks_quality_p_value=1	log10_base_likelihood=-14.6023	log10_qual_likelihood_position_model=27.7076	log10_strand_likelihood_position_model=16.5542	new_cov=35/0	polymorphism_quality=9.2	quality=9.2	quality_position_model=Inf	ref_cov=65/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=100/162
RA	150	.	NC_007779	547694	0	A	G	frequency=1	genotype_quality=1309.1	new_cov=171/148	quality=1309.1	ref_cov=0/1	tot_cov=171/149
RA	151	.	NC_007779	547831	1	.	G	frequency=1	genotype_quality=1146.6	new_cov=127/146	quality=1146.6	ref_cov=1/1	tot_cov=128/147
RA	152	.	NC_007779	556653	0	A	C	bias_e_value=1.58601e-20	bias_p_value=3.41347e-27	fisher_strand_p_value=5.16147e-29	frequency=9.438324e-02	genotype_quality=643.1	ks_quality_p_value=1	log10_base_likelihood=-13.0648	log10_qual_likelihood_position_model=38.3378	log10_strand_likelihood_position_model=28.2872	new_cov=0/37	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=174/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/56
RA	153	.	NC_007779	556858	0	A	T	frequency=1	genotype_quality=1411.7	new_cov=192/164	quality=1411.7	ref_cov=0/0	tot_cov=192/165
RA	154	.	NC_007779	569996	0	G	C	frequency=1	genotype_quality=1206.4	new_cov=140/139	quality=1206.4	ref_cov=0/0	tot_cov=140/139
RA	155	.	NC_007779	580450	0	A	C	frequency=1	genotype_quality=-0.2	new_cov=0/1	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	156	.	NC_007779	580451	0	T	G	frequency=1	genotype_quality=-0.1	new_cov=0/1	quality=-0.1	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	157	.	NC_007779	580455	0	C	T	frequency=1	genotype_quality=-0.2	new_cov=0/1	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	158	.	NC_007779	580461	0	G	T	frequency=1	genotype_quality=-0.2	new_cov=0/1	quality=-0.2	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	159	.	NC_007779	589157	0	T	G	bias_e_value=1.64843e-16	bias_p_value=3.54781e-23	fisher_strand_p_value=6.25369e-25	frequency=1.097236e-01	genotype_quality=587.0	ks_quality_p_value=1	log10_base_likelihood=-13.9334	log10_qual_likelihood_position_model=38.2687	log10_strand_likelihood_position_model=24.2039	new_cov=38/0	polymorphism_quality=8.6	quality=8.6	quality_position_model=Inf	ref_cov=28/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=67/153
RA	160	.	NC_007779	593216	0	T	G	bias_e_value=4.09877e-08	bias_p_value=8.82152e-15	fisher_strand_p_value=2.38602e-16	frequency=7.285070e-02	genotype_quality=506.5	ks_quality_p_value=1	log10_base_likelihood=-12.9233	log10_qual_likelihood_position_model=20.9825	log10_strand_likelihood_position_model=15.6223	new_cov=18/0	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=13/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=31/139
RA	161	.	NC_007779	595481	0	T	G	bias_e_value=2.08828e-12	bias_p_value=4.49447e-19	fisher_strand_p_value=9.5427e-21	frequency=1.014714e-01	genotype_quality=674.5	ks_quality_p_value=1	log10_base_likelihood=-10.297	log10_qual_likelihood_position_model=35.5242	log10_strand_likelihood_position_model=20.0296	new_cov=61/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=93/138	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/138
RA	162	.	NC_007779	598799	0	T	G	bias_e_value=1.02889e-15	bias_p_value=2.2144e-22	fisher_strand_p_value=4.03596e-24	frequency=1.454983e-01	genotype_quality=477.8	ks_quality_p_value=1	log10_base_likelihood=-20.9367	log10_qual_likelihood_position_model=34.0282	log10_strand_likelihood_position_model=23.3952	new_cov=31/1	polymorphism_quality=15.7	quality=15.7	quality_position_model=Inf	ref_cov=12/139	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=43/140
RA	163	.	NC_007779	606911	1	.	G	bias_e_value=507697	bias_p_value=0.109268	fisher_strand_p_value=0.0424445	frequency=1.158333e-02	genotype_quality=1268.7	ks_quality_p_value=0.538804	log10_base_likelihood=-12.6668	log10_qual_likelihood_position_model=2.46194	log10_strand_likelihood_position_model=1.37218	new_cov=3/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=7.8035e-11	ref_cov=88/168	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=91/168
RA	164	.	NC_007779	606915	0	T	G	bias_e_value=5.54128	bias_p_value=1.19261e-06	fisher_strand_p_value=6.97841e-08	frequency=2.638531e-02	genotype_quality=632.1	ks_quality_p_value=0.976481	log10_base_likelihood=-7.48826	log10_qual_likelihood_position_model=7.00134	log10_strand_likelihood_position_model=7.15624	new_cov=5/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=4/178	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=9/178
RA	165	.	NC_007779	612991	0	C	G	bias_e_value=1.53468e-11	bias_p_value=3.30299e-18	fisher_strand_p_value=7.33024e-20	frequency=9.935665e-02	genotype_quality=667.0	ks_quality_p_value=1	log10_base_likelihood=-30.0926	log10_qual_likelihood_position_model=21.9707	log10_strand_likelihood_position_model=19.1349	new_cov=0/19	polymorphism_quality=24.9	quality=24.9	quality_position_model=Inf	ref_cov=156/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/27
RA	166	.	NC_007779	616029	0	C	A	bias_e_value=6.20824e-05	bias_p_value=1.33616e-11	fisher_strand_p_value=4.54537e-13	frequency=6.878424e-02	genotype_quality=766.9	ks_quality_p_value=0.999175	log10_base_likelihood=-14.2644	log10_qual_likelihood_position_model=21.6169	log10_strand_likelihood_position_model=12.3424	new_cov=0/18	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=166/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=166/52
RA	167	.	NC_007779	623811	1	.	G	bias_e_value=2206410	bias_p_value=0.474871	fisher_strand_p_value=1	frequency=1.271152e-02	genotype_quality=1149.3	ks_quality_p_value=0.17206	log10_base_likelihood=-12.8287	log10_qual_likelihood_position_model=2.81653	log10_strand_likelihood_position_model=0.216647	new_cov=3/0	polymorphism_quality=7.4	quality=7.4	quality_position_model=8.08949e-12	ref_cov=197/36	reject=POLYMORPHISM_STRAND	tot_cov=200/36
RA	168	.	NC_007779	623841	1	.	G	bias_e_value=713547	bias_p_value=0.153572	fisher_strand_p_value=0.223809	frequency=3.061199e-02	genotype_quality=935.7	ks_quality_p_value=0.158036	log10_base_likelihood=-28.0976	log10_qual_likelihood_position_model=4.07431	log10_strand_likelihood_position_model=0.691241	new_cov=5/1	polymorphism_quality=22.9	quality=22.9	quality_position_model=1.54213e-25	ref_cov=183/7	reject=POLYMORPHISM_STRAND	tot_cov=188/8
RA	169	.	NC_007779	623849	0	C	T	bias_e_value=2752150	bias_p_value=0.592327	fisher_strand_p_value=1	frequency=2.195454e-02	genotype_quality=1013.1	ks_quality_p_value=0.24695	log10_base_likelihood=-9.80302	log10_qual_likelihood_position_model=5.36208	log10_strand_likelihood_position_model=0.40766	new_cov=5/1	polymorphism_quality=4.4	quality=4.4	quality_position_model=7.0981e-06	ref_cov=194/52	reject=POLYMORPHISM_STRAND	tot_cov=199/53
RA	170	.	NC_007779	623850	0	T	C	bias_e_value=4557640	bias_p_value=0.980911	fisher_strand_p_value=1	frequency=2.535248e-02	genotype_quality=958.0	ks_quality_p_value=0.811081	log10_base_likelihood=-12.2285	log10_qual_likelihood_position_model=6.4074	log10_strand_likelihood_position_model=0.462584	new_cov=6/1	polymorphism_quality=6.8	quality=6.8	quality_position_model=2.94423e-07	ref_cov=188/55	reject=POLYMORPHISM_STRAND	tot_cov=194/56
RA	171	.	NC_007779	623856	1	.	A	bias_e_value=3877280	bias_p_value=0.834481	fisher_strand_p_value=0.575485	frequency=1.587296e-02	genotype_quality=1206.1	ks_quality_p_value=0.839253	log10_base_likelihood=-17.6642	log10_qual_likelihood_position_model=2.44918	log10_strand_likelihood_position_model=0.53126	new_cov=4/0	polymorphism_quality=12.4	quality=12.4	quality_position_model=8.60453e-17	ref_cov=182/66	reject=POLYMORPHISM_STRAND	tot_cov=186/66
RA	172	.	NC_007779	623859	0	C	A	bias_e_value=4630610	bias_p_value=0.996615	fisher_strand_p_value=1	frequency=2.246857e-02	genotype_quality=1081.7	ks_quality_p_value=0.91886	log10_base_likelihood=-10.2141	log10_qual_likelihood_position_model=2.79878	log10_strand_likelihood_position_model=0.47413	new_cov=5/1	polymorphism_quality=4.8	quality=4.8	quality_position_model=6.81617e-09	ref_cov=188/71	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=193/72
RA	173	.	NC_007779	634377	1	.	T	bias_e_value=431947	bias_p_value=0.0929652	fisher_strand_p_value=0.502328	frequency=6.600380e-03	genotype_quality=1483.0	ks_quality_p_value=0.0371534	log10_base_likelihood=-8.11254	log10_qual_likelihood_position_model=2.05189	log10_strand_likelihood_position_model=0.529122	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.9477e-07	ref_cov=163/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/138
RA	174	.	NC_007779	645484	0	A	C	bias_e_value=1.29476e-06	bias_p_value=2.78662e-13	fisher_strand_p_value=8.33871e-15	frequency=5.556822e-02	genotype_quality=1016.4	ks_quality_p_value=1	log10_base_likelihood=-8.35965	log10_qual_likelihood_position_model=32.6664	log10_strand_likelihood_position_model=14.0789	new_cov=0/35	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=202/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=202/151
RA	175	.	NC_007779	645970	0	T	G	bias_e_value=1.68119e-11	bias_p_value=3.61831e-18	fisher_strand_p_value=8.0467e-20	frequency=1.055284e-01	genotype_quality=529.9	ks_quality_p_value=1	log10_base_likelihood=-18.8982	log10_qual_likelihood_position_model=25.7676	log10_strand_likelihood_position_model=19.0944	new_cov=23/0	polymorphism_quality=13.6	quality=13.6	quality_position_model=Inf	ref_cov=14/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/144
RA	176	.	NC_007779	646440	0	C	A	bias_e_value=8.98942e-19	bias_p_value=1.93473e-25	fisher_strand_p_value=3.11891e-27	frequency=1.220050e-01	genotype_quality=753.7	ks_quality_p_value=1	log10_base_likelihood=-75.753	log10_qual_likelihood_position_model=21.7793	log10_strand_likelihood_position_model=26.506	new_cov=0/28	polymorphism_quality=70.8	quality=70.8	quality_position_model=1.04129e-29	ref_cov=188/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=188/39
RA	177	.	NC_007779	649677	0	T	G	bias_e_value=3.45207e-14	bias_p_value=7.42966e-21	fisher_strand_p_value=1.44867e-22	frequency=9.292364e-02	genotype_quality=655.8	ks_quality_p_value=1	log10_base_likelihood=-12.151	log10_qual_likelihood_position_model=28.6741	log10_strand_likelihood_position_model=21.839	new_cov=38/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=42/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/166
RA	178	.	NC_007779	650004	0	C	T	bias_e_value=2.35005	bias_p_value=5.05786e-07	fisher_strand_p_value=2.74734e-08	frequency=5.463696e-02	genotype_quality=1030.3	ks_quality_p_value=1	log10_base_likelihood=-10.0007	log10_qual_likelihood_position_model=20.731	log10_strand_likelihood_position_model=7.56109	new_cov=21/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=117/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=139/165
RA	179	.	NC_007779	660356	0	T	G	bias_e_value=4.6236e-17	bias_p_value=9.95107e-24	fisher_strand_p_value=1.71495e-25	frequency=1.570425e-01	genotype_quality=512.4	ks_quality_p_value=1	log10_base_likelihood=-29.8116	log10_qual_likelihood_position_model=37.3925	log10_strand_likelihood_position_model=24.7657	new_cov=47/0	polymorphism_quality=24.6	quality=24.6	quality_position_model=Inf	ref_cov=36/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=83/137
RA	180	.	NC_007779	665062	0	C	A	bias_e_value=0.00145924	bias_p_value=3.14063e-10	fisher_strand_p_value=1.2691e-11	frequency=9.428835e-02	genotype_quality=679.2	ks_quality_p_value=0.946521	log10_base_likelihood=-21.6059	log10_qual_likelihood_position_model=29.627	log10_strand_likelihood_position_model=10.8965	new_cov=0/25	polymorphism_quality=16.3	quality=16.3	quality_position_model=Inf	ref_cov=134/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=135/90
RA	181	.	NC_007779	686495	0	A	C	bias_e_value=2.03478e-10	bias_p_value=4.37932e-17	fisher_strand_p_value=1.0325e-18	frequency=1.084518e-01	genotype_quality=601.4	ks_quality_p_value=1	log10_base_likelihood=-26.523	log10_qual_likelihood_position_model=28.4076	log10_strand_likelihood_position_model=17.9884	new_cov=1/26	polymorphism_quality=21.3	quality=21.3	quality_position_model=Inf	ref_cov=161/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/49
RA	182	.	NC_007779	687133	0	A	C	bias_e_value=0.00236824	bias_p_value=5.09701e-10	fisher_strand_p_value=1.9878e-11	frequency=4.807186e-02	genotype_quality=838.6	ks_quality_p_value=1	log10_base_likelihood=-16.2402	log10_qual_likelihood_position_model=22.7209	log10_strand_likelihood_position_model=10.7016	new_cov=0/19	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=188/61	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=188/81
RA	183	.	NC_007779	688155	0	T	G	bias_e_value=4.52857e-05	bias_p_value=9.74656e-12	fisher_strand_p_value=3.2765e-13	frequency=5.021095e-02	genotype_quality=864.1	ks_quality_p_value=1	log10_base_likelihood=-6.80788	log10_qual_likelihood_position_model=42.0005	log10_strand_likelihood_position_model=12.4846	new_cov=35/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=109/161	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/161
RA	184	.	NC_007779	693875	0	A	.	bias_e_value=4192740	bias_p_value=0.902376	fisher_strand_p_value=0.594357	frequency=9.510040e-03	genotype_quality=1254.0	ks_quality_p_value=0.9961	log10_base_likelihood=-7.30206	log10_qual_likelihood_position_model=4.61226	log10_strand_likelihood_position_model=0.466969	new_cov=1/2	polymorphism_quality=1.8	quality=1.8	quality_position_model=0.000598385	ref_cov=170/142	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=171/144
RA	185	.	NC_007779	704668	0	T	G	bias_e_value=1.94887e-07	bias_p_value=4.19443e-14	fisher_strand_p_value=1.18593e-15	frequency=4.715443e-02	genotype_quality=664.3	ks_quality_p_value=1	log10_base_likelihood=-7.20774	log10_qual_likelihood_position_model=26.9872	log10_strand_likelihood_position_model=14.9288	new_cov=21/1	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=25/173	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=47/174
RA	186	.	NC_007779	706282	0	T	G	bias_e_value=21528.6	bias_p_value=0.00463347	fisher_strand_p_value=0.000575303	frequency=1.903915e-02	genotype_quality=542.5	ks_quality_p_value=0.945694	log10_base_likelihood=-5.80723	log10_qual_likelihood_position_model=3.92614	log10_strand_likelihood_position_model=3.2401	new_cov=3/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=11/143	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=14/143
RA	187	.	NC_007779	706385	1	.	T	bias_e_value=1631160	bias_p_value=0.351065	fisher_strand_p_value=0.219572	frequency=1.954365e-02	genotype_quality=1438.9	ks_quality_p_value=0.4974	log10_base_likelihood=-26.3366	log10_qual_likelihood_position_model=3.67857	log10_strand_likelihood_position_model=0.930923	new_cov=1/5	polymorphism_quality=21.1	quality=21.1	quality_position_model=6.43068e-24	ref_cov=143/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/163
RA	188	.	NC_007779	706386	0	T	.	bias_e_value=3993210	bias_p_value=0.859432	fisher_strand_p_value=0.599099	frequency=9.604454e-03	genotype_quality=1216.6	ks_quality_p_value=0.866416	log10_base_likelihood=-7.49052	log10_qual_likelihood_position_model=2.75881	log10_strand_likelihood_position_model=0.458708	new_cov=2/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=3.98058e-06	ref_cov=143/166	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=145/167
RA	189	.	NC_007779	710864	0	T	G	bias_e_value=0.0108005	bias_p_value=2.32452e-09	fisher_strand_p_value=9.68202e-11	frequency=5.007124e-02	genotype_quality=651.2	ks_quality_p_value=0.997853	log10_base_likelihood=-16.7754	log10_qual_likelihood_position_model=13.3646	log10_strand_likelihood_position_model=10.014	new_cov=10/0	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=14/174	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=24/174
RA	190	.	NC_007779	719073	0	C	G	bias_e_value=0.156214	bias_p_value=3.36209e-08	fisher_strand_p_value=1.58103e-09	frequency=4.707289e-02	genotype_quality=704.3	ks_quality_p_value=1	log10_base_likelihood=-6.42908	log10_qual_likelihood_position_model=15.0518	log10_strand_likelihood_position_model=8.80106	new_cov=14/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=37/144	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=51/144
RA	191	.	NC_007779	749354	0	C	A	frequency=1	genotype_quality=1294.5	new_cov=173/152	quality=1294.5	ref_cov=1/0	tot_cov=174/152
RA	192	.	NC_007779	752693	0	A	C	bias_e_value=4.89583e-27	bias_p_value=1.0537e-33	fisher_strand_p_value=1.29556e-35	frequency=1.426926e-01	genotype_quality=781.7	ks_quality_p_value=1	log10_base_likelihood=-42.069	log10_qual_likelihood_position_model=52.8783	log10_strand_likelihood_position_model=34.8875	new_cov=0/57	polymorphism_quality=36.9	quality=36.9	quality_position_model=Inf	ref_cov=212/42	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=212/99
RA	193	.	NC_007779	753536	0	G	T	bias_e_value=0.0420639	bias_p_value=9.05315e-09	fisher_strand_p_value=3.99877e-10	frequency=4.663658e-02	genotype_quality=988.8	ks_quality_p_value=1	log10_base_likelihood=-8.15502	log10_qual_likelihood_position_model=20.0892	log10_strand_likelihood_position_model=9.39807	new_cov=0/20	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=178/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=178/101
RA	194	.	NC_007779	753547	0	T	A	bias_e_value=2.60509e-09	bias_p_value=5.60677e-16	fisher_strand_p_value=1.40869e-17	frequency=1.038580e-01	genotype_quality=916.2	ks_quality_p_value=1	log10_base_likelihood=-27.9631	log10_qual_likelihood_position_model=40.0678	log10_strand_likelihood_position_model=16.8512	new_cov=0/31	polymorphism_quality=22.7	quality=22.7	quality_position_model=Inf	ref_cov=188/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=188/91
RA	195	.	NC_007779	758440	0	C	A	frequency=1	genotype_quality=1218.2	new_cov=142/166	quality=1218.2	ref_cov=0/0	tot_cov=142/166
RA	196	.	NC_007779	759019	0	C	G	bias_e_value=3.15456e-22	bias_p_value=6.78936e-29	fisher_strand_p_value=9.89409e-31	frequency=1.340594e-01	genotype_quality=803.1	ks_quality_p_value=0.978757	log10_base_likelihood=-78.5815	log10_qual_likelihood_position_model=29.7624	log10_strand_likelihood_position_model=30.0046	new_cov=0/31	polymorphism_quality=73.6	quality=73.6	quality_position_model=5.6427e-21	ref_cov=191/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=191/40
RA	197	.	NC_007779	771319	0	T	G	bias_e_value=1.20899e-07	bias_p_value=2.60202e-14	fisher_strand_p_value=7.25615e-16	frequency=1.026416e-01	genotype_quality=559.6	ks_quality_p_value=1	log10_base_likelihood=-9.00053	log10_qual_likelihood_position_model=35.7749	log10_strand_likelihood_position_model=15.3504	new_cov=52/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=87/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=140/109
RA	198	.	NC_007779	781483	0	C	T	bias_e_value=1400320	bias_p_value=0.301381	fisher_strand_p_value=0.0877961	frequency=2.100563e-02	genotype_quality=1058.6	ks_quality_p_value=1	log10_base_likelihood=-6.23439	log10_qual_likelihood_position_model=8.62708	log10_strand_likelihood_position_model=1.31564	new_cov=2/7	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=149/126	reject=EVALUE	tot_cov=151/133
RA	199	.	NC_007779	800805	0	T	.	bias_e_value=4640010	bias_p_value=0.998638	fisher_strand_p_value=1	frequency=9.816170e-03	genotype_quality=1604.9	ks_quality_p_value=0.948271	log10_base_likelihood=-10.0654	log10_qual_likelihood_position_model=3.16303	log10_strand_likelihood_position_model=0.424254	new_cov=2/2	polymorphism_quality=4.6	quality=4.6	quality_position_model=2.04531e-08	ref_cov=206/197	reject=INDEL_HOMOPOLYMER	tot_cov=208/199
RA	200	.	NC_007779	827921	0	T	G	bias_e_value=1.09017e-19	bias_p_value=2.34629e-26	fisher_strand_p_value=3.65603e-28	frequency=1.079330e-01	genotype_quality=658.5	ks_quality_p_value=1	log10_base_likelihood=-11.8835	log10_qual_likelihood_position_model=45.5983	log10_strand_likelihood_position_model=27.437	new_cov=57/0	polymorphism_quality=6.5	quality=6.5	quality_position_model=Inf	ref_cov=55/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=113/166
RA	201	.	NC_007779	829585	0	G	T	bias_e_value=0.00326474	bias_p_value=7.02649e-10	fisher_strand_p_value=2.81341e-11	frequency=6.868601e-02	genotype_quality=703.5	ks_quality_p_value=0.986872	log10_base_likelihood=-16.229	log10_qual_likelihood_position_model=20.8222	log10_strand_likelihood_position_model=10.5508	new_cov=16/0	polymorphism_quality=10.9	quality=10.9	quality_position_model=Inf	ref_cov=35/154	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=51/154
RA	202	.	NC_007779	842195	0	C	A	bias_e_value=147.719	bias_p_value=3.17925e-05	fisher_strand_p_value=2.27171e-06	frequency=3.919983e-02	genotype_quality=1194.0	ks_quality_p_value=1	log10_base_likelihood=-6.80966	log10_qual_likelihood_position_model=25.1415	log10_strand_likelihood_position_model=5.70673	new_cov=25/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=194/143	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=220/144
RA	203	.	NC_007779	853114	0	C	G	bias_e_value=1.66567e-08	bias_p_value=3.58491e-15	fisher_strand_p_value=9.45965e-17	frequency=1.092315e-01	genotype_quality=690.1	ks_quality_p_value=1	log10_base_likelihood=-33.9318	log10_qual_likelihood_position_model=22.739	log10_strand_likelihood_position_model=16.0241	new_cov=0/22	polymorphism_quality=28.8	quality=28.8	quality_position_model=Inf	ref_cov=147/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/45
RA	204	.	NC_007779	881118	0	T	.	bias_e_value=3277830	bias_p_value=0.705467	fisher_strand_p_value=0.619528	frequency=8.762360e-03	genotype_quality=1338.4	ks_quality_p_value=0.546821	log10_base_likelihood=-7.56692	log10_qual_likelihood_position_model=1.53682	log10_strand_likelihood_position_model=0.429896	new_cov=1/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.65325e-07	ref_cov=172/167	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=173/169
RA	205	.	NC_007779	883947	0	C	A	bias_e_value=0.125199	bias_p_value=2.69457e-08	fisher_strand_p_value=1.25344e-09	frequency=4.595280e-02	genotype_quality=1004.9	ks_quality_p_value=1	log10_base_likelihood=-8.04874	log10_qual_likelihood_position_model=18.7227	log10_strand_likelihood_position_model=8.9019	new_cov=19/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=85/184	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=105/184
RA	206	.	NC_007779	887234	0	C	A	frequency=1	genotype_quality=884.4	new_cov=135/104	quality=884.4	ref_cov=0/0	tot_cov=135/104
RA	207	.	NC_007779	889984	0	A	.	bias_e_value=3692860	bias_p_value=0.794791	fisher_strand_p_value=1	frequency=1.196671e-02	genotype_quality=1320.8	ks_quality_p_value=0.432239	log10_base_likelihood=-10.7502	log10_qual_likelihood_position_model=2.84255	log10_strand_likelihood_position_model=0.424485	new_cov=2/2	polymorphism_quality=5.3	quality=5.3	quality_position_model=1.8884e-09	ref_cov=171/159	reject=INDEL_HOMOPOLYMER	tot_cov=173/161
RA	208	.	NC_007779	894943	0	T	G	bias_e_value=3.38338e-13	bias_p_value=7.28183e-20	fisher_strand_p_value=1.48739e-21	frequency=6.999254e-02	genotype_quality=638.2	ks_quality_p_value=1	log10_base_likelihood=-8.42991	log10_qual_likelihood_position_model=33.398	log10_strand_likelihood_position_model=20.8294	new_cov=29/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=21/168	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=51/169
RA	209	.	NC_007779	901814	0	A	C	bias_e_value=0.308697	bias_p_value=6.64389e-08	fisher_strand_p_value=3.23306e-09	frequency=4.193974e-02	genotype_quality=791.2	ks_quality_p_value=1	log10_base_likelihood=-5.77207	log10_qual_likelihood_position_model=19.7183	log10_strand_likelihood_position_model=8.49039	new_cov=0/21	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=161/94	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=161/115
RA	210	.	NC_007779	904838	0	C	A	bias_e_value=7.03943e-12	bias_p_value=1.51505e-18	fisher_strand_p_value=3.90178e-20	frequency=1.205664e-01	genotype_quality=1021.4	ks_quality_p_value=0.846765	log10_base_likelihood=-37.3584	log10_qual_likelihood_position_model=40.1575	log10_strand_likelihood_position_model=19.4087	new_cov=49/0	polymorphism_quality=32.2	quality=32.2	quality_position_model=Inf	ref_cov=103/189	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/189
RA	211	.	NC_007779	911333	0	T	G	bias_e_value=0.0243929	bias_p_value=5.24993e-09	fisher_strand_p_value=2.26196e-10	frequency=3.874683e-02	genotype_quality=607.4	ks_quality_p_value=1	log10_base_likelihood=-8.79221	log10_qual_likelihood_position_model=14.2325	log10_strand_likelihood_position_model=9.64551	new_cov=12/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=23/157	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=35/157
RA	212	.	NC_007779	915554	0	G	T	bias_e_value=17997.6	bias_p_value=0.0038735	fisher_strand_p_value=0.000446042	frequency=3.035736e-02	genotype_quality=508.8	ks_quality_p_value=0.995991	log10_base_likelihood=-6.39606	log10_qual_likelihood_position_model=5.34734	log10_strand_likelihood_position_model=3.35062	new_cov=0/6	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=119/42	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=119/48
RA	213	.	NC_007779	932754	1	.	A	bias_e_value=1681990	bias_p_value=0.362004	fisher_strand_p_value=0.224656	frequency=5.618095e-03	genotype_quality=1751.6	ks_quality_p_value=0.508358	log10_base_likelihood=-7.60503	log10_qual_likelihood_position_model=1.6614	log10_strand_likelihood_position_model=0.648482	new_cov=0/2	polymorphism_quality=2.1	quality=2.1	quality_position_model=3.42563e-07	ref_cov=187/167	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=187/169
RA	214	.	NC_007779	940808	0	G	C	bias_e_value=2.3887	bias_p_value=5.14105e-07	fisher_strand_p_value=2.79514e-08	frequency=6.316519e-02	genotype_quality=738.4	ks_quality_p_value=1	log10_base_likelihood=-9.87767	log10_qual_likelihood_position_model=14.701	log10_strand_likelihood_position_model=7.5536	new_cov=0/21	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=126/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=126/108
RA	215	.	NC_007779	947970	0	C	A	bias_e_value=0.520621	bias_p_value=1.1205e-07	fisher_strand_p_value=5.60248e-09	frequency=5.606127e-02	genotype_quality=901.3	ks_quality_p_value=1	log10_base_likelihood=-10.2226	log10_qual_likelihood_position_model=15.8017	log10_strand_likelihood_position_model=8.25162	new_cov=20/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=90/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=112/159
RA	216	.	NC_007779	954820	0	A	C	bias_e_value=1.00815e-10	bias_p_value=2.16978e-17	fisher_strand_p_value=5.03037e-19	frequency=1.463122e-01	genotype_quality=438.6	ks_quality_p_value=1	log10_base_likelihood=-12.2362	log10_qual_likelihood_position_model=30.6131	log10_strand_likelihood_position_model=18.2984	new_cov=0/46	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=103/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=103/94
RA	217	.	NC_007779	975142	0	T	G	bias_e_value=3.52151	bias_p_value=7.57911e-07	fisher_strand_p_value=4.22971e-08	frequency=3.202915e-02	genotype_quality=598.4	ks_quality_p_value=0.996479	log10_base_likelihood=-6.8363	log10_qual_likelihood_position_model=9.83006	log10_strand_likelihood_position_model=7.37369	new_cov=6/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=7/165	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=13/165
RA	218	.	NC_007779	985136	0	T	.	bias_e_value=840864	bias_p_value=0.180974	fisher_strand_p_value=0.0466807	frequency=1.097679e-02	genotype_quality=1426.8	ks_quality_p_value=0.939399	log10_base_likelihood=-10.1381	log10_qual_likelihood_position_model=3.00293	log10_strand_likelihood_position_model=1.33086	new_cov=0/4	polymorphism_quality=4.7	quality=4.7	quality_position_model=1.01617e-07	ref_cov=194/166	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=194/170
RA	219	.	NC_007779	986227	0	T	.	bias_e_value=1286490	bias_p_value=0.276883	fisher_strand_p_value=0.249218	frequency=8.327484e-03	genotype_quality=1397.1	ks_quality_p_value=0.312825	log10_base_likelihood=-6.7523	log10_qual_likelihood_position_model=3.65819	log10_strand_likelihood_position_model=0.853119	new_cov=3/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=0.000571841	ref_cov=184/172	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=187/172
RA	220	.	NC_007779	986260	1	.	A	bias_e_value=3573150	bias_p_value=0.769025	fisher_strand_p_value=1	frequency=6.600380e-03	genotype_quality=1483.9	ks_quality_p_value=0.402748	log10_base_likelihood=-7.72002	log10_qual_likelihood_position_model=1.7819	log10_strand_likelihood_position_model=0.303591	new_cov=1/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.52326e-07	ref_cov=165/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/137
RA	221	.	NC_007779	987436	0	A	C	bias_e_value=8.30896e-10	bias_p_value=1.78828e-16	fisher_strand_p_value=4.36454e-18	frequency=9.094238e-02	genotype_quality=755.8	ks_quality_p_value=1	log10_base_likelihood=-10.36	log10_qual_likelihood_position_model=44.2193	log10_strand_likelihood_position_model=17.3601	new_cov=0/47	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=154/92	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=154/142
RA	222	.	NC_007779	987574	0	G	T	frequency=1	genotype_quality=1236.6	new_cov=114/198	quality=1236.6	ref_cov=0/0	tot_cov=114/198
RA	223	.	NC_007779	987853	1	.	G	bias_e_value=3939400	bias_p_value=0.847851	fisher_strand_p_value=0.528032	frequency=5.916595e-03	genotype_quality=1670.5	ks_quality_p_value=0.950412	log10_base_likelihood=-7.80856	log10_qual_likelihood_position_model=1.5882	log10_strand_likelihood_position_model=0.414181	new_cov=2/0	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.01165e-07	ref_cov=208/128	reject=POLYMORPHISM_STRAND	tot_cov=210/128
RA	224	.	NC_007779	987916	0	T	G	bias_e_value=2.21921e-09	bias_p_value=4.77627e-16	fisher_strand_p_value=1.19509e-17	frequency=7.105112e-02	genotype_quality=655.2	ks_quality_p_value=1	log10_base_likelihood=-22.112	log10_qual_likelihood_position_model=21.6555	log10_strand_likelihood_position_model=16.9226	new_cov=17/0	polymorphism_quality=16.8	quality=16.8	quality_position_model=Inf	ref_cov=12/181	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=29/181
RA	225	.	NC_007779	991407	0	G	T	bias_e_value=0.386579	bias_p_value=8.3201e-08	fisher_strand_p_value=5.26065e-09	frequency=3.931522e-02	genotype_quality=1258.5	ks_quality_p_value=0.77859	log10_base_likelihood=-6.85588	log10_qual_likelihood_position_model=29.1693	log10_strand_likelihood_position_model=8.27896	new_cov=0/26	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=195/167	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=195/193
RA	226	.	NC_007779	1001437	1	.	A	bias_e_value=4600350	bias_p_value=0.990103	fisher_strand_p_value=1	frequency=6.230354e-03	genotype_quality=1573.2	ks_quality_p_value=0.862651	log10_base_likelihood=-7.55202	log10_qual_likelihood_position_model=3.08738	log10_strand_likelihood_position_model=0.299679	new_cov=1/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=5.16509e-06	ref_cov=159/160	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/161
RA	227	.	NC_007779	1002413	0	T	G	bias_e_value=1.18789e-23	bias_p_value=2.55661e-30	fisher_strand_p_value=3.48145e-32	frequency=1.621876e-01	genotype_quality=692.0	ks_quality_p_value=1	log10_base_likelihood=-31.7311	log10_qual_likelihood_position_model=49.1515	log10_strand_likelihood_position_model=31.4582	new_cov=66/0	polymorphism_quality=26.5	quality=26.5	quality_position_model=Inf	ref_cov=54/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/170
RA	228	.	NC_007779	1004576	0	G	.	bias_e_value=3171700	bias_p_value=0.682625	fisher_strand_p_value=1	frequency=1.023006e-02	genotype_quality=1226.0	ks_quality_p_value=0.318254	log10_base_likelihood=-7.93318	log10_qual_likelihood_position_model=2.22486	log10_strand_likelihood_position_model=0.355949	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.98772e-07	ref_cov=180/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=182/111
RA	229	.	NC_007779	1019391	0	A	.	bias_e_value=3142830	bias_p_value=0.676412	fisher_strand_p_value=1	frequency=9.794235e-03	genotype_quality=1203.2	ks_quality_p_value=0.312868	log10_base_likelihood=-7.77061	log10_qual_likelihood_position_model=1.64042	log10_strand_likelihood_position_model=0.37017	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.12931e-07	ref_cov=176/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=178/128
RA	230	.	NC_007779	1030153	1	.	A	bias_e_value=4112890	bias_p_value=0.88519	fisher_strand_p_value=1	frequency=7.575989e-03	genotype_quality=1236.8	ks_quality_p_value=0.56085	log10_base_likelihood=-7.76827	log10_qual_likelihood_position_model=2.11893	log10_strand_likelihood_position_model=0.299781	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=3.00786e-07	ref_cov=127/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/136
RA	231	.	NC_007779	1037604	0	C	G	bias_e_value=3.59596e-16	bias_p_value=7.73935e-23	fisher_strand_p_value=1.38357e-24	frequency=1.588941e-01	genotype_quality=625.8	ks_quality_p_value=1	log10_base_likelihood=-40.4052	log10_qual_likelihood_position_model=29.3311	log10_strand_likelihood_position_model=23.859	new_cov=33/0	polymorphism_quality=35.3	quality=35.3	quality_position_model=Inf	ref_cov=18/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=51/143
RA	232	.	NC_007779	1049998	0	C	A	bias_e_value=186.333	bias_p_value=4.01033e-05	fisher_strand_p_value=2.91772e-06	frequency=3.672791e-02	genotype_quality=768.7	ks_quality_p_value=1	log10_base_likelihood=-5.60557	log10_qual_likelihood_position_model=14.3274	log10_strand_likelihood_position_model=5.53496	new_cov=15/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=87/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/127
RA	233	.	NC_007779	1063614	0	A	C	bias_e_value=0.604308	bias_p_value=1.30061e-07	fisher_strand_p_value=6.55885e-09	frequency=5.290127e-02	genotype_quality=786.8	ks_quality_p_value=0.999333	log10_base_likelihood=-7.56995	log10_qual_likelihood_position_model=24.8168	log10_strand_likelihood_position_model=8.18317	new_cov=0/22	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=148/98	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=148/121
RA	234	.	NC_007779	1067257	0	T	C	bias_e_value=3716.17	bias_p_value=0.000799807	fisher_strand_p_value=7.63125e-05	frequency=2.718830e-02	genotype_quality=1028.4	ks_quality_p_value=1	log10_base_likelihood=-5.89984	log10_qual_likelihood_position_model=11.228	log10_strand_likelihood_position_model=4.1174	new_cov=0/12	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=163/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=164/141
RA	235	.	NC_007779	1067271	0	C	G	bias_e_value=244079	bias_p_value=0.0525316	fisher_strand_p_value=0.00924203	frequency=1.559067e-02	genotype_quality=1196.0	ks_quality_p_value=1	log10_base_likelihood=-6.41509	log10_qual_likelihood_position_model=7.45745	log10_strand_likelihood_position_model=2.03423	new_cov=0/6	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=165/136	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=165/142
RA	236	.	NC_007779	1070200	0	A	C	bias_e_value=0.13889	bias_p_value=2.98924e-08	fisher_strand_p_value=1.39759e-09	frequency=4.321480e-02	genotype_quality=603.4	ks_quality_p_value=1	log10_base_likelihood=-10.2792	log10_qual_likelihood_position_model=11.5852	log10_strand_likelihood_position_model=8.85462	new_cov=0/11	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=155/23	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/34
RA	237	.	NC_007779	1077331	0	A	C	bias_e_value=0.000117434	bias_p_value=2.52746e-11	fisher_strand_p_value=8.78803e-13	frequency=6.335878e-02	genotype_quality=813.0	ks_quality_p_value=1	log10_base_likelihood=-15.121	log10_qual_likelihood_position_model=31.8925	log10_strand_likelihood_position_model=12.0561	new_cov=0/32	polymorphism_quality=9.8	quality=9.8	quality_position_model=Inf	ref_cov=156/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/129
RA	238	.	NC_007779	1077754	0	G	C	bias_e_value=18262.8	bias_p_value=0.00393059	fisher_strand_p_value=0.000466459	frequency=2.608109e-02	genotype_quality=946.7	ks_quality_p_value=0.96827	log10_base_likelihood=-6.1809	log10_qual_likelihood_position_model=13.4862	log10_strand_likelihood_position_model=3.33119	new_cov=10/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=122/147	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=132/147
RA	239	.	NC_007779	1079882	0	T	G	bias_e_value=78.2979	bias_p_value=1.68516e-05	fisher_strand_p_value=1.18431e-06	frequency=2.364063e-02	genotype_quality=678.4	ks_quality_p_value=0.969451	log10_base_likelihood=-5.62162	log10_qual_likelihood_position_model=7.88558	log10_strand_likelihood_position_model=5.92653	new_cov=5/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=10/185	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=15/185
RA	240	.	NC_007779	1086017	0	A	C	bias_e_value=2.00667e-17	bias_p_value=4.31882e-24	fisher_strand_p_value=7.33564e-26	frequency=1.627526e-01	genotype_quality=597.1	ks_quality_p_value=1	log10_base_likelihood=-25.0175	log10_qual_likelihood_position_model=44.0417	log10_strand_likelihood_position_model=25.1346	new_cov=0/65	polymorphism_quality=19.8	quality=19.8	quality_position_model=Inf	ref_cov=137/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/132
RA	241	.	NC_007779	1093686	0	T	C	frequency=1	genotype_quality=1414.5	new_cov=135/192	quality=1414.5	ref_cov=0/0	tot_cov=135/192
RA	242	.	NC_007779	1097402	1	.	A	bias_e_value=3929890	bias_p_value=0.845805	fisher_strand_p_value=0.498904	frequency=4.784584e-03	genotype_quality=1667.1	ks_quality_p_value=0.999977	log10_base_likelihood=-7.15273	log10_qual_likelihood_position_model=2.83307	log10_strand_likelihood_position_model=0.590694	new_cov=0/2	polymorphism_quality=1.6	quality=1.6	quality_position_model=1.48245e-05	ref_cov=206/210	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=206/212
RA	243	.	NC_007779	1097580	0	C	T	bias_e_value=7001.93	bias_p_value=0.00150698	fisher_strand_p_value=0.0148327	frequency=1.733422e-01	genotype_quality=810.2	ks_quality_p_value=0.0103908	log10_base_likelihood=-162.399	log10_qual_likelihood_position_model=19.0328	log10_strand_likelihood_position_model=2.24303	new_cov=35/24	polymorphism_quality=157.6	quality=157.6	quality_position_model=1.02208e-143	ref_cov=117/163	tot_cov=154/187
RA	244	.	NC_007779	1097764	1	.	A	bias_e_value=4369150	bias_p_value=0.940343	fisher_strand_p_value=1	frequency=3.616333e-03	genotype_quality=2214.3	ks_quality_p_value=0.6751	log10_base_likelihood=-7.48972	log10_qual_likelihood_position_model=1.87146	log10_strand_likelihood_position_model=0.312704	new_cov=1/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=3.34143e-07	ref_cov=229/322	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=230/323
RA	245	.	NC_007779	1097765	0	A	.	bias_e_value=3425320	bias_p_value=0.73721	fisher_strand_p_value=1	frequency=5.368233e-03	genotype_quality=2004.7	ks_quality_p_value=0.369334	log10_base_likelihood=-6.56589	log10_qual_likelihood_position_model=2.7394	log10_strand_likelihood_position_model=0.370185	new_cov=1/2	polymorphism_quality=1.0	quality=1.0	quality_position_model=2.87453e-05	ref_cov=231/323	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=232/325
RA	246	.	NC_007779	1115100	0	C	G	bias_e_value=57003.9	bias_p_value=0.0122686	fisher_strand_p_value=0.0018025	frequency=3.045273e-02	genotype_quality=819.7	ks_quality_p_value=0.919471	log10_base_likelihood=-6.57394	log10_qual_likelihood_position_model=12.3053	log10_strand_likelihood_position_model=2.88146	new_cov=0/10	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=120/122	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=120/132
RA	247	.	NC_007779	1116582	0	G	C	bias_e_value=1.9638e-19	bias_p_value=4.22655e-26	fisher_strand_p_value=7.23569e-28	frequency=1.304073e-01	genotype_quality=556.4	ks_quality_p_value=0.918754	log10_base_likelihood=-45.1862	log10_qual_likelihood_position_model=19.3677	log10_strand_likelihood_position_model=27.1405	new_cov=0/23	polymorphism_quality=40.1	quality=40.1	quality_position_model=Inf	ref_cov=151/1	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=151/24
RA	248	.	NC_007779	1122985	1	.	G	bias_e_value=3540970	bias_p_value=0.7621	fisher_strand_p_value=0.498809	frequency=7.751465e-03	genotype_quality=1229.2	ks_quality_p_value=0.792312	log10_base_likelihood=-7.4629	log10_qual_likelihood_position_model=2.42015	log10_strand_likelihood_position_model=0.570596	new_cov=2/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=2.46435e-06	ref_cov=132/124	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/124
RA	249	.	NC_007779	1151485	0	C	A	bias_e_value=12.4447	bias_p_value=2.67839e-06	fisher_strand_p_value=1.6094e-07	frequency=4.708862e-02	genotype_quality=955.4	ks_quality_p_value=1	log10_base_likelihood=-9.65111	log10_qual_likelihood_position_model=13.7714	log10_strand_likelihood_position_model=6.79334	new_cov=20/0	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=117/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/151
RA	250	.	NC_007779	1158848	0	T	G	bias_e_value=7.84576e-25	bias_p_value=1.68859e-31	fisher_strand_p_value=2.21631e-33	frequency=1.617322e-01	genotype_quality=640.2	ks_quality_p_value=1	log10_base_likelihood=-27.5516	log10_qual_likelihood_position_model=49.2833	log10_strand_likelihood_position_model=32.6544	new_cov=65/0	polymorphism_quality=22.3	quality=22.3	quality_position_model=Inf	ref_cov=44/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=109/161
RA	251	.	NC_007779	1163018	0	T	G	bias_e_value=1.61873e-09	bias_p_value=3.48389e-16	fisher_strand_p_value=8.64718e-18	frequency=1.267762e-01	genotype_quality=747.8	ks_quality_p_value=1	log10_base_likelihood=-22.8998	log10_qual_likelihood_position_model=38.7581	log10_strand_likelihood_position_model=17.0631	new_cov=46/0	polymorphism_quality=17.6	quality=17.6	quality_position_model=Inf	ref_cov=91/153	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=138/153
RA	252	.	NC_007779	1164942	0	A	G	bias_e_value=0.313597	bias_p_value=6.74934e-08	fisher_strand_p_value=3.28702e-09	frequency=5.109739e-02	genotype_quality=598.0	ks_quality_p_value=1	log10_base_likelihood=-6.52594	log10_qual_likelihood_position_model=14.6981	log10_strand_likelihood_position_model=8.4832	new_cov=10/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=18/141	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=28/141
RA	253	.	NC_007779	1164944	0	T	G	bias_e_value=0.0168041	bias_p_value=3.61663e-09	fisher_strand_p_value=1.53254e-10	frequency=5.821228e-02	genotype_quality=523.9	ks_quality_p_value=1	log10_base_likelihood=-10.1569	log10_qual_likelihood_position_model=16.6724	log10_strand_likelihood_position_model=9.81459	new_cov=12/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=18/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=30/135
RA	254	.	NC_007779	1170375	1	.	T	bias_e_value=3222490	bias_p_value=0.693555	fisher_strand_p_value=0.534308	frequency=8.695602e-03	genotype_quality=1105.7	ks_quality_p_value=0.613744	log10_base_likelihood=-8.24535	log10_qual_likelihood_position_model=1.41108	log10_strand_likelihood_position_model=0.395842	new_cov=0/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=2.24754e-08	ref_cov=84/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=84/146
RA	255	.	NC_007779	1170573	0	C	T	frequency=1	genotype_quality=1402.4	new_cov=220/125	quality=1402.4	ref_cov=0/0	tot_cov=221/125
RA	256	.	NC_007779	1177683	0	A	G	bias_e_value=2.98144e-13	bias_p_value=6.41675e-20	fisher_strand_p_value=1.30724e-21	frequency=1.523037e-01	genotype_quality=579.2	ks_quality_p_value=1	log10_base_likelihood=-44.7291	log10_qual_likelihood_position_model=28.0432	log10_strand_likelihood_position_model=20.8836	new_cov=33/0	polymorphism_quality=39.6	quality=39.6	quality_position_model=Inf	ref_cov=28/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=61/144
RA	257	.	NC_007779	1224173	0	G	A	bias_e_value=1.69966e-06	bias_p_value=3.65808e-13	fisher_strand_p_value=1.10391e-14	frequency=1.252298e-01	genotype_quality=694.7	ks_quality_p_value=1	log10_base_likelihood=-28.0914	log10_qual_likelihood_position_model=26.4	log10_strand_likelihood_position_model=13.9571	new_cov=0/32	polymorphism_quality=22.9	quality=22.9	quality_position_model=Inf	ref_cov=138/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/96
RA	258	.	NC_007779	1231130	1	.	T	bias_e_value=4373290	bias_p_value=0.941235	fisher_strand_p_value=1	frequency=7.066727e-03	genotype_quality=1389.0	ks_quality_p_value=0.67738	log10_base_likelihood=-7.77953	log10_qual_likelihood_position_model=1.41774	log10_strand_likelihood_position_model=0.299498	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=5.497e-08	ref_cov=140/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/142
RA	259	.	NC_007779	1262472	0	A	C	bias_e_value=2.61559e-13	bias_p_value=5.62938e-20	fisher_strand_p_value=1.14372e-21	frequency=1.256742e-01	genotype_quality=597.8	ks_quality_p_value=1	log10_base_likelihood=-16.2829	log10_qual_likelihood_position_model=38.1222	log10_strand_likelihood_position_model=20.9417	new_cov=0/50	polymorphism_quality=11.0	quality=11.0	quality_position_model=Inf	ref_cov=136/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/111
RA	260	.	NC_007779	1273399	0	T	G	bias_e_value=6.66056e-35	bias_p_value=1.43351e-41	fisher_strand_p_value=1.43858e-43	frequency=1.736994e-01	genotype_quality=618.6	ks_quality_p_value=1	log10_base_likelihood=-33.643	log10_qual_likelihood_position_model=52.8815	log10_strand_likelihood_position_model=42.8421	new_cov=61/0	polymorphism_quality=28.5	quality=28.5	quality_position_model=Inf	ref_cov=18/181	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/181
RA	261	.	NC_007779	1288364	0	G	A	deleted=1	frequency=1	genotype_quality=89.9	new_cov=18/13	quality=89.9	ref_cov=1/0	tot_cov=19/13
RA	262	.	NC_007779	1288370	0	A	G	deleted=1	frequency=1	genotype_quality=28.6	new_cov=11/2	quality=28.6	ref_cov=0/0	tot_cov=11/2
RA	263	.	NC_007779	1288373	0	T	C	deleted=1	frequency=1	genotype_quality=0.1	new_cov=1/0	quality=0.1	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	264	.	NC_007779	1288462	0	T	C	deleted=1	frequency=1	genotype_quality=32.7	new_cov=5/11	quality=32.7	ref_cov=0/0	tot_cov=5/11
RA	265	.	NC_007779	1288911	0	T	G	bias_e_value=0.127385	bias_p_value=2.74162e-08	fisher_strand_p_value=1.27641e-09	frequency=3.442955e-02	genotype_quality=1039.0	ks_quality_p_value=1	log10_base_likelihood=-7.04452	log10_qual_likelihood_position_model=28.9473	log10_strand_likelihood_position_model=8.90386	new_cov=26/1	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=117/188	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/189
RA	266	.	NC_007779	1302370	0	A	C	bias_e_value=4636450	bias_p_value=0.997874	deleted=1	error=polymorphic_without_reference_base	fisher_strand_p_value=1	frequency=3.625426e-01	genotype_quality=2.7	ks_quality_p_value=0.935507	log10_base_likelihood=-7.82864	log10_qual_likelihood_position_model=0.69897	log10_strand_likelihood_position_model=0.221849	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=7.37723e-09	ref_cov=2/1	reject=POLYMORPHISM_STRAND	tot_cov=4/3
RA	267	.	NC_007779	1302371	0	T	.	bias_e_value=4646330	bias_p_value=1	deleted=1	error=polymorphic_without_reference_base	fisher_strand_p_value=1	frequency=3.367963e-01	genotype_quality=3.1	ks_quality_p_value=1	log10_base_likelihood=-8.42814	log10_qual_likelihood_position_model=0.778151	log10_strand_likelihood_position_model=0.176091	new_cov=1/1	polymorphism_quality=3.0	quality=3.0	quality_position_model=1.93028e-09	ref_cov=1/1	reject=POLYMORPHISM_STRAND	tot_cov=4/2
RA	268	.	NC_007779	1318876	0	G	A	frequency=1	genotype_quality=1169.4	new_cov=160/135	quality=1169.4	ref_cov=0/0	tot_cov=160/135
RA	269	.	NC_007779	1324190	0	T	C	bias_e_value=6.25026e-06	bias_p_value=1.3452e-12	fisher_strand_p_value=4.23103e-14	frequency=8.228445e-02	genotype_quality=787.9	ks_quality_p_value=1	log10_base_likelihood=-12.0437	log10_qual_likelihood_position_model=22.8304	log10_strand_likelihood_position_model=13.3736	new_cov=0/32	polymorphism_quality=6.6	quality=6.6	quality_position_model=Inf	ref_cov=160/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/115
RA	270	.	NC_007779	1325276	0	G	T	bias_e_value=2.20303	bias_p_value=4.74144e-07	fisher_strand_p_value=2.5761e-08	frequency=4.920816e-02	genotype_quality=1110.2	ks_quality_p_value=0.996057	log10_base_likelihood=-13.6262	log10_qual_likelihood_position_model=19.5221	log10_strand_likelihood_position_model=7.58904	new_cov=0/21	polymorphism_quality=8.3	quality=8.3	quality_position_model=Inf	ref_cov=175/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/146
RA	271	.	NC_007779	1330179	0	T	G	bias_e_value=6.33445e-05	bias_p_value=1.36332e-11	fisher_strand_p_value=4.63724e-13	frequency=7.606602e-02	genotype_quality=706.8	ks_quality_p_value=1	log10_base_likelihood=-11.6037	log10_qual_likelihood_position_model=31.3761	log10_strand_likelihood_position_model=12.3337	new_cov=35/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=89/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/133
RA	272	.	NC_007779	1336531	0	G	T	bias_e_value=8.4629	bias_p_value=1.82141e-06	fisher_strand_p_value=1.06814e-07	frequency=6.380939e-02	genotype_quality=970.6	ks_quality_p_value=1	log10_base_likelihood=-11.2855	log10_qual_likelihood_position_model=20.9817	log10_strand_likelihood_position_model=7.0372	new_cov=0/29	polymorphism_quality=5.9	quality=5.9	quality_position_model=Inf	ref_cov=127/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=127/184
RA	273	.	NC_007779	1345020	1	.	T	bias_e_value=4035120	bias_p_value=0.868453	fisher_strand_p_value=1	frequency=6.872177e-03	genotype_quality=1425.0	ks_quality_p_value=0.533114	log10_base_likelihood=-7.82212	log10_qual_likelihood_position_model=1.59466	log10_strand_likelihood_position_model=0.299581	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=7.57027e-08	ref_cov=146/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=147/144
RA	274	.	NC_007779	1352913	1	.	T	bias_e_value=111073	bias_p_value=0.0239055	fisher_strand_p_value=0.00573096	frequency=2.162170e-02	genotype_quality=860.2	ks_quality_p_value=0.629685	log10_base_likelihood=-17.802	log10_qual_likelihood_position_model=1.97242	log10_strand_likelihood_position_model=2.24177	new_cov=4/0	polymorphism_quality=12.5	quality=12.5	quality_position_model=1.11439e-15	ref_cov=48/133	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=52/133
RA	275	.	NC_007779	1371749	1	.	T	bias_e_value=4371520	bias_p_value=0.940853	fisher_strand_p_value=1	frequency=3.816795e-02	genotype_quality=1758.0	ks_quality_p_value=0.676401	log10_base_likelihood=-70.3818	log10_qual_likelihood_position_model=5.92381	log10_strand_likelihood_position_model=0.685853	new_cov=7/8	polymorphism_quality=65.4	quality=65.4	quality_position_model=3.40552e-66	ref_cov=181/197	reject=INDEL_HOMOPOLYMER	tot_cov=188/205
RA	276	.	NC_007779	1374596	0	C	A	bias_e_value=31.5662	bias_p_value=6.79379e-06	fisher_strand_p_value=4.5199e-07	frequency=5.343771e-02	genotype_quality=968.8	ks_quality_p_value=0.960438	log10_base_likelihood=-14.1394	log10_qual_likelihood_position_model=19.6851	log10_strand_likelihood_position_model=6.6146	new_cov=21/0	polymorphism_quality=8.8	quality=8.8	quality_position_model=Inf	ref_cov=130/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=152/150
RA	277	.	NC_007779	1378219	0	A	C	bias_e_value=5.42898e-09	bias_p_value=1.16845e-15	fisher_strand_p_value=2.99234e-17	frequency=8.454752e-02	genotype_quality=734.6	ks_quality_p_value=1	log10_base_likelihood=-10.8072	log10_qual_likelihood_position_model=39.8167	log10_strand_likelihood_position_model=16.524	new_cov=0/34	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=156/59	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/93
RA	278	.	NC_007779	1378854	0	A	C	bias_e_value=2.01604e-21	bias_p_value=4.33899e-28	fisher_strand_p_value=6.35958e-30	frequency=1.060448e-01	genotype_quality=679.5	ks_quality_p_value=1	log10_base_likelihood=-13.532	log10_qual_likelihood_position_model=46.2804	log10_strand_likelihood_position_model=29.1966	new_cov=0/61	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=170/56	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/117
RA	279	.	NC_007779	1385448	0	A	C	bias_e_value=1.56813e-11	bias_p_value=3.37499e-18	fisher_strand_p_value=7.49371e-20	frequency=5.514050e-02	genotype_quality=854.3	ks_quality_p_value=1	log10_base_likelihood=-8.14545	log10_qual_likelihood_position_model=31.1192	log10_strand_likelihood_position_model=19.1253	new_cov=0/43	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=191/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=191/129
RA	280	.	NC_007779	1385794	1	.	T	bias_e_value=429365	bias_p_value=0.0924095	fisher_strand_p_value=0.563097	frequency=1.153851e-02	genotype_quality=1255.1	ks_quality_p_value=0.0328962	log10_base_likelihood=-12.573	log10_qual_likelihood_position_model=2.35879	log10_strand_likelihood_position_model=0.551193	new_cov=2/1	polymorphism_quality=7.2	quality=7.2	quality_position_model=1.10476e-11	ref_cov=100/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=102/158
RA	281	.	NC_007779	1386502	0	T	G	bias_e_value=3.49136e-08	bias_p_value=7.51424e-15	fisher_strand_p_value=2.02341e-16	frequency=1.262383e-01	genotype_quality=571.1	ks_quality_p_value=1	log10_base_likelihood=-23.7832	log10_qual_likelihood_position_model=36.7379	log10_strand_likelihood_position_model=15.6939	new_cov=42/0	polymorphism_quality=18.5	quality=18.5	quality_position_model=Inf	ref_cov=72/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/126
RA	282	.	NC_007779	1405508	0	G	T	bias_e_value=1.31379e-06	bias_p_value=2.82758e-13	fisher_strand_p_value=8.61587e-15	frequency=1.270146e-01	genotype_quality=498.3	ks_quality_p_value=0.982499	log10_base_likelihood=-46.095	log10_qual_likelihood_position_model=20.7027	log10_strand_likelihood_position_model=14.0668	new_cov=18/1	polymorphism_quality=41.0	quality=41.0	quality_position_model=2.22662e-13	ref_cov=11/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=29/120
RA	283	.	NC_007779	1409137	0	G	T	bias_e_value=2.6977e-10	bias_p_value=5.8061e-17	fisher_strand_p_value=1.38033e-18	frequency=1.505265e-01	genotype_quality=795.7	ks_quality_p_value=0.998516	log10_base_likelihood=-32.5924	log10_qual_likelihood_position_model=28.1984	log10_strand_likelihood_position_model=17.8649	new_cov=0/54	polymorphism_quality=27.4	quality=27.4	quality_position_model=Inf	ref_cov=144/100	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/156
RA	284	.	NC_007779	1410956	1	.	T	bias_e_value=4605700	bias_p_value=0.991256	fisher_strand_p_value=1	frequency=6.622314e-03	genotype_quality=1453.9	ks_quality_p_value=0.870703	log10_base_likelihood=-7.6714	log10_qual_likelihood_position_model=2.34579	log10_strand_likelihood_position_model=0.299609	new_cov=1/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=6.52254e-07	ref_cov=149/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/152
RA	285	.	NC_007779	1430015	0	C	G	deleted=1	frequency=1	genotype_quality=1.3	new_cov=0/1	quality=1.3	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	286	.	NC_007779	1437441	0	G	A	bias_e_value=0.0573772	bias_p_value=1.23489e-08	fisher_strand_p_value=5.53392e-10	frequency=3.855801e-02	genotype_quality=923.2	ks_quality_p_value=1	log10_base_likelihood=-10.6326	log10_qual_likelihood_position_model=14.5615	log10_strand_likelihood_position_model=9.25697	new_cov=0/10	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=203/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=203/32
RA	287	.	NC_007779	1437447	0	G	C	bias_e_value=4.3654e-26	bias_p_value=9.39538e-33	fisher_strand_p_value=1.18754e-34	frequency=1.601138e-01	genotype_quality=812.4	ks_quality_p_value=1	log10_base_likelihood=-37.2738	log10_qual_likelihood_position_model=40.7375	log10_strand_likelihood_position_model=33.9254	new_cov=0/53	polymorphism_quality=32.1	quality=32.1	quality_position_model=Inf	ref_cov=190/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=190/85
RA	288	.	NC_007779	1438937	0	T	.	bias_e_value=4079640	bias_p_value=0.878035	fisher_strand_p_value=0.646024	frequency=1.453495e-02	genotype_quality=1082.2	ks_quality_p_value=0.849358	log10_base_likelihood=-10.789	log10_qual_likelihood_position_model=2.49017	log10_strand_likelihood_position_model=0.472215	new_cov=3/1	polymorphism_quality=5.4	quality=5.4	quality_position_model=8.3828e-10	ref_cov=159/112	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/113
RA	289	.	NC_007779	1442205	0	G	C	bias_e_value=2.22937e-06	bias_p_value=4.79813e-13	fisher_strand_p_value=1.46211e-14	frequency=9.153318e-02	genotype_quality=644.2	ks_quality_p_value=0.998752	log10_base_likelihood=-15.9773	log10_qual_likelihood_position_model=20.8725	log10_strand_likelihood_position_model=13.835	new_cov=0/18	polymorphism_quality=10.6	quality=10.6	quality_position_model=Inf	ref_cov=141/20	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/38
RA	290	.	NC_007779	1455220	0	T	G	bias_e_value=5.95199e-05	bias_p_value=1.28101e-11	fisher_strand_p_value=4.35081e-13	frequency=6.121445e-02	genotype_quality=882.9	ks_quality_p_value=0.999287	log10_base_likelihood=-14.4931	log10_qual_likelihood_position_model=22.7317	log10_strand_likelihood_position_model=12.3614	new_cov=0/20	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=180/47	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=180/67
RA	291	.	NC_007779	1467852	0	G	A	bias_e_value=2088680	bias_p_value=0.449533	fisher_strand_p_value=0.622697	frequency=1.033783e-02	genotype_quality=1247.1	ks_quality_p_value=0.253733	log10_base_likelihood=-5.68085	log10_qual_likelihood_position_model=3.80642	log10_strand_likelihood_position_model=0.593904	new_cov=1/3	polymorphism_quality=0.1	quality=0.1	quality_position_model=0.00663712	ref_cov=157/158	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=158/161
RA	292	.	NC_007779	1483588	0	G	A	frequency=1	genotype_quality=739.0	new_cov=152/45	quality=739.0	ref_cov=0/0	tot_cov=152/45
RA	293	.	NC_007779	1483616	0	C	G	bias_e_value=1.12742	bias_p_value=2.42648e-07	fisher_strand_p_value=1.26472e-08	frequency=4.495811e-02	genotype_quality=697.9	ks_quality_p_value=1	log10_base_likelihood=-12.2068	log10_qual_likelihood_position_model=10.2779	log10_strand_likelihood_position_model=7.898	new_cov=0/9	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=156/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/28
RA	294	.	NC_007779	1492812	0	A	C	bias_e_value=8.0771e-09	bias_p_value=1.73838e-15	fisher_strand_p_value=4.49891e-17	frequency=6.609774e-02	genotype_quality=663.8	ks_quality_p_value=1	log10_base_likelihood=-7.03039	log10_qual_likelihood_position_model=45.0697	log10_strand_likelihood_position_model=16.3666	new_cov=0/49	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=134/92	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=134/141
RA	295	.	NC_007779	1493616	0	G	A	bias_e_value=4979.36	bias_p_value=0.00107168	fisher_strand_p_value=0.000105515	frequency=2.989101e-02	genotype_quality=1042.3	ks_quality_p_value=1	log10_base_likelihood=-6.41744	log10_qual_likelihood_position_model=14.6123	log10_strand_likelihood_position_model=3.97669	new_cov=0/10	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=164/104	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=164/114
RA	296	.	NC_007779	1493621	0	T	C	bias_e_value=1.34933	bias_p_value=2.90407e-07	fisher_strand_p_value=1.52876e-08	frequency=5.081940e-02	genotype_quality=923.3	ks_quality_p_value=1	log10_base_likelihood=-11.1976	log10_qual_likelihood_position_model=19.6784	log10_strand_likelihood_position_model=7.81566	new_cov=0/19	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=167/96	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/115
RA	297	.	NC_007779	1496775	0	T	.	frequency=1	genotype_quality=1274.4	new_cov=111/147	quality=1274.4	ref_cov=0/0	tot_cov=111/147
RA	298	.	NC_007779	1512495	0	A	.	bias_e_value=3569320	bias_p_value=0.768202	fisher_strand_p_value=1	frequency=1.085949e-02	genotype_quality=1097.3	ks_quality_p_value=0.401845	log10_base_likelihood=-7.84312	log10_qual_likelihood_position_model=2.18512	log10_strand_likelihood_position_model=0.382299	new_cov=1/2	polymorphism_quality=2.4	quality=2.4	quality_position_model=3.58864e-07	ref_cov=121/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/154
RA	299	.	NC_007779	1515709	0	A	G	bias_e_value=7.5607e-17	bias_p_value=1.62724e-23	fisher_strand_p_value=2.82876e-25	frequency=2.059536e-01	genotype_quality=590.5	ks_quality_p_value=1	log10_base_likelihood=-55.1927	log10_qual_likelihood_position_model=47.9551	log10_strand_likelihood_position_model=24.5484	new_cov=56/0	polymorphism_quality=50.1	quality=50.1	quality_position_model=Inf	ref_cov=54/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/140
RA	300	.	NC_007779	1515714	0	A	T	bias_e_value=230.671	bias_p_value=4.96459e-05	fisher_strand_p_value=3.67357e-06	frequency=5.103064e-02	genotype_quality=743.4	ks_quality_p_value=1	log10_base_likelihood=-8.52178	log10_qual_likelihood_position_model=15.9592	log10_strand_likelihood_position_model=5.43491	new_cov=14/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=84/132	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=98/132
RA	301	.	NC_007779	1527466	0	T	A	bias_e_value=31.0438	bias_p_value=6.68136e-06	fisher_strand_p_value=4.26439e-07	frequency=4.763937e-02	genotype_quality=937.4	ks_quality_p_value=1	log10_base_likelihood=-11.0843	log10_qual_likelihood_position_model=17.8689	log10_strand_likelihood_position_model=6.37014	new_cov=0/15	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=164/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=164/106
RA	302	.	NC_007779	1527474	0	G	A	bias_e_value=4.45676e-12	bias_p_value=9.59199e-19	fisher_strand_p_value=2.07064e-20	frequency=1.455431e-01	genotype_quality=877.9	ks_quality_p_value=1	log10_base_likelihood=-54.0107	log10_qual_likelihood_position_model=41.4547	log10_strand_likelihood_position_model=19.6839	new_cov=0/47	polymorphism_quality=48.9	quality=48.9	quality_position_model=Inf	ref_cov=175/85	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=175/132
RA	303	.	NC_007779	1527479	0	C	A	bias_e_value=0.00244255	bias_p_value=5.25695e-10	fisher_strand_p_value=2.35331e-11	frequency=7.267094e-02	genotype_quality=1050.6	ks_quality_p_value=0.872284	log10_base_likelihood=-20.7296	log10_qual_likelihood_position_model=33.4166	log10_strand_likelihood_position_model=10.6283	new_cov=0/27	polymorphism_quality=15.5	quality=15.5	quality_position_model=Inf	ref_cov=178/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=178/134
RA	304	.	NC_007779	1531018	0	A	C	bias_e_value=1.75364e-06	bias_p_value=3.77424e-13	fisher_strand_p_value=1.14008e-14	frequency=1.017480e-01	genotype_quality=485.5	ks_quality_p_value=1	log10_base_likelihood=-15.8105	log10_qual_likelihood_position_model=22.4185	log10_strand_likelihood_position_model=13.9431	new_cov=0/22	polymorphism_quality=10.5	quality=10.5	quality_position_model=Inf	ref_cov=125/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=125/50
RA	305	.	NC_007779	1537499	0	A	G	bias_e_value=6.9419e-13	bias_p_value=1.49406e-19	fisher_strand_p_value=3.0982e-21	frequency=1.501951e-01	genotype_quality=691.6	ks_quality_p_value=1	log10_base_likelihood=-27.3208	log10_qual_likelihood_position_model=34.3451	log10_strand_likelihood_position_model=20.5089	new_cov=49/0	polymorphism_quality=22.1	quality=22.1	quality_position_model=Inf	ref_cov=69/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/150
RA	306	.	NC_007779	1552377	0	A	C	bias_e_value=6.20709e-16	bias_p_value=1.33591e-22	fisher_strand_p_value=2.4122e-24	frequency=1.740522e-01	genotype_quality=431.4	ks_quality_p_value=1	log10_base_likelihood=-26.0228	log10_qual_likelihood_position_model=32.8693	log10_strand_likelihood_position_model=23.6176	new_cov=0/40	polymorphism_quality=20.8	quality=20.8	quality_position_model=Inf	ref_cov=117/22	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/62
RA	307	.	NC_007779	1562465	0	T	G	bias_e_value=13.9637	bias_p_value=3.00532e-06	fisher_strand_p_value=1.81924e-07	frequency=6.804514e-02	genotype_quality=466.2	ks_quality_p_value=1	log10_base_likelihood=-8.06525	log10_qual_likelihood_position_model=14.0432	log10_strand_likelihood_position_model=6.74011	new_cov=15/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=49/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=64/104
RA	308	.	NC_007779	1595838	1	.	C	bias_e_value=3739740	bias_p_value=0.804879	fisher_strand_p_value=1	frequency=9.433746e-03	genotype_quality=1019.3	ks_quality_p_value=0.444471	log10_base_likelihood=-8.35787	log10_qual_likelihood_position_model=1.50325	log10_strand_likelihood_position_model=0.299944	new_cov=1/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.70528e-08	ref_cov=110/100	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=111/101
RA	309	.	NC_007779	1602599	0	C	A	bias_e_value=4854.76	bias_p_value=0.00104486	fisher_strand_p_value=0.00010259	frequency=4.805231e-02	genotype_quality=791.7	ks_quality_p_value=1	log10_base_likelihood=-8.81121	log10_qual_likelihood_position_model=15.1868	log10_strand_likelihood_position_model=4.06994	new_cov=16/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=126/107	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/107
RA	310	.	NC_007779	1607452	0	C	A	bias_e_value=280.279	bias_p_value=6.03226e-05	fisher_strand_p_value=4.57052e-06	frequency=4.053783e-02	genotype_quality=787.8	ks_quality_p_value=0.992058	log10_base_likelihood=-8.28947	log10_qual_likelihood_position_model=16.0201	log10_strand_likelihood_position_model=5.34003	new_cov=0/13	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=140/82	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=140/95
RA	311	.	NC_007779	1615814	0	C	A	frequency=1	genotype_quality=864.0	new_cov=104/126	quality=864.0	ref_cov=0/0	tot_cov=105/126
RA	312	.	NC_007779	1624530	1	.	A	bias_e_value=2095440	bias_p_value=0.450987	fisher_strand_p_value=1	frequency=8.658409e-03	genotype_quality=1066.6	ks_quality_p_value=0.158788	log10_base_likelihood=-8.19488	log10_qual_likelihood_position_model=2.21748	log10_strand_likelihood_position_model=0.300132	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.37565e-07	ref_cov=109/120	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=110/121
RA	313	.	NC_007779	1626064	0	T	.	bias_e_value=3316020	bias_p_value=0.713686	fisher_strand_p_value=1	frequency=1.586342e-02	genotype_quality=989.0	ks_quality_p_value=0.346443	log10_base_likelihood=-11.1835	log10_qual_likelihood_position_model=3.05371	log10_strand_likelihood_position_model=0.426038	new_cov=2/2	polymorphism_quality=5.8	quality=5.8	quality_position_model=1.12077e-09	ref_cov=132/116	reject=INDEL_HOMOPOLYMER	tot_cov=134/118
RA	314	.	NC_007779	1628027	0	G	T	bias_e_value=0.000117708	bias_p_value=2.53335e-11	fisher_strand_p_value=9.3589e-13	frequency=2.390523e-01	genotype_quality=227.5	ks_quality_p_value=0.941269	log10_base_likelihood=-57.0159	log10_qual_likelihood_position_model=15.9872	log10_strand_likelihood_position_model=12.0288	new_cov=23/0	polymorphism_quality=52.0	quality=52.0	quality_position_model=2.97732e-31	ref_cov=14/58	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/58
RA	315	.	NC_007779	1636114	0	C	T	frequency=1	genotype_quality=1.9	new_cov=0/1	quality=1.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	316	.	NC_007779	1636118	0	A	G	frequency=1	genotype_quality=1.9	new_cov=0/1	quality=1.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	317	.	NC_007779	1636135	0	A	G	frequency=1	genotype_quality=1.9	new_cov=0/1	quality=1.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	318	.	NC_007779	1636148	0	G	A	frequency=1	genotype_quality=1.9	new_cov=0/1	quality=1.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	319	.	NC_007779	1636162	0	C	T	frequency=1	genotype_quality=1.9	new_cov=0/1	quality=1.9	ref_cov=0/0	reject=EVALUE	tot_cov=0/1
RA	320	.	NC_007779	1646737	0	T	A	bias_e_value=1080.39	bias_p_value=0.000232525	fisher_strand_p_value=1.96426e-05	frequency=5.088377e-02	genotype_quality=1002.6	ks_quality_p_value=1	log10_base_likelihood=-12.077	log10_qual_likelihood_position_model=25.5443	log10_strand_likelihood_position_model=5.00783	new_cov=0/16	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=144/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/144
RA	321	.	NC_007779	1646748	0	A	C	bias_e_value=5.18155e-06	bias_p_value=1.11519e-12	fisher_strand_p_value=3.48636e-14	frequency=8.946180e-02	genotype_quality=686.0	ks_quality_p_value=1	log10_base_likelihood=-16.7411	log10_qual_likelihood_position_model=27.8555	log10_strand_likelihood_position_model=13.4576	new_cov=0/36	polymorphism_quality=11.4	quality=11.4	quality_position_model=Inf	ref_cov=132/79	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=132/115
RA	322	.	NC_007779	1651009	0	T	G	bias_e_value=1.05267e-05	bias_p_value=2.2656e-12	fisher_strand_p_value=7.24866e-14	frequency=1.123943e-01	genotype_quality=377.1	ks_quality_p_value=1	log10_base_likelihood=-14.2215	log10_qual_likelihood_position_model=21.4472	log10_strand_likelihood_position_model=13.1397	new_cov=19/0	polymorphism_quality=8.9	quality=8.9	quality_position_model=Inf	ref_cov=16/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/99
RA	323	.	NC_007779	1660545	0	G	T	bias_e_value=320.718	bias_p_value=6.90262e-05	fisher_strand_p_value=5.24592e-06	frequency=4.241753e-02	genotype_quality=941.8	ks_quality_p_value=1	log10_base_likelihood=-7.24036	log10_qual_likelihood_position_model=18.1478	log10_strand_likelihood_position_model=5.3802	new_cov=0/18	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=137/129	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/149
RA	324	.	NC_007779	1669599	0	C	.	frequency=1	genotype_quality=1239.9	new_cov=126/124	quality=1239.9	ref_cov=0/0	tot_cov=126/124
RA	325	.	NC_007779	1671093	0	G	T	bias_e_value=3.20382	bias_p_value=6.89537e-07	fisher_strand_p_value=3.81335e-08	frequency=5.912161e-02	genotype_quality=839.2	ks_quality_p_value=1	log10_base_likelihood=-9.45518	log10_qual_likelihood_position_model=19.3538	log10_strand_likelihood_position_model=7.64096	new_cov=0/24	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=130/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/132
RA	326	.	NC_007779	1677110	0	G	T	bias_e_value=2.53593	bias_p_value=5.45792e-07	fisher_strand_p_value=4.08186e-08	frequency=5.717468e-02	genotype_quality=702.9	ks_quality_p_value=0.729486	log10_base_likelihood=-6.02647	log10_qual_likelihood_position_model=23.7353	log10_strand_likelihood_position_model=7.38914	new_cov=0/21	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=122/87	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=122/109
RA	327	.	NC_007779	1681026	0	A	C	bias_e_value=1.97246e-11	bias_p_value=4.24519e-18	fisher_strand_p_value=9.47524e-20	frequency=7.996988e-02	genotype_quality=599.0	ks_quality_p_value=1	log10_base_likelihood=-11.0611	log10_qual_likelihood_position_model=32.1598	log10_strand_likelihood_position_model=19.0234	new_cov=0/46	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=137/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=137/111
RA	328	.	NC_007779	1681402	0	T	G	bias_e_value=0.000565999	bias_p_value=1.21816e-10	fisher_strand_p_value=4.49024e-12	frequency=6.548166e-02	genotype_quality=671.6	ks_quality_p_value=1	log10_base_likelihood=-14.7361	log10_qual_likelihood_position_model=24.3119	log10_strand_likelihood_position_model=11.3477	new_cov=23/0	polymorphism_quality=9.4	quality=9.4	quality_position_model=Inf	ref_cov=57/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=81/145
RA	329	.	NC_007779	1686463	0	A	C	bias_e_value=1.35164e-09	bias_p_value=2.90904e-16	fisher_strand_p_value=7.1874e-18	frequency=1.160231e-01	genotype_quality=505.2	ks_quality_p_value=1	log10_base_likelihood=-14.6388	log10_qual_likelihood_position_model=27.2426	log10_strand_likelihood_position_model=17.1434	new_cov=0/38	polymorphism_quality=9.3	quality=9.3	quality_position_model=Inf	ref_cov=121/48	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/88
RA	330	.	NC_007779	1699348	0	T	.	bias_e_value=3795640	bias_p_value=0.816911	fisher_strand_p_value=1	frequency=9.337425e-03	genotype_quality=1290.4	ks_quality_p_value=0.459624	log10_base_likelihood=-7.78036	log10_qual_likelihood_position_model=2.51075	log10_strand_likelihood_position_model=0.384595	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=9.14382e-07	ref_cov=176/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=178/143
RA	331	.	NC_007779	1703335	0	G	C	bias_e_value=8.45964e-14	bias_p_value=1.82071e-20	fisher_strand_p_value=3.61883e-22	frequency=1.054931e-01	genotype_quality=739.2	ks_quality_p_value=0.998816	log10_base_likelihood=-37.3501	log10_qual_likelihood_position_model=24.3603	log10_strand_likelihood_position_model=21.4414	new_cov=22/0	polymorphism_quality=32.2	quality=32.2	quality_position_model=Inf	ref_cov=10/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=32/172
RA	332	.	NC_007779	1704412	0	T	.	bias_e_value=3098240	bias_p_value=0.666813	fisher_strand_p_value=0.608803	frequency=1.026440e-02	genotype_quality=1143.3	ks_quality_p_value=0.50049	log10_base_likelihood=-7.79754	log10_qual_likelihood_position_model=1.97181	log10_strand_likelihood_position_model=0.443566	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=2.78246e-07	ref_cov=138/151	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/152
RA	333	.	NC_007779	1713510	0	A	C	bias_e_value=1.93655e-12	bias_p_value=4.16792e-19	fisher_strand_p_value=8.83491e-21	frequency=1.179299e-01	genotype_quality=710.9	ks_quality_p_value=1	log10_base_likelihood=-15.4611	log10_qual_likelihood_position_model=50.2237	log10_strand_likelihood_position_model=20.0538	new_cov=0/51	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=151/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/130
RA	334	.	NC_007779	1716031	1	.	T	bias_e_value=1520060	bias_p_value=0.327153	fisher_strand_p_value=0.598639	frequency=1.071453e-02	genotype_quality=1342.8	ks_quality_p_value=0.1648	log10_base_likelihood=-12.2296	log10_qual_likelihood_position_model=2.9066	log10_strand_likelihood_position_model=0.459061	new_cov=1/2	polymorphism_quality=6.8	quality=6.8	quality_position_model=7.24932e-11	ref_cov=149/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/130
RA	335	.	NC_007779	1716032	0	T	.	bias_e_value=4631980	bias_p_value=0.996912	fisher_strand_p_value=1	frequency=1.047897e-02	genotype_quality=1131.1	ks_quality_p_value=0.922444	log10_base_likelihood=-7.71489	log10_qual_likelihood_position_model=1.77464	log10_strand_likelihood_position_model=0.402006	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.91672e-07	ref_cov=149/134	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/135
RA	336	.	NC_007779	1722510	0	G	T	bias_e_value=32500.2	bias_p_value=0.00699481	fisher_strand_p_value=0.000869237	frequency=2.153015e-02	genotype_quality=1155.1	ks_quality_p_value=0.999884	log10_base_likelihood=-6.20164	log10_qual_likelihood_position_model=11.828	log10_strand_likelihood_position_model=3.17318	new_cov=0/13	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=141/180	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/193
RA	337	.	NC_007779	1732512	0	T	G	bias_e_value=4.56175e-08	bias_p_value=9.81796e-15	fisher_strand_p_value=2.66346e-16	frequency=8.135796e-02	genotype_quality=720.1	ks_quality_p_value=1	log10_base_likelihood=-8.88157	log10_qual_likelihood_position_model=29.4057	log10_strand_likelihood_position_model=15.5796	new_cov=40/1	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=76/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=116/159
RA	338	.	NC_007779	1732516	0	T	G	bias_e_value=1.57979e-11	bias_p_value=3.40008e-18	fisher_strand_p_value=7.55069e-20	frequency=7.446861e-02	genotype_quality=684.3	ks_quality_p_value=1	log10_base_likelihood=-7.58241	log10_qual_likelihood_position_model=35.5652	log10_strand_likelihood_position_model=19.122	new_cov=42/0	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=66/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=108/160
RA	339	.	NC_007779	1752711	0	C	T	bias_e_value=1847140	bias_p_value=0.397547	fisher_strand_p_value=0.131267	frequency=1.389027e-02	genotype_quality=1132.2	ks_quality_p_value=0.999027	log10_base_likelihood=-5.77501	log10_qual_likelihood_position_model=3.98441	log10_strand_likelihood_position_model=1.03135	new_cov=4/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.0275656	ref_cov=148/122	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=152/122
RA	340	.	NC_007779	1763744	0	C	A	bias_e_value=301.622	bias_p_value=6.49162e-05	fisher_strand_p_value=4.91529e-06	frequency=2.818203e-02	genotype_quality=1058.5	ks_quality_p_value=0.998678	log10_base_likelihood=-5.75186	log10_qual_likelihood_position_model=14.6026	log10_strand_likelihood_position_model=5.50474	new_cov=18/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=154/167	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/167
RA	341	.	NC_007779	1766507	0	A	C	bias_e_value=1.56551e-08	bias_p_value=3.36935e-15	fisher_strand_p_value=8.87592e-17	frequency=6.628323e-02	genotype_quality=576.2	ks_quality_p_value=1	log10_base_likelihood=-9.97609	log10_qual_likelihood_position_model=27.0325	log10_strand_likelihood_position_model=16.0518	new_cov=0/24	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=142/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=142/51
RA	342	.	NC_007779	1773949	0	A	.	bias_e_value=4141750	bias_p_value=0.891403	fisher_strand_p_value=0.607488	frequency=9.665489e-03	genotype_quality=1218.1	ks_quality_p_value=0.941213	log10_base_likelihood=-7.43789	log10_qual_likelihood_position_model=1.78815	log10_strand_likelihood_position_model=0.445656	new_cov=2/1	polymorphism_quality=1.9	quality=1.9	quality_position_model=4.25905e-07	ref_cov=146/161	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=148/162
RA	343	.	NC_007779	1777181	0	A	C	bias_e_value=2.6469e-10	bias_p_value=5.69675e-17	fisher_strand_p_value=1.3517e-18	frequency=8.458233e-02	genotype_quality=750.0	ks_quality_p_value=1	log10_base_likelihood=-11.4686	log10_qual_likelihood_position_model=65.3625	log10_strand_likelihood_position_model=17.8962	new_cov=0/67	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=143/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=143/205
RA	344	.	NC_007779	1788809	0	C	G	bias_e_value=548.869	bias_p_value=0.00011813	fisher_strand_p_value=9.77413e-06	frequency=4.190826e-02	genotype_quality=837.0	ks_quality_p_value=0.961072	log10_base_likelihood=-5.98568	log10_qual_likelihood_position_model=18.1087	log10_strand_likelihood_position_model=5.00992	new_cov=0/15	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=133/107	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/123
RA	345	.	NC_007779	1790245	0	A	C	bias_e_value=0.133161	bias_p_value=2.86593e-08	fisher_strand_p_value=1.33718e-09	frequency=8.029366e-02	genotype_quality=655.2	ks_quality_p_value=1	log10_base_likelihood=-9.05293	log10_qual_likelihood_position_model=25.8942	log10_strand_likelihood_position_model=9.03536	new_cov=0/28	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=118/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/121
RA	346	.	NC_007779	1801443	0	A	C	bias_e_value=8.79977e-20	bias_p_value=1.89392e-26	fisher_strand_p_value=2.94116e-28	frequency=1.591353e-01	genotype_quality=589.5	ks_quality_p_value=1	log10_base_likelihood=-22.124	log10_qual_likelihood_position_model=49.5784	log10_strand_likelihood_position_model=27.5315	new_cov=0/62	polymorphism_quality=16.9	quality=16.9	quality_position_model=Inf	ref_cov=142/51	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=142/113
RA	347	.	NC_007779	1801456	0	C	G	bias_e_value=0.0497245	bias_p_value=1.07019e-08	fisher_strand_p_value=4.95322e-10	frequency=9.565115e-02	genotype_quality=917.3	ks_quality_p_value=0.961767	log10_base_likelihood=-28.8217	log10_qual_likelihood_position_model=26.6765	log10_strand_likelihood_position_model=9.3242	new_cov=0/33	polymorphism_quality=23.6	quality=23.6	quality_position_model=Inf	ref_cov=138/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=139/167
RA	348	.	NC_007779	1820099	0	A	C	bias_e_value=8.2863e-18	bias_p_value=1.78341e-24	fisher_strand_p_value=2.98358e-26	frequency=1.537123e-01	genotype_quality=690.1	ks_quality_p_value=1	log10_base_likelihood=-32.7377	log10_qual_likelihood_position_model=42.6905	log10_strand_likelihood_position_model=25.5253	new_cov=0/53	polymorphism_quality=27.6	quality=27.6	quality_position_model=Inf	ref_cov=173/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=173/114
RA	349	.	NC_007779	1820258	0	C	.	bias_e_value=4471940	bias_p_value=0.962467	fisher_strand_p_value=1	frequency=1.063061e-02	genotype_quality=1162.9	ks_quality_p_value=0.738838	log10_base_likelihood=-8.16091	log10_qual_likelihood_position_model=1.17272	log10_strand_likelihood_position_model=0.412541	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.62242e-08	ref_cov=136/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/145
RA	350	.	NC_007779	1826779	1	.	C	bias_e_value=2686200	bias_p_value=0.578134	fisher_strand_p_value=0.247148	frequency=1.135921e-02	genotype_quality=1223.2	ks_quality_p_value=0.95873	log10_base_likelihood=-8.99501	log10_qual_likelihood_position_model=2.89738	log10_strand_likelihood_position_model=0.908072	new_cov=0/3	polymorphism_quality=3.5	quality=3.5	quality_position_model=4.40961e-07	ref_cov=132/129	reject=POLYMORPHISM_STRAND	tot_cov=132/132
RA	351	.	NC_007779	1837206	0	G	T	bias_e_value=8.80646e-12	bias_p_value=1.89536e-18	fisher_strand_p_value=4.17569e-20	frequency=1.263013e-01	genotype_quality=774.4	ks_quality_p_value=0.994798	log10_base_likelihood=-37.9873	log10_qual_likelihood_position_model=35.921	log10_strand_likelihood_position_model=19.3793	new_cov=34/0	polymorphism_quality=32.8	quality=32.8	quality_position_model=Inf	ref_cov=45/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=79/167
RA	352	.	NC_007779	1844073	0	G	A	frequency=1	genotype_quality=1294.2	new_cov=155/175	quality=1294.2	ref_cov=1/0	tot_cov=156/175
RA	353	.	NC_007779	1844628	0	A	G	bias_e_value=0.344588	bias_p_value=7.41633e-08	fisher_strand_p_value=3.63159e-09	frequency=4.493332e-02	genotype_quality=602.9	ks_quality_p_value=0.99939	log10_base_likelihood=-9.41004	log10_qual_likelihood_position_model=10.8768	log10_strand_likelihood_position_model=8.4399	new_cov=8/0	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=10/148	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=18/148
RA	354	.	NC_007779	1846634	0	A	.	bias_e_value=4016030	bias_p_value=0.864343	fisher_strand_p_value=1	frequency=3.675652e-02	genotype_quality=1059.8	ks_quality_p_value=0.526643	log10_base_likelihood=-32.1914	log10_qual_likelihood_position_model=4.23394	log10_strand_likelihood_position_model=0.610602	new_cov=5/5	polymorphism_quality=27.0	quality=27.0	quality_position_model=1.37851e-29	ref_cov=140/122	reject=INDEL_HOMOPOLYMER	tot_cov=145/127
RA	355	.	NC_007779	1861399	0	A	C	bias_e_value=7.68941e-08	bias_p_value=1.65494e-14	fisher_strand_p_value=4.55594e-16	frequency=6.562090e-02	genotype_quality=477.2	ks_quality_p_value=1	log10_base_likelihood=-5.90147	log10_qual_likelihood_position_model=24.5546	log10_strand_likelihood_position_model=15.3414	new_cov=0/23	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=121/22	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/45
RA	356	.	NC_007779	1879404	0	A	C	bias_e_value=8.88193e-10	bias_p_value=1.9116e-16	fisher_strand_p_value=4.67841e-18	frequency=9.082556e-02	genotype_quality=658.0	ks_quality_p_value=0.998909	log10_base_likelihood=-21.4882	log10_qual_likelihood_position_model=28.7344	log10_strand_likelihood_position_model=17.3299	new_cov=0/24	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=170/28	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/52
RA	357	.	NC_007779	1879996	0	G	T	bias_e_value=1.12391	bias_p_value=2.41893e-07	fisher_strand_p_value=1.26057e-08	frequency=6.377029e-02	genotype_quality=885.3	ks_quality_p_value=1	log10_base_likelihood=-15.3916	log10_qual_likelihood_position_model=15.9314	log10_strand_likelihood_position_model=7.89943	new_cov=18/0	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=84/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=102/163
RA	358	.	NC_007779	1889730	0	A	.	bias_e_value=3760250	bias_p_value=0.809294	fisher_strand_p_value=1	frequency=2.340221e-02	genotype_quality=1164.3	ks_quality_p_value=0.449956	log10_base_likelihood=-20.7434	log10_qual_likelihood_position_model=5.28148	log10_strand_likelihood_position_model=0.528708	new_cov=4/3	polymorphism_quality=15.5	quality=15.5	quality_position_model=4.80517e-17	ref_cov=172/120	reject=INDEL_HOMOPOLYMER	tot_cov=176/123
RA	359	.	NC_007779	1896056	0	A	.	bias_e_value=2540460	bias_p_value=0.546767	fisher_strand_p_value=0.660637	frequency=1.518822e-02	genotype_quality=1312.4	ks_quality_p_value=0.326712	log10_base_likelihood=-13.9916	log10_qual_likelihood_position_model=2.09287	log10_strand_likelihood_position_model=0.557835	new_cov=3/2	polymorphism_quality=8.6	quality=8.6	quality_position_model=2.1475e-13	ref_cov=145/179	reject=INDEL_HOMOPOLYMER	tot_cov=148/181
RA	360	.	NC_007779	1906475	1	.	C	bias_e_value=406054	bias_p_value=0.0873923	fisher_strand_p_value=0.0594263	frequency=1.041698e-02	genotype_quality=1377.3	ks_quality_p_value=0.290724	log10_base_likelihood=-13.0193	log10_qual_likelihood_position_model=2.29738	log10_strand_likelihood_position_model=1.22602	new_cov=3/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=1.63687e-11	ref_cov=110/175	reject=POLYMORPHISM_STRAND	tot_cov=113/175
RA	361	.	NC_007779	1906477	1	.	G	bias_e_value=19423.7	bias_p_value=0.00418043	fisher_strand_p_value=0.000494108	frequency=2.621651e-02	genotype_quality=1248.4	ks_quality_p_value=0.980035	log10_base_likelihood=-27.9018	log10_qual_likelihood_position_model=8.62007	log10_strand_likelihood_position_model=3.30618	new_cov=7/0	polymorphism_quality=22.7	quality=22.7	quality_position_model=4.21796e-18	ref_cov=85/175	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=92/175
RA	362	.	NC_007779	1906488	0	G	T	bias_e_value=0.168275	bias_p_value=3.62168e-08	fisher_strand_p_value=1.70938e-09	frequency=6.299543e-02	genotype_quality=930.6	ks_quality_p_value=1	log10_base_likelihood=-12.2173	log10_qual_likelihood_position_model=21.7079	log10_strand_likelihood_position_model=8.7755	new_cov=20/1	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=70/171	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=91/172
RA	363	.	NC_007779	1918872	0	T	A	frequency=1	genotype_quality=1098.7	new_cov=152/139	quality=1098.7	ref_cov=0/0	tot_cov=153/140
RA	364	.	NC_007779	1938748	1	.	A	bias_e_value=2077900	bias_p_value=0.447213	fisher_strand_p_value=0.219353	frequency=7.220268e-03	genotype_quality=1329.3	ks_quality_p_value=0.714574	log10_base_likelihood=-7.99294	log10_qual_likelihood_position_model=1.49778	log10_strand_likelihood_position_model=0.658856	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=9.41575e-08	ref_cov=128/147	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=130/147
RA	365	.	NC_007779	1956118	0	C	A	bias_e_value=0.0161064	bias_p_value=3.46647e-09	fisher_strand_p_value=1.48932e-10	frequency=5.019283e-02	genotype_quality=676.1	ks_quality_p_value=0.984448	log10_base_likelihood=-15.6816	log10_qual_likelihood_position_model=12.7357	log10_strand_likelihood_position_model=9.82701	new_cov=0/9	polymorphism_quality=10.3	quality=10.3	quality_position_model=Inf	ref_cov=156/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/18
RA	366	.	NC_007779	1971508	0	A	C	bias_e_value=4.15437e-15	bias_p_value=8.94119e-22	fisher_strand_p_value=1.67297e-23	frequency=1.679301e-01	genotype_quality=401.1	ks_quality_p_value=1	log10_base_likelihood=-48.4321	log10_qual_likelihood_position_model=26.6765	log10_strand_likelihood_position_model=22.7765	new_cov=0/29	polymorphism_quality=43.3	quality=43.3	quality_position_model=Inf	ref_cov=124/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=124/40
RA	367	.	NC_007779	1973476	0	G	A	frequency=1	genotype_quality=1051.4	new_cov=135/138	quality=1051.4	ref_cov=0/0	tot_cov=135/138
RA	368	.	NC_007779	1980091	0	C	T	bias_e_value=83728.1	bias_p_value=0.0180203	fisher_strand_p_value=0.00425076	frequency=1.946640e-02	genotype_quality=2311.4	ks_quality_p_value=0.60946	log10_base_likelihood=-21.4314	log10_qual_likelihood_position_model=4.59395	log10_strand_likelihood_position_model=2.43762	new_cov=11/0	polymorphism_quality=16.2	quality=16.2	quality_position_model=1.67023e-16	ref_cov=329/223	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=340/224
RA	369	.	NC_007779	1980208	0	A	G	bias_e_value=1426670	bias_p_value=0.307053	fisher_strand_p_value=0.117657	frequency=4.496193e-02	genotype_quality=689.0	ks_quality_p_value=0.766124	log10_base_likelihood=-22.7308	log10_qual_likelihood_position_model=4.00842	log10_strand_likelihood_position_model=1.0982	new_cov=9/0	polymorphism_quality=17.5	quality=17.5	quality_position_model=9.02971e-20	ref_cov=143/48	reject=POLYMORPHISM_STRAND	tot_cov=152/48
RA	370	.	NC_007779	1981406	0	A	.	bias_e_value=146.719	bias_p_value=3.15775e-05	fisher_strand_p_value=2.59913e-06	frequency=7.983923e-02	genotype_quality=975.8	ks_quality_p_value=0.867663	log10_base_likelihood=-74.1905	log10_qual_likelihood_position_model=5.85011	log10_strand_likelihood_position_model=5.66766	new_cov=0/21	polymorphism_quality=69.2	quality=69.2	quality_position_model=4.3185e-65	ref_cov=117/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=117/146
RA	371	.	NC_007779	1981408	0	C	G	bias_e_value=129.93	bias_p_value=2.7964e-05	fisher_strand_p_value=2.3604e-06	frequency=7.689571e-02	genotype_quality=1083.2	ks_quality_p_value=0.838254	log10_base_likelihood=-66.6274	log10_qual_likelihood_position_model=6.39798	log10_strand_likelihood_position_model=5.75651	new_cov=0/21	polymorphism_quality=61.6	quality=61.6	quality_position_model=7.33468e-57	ref_cov=123/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=123/150
RA	372	.	NC_007779	1981413	0	A	G	bias_e_value=117.853	bias_p_value=2.53647e-05	fisher_strand_p_value=2.17557e-06	frequency=7.442522e-02	genotype_quality=982.2	ks_quality_p_value=0.818853	log10_base_likelihood=-58.734	log10_qual_likelihood_position_model=5.34303	log10_strand_likelihood_position_model=5.93394	new_cov=0/21	polymorphism_quality=53.7	quality=53.7	quality_position_model=8.14621e-50	ref_cov=130/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/152
RA	373	.	NC_007779	1986832	1	.	C	bias_e_value=2569150	bias_p_value=0.552941	fisher_strand_p_value=0.219889	frequency=7.501602e-03	genotype_quality=1245.7	ks_quality_p_value=1	log10_base_likelihood=-5.6825	log10_qual_likelihood_position_model=2.9908	log10_strand_likelihood_position_model=0.657796	new_cov=0/2	polymorphism_quality=0.1	quality=0.1	quality_position_model=0.000960798	ref_cov=141/123	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/125
RA	374	.	NC_007779	1993891	1	.	C	bias_e_value=1589370	bias_p_value=0.34207	fisher_strand_p_value=0.109587	frequency=9.856224e-03	genotype_quality=1436.9	ks_quality_p_value=0.959847	log10_base_likelihood=-7.96379	log10_qual_likelihood_position_model=3.84663	log10_strand_likelihood_position_model=0.96024	new_cov=0/3	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.96539e-05	ref_cov=158/143	reject=POLYMORPHISM_STRAND	tot_cov=158/146
RA	375	.	NC_007779	1993894	0	A	C	bias_e_value=0.019468	bias_p_value=4.18998e-09	fisher_strand_p_value=1.78713e-10	frequency=5.993700e-02	genotype_quality=1012.1	ks_quality_p_value=1	log10_base_likelihood=-20.5787	log10_qual_likelihood_position_model=27.6995	log10_strand_likelihood_position_model=9.74784	new_cov=0/29	polymorphism_quality=15.3	quality=15.3	quality_position_model=Inf	ref_cov=169/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=169/160
RA	376	.	NC_007779	1999251	0	T	G	bias_e_value=0.054264	bias_p_value=1.16789e-08	fisher_strand_p_value=5.22e-10	frequency=9.111071e-02	genotype_quality=532.8	ks_quality_p_value=1	log10_base_likelihood=-7.67705	log10_qual_likelihood_position_model=27.0957	log10_strand_likelihood_position_model=9.54891	new_cov=40/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=91/81	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/81
RA	377	.	NC_007779	2004055	0	A	C	bias_e_value=1.2874e-35	bias_p_value=2.77079e-42	fisher_strand_p_value=2.73502e-44	frequency=2.519608e-01	genotype_quality=585.7	ks_quality_p_value=1	log10_base_likelihood=-73.3615	log10_qual_likelihood_position_model=60.1961	log10_strand_likelihood_position_model=43.5641	new_cov=1/91	polymorphism_quality=68.4	quality=68.4	quality_position_model=Inf	ref_cov=170/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/131
RA	378	.	NC_007779	2005401	0	C	T	frequency=1	genotype_quality=1457.5	new_cov=185/176	quality=1457.5	ref_cov=0/0	tot_cov=185/176
RA	379	.	NC_007779	2005920	1	.	A	bias_e_value=4631030	bias_p_value=0.996706	fisher_strand_p_value=1	frequency=8.522034e-03	genotype_quality=1714.0	ks_quality_p_value=0.919945	log10_base_likelihood=-11.8606	log10_qual_likelihood_position_model=2.95186	log10_strand_likelihood_position_model=0.402004	new_cov=2/1	polymorphism_quality=6.5	quality=6.5	quality_position_model=1.6828e-10	ref_cov=184/165	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=186/166
RA	380	.	NC_007779	2027359	0	T	A	bias_e_value=100547	bias_p_value=0.0216402	fisher_strand_p_value=0.00321	frequency=2.239132e-02	genotype_quality=1171.0	ks_quality_p_value=1	log10_base_likelihood=-5.98151	log10_qual_likelihood_position_model=13.3309	log10_strand_likelihood_position_model=2.49349	new_cov=0/8	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=159/147	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=159/155
RA	381	.	NC_007779	2027367	0	T	C	bias_e_value=2226.03	bias_p_value=0.000479094	fisher_strand_p_value=4.3374e-05	frequency=2.793503e-02	genotype_quality=1080.2	ks_quality_p_value=1	log10_base_likelihood=-5.85368	log10_qual_likelihood_position_model=18.7352	log10_strand_likelihood_position_model=4.6638	new_cov=0/15	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=161/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/162
RA	382	.	NC_007779	2032185	0	G	C	bias_e_value=61.6614	bias_p_value=1.3271e-05	fisher_strand_p_value=8.95603e-07	frequency=3.390503e-02	genotype_quality=587.5	ks_quality_p_value=0.992258	log10_base_likelihood=-8.13712	log10_qual_likelihood_position_model=7.93438	log10_strand_likelihood_position_model=6.04788	new_cov=5/0	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=6/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=11/135
RA	383	.	NC_007779	2036124	0	T	.	bias_e_value=3638780	bias_p_value=0.783151	fisher_strand_p_value=1	frequency=1.394463e-02	genotype_quality=866.5	ks_quality_p_value=0.41862	log10_base_likelihood=-8.34025	log10_qual_likelihood_position_model=1.39232	log10_strand_likelihood_position_model=0.356569	new_cov=2/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=1.56303e-08	ref_cov=152/60	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=154/61
RA	384	.	NC_007779	2047442	0	A	.	bias_e_value=3380310	bias_p_value=0.727522	fisher_strand_p_value=0.617751	frequency=1.161289e-02	genotype_quality=1014.4	ks_quality_p_value=0.582329	log10_base_likelihood=-7.59335	log10_qual_likelihood_position_model=3.6523	log10_strand_likelihood_position_model=0.431226	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=2.52368e-05	ref_cov=125/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/131
RA	385	.	NC_007779	2050720	0	G	T	bias_e_value=252.901	bias_p_value=5.44302e-05	fisher_strand_p_value=4.05992e-06	frequency=4.502869e-02	genotype_quality=819.7	ks_quality_p_value=0.999385	log10_base_likelihood=-8.09326	log10_qual_likelihood_position_model=13.7235	log10_strand_likelihood_position_model=5.6036	new_cov=0/18	polymorphism_quality=2.6	quality=2.6	quality_position_model=Inf	ref_cov=124/109	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/127
RA	386	.	NC_007779	2068312	0	T	C	bias_e_value=634683	bias_p_value=0.136599	fisher_strand_p_value=0.0512289	frequency=1.418972e-02	genotype_quality=1011.6	ks_quality_p_value=0.593426	log10_base_likelihood=-7.01183	log10_qual_likelihood_position_model=3.48092	log10_strand_likelihood_position_model=1.29049	new_cov=4/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=0.000572655	ref_cov=130/146	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=134/146
RA	387	.	NC_007779	2089543	0	A	C	bias_e_value=0.000248291	bias_p_value=5.34381e-11	fisher_strand_p_value=1.90958e-12	frequency=5.162191e-02	genotype_quality=832.6	ks_quality_p_value=1	log10_base_likelihood=-7.11187	log10_qual_likelihood_position_model=24.346	log10_strand_likelihood_position_model=11.7191	new_cov=0/25	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=178/79	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=178/105
RA	388	.	NC_007779	2095582	0	G	T	bias_e_value=36.0718	bias_p_value=7.7635e-06	fisher_strand_p_value=5.00632e-07	frequency=4.964495e-02	genotype_quality=999.4	ks_quality_p_value=1	log10_base_likelihood=-9.60695	log10_qual_likelihood_position_model=18.9933	log10_strand_likelihood_position_model=6.44607	new_cov=0/25	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=136/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/181
RA	389	.	NC_007779	2116876	0	A	.	bias_e_value=2651280	bias_p_value=0.570618	fisher_strand_p_value=0.253203	frequency=1.005650e-02	genotype_quality=1193.1	ks_quality_p_value=0.915345	log10_base_likelihood=-7.65239	log10_qual_likelihood_position_model=2.56559	log10_strand_likelihood_position_model=0.797804	new_cov=3/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=3.83004e-06	ref_cov=159/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/136
RA	390	.	NC_007779	2157800	0	A	C	bias_e_value=2299.8	bias_p_value=0.000494971	fisher_strand_p_value=4.49574e-05	frequency=2.277374e-02	genotype_quality=768.3	ks_quality_p_value=1	log10_base_likelihood=-6.6622	log10_qual_likelihood_position_model=8.53658	log10_strand_likelihood_position_model=4.3472	new_cov=0/9	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=155/71	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/80
RA	391	.	NC_007779	2170094	0	C	A	frequency=1	genotype_quality=1425.2	new_cov=141/211	quality=1425.2	ref_cov=0/0	tot_cov=141/211
RA	392	.	NC_007779	2174678	0	C	G	bias_e_value=1.00722e-22	bias_p_value=2.16777e-29	fisher_strand_p_value=3.04173e-31	frequency=1.714964e-01	genotype_quality=741.6	ks_quality_p_value=1	log10_base_likelihood=-66.4371	log10_qual_likelihood_position_model=38.7749	log10_strand_likelihood_position_model=30.5169	new_cov=0/41	polymorphism_quality=61.4	quality=61.4	quality_position_model=Inf	ref_cov=172/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=172/60
RA	393	.	NC_007779	2178210	0	A	C	bias_e_value=4646270	bias_p_value=0.999987	fisher_strand_p_value=1	frequency=3.273392e-02	genotype_quality=1296.0	ks_quality_p_value=0.994915	log10_base_likelihood=-26.2294	log10_qual_likelihood_position_model=7.66343	log10_strand_likelihood_position_model=0.619793	new_cov=5/6	polymorphism_quality=21.0	quality=21.0	quality_position_model=4.26417e-20	ref_cov=148/175	tot_cov=153/181
RA	394	.	NC_007779	2199432	0	G	C	bias_e_value=6.00299e-19	bias_p_value=1.29198e-25	fisher_strand_p_value=2.06907e-27	frequency=1.486449e-01	genotype_quality=684.3	ks_quality_p_value=1	log10_base_likelihood=-61.9728	log10_qual_likelihood_position_model=26.1071	log10_strand_likelihood_position_model=26.6842	new_cov=0/30	polymorphism_quality=56.9	quality=56.9	quality_position_model=3.43096e-11	ref_cov=160/10	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=160/40
RA	395	.	NC_007779	2200802	0	A	.	bias_e_value=1678620	bias_p_value=0.361279	fisher_strand_p_value=0.127349	frequency=1.341438e-02	genotype_quality=1193.2	ks_quality_p_value=0.894172	log10_base_likelihood=-11.1674	log10_qual_likelihood_position_model=2.16713	log10_strand_likelihood_position_model=1.07709	new_cov=0/4	polymorphism_quality=5.8	quality=5.8	quality_position_model=6.67245e-10	ref_cov=137/157	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=137/161
RA	396	.	NC_007779	2203514	0	A	G	bias_e_value=0.122575	bias_p_value=2.6381e-08	fisher_strand_p_value=1.22591e-09	frequency=6.756306e-02	genotype_quality=655.3	ks_quality_p_value=1	log10_base_likelihood=-8.71058	log10_qual_likelihood_position_model=25.5276	log10_strand_likelihood_position_model=8.91154	new_cov=20/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=63/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=83/131
RA	397	.	NC_007779	2203516	0	T	G	bias_e_value=8.65403e-09	bias_p_value=1.86255e-15	fisher_strand_p_value=4.82911e-17	frequency=8.416986e-02	genotype_quality=575.3	ks_quality_p_value=1	log10_base_likelihood=-6.97013	log10_qual_likelihood_position_model=33.1438	log10_strand_likelihood_position_model=16.3161	new_cov=35/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=49/127	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/127
RA	398	.	NC_007779	2211749	0	G	C	bias_e_value=0.875638	bias_p_value=1.88458e-07	fisher_strand_p_value=9.68818e-09	frequency=5.205774e-02	genotype_quality=792.5	ks_quality_p_value=1	log10_base_likelihood=-18.3926	log10_qual_likelihood_position_model=13.6474	log10_strand_likelihood_position_model=8.01376	new_cov=12/0	polymorphism_quality=13.1	quality=13.1	quality_position_model=Inf	ref_cov=38/162	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=50/162
RA	399	.	NC_007779	2212417	0	G	T	bias_e_value=4.63122e-05	bias_p_value=9.96748e-12	fisher_strand_p_value=3.35338e-13	frequency=6.846189e-02	genotype_quality=702.6	ks_quality_p_value=1	log10_base_likelihood=-26.1669	log10_qual_likelihood_position_model=17.0145	log10_strand_likelihood_position_model=12.4745	new_cov=13/0	polymorphism_quality=20.9	quality=20.9	quality_position_model=Inf	ref_cov=13/159	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=26/160
RA	400	.	NC_007779	2213136	0	G	T	bias_e_value=5.64661e-08	bias_p_value=1.21528e-14	fisher_strand_p_value=3.38362e-16	frequency=1.507440e-01	genotype_quality=485.2	ks_quality_p_value=0.980193	log10_base_likelihood=-51.3018	log10_qual_likelihood_position_model=21.3638	log10_strand_likelihood_position_model=15.4706	new_cov=25/0	polymorphism_quality=46.2	quality=46.2	quality_position_model=1.42635e-16	ref_cov=24/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=49/115
RA	401	.	NC_007779	2213138	0	C	G	bias_e_value=337.469	bias_p_value=7.26312e-05	fisher_strand_p_value=5.67955e-06	frequency=6.193256e-02	genotype_quality=522.9	ks_quality_p_value=0.975978	log10_base_likelihood=-9.71263	log10_qual_likelihood_position_model=11.073	log10_strand_likelihood_position_model=5.2562	new_cov=10/1	polymorphism_quality=4.3	quality=4.3	quality_position_model=Inf	ref_cov=31/114	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=41/115
RA	402	.	NC_007779	2214952	0	A	.	bias_e_value=2496880	bias_p_value=0.537388	fisher_strand_p_value=0.259258	frequency=8.164406e-03	genotype_quality=1463.3	ks_quality_p_value=0.809146	log10_base_likelihood=-7.41902	log10_qual_likelihood_position_model=1.81337	log10_strand_likelihood_position_model=0.755189	new_cov=3/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=9.9337e-07	ref_cov=203/161	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=206/161
RA	403	.	NC_007779	2225700	0	T	G	bias_e_value=0.00105941	bias_p_value=2.2801e-10	fisher_strand_p_value=8.62469e-12	frequency=3.085995e-02	genotype_quality=722.8	ks_quality_p_value=0.99845	log10_base_likelihood=-8.61156	log10_qual_likelihood_position_model=12.0998	log10_strand_likelihood_position_model=11.0643	new_cov=9/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=8/203	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=17/204
RA	404	.	NC_007779	2226024	0	C	A	bias_e_value=0.195112	bias_p_value=4.19927e-08	fisher_strand_p_value=1.99663e-09	frequency=4.612732e-02	genotype_quality=1089.1	ks_quality_p_value=1	log10_base_likelihood=-9.21705	log10_qual_likelihood_position_model=18.9832	log10_strand_likelihood_position_model=8.6997	new_cov=23/0	polymorphism_quality=3.8	quality=3.8	quality_position_model=Inf	ref_cov=125/190	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=156/190
RA	405	.	NC_007779	2226744	0	T	G	bias_e_value=1.70792e-14	bias_p_value=3.67585e-21	fisher_strand_p_value=7.06843e-23	frequency=1.422563e-01	genotype_quality=811.5	ks_quality_p_value=1	log10_base_likelihood=-33.2175	log10_qual_likelihood_position_model=44.4742	log10_strand_likelihood_position_model=22.1507	new_cov=61/0	polymorphism_quality=28.0	quality=28.0	quality_position_model=Inf	ref_cov=103/173	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=164/173
RA	406	.	NC_007779	2230225	0	A	C	bias_e_value=26.0263	bias_p_value=5.60148e-06	fisher_strand_p_value=3.53271e-07	frequency=4.135799e-02	genotype_quality=1003.4	ks_quality_p_value=1	log10_base_likelihood=-9.47235	log10_qual_likelihood_position_model=25.0423	log10_strand_likelihood_position_model=6.55501	new_cov=1/23	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=177/142	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=178/165
RA	407	.	NC_007779	2231556	0	T	G	bias_e_value=0.00414089	bias_p_value=8.91217e-10	fisher_strand_p_value=3.55638e-11	frequency=5.011129e-02	genotype_quality=714.3	ks_quality_p_value=1	log10_base_likelihood=-10.2858	log10_qual_likelihood_position_model=20.4419	log10_strand_likelihood_position_model=10.449	new_cov=21/0	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=63/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=84/158
RA	408	.	NC_007779	2245262	0	G	C	bias_e_value=2.79016e-06	bias_p_value=6.00508e-13	fisher_strand_p_value=1.84057e-14	frequency=9.720612e-02	genotype_quality=570.6	ks_quality_p_value=1	log10_base_likelihood=-17.8566	log10_qual_likelihood_position_model=17.0071	log10_strand_likelihood_position_model=13.735	new_cov=0/17	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=127/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=127/32
RA	409	.	NC_007779	2249963	0	T	G	bias_e_value=2.83325e-26	bias_p_value=6.09783e-33	fisher_strand_p_value=7.66504e-35	frequency=2.781529e-01	genotype_quality=474.0	ks_quality_p_value=1	log10_base_likelihood=-81.435	log10_qual_likelihood_position_model=60.6244	log10_strand_likelihood_position_model=34.2005	new_cov=88/0	polymorphism_quality=76.5	quality=76.5	quality_position_model=Inf	ref_cov=53/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/134
RA	410	.	NC_007779	2264335	0	A	C	bias_e_value=7.71853e-07	bias_p_value=1.66121e-13	fisher_strand_p_value=4.89297e-15	frequency=5.252886e-02	genotype_quality=783.2	ks_quality_p_value=1	log10_base_likelihood=-8.281	log10_qual_likelihood_position_model=31.6911	log10_strand_likelihood_position_model=14.3104	new_cov=0/33	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=160/77	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=160/111
RA	411	.	NC_007779	2271204	0	G	A	bias_e_value=1015.85	bias_p_value=0.000218635	fisher_strand_p_value=1.85112e-05	frequency=4.172897e-02	genotype_quality=1135.3	ks_quality_p_value=0.992095	log10_base_likelihood=-12.3984	log10_qual_likelihood_position_model=19.8141	log10_strand_likelihood_position_model=4.73257	new_cov=0/15	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=159/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/156
RA	412	.	NC_007779	2278432	0	T	G	bias_e_value=0.0378859	bias_p_value=8.15393e-09	fisher_strand_p_value=3.58425e-10	frequency=5.785465e-02	genotype_quality=818.9	ks_quality_p_value=1	log10_base_likelihood=-6.47606	log10_qual_likelihood_position_model=26.2233	log10_strand_likelihood_position_model=9.69989	new_cov=30/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=117/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=147/146
RA	413	.	NC_007779	2278635	0	C	A	bias_e_value=3251.32	bias_p_value=0.000699761	fisher_strand_p_value=6.58395e-05	frequency=2.791691e-02	genotype_quality=1020.2	ks_quality_p_value=1	log10_base_likelihood=-6.40342	log10_qual_likelihood_position_model=9.45647	log10_strand_likelihood_position_model=4.18151	new_cov=12/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=126/163	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=138/163
RA	414	.	NC_007779	2278884	0	T	G	bias_e_value=6.13218e-13	bias_p_value=1.31979e-19	fisher_strand_p_value=2.72965e-21	frequency=1.068282e-01	genotype_quality=736.4	ks_quality_p_value=1	log10_base_likelihood=-13.8171	log10_qual_likelihood_position_model=49.1946	log10_strand_likelihood_position_model=20.5639	new_cov=52/0	polymorphism_quality=8.5	quality=8.5	quality_position_model=Inf	ref_cov=80/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/156
RA	415	.	NC_007779	2287114	0	C	A	bias_e_value=0.00650328	bias_p_value=1.39966e-09	fisher_strand_p_value=6.47632e-11	frequency=6.255913e-02	genotype_quality=1013.8	ks_quality_p_value=0.878915	log10_base_likelihood=-12.9297	log10_qual_likelihood_position_model=28.8654	log10_strand_likelihood_position_model=10.1887	new_cov=0/25	polymorphism_quality=7.5	quality=7.5	quality_position_model=Inf	ref_cov=180/103	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=180/128
RA	416	.	NC_007779	2287403	1	.	A	bias_e_value=1828990	bias_p_value=0.393641	fisher_strand_p_value=0.231716	frequency=5.951881e-03	genotype_quality=1647.7	ks_quality_p_value=0.557677	log10_base_likelihood=-7.48287	log10_qual_likelihood_position_model=3.14829	log10_strand_likelihood_position_model=0.635043	new_cov=0/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.59211e-05	ref_cov=174/160	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=174/162
RA	417	.	NC_007779	2300442	0	C	.	bias_e_value=3584700	bias_p_value=0.771512	fisher_strand_p_value=0.601598	frequency=8.998871e-03	genotype_quality=1352.8	ks_quality_p_value=0.674027	log10_base_likelihood=-7.59278	log10_qual_likelihood_position_model=2.57574	log10_strand_likelihood_position_model=0.454859	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.98468e-06	ref_cov=154/176	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/177
RA	418	.	NC_007779	2302609	0	G	T	bias_e_value=2747.61	bias_p_value=0.000591351	fisher_strand_p_value=5.46841e-05	frequency=2.936554e-02	genotype_quality=1097.8	ks_quality_p_value=1	log10_base_likelihood=-5.5725	log10_qual_likelihood_position_model=16.2096	log10_strand_likelihood_position_model=4.38625	new_cov=1/16	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=168/137	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/154
RA	419	.	NC_007779	2307309	0	T	C	bias_e_value=2.6952e-15	bias_p_value=5.8007e-22	fisher_strand_p_value=1.07648e-23	frequency=1.033201e-01	genotype_quality=812.1	ks_quality_p_value=1	log10_base_likelihood=-46.5153	log10_qual_likelihood_position_model=19.7615	log10_strand_likelihood_position_model=22.968	new_cov=0/29	polymorphism_quality=41.4	quality=41.4	quality_position_model=1.29173e-05	ref_cov=213/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=213/56
RA	420	.	NC_007779	2314183	0	A	C	bias_e_value=0.0311896	bias_p_value=6.71273e-09	fisher_strand_p_value=2.92459e-10	frequency=6.676197e-02	genotype_quality=648.9	ks_quality_p_value=1	log10_base_likelihood=-6.79866	log10_qual_likelihood_position_model=23.1017	log10_strand_likelihood_position_model=9.54596	new_cov=0/31	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=114/95	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/127
RA	421	.	NC_007779	2316502	1	.	T	bias_e_value=3077370	bias_p_value=0.662323	fisher_strand_p_value=0.498525	frequency=5.951881e-03	genotype_quality=1650.0	ks_quality_p_value=0.603662	log10_base_likelihood=-7.50942	log10_qual_likelihood_position_model=3.06016	log10_strand_likelihood_position_model=0.598188	new_cov=0/2	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.10282e-05	ref_cov=167/167	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=167/169
RA	422	.	NC_007779	2331120	0	T	G	bias_e_value=7.03019e-31	bias_p_value=1.51306e-37	fisher_strand_p_value=1.67588e-39	frequency=2.589636e-01	genotype_quality=457.6	ks_quality_p_value=1	log10_base_likelihood=-47.5382	log10_qual_likelihood_position_model=53.141	log10_strand_likelihood_position_model=38.7758	new_cov=82/0	polymorphism_quality=42.4	quality=42.4	quality_position_model=Inf	ref_cov=32/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=116/134
RA	423	.	NC_007779	2332580	0	A	C	bias_e_value=1.43615e-27	bias_p_value=3.09093e-34	fisher_strand_p_value=3.74326e-36	frequency=1.965137e-01	genotype_quality=530.2	ks_quality_p_value=1	log10_base_likelihood=-27.9767	log10_qual_likelihood_position_model=46.4637	log10_strand_likelihood_position_model=35.4267	new_cov=0/75	polymorphism_quality=22.8	quality=22.8	quality_position_model=Inf	ref_cov=143/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/114
RA	424	.	NC_007779	2334630	0	C	A	bias_e_value=80.1762	bias_p_value=1.72558e-05	fisher_strand_p_value=1.17771e-06	frequency=4.179192e-02	genotype_quality=1010.9	ks_quality_p_value=1	log10_base_likelihood=-6.39233	log10_qual_likelihood_position_model=17.4983	log10_strand_likelihood_position_model=6.03981	new_cov=20/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=140/151	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/151
RA	425	.	NC_007779	2337256	0	G	C	bias_e_value=1.48188	bias_p_value=3.18936e-07	fisher_strand_p_value=1.68859e-08	frequency=4.161930e-02	genotype_quality=734.4	ks_quality_p_value=0.999493	log10_base_likelihood=-11.6342	log10_qual_likelihood_position_model=11.9738	log10_strand_likelihood_position_model=7.77248	new_cov=9/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=21/163	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=31/163
RA	426	.	NC_007779	2341297	1	.	T	bias_e_value=942225	bias_p_value=0.202789	fisher_strand_p_value=0.503745	frequency=7.575989e-03	genotype_quality=1285.5	ks_quality_p_value=0.101253	log10_base_likelihood=-8.082	log10_qual_likelihood_position_model=1.59902	log10_strand_likelihood_position_model=0.515839	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=6.89449e-08	ref_cov=144/118	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=146/118
RA	427	.	NC_007779	2342393	0	A	C	bias_e_value=2.03729e-16	bias_p_value=4.38472e-23	fisher_strand_p_value=7.7584e-25	frequency=9.919500e-02	genotype_quality=674.5	ks_quality_p_value=1	log10_base_likelihood=-10.9306	log10_qual_likelihood_position_model=37.652	log10_strand_likelihood_position_model=24.1102	new_cov=0/41	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=171/40	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/82
RA	428	.	NC_007779	2347976	0	A	C	bias_e_value=2.46792e-21	bias_p_value=5.31155e-28	fisher_strand_p_value=7.80854e-30	frequency=1.083517e-01	genotype_quality=732.9	ks_quality_p_value=1	log10_base_likelihood=-16.8023	log10_qual_likelihood_position_model=40.8159	log10_strand_likelihood_position_model=29.1074	new_cov=0/53	polymorphism_quality=11.5	quality=11.5	quality_position_model=Inf	ref_cov=188/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=188/102
RA	429	.	NC_007779	2354291	0	A	C	bias_e_value=1.47592e-26	bias_p_value=3.17654e-33	fisher_strand_p_value=3.96007e-35	frequency=1.923466e-01	genotype_quality=723.1	ks_quality_p_value=1	log10_base_likelihood=-54.6741	log10_qual_likelihood_position_model=52.4093	log10_strand_likelihood_position_model=34.4023	new_cov=0/73	polymorphism_quality=49.6	quality=49.6	quality_position_model=Inf	ref_cov=192/64	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=192/137
RA	430	.	NC_007779	2359978	0	T	.	bias_e_value=2486760	bias_p_value=0.535209	fisher_strand_p_value=0.578607	frequency=8.893013e-03	genotype_quality=1297.3	ks_quality_p_value=0.36015	log10_base_likelihood=-7.74912	log10_qual_likelihood_position_model=2.40657	log10_strand_likelihood_position_model=0.50101	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.01486e-06	ref_cov=142/191	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/193
RA	431	.	NC_007779	2362564	0	C	A	bias_e_value=3716.11	bias_p_value=0.000799795	fisher_strand_p_value=8.00156e-05	frequency=3.290653e-02	genotype_quality=1050.3	ks_quality_p_value=0.953705	log10_base_likelihood=-5.6383	log10_qual_likelihood_position_model=20.8973	log10_strand_likelihood_position_model=4.15718	new_cov=1/16	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=167/146	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=168/163
RA	432	.	NC_007779	2374921	0	T	G	bias_e_value=2.1511e-08	bias_p_value=4.62967e-15	fisher_strand_p_value=1.23018e-16	frequency=7.910109e-02	genotype_quality=658.7	ks_quality_p_value=1	log10_base_likelihood=-13.4893	log10_qual_likelihood_position_model=25.3311	log10_strand_likelihood_position_model=15.91	new_cov=23/0	polymorphism_quality=8.1	quality=8.1	quality_position_model=Inf	ref_cov=31/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=54/167
RA	433	.	NC_007779	2386047	0	T	.	bias_e_value=4491170	bias_p_value=0.966606	fisher_strand_p_value=1	frequency=9.795189e-03	genotype_quality=1207.8	ks_quality_p_value=0.752957	log10_base_likelihood=-7.74621	log10_qual_likelihood_position_model=1.59289	log10_strand_likelihood_position_model=0.407088	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.16705e-07	ref_cov=157/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/146
RA	434	.	NC_007779	2406075	0	C	T	frequency=1	genotype_quality=1145.5	new_cov=145/149	quality=1145.5	ref_cov=0/0	tot_cov=145/149
RA	435	.	NC_007779	2409404	0	A	C	bias_e_value=4.72694e-10	bias_p_value=1.01735e-16	fisher_strand_p_value=2.44843e-18	frequency=1.083951e-01	genotype_quality=621.6	ks_quality_p_value=1	log10_base_likelihood=-16.6417	log10_qual_likelihood_position_model=29.6948	log10_strand_likelihood_position_model=17.6111	new_cov=0/33	polymorphism_quality=11.3	quality=11.3	quality_position_model=Inf	ref_cov=150/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=150/79
RA	436	.	NC_007779	2410310	0	T	A	bias_e_value=2905.73	bias_p_value=0.000625382	fisher_strand_p_value=5.81628e-05	frequency=3.012943e-02	genotype_quality=1175.0	ks_quality_p_value=1	log10_base_likelihood=-5.93717	log10_qual_likelihood_position_model=18.5545	log10_strand_likelihood_position_model=4.23535	new_cov=0/13	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=172/147	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/160
RA	437	.	NC_007779	2410316	0	A	C	bias_e_value=1.85707e-18	bias_p_value=3.99686e-25	fisher_strand_p_value=6.52071e-27	frequency=1.550641e-01	genotype_quality=793.8	ks_quality_p_value=1	log10_base_likelihood=-55.1731	log10_qual_likelihood_position_model=50.5502	log10_strand_likelihood_position_model=26.1857	new_cov=0/70	polymorphism_quality=50.1	quality=50.1	quality_position_model=Inf	ref_cov=178/97	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=178/167
RA	438	.	NC_007779	2416102	0	G	A	frequency=1	genotype_quality=1116.2	new_cov=129/159	quality=1116.2	ref_cov=0/0	tot_cov=129/159
RA	439	.	NC_007779	2417605	0	C	A	bias_e_value=26.7933	bias_p_value=5.76654e-06	fisher_strand_p_value=4.6462e-07	frequency=5.648708e-02	genotype_quality=960.1	ks_quality_p_value=0.784283	log10_base_likelihood=-12.1625	log10_qual_likelihood_position_model=27.8293	log10_strand_likelihood_position_model=6.57036	new_cov=25/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=Inf	ref_cov=152/137	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/137
RA	440	.	NC_007779	2418805	1	.	A	bias_e_value=4644210	bias_p_value=0.999544	fisher_strand_p_value=1	frequency=1.013470e-02	genotype_quality=1443.4	ks_quality_p_value=0.969952	log10_base_likelihood=-12.3192	log10_qual_likelihood_position_model=3.31492	log10_strand_likelihood_position_model=0.382741	new_cov=2/1	polymorphism_quality=6.9	quality=6.9	quality_position_model=1.28365e-10	ref_cov=163/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=165/131
RA	441	.	NC_007779	2420902	0	G	C	bias_e_value=0.0248791	bias_p_value=5.35456e-09	fisher_strand_p_value=2.48215e-10	frequency=6.958199e-02	genotype_quality=789.2	ks_quality_p_value=0.930279	log10_base_likelihood=-17.4568	log10_qual_likelihood_position_model=21.0873	log10_strand_likelihood_position_model=9.60517	new_cov=19/0	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=62/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=81/158
RA	442	.	NC_007779	2426889	0	A	C	bias_e_value=848.664	bias_p_value=0.000182652	fisher_strand_p_value=1.50937e-05	frequency=2.225971e-02	genotype_quality=581.3	ks_quality_p_value=1	log10_base_likelihood=-6.94103	log10_qual_likelihood_position_model=5.62371	log10_strand_likelihood_position_model=4.8212	new_cov=0/4	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=157/8	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/12
RA	443	.	NC_007779	2446437	0	A	C	bias_e_value=3.97779e-07	bias_p_value=8.56114e-14	fisher_strand_p_value=2.4719e-15	frequency=6.819010e-02	genotype_quality=846.5	ks_quality_p_value=1	log10_base_likelihood=-7.70806	log10_qual_likelihood_position_model=30.7042	log10_strand_likelihood_position_model=14.607	new_cov=0/33	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=176/83	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=176/117
RA	444	.	NC_007779	2454645	0	C	G	bias_e_value=2202360	bias_p_value=0.474	fisher_strand_p_value=0.171566	frequency=2.908134e-02	genotype_quality=726.9	ks_quality_p_value=1	log10_base_likelihood=-7.51003	log10_qual_likelihood_position_model=9.22441	log10_strand_likelihood_position_model=0.971109	new_cov=5/4	polymorphism_quality=2.0	quality=2.0	quality_position_model=Inf	ref_cov=67/136	reject=SURROUNDING_HOMOPOLYMER	tot_cov=72/141
RA	445	.	NC_007779	2458860	0	T	G	bias_e_value=699.305	bias_p_value=0.000150507	fisher_strand_p_value=1.22243e-05	frequency=2.143192e-02	genotype_quality=489.6	ks_quality_p_value=1	log10_base_likelihood=-6.48294	log10_qual_likelihood_position_model=5.08887	log10_strand_likelihood_position_model=4.91278	new_cov=4/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=6/134	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=10/134
RA	446	.	NC_007779	2465370	0	C	A	bias_e_value=1.37993e-10	bias_p_value=2.96993e-17	fisher_strand_p_value=6.95318e-19	frequency=1.420536e-01	genotype_quality=505.5	ks_quality_p_value=0.99769	log10_base_likelihood=-36.543	log10_qual_likelihood_position_model=23.7747	log10_strand_likelihood_position_model=18.1578	new_cov=0/23	polymorphism_quality=31.4	quality=31.4	quality_position_model=Inf	ref_cov=118/12	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/35
RA	447	.	NC_007779	2468327	0	C	.	bias_e_value=3862920	bias_p_value=0.831391	fisher_strand_p_value=0.651807	frequency=1.975536e-02	genotype_quality=1013.7	ks_quality_p_value=0.734507	log10_base_likelihood=-15.0259	log10_qual_likelihood_position_model=2.4805	log10_strand_likelihood_position_model=0.609695	new_cov=3/2	polymorphism_quality=9.7	quality=9.7	quality_position_model=5.326e-14	ref_cov=102/146	reject=INDEL_HOMOPOLYMER	tot_cov=105/148
RA	448	.	NC_007779	2475172	0	T	.	bias_e_value=1945360	bias_p_value=0.418686	fisher_strand_p_value=1	frequency=1.713467e-02	genotype_quality=697.2	ks_quality_p_value=0.14175	log10_base_likelihood=-8.63972	log10_qual_likelihood_position_model=1.44726	log10_strand_likelihood_position_model=0.368268	new_cov=2/1	polymorphism_quality=3.2	quality=3.2	quality_position_model=8.99539e-09	ref_cov=100/72	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=102/73
RA	449	.	NC_007779	2484034	0	G	T	bias_e_value=9621.55	bias_p_value=0.00207078	fisher_strand_p_value=0.000224381	frequency=3.616333e-02	genotype_quality=848.0	ks_quality_p_value=0.979403	log10_base_likelihood=-7.35115	log10_qual_likelihood_position_model=13.3938	log10_strand_likelihood_position_model=3.73591	new_cov=0/13	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=120/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=120/135
RA	450	.	NC_007779	2485817	0	T	G	bias_e_value=0.000459518	bias_p_value=9.88991e-11	fisher_strand_p_value=3.62225e-12	frequency=5.865479e-02	genotype_quality=465.5	ks_quality_p_value=0.998454	log10_base_likelihood=-10.2451	log10_qual_likelihood_position_model=16.1792	log10_strand_likelihood_position_model=11.441	new_cov=17/0	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=23/117	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=40/117
RA	451	.	NC_007779	2512935	0	A	C	bias_e_value=34242.1	bias_p_value=0.00736971	fisher_strand_p_value=0.00101505	frequency=1.868248e-02	genotype_quality=554.7	ks_quality_p_value=0.908881	log10_base_likelihood=-5.65247	log10_qual_likelihood_position_model=4.3489	log10_strand_likelihood_position_model=2.99351	new_cov=0/3	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=143/14	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=143/17
RA	452	.	NC_007779	2517215	0	A	C	bias_e_value=1.72458e-07	bias_p_value=3.71171e-14	fisher_strand_p_value=1.04573e-15	frequency=4.735327e-02	genotype_quality=652.1	ks_quality_p_value=1	log10_base_likelihood=-5.56723	log10_qual_likelihood_position_model=22.9665	log10_strand_likelihood_position_model=14.9806	new_cov=0/22	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=163/32	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/54
RA	453	.	NC_007779	2517218	0	A	C	bias_e_value=1.5999e-19	bias_p_value=3.44336e-26	fisher_strand_p_value=5.39828e-28	frequency=1.187367e-01	genotype_quality=598.0	ks_quality_p_value=1	log10_base_likelihood=-16.4335	log10_qual_likelihood_position_model=41.9037	log10_strand_likelihood_position_model=27.2677	new_cov=0/38	polymorphism_quality=11.1	quality=11.1	quality_position_model=Inf	ref_cov=163/21	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/59
RA	454	.	NC_007779	2519319	0	T	G	bias_e_value=2.61482e-05	bias_p_value=5.62772e-12	fisher_strand_p_value=1.85642e-13	frequency=7.563591e-02	genotype_quality=817.2	ks_quality_p_value=1	log10_base_likelihood=-12.4441	log10_qual_likelihood_position_model=30.4313	log10_strand_likelihood_position_model=12.7313	new_cov=30/0	polymorphism_quality=7.1	quality=7.1	quality_position_model=Inf	ref_cov=84/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=114/164
RA	455	.	NC_007779	2522930	0	T	G	bias_e_value=0.164297	bias_p_value=3.53606e-08	fisher_strand_p_value=1.66699e-09	frequency=9.473705e-02	genotype_quality=753.3	ks_quality_p_value=1	log10_base_likelihood=-14.0251	log10_qual_likelihood_position_model=27.4395	log10_strand_likelihood_position_model=8.98868	new_cov=37/0	polymorphism_quality=8.7	quality=8.7	quality_position_model=Inf	ref_cov=135/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/115
RA	456	.	NC_007779	2536601	0	T	G	bias_e_value=5.45013e-13	bias_p_value=1.173e-19	fisher_strand_p_value=2.42002e-21	frequency=1.354585e-01	genotype_quality=652.1	ks_quality_p_value=1	log10_base_likelihood=-34.9072	log10_qual_likelihood_position_model=32.2075	log10_strand_likelihood_position_model=20.6162	new_cov=41/0	polymorphism_quality=29.7	quality=29.7	quality_position_model=Inf	ref_cov=54/161	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=95/161
RA	457	.	NC_007779	2538628	0	C	T	frequency=1	genotype_quality=1340.5	new_cov=165/174	quality=1340.5	ref_cov=0/0	tot_cov=165/174
RA	458	.	NC_007779	2556426	0	G	T	bias_e_value=2.59233e-10	bias_p_value=5.5793e-17	fisher_strand_p_value=2.2309e-18	frequency=1.155920e-01	genotype_quality=1053.2	ks_quality_p_value=0.593106	log10_base_likelihood=-36.041	log10_qual_likelihood_position_model=43.0519	log10_strand_likelihood_position_model=17.6515	new_cov=0/50	polymorphism_quality=30.9	quality=30.9	quality_position_model=Inf	ref_cov=185/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=185/173
RA	459	.	NC_007779	2570517	0	G	T	bias_e_value=2193290	bias_p_value=0.472047	fisher_strand_p_value=1	frequency=9.143829e-03	genotype_quality=1327.3	ks_quality_p_value=0.17046	log10_base_likelihood=-5.75757	log10_qual_likelihood_position_model=2.27146	log10_strand_likelihood_position_model=0.388799	new_cov=2/1	polymorphism_quality=0.2	quality=0.2	quality_position_model=6.90176e-05	ref_cov=176/146	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=178/147
RA	460	.	NC_007779	2577496	0	A	.	bias_e_value=4132840	bias_p_value=0.889485	fisher_strand_p_value=1	frequency=9.666443e-03	genotype_quality=1204.5	ks_quality_p_value=0.568362	log10_base_likelihood=-7.56957	log10_qual_likelihood_position_model=2.58887	log10_strand_likelihood_position_model=0.392436	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.86408e-06	ref_cov=166/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=168/142
RA	461	.	NC_007779	2593271	0	A	C	bias_e_value=0.000609685	bias_p_value=1.31219e-10	fisher_strand_p_value=4.85062e-12	frequency=4.218674e-02	genotype_quality=747.8	ks_quality_p_value=1	log10_base_likelihood=-6.312	log10_qual_likelihood_position_model=33.3976	log10_strand_likelihood_position_model=11.3142	new_cov=0/28	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=149/83	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=149/113
RA	462	.	NC_007779	2593281	0	A	C	bias_e_value=0.158531	bias_p_value=3.41197e-08	fisher_strand_p_value=1.60565e-09	frequency=5.471563e-02	genotype_quality=743.6	ks_quality_p_value=1	log10_base_likelihood=-7.87716	log10_qual_likelihood_position_model=21.6071	log10_strand_likelihood_position_model=8.79435	new_cov=0/23	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=145/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=145/114
RA	463	.	NC_007779	2595934	0	T	G	bias_e_value=444.137	bias_p_value=9.55887e-05	fisher_strand_p_value=7.46878e-06	frequency=3.108978e-02	genotype_quality=473.5	ks_quality_p_value=0.999463	log10_base_likelihood=-6.12172	log10_qual_likelihood_position_model=6.01102	log10_strand_likelihood_position_model=5.12675	new_cov=5/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=10/124	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=15/124
RA	464	.	NC_007779	2600440	0	A	G	bias_e_value=6.09124e-07	bias_p_value=1.31098e-13	fisher_strand_p_value=3.83384e-15	frequency=9.027529e-02	genotype_quality=845.5	ks_quality_p_value=1	log10_base_likelihood=-12.623	log10_qual_likelihood_position_model=24.5639	log10_strand_likelihood_position_model=14.4164	new_cov=35/0	polymorphism_quality=7.2	quality=7.2	quality_position_model=Inf	ref_cov=87/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=122/165
RA	465	.	NC_007779	2601998	0	A	C	bias_e_value=0.0575633	bias_p_value=1.2389e-08	fisher_strand_p_value=5.56278e-10	frequency=4.158401e-02	genotype_quality=751.0	ks_quality_p_value=0.998191	log10_base_likelihood=-9.99935	log10_qual_likelihood_position_model=15.4262	log10_strand_likelihood_position_model=9.25471	new_cov=0/11	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=189/26	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=189/38
RA	466	.	NC_007779	2606900	0	T	G	bias_e_value=5.79523e-09	bias_p_value=1.24727e-15	fisher_strand_p_value=3.1997e-17	frequency=6.117916e-02	genotype_quality=672.8	ks_quality_p_value=1	log10_base_likelihood=-5.609	log10_qual_likelihood_position_model=35.4796	log10_strand_likelihood_position_model=16.4949	new_cov=45/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=83/139	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/139
RA	467	.	NC_007779	2610583	0	G	C	bias_e_value=23.3272	bias_p_value=5.02056e-06	fisher_strand_p_value=3.14318e-07	frequency=3.634548e-02	genotype_quality=738.7	ks_quality_p_value=1	log10_base_likelihood=-5.69719	log10_qual_likelihood_position_model=11.7327	log10_strand_likelihood_position_model=6.50263	new_cov=0/10	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=154/39	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=155/49
RA	468	.	NC_007779	2616347	0	A	C	bias_e_value=2.40729e-10	bias_p_value=5.18105e-17	fisher_strand_p_value=1.22651e-18	frequency=7.517529e-02	genotype_quality=622.6	ks_quality_p_value=1	log10_base_likelihood=-16.1446	log10_qual_likelihood_position_model=26.0012	log10_strand_likelihood_position_model=17.9132	new_cov=1/23	polymorphism_quality=10.8	quality=10.8	quality_position_model=Inf	ref_cov=170/18	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=171/41
RA	469	.	NC_007779	2623159	0	T	G	bias_e_value=3.44151e-20	bias_p_value=7.40694e-27	fisher_strand_p_value=1.13348e-28	frequency=1.916485e-01	genotype_quality=502.1	ks_quality_p_value=1	log10_base_likelihood=-35.4063	log10_qual_likelihood_position_model=42.5994	log10_strand_likelihood_position_model=27.9456	new_cov=56/0	polymorphism_quality=30.2	quality=30.2	quality_position_model=Inf	ref_cov=36/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=92/133
RA	470	.	NC_007779	2623170	0	A	T	bias_e_value=2945.76	bias_p_value=0.000633997	fisher_strand_p_value=5.90468e-05	frequency=3.903961e-02	genotype_quality=741.9	ks_quality_p_value=1	log10_base_likelihood=-6.88849	log10_qual_likelihood_position_model=8.78976	log10_strand_likelihood_position_model=4.2288	new_cov=11/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=84/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=95/128
RA	471	.	NC_007779	2623173	0	G	T	bias_e_value=2.05082	bias_p_value=4.41385e-07	fisher_strand_p_value=2.37892e-08	frequency=7.596827e-02	genotype_quality=765.8	ks_quality_p_value=1	log10_base_likelihood=-12.6901	log10_qual_likelihood_position_model=17.727	log10_strand_likelihood_position_model=7.62362	new_cov=20/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=78/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=98/124
RA	472	.	NC_007779	2640922	0	T	G	bias_e_value=2.25605e-09	bias_p_value=4.85555e-16	fisher_strand_p_value=1.21544e-17	frequency=8.539152e-02	genotype_quality=591.8	ks_quality_p_value=1	log10_base_likelihood=-10.1694	log10_qual_likelihood_position_model=37.3147	log10_strand_likelihood_position_model=16.9153	new_cov=35/0	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=52/141	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=87/141
RA	473	.	NC_007779	2641345	0	T	G	bias_e_value=5.03717	bias_p_value=1.08412e-06	fisher_strand_p_value=6.15878e-08	frequency=5.912256e-02	genotype_quality=437.5	ks_quality_p_value=1	log10_base_likelihood=-11.6437	log10_qual_likelihood_position_model=11.6381	log10_strand_likelihood_position_model=7.21486	new_cov=9/1	polymorphism_quality=6.2	quality=6.2	quality_position_model=Inf	ref_cov=12/118	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=21/119
RA	474	.	NC_007779	2646804	0	A	C	bias_e_value=1.34969e-16	bias_p_value=2.90486e-23	fisher_strand_p_value=5.10206e-25	frequency=1.143527e-01	genotype_quality=775.3	ks_quality_p_value=1	log10_base_likelihood=-22.7177	log10_qual_likelihood_position_model=52.7554	log10_strand_likelihood_position_model=24.2923	new_cov=0/55	polymorphism_quality=17.5	quality=17.5	quality_position_model=Inf	ref_cov=177/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=177/131
RA	475	.	NC_007779	2648595	0	A	C	bias_e_value=9.03591e-13	bias_p_value=1.94474e-19	fisher_strand_p_value=4.05541e-21	frequency=1.160951e-01	genotype_quality=472.7	ks_quality_p_value=1	log10_base_likelihood=-21.5986	log10_qual_likelihood_position_model=24.8091	log10_strand_likelihood_position_model=20.392	new_cov=0/22	polymorphism_quality=16.3	quality=16.3	quality_position_model=Inf	ref_cov=136/8	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/30
RA	476	.	NC_007779	2672817	0	A	C	bias_e_value=9.28437e-22	bias_p_value=1.99821e-28	fisher_strand_p_value=2.89536e-30	frequency=1.788821e-01	genotype_quality=570.2	ks_quality_p_value=1	log10_base_likelihood=-36.6593	log10_qual_likelihood_position_model=47.0848	log10_strand_likelihood_position_model=29.5383	new_cov=0/61	polymorphism_quality=31.5	quality=31.5	quality_position_model=Inf	ref_cov=150/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=150/106
RA	477	.	NC_007779	2700681	0	T	G	bias_e_value=0.000113537	bias_p_value=2.44358e-11	fisher_strand_p_value=8.48606e-13	frequency=9.906816e-02	genotype_quality=690.9	ks_quality_p_value=1	log10_base_likelihood=-17.0495	log10_qual_likelihood_position_model=30.2376	log10_strand_likelihood_position_model=12.0713	new_cov=35/0	polymorphism_quality=11.7	quality=11.7	quality_position_model=Inf	ref_cov=94/135	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=131/135
RA	478	.	NC_007779	2708932	0	T	C	bias_e_value=0.000360829	bias_p_value=7.7659e-11	fisher_strand_p_value=2.8141e-12	frequency=7.427645e-02	genotype_quality=755.3	ks_quality_p_value=1	log10_base_likelihood=-6.62432	log10_qual_likelihood_position_model=26.1085	log10_strand_likelihood_position_model=11.5507	new_cov=0/33	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=143/99	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=143/132
RA	479	.	NC_007779	2708935	0	A	C	bias_e_value=3.9546e-16	bias_p_value=8.51122e-23	fisher_strand_p_value=1.5242e-24	frequency=1.995468e-01	genotype_quality=582.8	ks_quality_p_value=1	log10_base_likelihood=-49.0111	log10_qual_likelihood_position_model=44.4519	log10_strand_likelihood_position_model=23.817	new_cov=0/63	polymorphism_quality=43.9	quality=43.9	quality_position_model=Inf	ref_cov=144/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=144/137
RA	480	.	NC_007779	2733944	0	G	.	bias_e_value=2680160	bias_p_value=0.576834	fisher_strand_p_value=0.247293	frequency=1.093578e-02	genotype_quality=1131.5	ks_quality_p_value=0.954524	log10_base_likelihood=-7.48055	log10_qual_likelihood_position_model=2.99176	log10_strand_likelihood_position_model=0.898344	new_cov=0/3	polymorphism_quality=2.0	quality=2.0	quality_position_model=2.07466e-05	ref_cov=136/135	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/138
RA	481	.	NC_007779	2743745	0	A	C	bias_e_value=0.0213728	bias_p_value=4.59993e-09	fisher_strand_p_value=1.97018e-10	frequency=5.081463e-02	genotype_quality=765.7	ks_quality_p_value=1	log10_base_likelihood=-6.40179	log10_qual_likelihood_position_model=25.2858	log10_strand_likelihood_position_model=9.70549	new_cov=0/24	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=154/88	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=154/114
RA	482	.	NC_007779	2750349	1	.	A	bias_e_value=3348030	bias_p_value=0.720575	fisher_strand_p_value=0.503554	frequency=7.967949e-03	genotype_quality=1210.5	ks_quality_p_value=0.701018	log10_base_likelihood=-7.60929	log10_qual_likelihood_position_model=2.47955	log10_strand_likelihood_position_model=0.379379	new_cov=1/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.263e-06	ref_cov=73/176	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=74/177
RA	483	.	NC_007779	2756639	0	T	.	bias_e_value=332159	bias_p_value=0.0714885	fisher_strand_p_value=0.343876	frequency=1.383305e-02	genotype_quality=1136.3	ks_quality_p_value=0.0391706	log10_base_likelihood=-11.1985	log10_qual_likelihood_position_model=2.17683	log10_strand_likelihood_position_model=0.660444	new_cov=3/1	polymorphism_quality=5.8	quality=5.8	quality_position_model=2.37199e-10	ref_cov=132/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/153
RA	484	.	NC_007779	2767290	0	A	T	bias_e_value=205775	bias_p_value=0.0442877	fisher_strand_p_value=0.00751866	frequency=4.284477e-02	genotype_quality=937.8	ks_quality_p_value=1	log10_base_likelihood=-10.1537	log10_qual_likelihood_position_model=17.8995	log10_strand_likelihood_position_model=2.42768	new_cov=12/1	polymorphism_quality=4.7	quality=4.7	quality_position_model=Inf	ref_cov=133/118	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=146/119
RA	485	.	NC_007779	2771144	0	G	T	bias_e_value=0.000118615	bias_p_value=2.55288e-11	fisher_strand_p_value=1.084e-12	frequency=8.333302e-02	genotype_quality=933.0	ks_quality_p_value=0.819156	log10_base_likelihood=-20.8039	log10_qual_likelihood_position_model=27.7969	log10_strand_likelihood_position_model=11.965	new_cov=0/33	polymorphism_quality=15.5	quality=15.5	quality_position_model=Inf	ref_cov=165/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=165/144
RA	486	.	NC_007779	2774179	0	A	T	bias_e_value=55481	bias_p_value=0.0119408	fisher_strand_p_value=0.00160628	frequency=3.874588e-02	genotype_quality=930.2	ks_quality_p_value=1	log10_base_likelihood=-8.91766	log10_qual_likelihood_position_model=18.4501	log10_strand_likelihood_position_model=2.91997	new_cov=12/0	polymorphism_quality=3.5	quality=3.5	quality_position_model=Inf	ref_cov=140/110	reject=POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=152/110
RA	487	.	NC_007779	2780301	0	A	C	bias_e_value=9.66058e-14	bias_p_value=2.07918e-20	fisher_strand_p_value=4.13879e-22	frequency=8.047676e-02	genotype_quality=929.3	ks_quality_p_value=1	log10_base_likelihood=-10.8911	log10_qual_likelihood_position_model=39.0308	log10_strand_likelihood_position_model=21.3831	new_cov=0/55	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=195/108	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=195/163
RA	488	.	NC_007779	2781165	0	A	C	bias_e_value=2.78008e-08	bias_p_value=5.98339e-15	fisher_strand_p_value=1.60109e-16	frequency=4.337502e-02	genotype_quality=1081.0	ks_quality_p_value=1	log10_base_likelihood=-8.54946	log10_qual_likelihood_position_model=29.6753	log10_strand_likelihood_position_model=15.7956	new_cov=0/41	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=219/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=219/175
RA	489	.	NC_007779	2791171	0	G	T	bias_e_value=0.000110372	bias_p_value=2.37547e-11	fisher_strand_p_value=8.24116e-13	frequency=5.727196e-02	genotype_quality=1165.7	ks_quality_p_value=1	log10_base_likelihood=-9.11096	log10_qual_likelihood_position_model=27.1343	log10_strand_likelihood_position_model=12.084	new_cov=0/33	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=194/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=194/163
RA	490	.	NC_007779	2791635	0	C	T	bias_e_value=4.86118e-22	bias_p_value=1.04624e-28	fisher_strand_p_value=1.50169e-30	frequency=1.684608e-01	genotype_quality=801.6	ks_quality_p_value=1	log10_base_likelihood=-47.8727	log10_qual_likelihood_position_model=42.3057	log10_strand_likelihood_position_model=29.8234	new_cov=0/52	polymorphism_quality=42.8	quality=42.8	quality_position_model=Inf	ref_cov=185/43	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=185/96
RA	491	.	NC_007779	2791639	0	C	G	bias_e_value=6.10229e-05	bias_p_value=1.31336e-11	fisher_strand_p_value=4.46425e-13	frequency=7.674789e-02	genotype_quality=990.8	ks_quality_p_value=0.999364	log10_base_likelihood=-25.0152	log10_qual_likelihood_position_model=26.6844	log10_strand_likelihood_position_model=12.3503	new_cov=0/24	polymorphism_quality=19.8	quality=19.8	quality_position_model=Inf	ref_cov=191/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=191/96
RA	492	.	NC_007779	2793036	1	.	G	bias_e_value=2178460	bias_p_value=0.468855	fisher_strand_p_value=0.186767	frequency=5.586624e-03	genotype_quality=1756.1	ks_quality_p_value=0.903056	log10_base_likelihood=-7.36609	log10_qual_likelihood_position_model=0.990209	log10_strand_likelihood_position_model=0.728699	new_cov=2/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.47798e-07	ref_cov=153/203	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=155/203
RA	493	.	NC_007779	2797644	0	C	A	bias_e_value=0.000489011	bias_p_value=1.05247e-10	fisher_strand_p_value=3.85789e-12	frequency=5.482483e-02	genotype_quality=1222.5	ks_quality_p_value=1	log10_base_likelihood=-17.5764	log10_qual_likelihood_position_model=20.1513	log10_strand_likelihood_position_model=11.4137	new_cov=0/22	polymorphism_quality=12.3	quality=12.3	quality_position_model=Inf	ref_cov=240/93	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=240/115
RA	494	.	NC_007779	2811282	0	A	.	bias_e_value=1171770	bias_p_value=0.252193	fisher_strand_p_value=0.248055	frequency=9.794235e-03	genotype_quality=1217.2	ks_quality_p_value=0.276223	log10_base_likelihood=-7.6627	log10_qual_likelihood_position_model=2.4029	log10_strand_likelihood_position_model=0.873539	new_cov=3/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=3.03018e-06	ref_cov=154/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/149
RA	495	.	NC_007779	2815241	0	A	.	bias_e_value=2406690	bias_p_value=0.517976	fisher_strand_p_value=0.247512	frequency=1.090050e-02	genotype_quality=1091.2	ks_quality_p_value=0.79826	log10_base_likelihood=-8.02817	log10_qual_likelihood_position_model=1.50981	log10_strand_likelihood_position_model=0.884224	new_cov=0/3	polymorphism_quality=2.5	quality=2.5	quality_position_model=1.52469e-07	ref_cov=135/137	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/140
RA	496	.	NC_007779	2816613	1	.	C	bias_e_value=2100960	bias_p_value=0.452176	fisher_strand_p_value=0.160784	frequency=6.534576e-03	genotype_quality=1239.6	ks_quality_p_value=0.991607	log10_base_likelihood=-6.69363	log10_qual_likelihood_position_model=3.89084	log10_strand_likelihood_position_model=0.793756	new_cov=2/0	polymorphism_quality=1.2	quality=1.2	quality_position_model=0.00102286	ref_cov=121/183	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=123/183
RA	497	.	NC_007779	2816615	0	G	C	bias_e_value=7.32961e-15	bias_p_value=1.5775e-21	fisher_strand_p_value=3.11735e-23	frequency=1.325517e-01	genotype_quality=851.6	ks_quality_p_value=0.957209	log10_base_likelihood=-58.3425	log10_qual_likelihood_position_model=31.2156	log10_strand_likelihood_position_model=22.5062	new_cov=37/0	polymorphism_quality=53.3	quality=53.3	quality_position_model=1.72446e-06	ref_cov=43/186	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=80/186
RA	498	.	NC_007779	2817028	1	.	C	bias_e_value=2362710	bias_p_value=0.508511	fisher_strand_p_value=0.191795	frequency=5.695343e-03	genotype_quality=1358.5	ks_quality_p_value=1	log10_base_likelihood=-6.05528	log10_qual_likelihood_position_model=4.31122	log10_strand_likelihood_position_model=0.717163	new_cov=2/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.0130751	ref_cov=152/197	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=154/197
RA	499	.	NC_007779	2817030	0	G	C	bias_e_value=6.10198e-38	bias_p_value=1.31329e-44	fisher_strand_p_value=1.32989e-46	frequency=2.494960e-01	genotype_quality=804.5	ks_quality_p_value=0.925408	log10_base_likelihood=-143.233	log10_qual_likelihood_position_model=55.2589	log10_strand_likelihood_position_model=45.8762	new_cov=82/0	polymorphism_quality=138.4	quality=138.4	quality_position_model=1.97628e-44	ref_cov=39/199	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=121/199
RA	500	.	NC_007779	2817034	0	T	C	bias_e_value=2.60832	bias_p_value=5.61372e-07	fisher_strand_p_value=3.06765e-08	frequency=2.534008e-02	genotype_quality=807.5	ks_quality_p_value=1	log10_base_likelihood=-5.65461	log10_qual_likelihood_position_model=11.2191	log10_strand_likelihood_position_model=7.51319	new_cov=8/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=22/203	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=30/203
RA	501	.	NC_007779	2833875	0	A	C	bias_e_value=1.05164e-08	bias_p_value=2.26337e-15	fisher_strand_p_value=5.89893e-17	frequency=5.982447e-02	genotype_quality=894.0	ks_quality_p_value=1	log10_base_likelihood=-9.01874	log10_qual_likelihood_position_model=35.7765	log10_strand_likelihood_position_model=16.2292	new_cov=0/40	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=171/91	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/131
RA	502	.	NC_007779	2833904	0	A	C	bias_e_value=1.51143e-10	bias_p_value=3.25296e-17	fisher_strand_p_value=7.61478e-19	frequency=7.022810e-02	genotype_quality=758.2	ks_quality_p_value=1	log10_base_likelihood=-10.7451	log10_qual_likelihood_position_model=34.6355	log10_strand_likelihood_position_model=18.1183	new_cov=0/46	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=163/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/137
RA	503	.	NC_007779	2833989	0	A	C	bias_e_value=1.27061e-10	bias_p_value=2.73465e-17	fisher_strand_p_value=6.37495e-19	frequency=7.160139e-02	genotype_quality=656.9	ks_quality_p_value=1	log10_base_likelihood=-12.2508	log10_qual_likelihood_position_model=26.4963	log10_strand_likelihood_position_model=18.1955	new_cov=0/21	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=173/17	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/38
RA	504	.	NC_007779	2839296	0	A	G	bias_e_value=2.56207e-12	bias_p_value=5.51417e-19	fisher_strand_p_value=1.17599e-20	frequency=1.178746e-01	genotype_quality=725.4	ks_quality_p_value=1	log10_base_likelihood=-27.3618	log10_qual_likelihood_position_model=33.1071	log10_strand_likelihood_position_model=19.9296	new_cov=33/0	polymorphism_quality=22.1	quality=22.1	quality_position_model=Inf	ref_cov=41/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=74/172
RA	505	.	NC_007779	2839396	1	.	G	bias_e_value=1821220	bias_p_value=0.39197	fisher_strand_p_value=0.232801	frequency=6.078720e-03	genotype_quality=1579.7	ks_quality_p_value=0.551577	log10_base_likelihood=-7.36933	log10_qual_likelihood_position_model=1.94316	log10_strand_likelihood_position_model=0.633016	new_cov=2/0	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.13976e-06	ref_cov=157/170	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/170
RA	506	.	NC_007779	2847445	0	G	T	bias_e_value=1.17833	bias_p_value=2.53603e-07	fisher_strand_p_value=1.32504e-08	frequency=4.351807e-02	genotype_quality=1162.7	ks_quality_p_value=1	log10_base_likelihood=-9.93094	log10_qual_likelihood_position_model=20.1498	log10_strand_likelihood_position_model=7.88883	new_cov=1/23	polymorphism_quality=4.5	quality=4.5	quality_position_model=Inf	ref_cov=201/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=202/148
RA	507	.	NC_007779	2866111	0	A	G	frequency=1	genotype_quality=1217.5	new_cov=145/142	quality=1217.5	ref_cov=0/0	tot_cov=145/142
RA	508	.	NC_007779	2892687	0	T	.	bias_e_value=3979350	bias_p_value=0.85645	fisher_strand_p_value=1	frequency=9.956360e-03	genotype_quality=1149.5	ks_quality_p_value=0.514552	log10_base_likelihood=-7.68005	log10_qual_likelihood_position_model=2.69666	log10_strand_likelihood_position_model=0.423078	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.99357e-06	ref_cov=149/149	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/150
RA	509	.	NC_007779	2895131	0	A	C	bias_e_value=2.76342e-08	bias_p_value=5.94754e-15	fisher_strand_p_value=1.59124e-16	frequency=5.815554e-02	genotype_quality=825.3	ks_quality_p_value=1	log10_base_likelihood=-10.7817	log10_qual_likelihood_position_model=33.2404	log10_strand_likelihood_position_model=15.7983	new_cov=0/25	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=192/46	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=192/72
RA	510	.	NC_007779	2895144	0	G	C	bias_e_value=0.000824989	bias_p_value=1.77557e-10	fisher_strand_p_value=6.66013e-12	frequency=6.629705e-02	genotype_quality=813.8	ks_quality_p_value=0.997078	log10_base_likelihood=-12.4149	log10_qual_likelihood_position_model=19.8489	log10_strand_likelihood_position_model=11.1765	new_cov=0/18	polymorphism_quality=7.0	quality=7.0	quality_position_model=Inf	ref_cov=169/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=169/62
RA	511	.	NC_007779	2895155	0	T	.	bias_e_value=4200260	bias_p_value=0.903995	fisher_strand_p_value=0.600341	frequency=8.728981e-03	genotype_quality=1340.6	ks_quality_p_value=0.991343	log10_base_likelihood=-6.88474	log10_qual_likelihood_position_model=4.09153	log10_strand_likelihood_position_model=0.456985	new_cov=1/2	polymorphism_quality=1.4	quality=1.4	quality_position_model=0.000450986	ref_cov=182/158	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=183/160
RA	512	.	NC_007779	2898953	1	.	A	bias_e_value=2496090	bias_p_value=0.537217	fisher_strand_p_value=0.598124	frequency=1.045227e-02	genotype_quality=1381.4	ks_quality_p_value=0.350542	log10_base_likelihood=-12.1053	log10_qual_likelihood_position_model=2.50637	log10_strand_likelihood_position_model=0.460025	new_cov=2/1	polymorphism_quality=6.7	quality=6.7	quality_position_model=3.79295e-11	ref_cov=131/153	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/154
RA	513	.	NC_007779	2898954	0	A	.	bias_e_value=2465210	bias_p_value=0.530572	fisher_strand_p_value=0.596297	frequency=1.029968e-02	genotype_quality=1156.6	ks_quality_p_value=0.344528	log10_base_likelihood=-7.83636	log10_qual_likelihood_position_model=1.55061	log10_strand_likelihood_position_model=0.463211	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=9.72971e-08	ref_cov=132/156	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/157
RA	514	.	NC_007779	2915479	0	C	G	bias_e_value=0.180469	bias_p_value=3.88412e-08	fisher_strand_p_value=1.84075e-09	frequency=5.226469e-02	genotype_quality=774.3	ks_quality_p_value=0.999384	log10_base_likelihood=-12.8276	log10_qual_likelihood_position_model=15.2304	log10_strand_likelihood_position_model=8.735	new_cov=0/13	polymorphism_quality=7.4	quality=7.4	quality_position_model=Inf	ref_cov=162/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=162/50
RA	515	.	NC_007779	2926157	0	T	G	bias_e_value=8.43959e-14	bias_p_value=1.8164e-20	fisher_strand_p_value=3.6058e-22	frequency=6.929970e-02	genotype_quality=686.6	ks_quality_p_value=1	log10_base_likelihood=-12.9956	log10_qual_likelihood_position_model=26.8274	log10_strand_likelihood_position_model=21.443	new_cov=23/0	polymorphism_quality=7.6	quality=7.6	quality_position_model=Inf	ref_cov=14/189	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=37/189
RA	516	.	NC_007779	2939008	0	A	C	bias_e_value=3.23959e-16	bias_p_value=6.97237e-23	fisher_strand_p_value=1.24539e-24	frequency=1.043301e-01	genotype_quality=865.0	ks_quality_p_value=0.998964	log10_base_likelihood=-19.928	log10_qual_likelihood_position_model=37.8811	log10_strand_likelihood_position_model=23.9047	new_cov=0/45	polymorphism_quality=14.6	quality=14.6	quality_position_model=Inf	ref_cov=208/65	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=208/112
RA	517	.	NC_007779	2942976	0	G	T	bias_e_value=322.25	bias_p_value=6.93558e-05	fisher_strand_p_value=5.27304e-06	frequency=3.298283e-02	genotype_quality=1181.6	ks_quality_p_value=1	log10_base_likelihood=-9.18454	log10_qual_likelihood_position_model=14.12	log10_strand_likelihood_position_model=5.43242	new_cov=0/18	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=174/164	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=174/182
RA	518	.	NC_007779	2953753	0	C	.	bias_e_value=1616350	bias_p_value=0.347876	fisher_strand_p_value=0.612529	frequency=1.126385e-02	genotype_quality=1060.0	ks_quality_p_value=0.175958	log10_base_likelihood=-7.63489	log10_qual_likelihood_position_model=4.24854	log10_strand_likelihood_position_model=0.43809	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=9.94413e-05	ref_cov=127/136	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=129/137
RA	519	.	NC_007779	2974959	1	.	A	bias_e_value=715126	bias_p_value=0.153912	fisher_strand_p_value=0.243273	frequency=7.721901e-03	genotype_quality=1255.2	ks_quality_p_value=0.14581	log10_base_likelihood=-8.03472	log10_qual_likelihood_position_model=1.93171	log10_strand_likelihood_position_model=0.613906	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.15529e-07	ref_cov=126/131	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/131
RA	520	.	NC_007779	2983097	0	A	C	bias_e_value=4.29381e-14	bias_p_value=9.24128e-21	fisher_strand_p_value=1.80976e-22	frequency=1.424136e-01	genotype_quality=487.1	ks_quality_p_value=1	log10_base_likelihood=-16.06	log10_qual_likelihood_position_model=39.6885	log10_strand_likelihood_position_model=21.7424	new_cov=0/41	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=120/31	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=120/73
RA	521	.	NC_007779	2987535	0	A	C	bias_e_value=1.57106e-43	bias_p_value=3.38129e-50	fisher_strand_p_value=2.8249e-52	frequency=3.709598e-01	genotype_quality=354.7	ks_quality_p_value=1	log10_base_likelihood=-106.393	log10_qual_likelihood_position_model=67.1073	log10_strand_likelihood_position_model=51.549	new_cov=0/106	polymorphism_quality=101.5	quality=101.5	quality_position_model=Inf	ref_cov=134/21	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/127
RA	522	.	NC_007779	2988137	0	A	.	bias_e_value=3862380	bias_p_value=0.831275	fisher_strand_p_value=0.560929	frequency=1.594734e-02	genotype_quality=743.8	ks_quality_p_value=0.853226	log10_base_likelihood=-8.31638	log10_qual_likelihood_position_model=2.18458	log10_strand_likelihood_position_model=0.557038	new_cov=1/2	polymorphism_quality=2.8	quality=2.8	quality_position_model=1.75672e-07	ref_cov=114/71	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=115/73
RA	523	.	NC_007779	2994663	1	.	T	bias_e_value=4239800	bias_p_value=0.912504	fisher_strand_p_value=1	frequency=7.272720e-03	genotype_quality=1349.1	ks_quality_p_value=0.611996	log10_base_likelihood=-8.16548	log10_qual_likelihood_position_model=1.85342	log10_strand_likelihood_position_model=0.300419	new_cov=1/1	polymorphism_quality=2.7	quality=2.7	quality_position_model=6.20141e-08	ref_cov=143/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=144/131
RA	524	.	NC_007779	2999826	0	A	C	bias_e_value=6.05069e-06	bias_p_value=1.30225e-12	fisher_strand_p_value=4.09162e-14	frequency=7.935476e-02	genotype_quality=471.1	ks_quality_p_value=1	log10_base_likelihood=-7.43583	log10_qual_likelihood_position_model=24.7777	log10_strand_likelihood_position_model=13.3881	new_cov=0/25	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=115/35	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/60
RA	525	.	NC_007779	3003330	0	G	A	frequency=1	genotype_quality=1036.5	new_cov=143/117	quality=1036.5	ref_cov=0/0	tot_cov=143/117
RA	526	.	NC_007779	3029385	0	C	A	bias_e_value=0.0020959	bias_p_value=4.51086e-10	fisher_strand_p_value=1.80822e-11	frequency=4.532814e-02	genotype_quality=922.8	ks_quality_p_value=0.968096	log10_base_likelihood=-21.5138	log10_qual_likelihood_position_model=12.784	log10_strand_likelihood_position_model=10.7427	new_cov=0/11	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=210/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=210/30
RA	527	.	NC_007779	3034413	0	A	C	bias_e_value=2.26637e-24	bias_p_value=4.87777e-31	fisher_strand_p_value=6.49378e-33	frequency=1.668959e-01	genotype_quality=548.7	ks_quality_p_value=1	log10_base_likelihood=-33.6367	log10_qual_likelihood_position_model=44.1211	log10_strand_likelihood_position_model=32.1875	new_cov=0/51	polymorphism_quality=28.5	quality=28.5	quality_position_model=Inf	ref_cov=158/25	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/76
RA	528	.	NC_007779	3035390	0	T	C	bias_e_value=2.17992e-22	bias_p_value=4.69171e-29	fisher_strand_p_value=7.62474e-31	frequency=2.446342e-01	genotype_quality=319.6	ks_quality_p_value=0.872995	log10_base_likelihood=-88.6172	log10_qual_likelihood_position_model=22.7249	log10_strand_likelihood_position_model=30.1178	new_cov=0/43	polymorphism_quality=83.7	quality=83.7	quality_position_model=4.51017e-38	ref_cov=120/11	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/54
RA	529	.	NC_007779	3044712	0	T	C	bias_e_value=11.1345	bias_p_value=2.39641e-06	fisher_strand_p_value=1.43487e-07	frequency=3.439903e-02	genotype_quality=621.4	ks_quality_p_value=0.996459	log10_base_likelihood=-6.93289	log10_qual_likelihood_position_model=10.5002	log10_strand_likelihood_position_model=6.84319	new_cov=7/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=16/169	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=23/170
RA	530	.	NC_007779	3044714	0	A	C	bias_e_value=4610.65	bias_p_value=0.00099232	fisher_strand_p_value=9.68877e-05	frequency=3.265476e-02	genotype_quality=569.3	ks_quality_p_value=1	log10_base_likelihood=-5.95377	log10_qual_likelihood_position_model=12.7329	log10_strand_likelihood_position_model=4.03993	new_cov=7/4	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=20/166	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=27/173
RA	531	.	NC_007779	3048743	0	C	T	bias_e_value=2936560	bias_p_value=0.632016	fisher_strand_p_value=0.277149	frequency=2.111340e-02	genotype_quality=1283.2	ks_quality_p_value=0.997835	log10_base_likelihood=-10.3824	log10_qual_likelihood_position_model=7.17235	log10_strand_likelihood_position_model=0.807187	new_cov=2/5	polymorphism_quality=5.0	quality=5.0	quality_position_model=0.000382104	ref_cov=163/155	tot_cov=165/160
RA	532	.	NC_007779	3049815	0	G	T	frequency=1	genotype_quality=1178.9	new_cov=148/151	quality=1178.9	ref_cov=0/0	tot_cov=148/151
RA	533	.	NC_007779	3059421	0	T	.	bias_e_value=4494790	bias_p_value=0.967384	fisher_strand_p_value=1	frequency=8.711815e-03	genotype_quality=1346.3	ks_quality_p_value=0.755714	log10_base_likelihood=-7.6304	log10_qual_likelihood_position_model=1.62185	log10_strand_likelihood_position_model=0.412555	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.66993e-07	ref_cov=175/166	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=177/167
RA	534	.	NC_007779	3074129	0	G	T	bias_e_value=32.8842	bias_p_value=7.07746e-06	fisher_strand_p_value=4.53501e-07	frequency=4.616737e-02	genotype_quality=949.3	ks_quality_p_value=1	log10_base_likelihood=-6.92944	log10_qual_likelihood_position_model=16.1965	log10_strand_likelihood_position_model=6.65035	new_cov=0/25	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=135/147	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=135/175
RA	535	.	NC_007779	3082392	0	C	G	bias_e_value=67.4849	bias_p_value=1.45243e-05	fisher_strand_p_value=9.78941e-07	frequency=6.321096e-02	genotype_quality=817.9	ks_quality_p_value=1	log10_base_likelihood=-8.40781	log10_qual_likelihood_position_model=21.6432	log10_strand_likelihood_position_model=6.05704	new_cov=24/1	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=112/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=136/123
RA	536	.	NC_007779	3084663	0	C	A	bias_e_value=20.5105	bias_p_value=4.41434e-06	fisher_strand_p_value=2.7401e-07	frequency=3.387070e-02	genotype_quality=1140.5	ks_quality_p_value=1	log10_base_likelihood=-5.67888	log10_qual_likelihood_position_model=16.7458	log10_strand_likelihood_position_model=6.57849	new_cov=23/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=162/162	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=185/163
RA	537	.	NC_007779	3089270	0	C	A	bias_e_value=0.198433	bias_p_value=4.27075e-08	fisher_strand_p_value=2.03233e-09	frequency=4.912996e-02	genotype_quality=1037.1	ks_quality_p_value=1	log10_base_likelihood=-8.38565	log10_qual_likelihood_position_model=19.3887	log10_strand_likelihood_position_model=8.69201	new_cov=24/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=116/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/167
RA	538	.	NC_007779	3091181	0	C	G	bias_e_value=1283490	bias_p_value=0.276236	fisher_strand_p_value=0.148585	frequency=3.011894e-02	genotype_quality=415.7	ks_quality_p_value=0.522986	log10_base_likelihood=-5.76391	log10_qual_likelihood_position_model=5.30402	log10_strand_likelihood_position_model=0.905352	new_cov=0/4	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=53/75	reject=EVALUE,POLYMORPHISM_STRAND,SURROUNDING_HOMOPOLYMER	tot_cov=53/79
RA	539	.	NC_007779	3099689	0	C	.	bias_e_value=4083080	bias_p_value=0.878774	fisher_strand_p_value=1	frequency=9.028435e-03	genotype_quality=1360.1	ks_quality_p_value=0.549939	log10_base_likelihood=-7.89178	log10_qual_likelihood_position_model=1.92943	log10_strand_likelihood_position_model=0.370485	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=1.6865e-07	ref_cov=191/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=193/139
RA	540	.	NC_007779	3110532	0	C	A	bias_e_value=0.337118	bias_p_value=7.25558e-08	fisher_strand_p_value=3.72263e-09	frequency=5.288887e-02	genotype_quality=721.7	ks_quality_p_value=0.952743	log10_base_likelihood=-22.6457	log10_qual_likelihood_position_model=11.8122	log10_strand_likelihood_position_model=8.42915	new_cov=0/10	polymorphism_quality=17.4	quality=17.4	quality_position_model=0.000380691	ref_cov=157/21	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/31
RA	541	.	NC_007779	3124046	0	C	A	bias_e_value=6.47745	bias_p_value=1.3941e-06	fisher_strand_p_value=8.04544e-08	frequency=3.742123e-02	genotype_quality=1000.5	ks_quality_p_value=0.999525	log10_base_likelihood=-6.0468	log10_qual_likelihood_position_model=16.9581	log10_strand_likelihood_position_model=7.09445	new_cov=21/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=126/161	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/161
RA	542	.	NC_007779	3124070	0	G	.	bias_e_value=4151350	bias_p_value=0.893469	fisher_strand_p_value=0.607793	frequency=1.015091e-02	genotype_quality=1192.1	ks_quality_p_value=0.946856	log10_base_likelihood=-7.01921	log10_qual_likelihood_position_model=3.57767	log10_strand_likelihood_position_model=0.445048	new_cov=2/1	polymorphism_quality=1.5	quality=1.5	quality_position_model=8.83465e-05	ref_cov=139/153	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=141/154
RA	543	.	NC_007779	3124071	0	C	.	bias_e_value=4132110	bias_p_value=0.889326	fisher_strand_p_value=0.605357	frequency=1.022339e-02	genotype_quality=1181.3	ks_quality_p_value=0.938425	log10_base_likelihood=-7.19546	log10_qual_likelihood_position_model=4.12384	log10_strand_likelihood_position_model=0.448608	new_cov=2/1	polymorphism_quality=1.7	quality=1.7	quality_position_model=0.000221465	ref_cov=137/153	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=139/154
RA	544	.	NC_007779	3136120	0	G	T	deleted=1	frequency=1	genotype_quality=1.2	new_cov=1/0	quality=1.2	ref_cov=0/0	reject=EVALUE	tot_cov=1/0
RA	545	.	NC_007779	3149201	0	A	.	bias_e_value=1447330	bias_p_value=0.311499	fisher_strand_p_value=1	frequency=9.221077e-03	genotype_quality=1280.1	ks_quality_p_value=0.091996	log10_base_likelihood=-7.59372	log10_qual_likelihood_position_model=2.9389	log10_strand_likelihood_position_model=0.383196	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=3.99379e-06	ref_cov=179/143	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=181/144
RA	546	.	NC_007779	3152854	1	.	A	bias_e_value=2151410	bias_p_value=0.463034	fisher_strand_p_value=0.181397	frequency=1.700687e-02	genotype_quality=1395.5	ks_quality_p_value=0.911857	log10_base_likelihood=-21.8173	log10_qual_likelihood_position_model=4.14656	log10_strand_likelihood_position_model=0.934997	new_cov=4/1	polymorphism_quality=16.6	quality=16.6	quality_position_model=7.16268e-19	ref_cov=130/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/160
RA	547	.	NC_007779	3152855	0	A	.	bias_e_value=881204	bias_p_value=0.189656	fisher_strand_p_value=0.663646	frequency=1.659966e-02	genotype_quality=1165.5	ks_quality_p_value=0.0703032	log10_base_likelihood=-13.6656	log10_qual_likelihood_position_model=4.03921	log10_strand_likelihood_position_model=0.54649	new_cov=3/2	polymorphism_quality=8.3	quality=8.3	quality_position_model=4.35849e-11	ref_cov=135/161	reject=INDEL_HOMOPOLYMER	tot_cov=138/163
RA	548	.	NC_007779	3160153	0	G	C	bias_e_value=1.31222e-07	bias_p_value=2.8242e-14	fisher_strand_p_value=7.90257e-16	frequency=8.422089e-02	genotype_quality=651.6	ks_quality_p_value=0.998953	log10_base_likelihood=-26.1432	log10_qual_likelihood_position_model=15.5595	log10_strand_likelihood_position_model=15.1022	new_cov=16/0	polymorphism_quality=20.9	quality=20.9	quality_position_model=Inf	ref_cov=12/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=28/155
RA	549	.	NC_007779	3162929	0	G	C	bias_e_value=0.0212476	bias_p_value=4.57297e-09	fisher_strand_p_value=2.19688e-10	frequency=8.838415e-02	genotype_quality=733.7	ks_quality_p_value=0.891319	log10_base_likelihood=-21.5972	log10_qual_likelihood_position_model=24.7466	log10_strand_likelihood_position_model=9.65819	new_cov=24/0	polymorphism_quality=16.3	quality=16.3	quality_position_model=Inf	ref_cov=77/136	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=101/136
RA	550	.	NC_007779	3188902	1	.	A	bias_e_value=2259660	bias_p_value=0.486332	fisher_strand_p_value=1	frequency=9.933472e-03	genotype_quality=1460.6	ks_quality_p_value=0.178643	log10_base_likelihood=-12.4256	log10_qual_likelihood_position_model=2.83472	log10_strand_likelihood_position_model=0.421662	new_cov=1/2	polymorphism_quality=7.0	quality=7.0	quality_position_model=3.53168e-11	ref_cov=149/150	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/152
RA	551	.	NC_007779	3195467	0	A	C	bias_e_value=2.40192e-09	bias_p_value=5.16949e-16	fisher_strand_p_value=1.29611e-17	frequency=8.637333e-02	genotype_quality=836.1	ks_quality_p_value=1	log10_base_likelihood=-17.3955	log10_qual_likelihood_position_model=35.2803	log10_strand_likelihood_position_model=16.8874	new_cov=0/34	polymorphism_quality=12.1	quality=12.1	quality_position_model=Inf	ref_cov=192/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=192/108
RA	552	.	NC_007779	3212355	0	G	C	bias_e_value=4.71802e-12	bias_p_value=1.01543e-18	fisher_strand_p_value=2.421e-20	frequency=1.416583e-01	genotype_quality=754.4	ks_quality_p_value=0.90656	log10_base_likelihood=-39.4915	log10_qual_likelihood_position_model=34.2716	log10_strand_likelihood_position_model=19.616	new_cov=37/0	polymorphism_quality=34.4	quality=34.4	quality_position_model=Inf	ref_cov=47/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=84/156
RA	553	.	NC_007779	3220025	0	C	A	bias_e_value=0.0789435	bias_p_value=1.69905e-08	fisher_strand_p_value=7.73226e-10	frequency=3.633976e-02	genotype_quality=1380.0	ks_quality_p_value=0.99967	log10_base_likelihood=-8.57801	log10_qual_likelihood_position_model=25.3151	log10_strand_likelihood_position_model=9.11169	new_cov=26/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=164/220	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=190/220
RA	554	.	NC_007779	3220087	0	G	.	bias_e_value=3884460	bias_p_value=0.836028	fisher_strand_p_value=0.580106	frequency=7.907867e-03	genotype_quality=1613.8	ks_quality_p_value=0.836243	log10_base_likelihood=-7.69739	log10_qual_likelihood_position_model=1.64638	log10_strand_likelihood_position_model=0.497759	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.84927e-07	ref_cov=161/214	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=163/216
RA	555	.	NC_007779	3231302	0	C	G	bias_e_value=8.59911e-07	bias_p_value=1.85073e-13	fisher_strand_p_value=5.49297e-15	frequency=1.008053e-01	genotype_quality=755.3	ks_quality_p_value=0.995657	log10_base_likelihood=-23.4593	log10_qual_likelihood_position_model=26.249	log10_strand_likelihood_position_model=14.2602	new_cov=0/26	polymorphism_quality=18.2	quality=18.2	quality_position_model=Inf	ref_cov=157/49	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=157/76
RA	556	.	NC_007779	3231832	1	.	G	bias_e_value=414521	bias_p_value=0.0892147	fisher_strand_p_value=0.0212324	frequency=1.149368e-02	genotype_quality=1269.6	ks_quality_p_value=0.834909	log10_base_likelihood=-12.1452	log10_qual_likelihood_position_model=1.76163	log10_strand_likelihood_position_model=1.673	new_cov=3/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=1.04059e-10	ref_cov=70/188	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=73/188
RA	557	.	NC_007779	3238315	1	.	T	bias_e_value=1806690	bias_p_value=0.388842	fisher_strand_p_value=0.158266	frequency=2.285671e-02	genotype_quality=764.1	ks_quality_p_value=0.801741	log10_base_likelihood=-17.2238	log10_qual_likelihood_position_model=4.09752	log10_strand_likelihood_position_model=0.86425	new_cov=4/0	polymorphism_quality=11.9	quality=11.9	quality_position_model=2.47977e-14	ref_cov=103/68	reject=POLYMORPHISM_STRAND	tot_cov=107/68
RA	558	.	NC_007779	3238322	0	T	C	bias_e_value=2189.2	bias_p_value=0.000471168	fisher_strand_p_value=4.25858e-05	frequency=8.648157e-02	genotype_quality=423.9	ks_quality_p_value=1	log10_base_likelihood=-16.9631	log10_qual_likelihood_position_model=15.1208	log10_strand_likelihood_position_model=4.38846	new_cov=14/1	polymorphism_quality=11.6	quality=11.6	quality_position_model=Inf	ref_cov=55/87	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=69/88
RA	559	.	NC_007779	3238324	0	A	C	bias_e_value=955.018	bias_p_value=0.000205542	fisher_strand_p_value=1.71679e-05	frequency=9.068203e-02	genotype_quality=436.6	ks_quality_p_value=1	log10_base_likelihood=-14.9866	log10_qual_likelihood_position_model=17.0234	log10_strand_likelihood_position_model=4.84349	new_cov=18/2	polymorphism_quality=9.6	quality=9.6	quality_position_model=Inf	ref_cov=58/89	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=76/91
RA	560	.	NC_007779	3243783	1	.	T	bias_e_value=3717240	bias_p_value=0.800039	fisher_strand_p_value=1	frequency=6.557465e-03	genotype_quality=1436.7	ks_quality_p_value=0.43855	log10_base_likelihood=-7.72477	log10_qual_likelihood_position_model=2.00718	log10_strand_likelihood_position_model=0.30208	new_cov=1/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=2.56939e-07	ref_cov=140/163	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=141/164
RA	561	.	NC_007779	3259711	0	A	C	bias_e_value=1.57562e-17	bias_p_value=3.39111e-24	fisher_strand_p_value=5.73593e-26	frequency=1.265097e-01	genotype_quality=617.3	ks_quality_p_value=1	log10_base_likelihood=-20.0835	log10_qual_likelihood_position_model=38.8602	log10_strand_likelihood_position_model=25.2414	new_cov=0/48	polymorphism_quality=14.8	quality=14.8	quality_position_model=Inf	ref_cov=157/44	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=157/93
RA	562	.	NC_007779	3266843	0	C	G	bias_e_value=0.000600622	bias_p_value=1.29268e-10	fisher_strand_p_value=4.77908e-12	frequency=6.325150e-02	genotype_quality=829.4	ks_quality_p_value=0.999307	log10_base_likelihood=-15.4765	log10_qual_likelihood_position_model=16.9469	log10_strand_likelihood_position_model=11.3207	new_cov=0/16	polymorphism_quality=10.1	quality=10.1	quality_position_model=Inf	ref_cov=173/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/50
RA	563	.	NC_007779	3269805	0	C	A	bias_e_value=34561.8	bias_p_value=0.00743851	fisher_strand_p_value=0.000932409	frequency=2.043247e-02	genotype_quality=1309.2	ks_quality_p_value=1	log10_base_likelihood=-6.7281	log10_qual_likelihood_position_model=12.983	log10_strand_likelihood_position_model=3.16362	new_cov=0/11	polymorphism_quality=1.2	quality=1.2	quality_position_model=Inf	ref_cov=169/174	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=169/185
RA	564	.	NC_007779	3269811	0	T	A	bias_e_value=69114.8	bias_p_value=0.0148751	fisher_strand_p_value=0.00207196	frequency=3.027439e-02	genotype_quality=1189.5	ks_quality_p_value=1	log10_base_likelihood=-9.31685	log10_qual_likelihood_position_model=14.1788	log10_strand_likelihood_position_model=2.7847	new_cov=1/13	polymorphism_quality=3.9	quality=3.9	quality_position_model=Inf	ref_cov=172/186	reject=POLYMORPHISM_STRAND	tot_cov=175/199
RA	565	.	NC_007779	3280326	0	A	C	bias_e_value=4.14246e-30	bias_p_value=8.91556e-37	fisher_strand_p_value=1.00751e-38	frequency=1.792483e-01	genotype_quality=610.8	ks_quality_p_value=1	log10_base_likelihood=-36.0267	log10_qual_likelihood_position_model=49.3408	log10_strand_likelihood_position_model=37.9967	new_cov=0/67	polymorphism_quality=30.9	quality=30.9	quality_position_model=Inf	ref_cov=173/34	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=173/101
RA	566	.	NC_007779	3284776	0	T	G	bias_e_value=8748.39	bias_p_value=0.00188286	fisher_strand_p_value=0.000242601	frequency=2.711773e-02	genotype_quality=624.1	ks_quality_p_value=0.814446	log10_base_likelihood=-10.5265	log10_qual_likelihood_position_model=6.12074	log10_strand_likelihood_position_model=3.62182	new_cov=4/1	polymorphism_quality=5.1	quality=5.1	quality_position_model=0.0256847	ref_cov=13/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=17/167
RA	567	.	NC_007779	3287872	1	.	G	bias_e_value=482660	bias_p_value=0.10388	fisher_strand_p_value=0.501648	frequency=7.220268e-03	genotype_quality=1350.3	ks_quality_p_value=0.0427685	log10_base_likelihood=-8.35776	log10_qual_likelihood_position_model=1.88688	log10_strand_likelihood_position_model=0.534111	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=7.4116e-08	ref_cov=148/127	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/127
RA	568	.	NC_007779	3288865	1	.	A	bias_e_value=1000280	bias_p_value=0.215284	fisher_strand_p_value=1	frequency=5.509377e-03	genotype_quality=1775.2	ks_quality_p_value=0.0552625	log10_base_likelihood=-7.77905	log10_qual_likelihood_position_model=1.64586	log10_strand_likelihood_position_model=0.305969	new_cov=1/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=9.62169e-08	ref_cov=159/202	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=160/203
RA	569	.	NC_007779	3295552	0	A	G	bias_e_value=0.550423	bias_p_value=1.18464e-07	fisher_strand_p_value=5.94059e-09	frequency=5.477190e-02	genotype_quality=742.1	ks_quality_p_value=1	log10_base_likelihood=-6.38428	log10_qual_likelihood_position_model=18.7546	log10_strand_likelihood_position_model=8.22617	new_cov=16/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=57/148	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=73/148
RA	570	.	NC_007779	3297572	0	A	C	bias_e_value=0.121884	bias_p_value=2.62322e-08	fisher_strand_p_value=1.21866e-09	frequency=4.723215e-02	genotype_quality=773.2	ks_quality_p_value=1	log10_base_likelihood=-8.30612	log10_qual_likelihood_position_model=19.2837	log10_strand_likelihood_position_model=8.91412	new_cov=0/22	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=153/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=153/110
RA	571	.	NC_007779	3300073	0	T	G	bias_e_value=8.36551e-16	bias_p_value=1.80046e-22	fisher_strand_p_value=3.26894e-24	frequency=1.650863e-01	genotype_quality=492.4	ks_quality_p_value=1	log10_base_likelihood=-18.9105	log10_qual_likelihood_position_model=44.1464	log10_strand_likelihood_position_model=23.4856	new_cov=54/0	polymorphism_quality=13.6	quality=13.6	quality_position_model=Inf	ref_cov=44/119	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=101/119
RA	572	.	NC_007779	3310088	0	G	C	bias_e_value=0.000305591	bias_p_value=6.57704e-11	fisher_strand_p_value=2.3685e-12	frequency=4.898548e-02	genotype_quality=782.2	ks_quality_p_value=1	log10_base_likelihood=-7.88997	log10_qual_likelihood_position_model=17.2636	log10_strand_likelihood_position_model=11.6255	new_cov=0/12	polymorphism_quality=2.4	quality=2.4	quality_position_model=Inf	ref_cov=176/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=176/27
RA	573	.	NC_007779	3333612	0	T	G	bias_e_value=0.00505137	bias_p_value=1.08717e-09	fisher_strand_p_value=4.37448e-11	frequency=4.217815e-02	genotype_quality=635.0	ks_quality_p_value=1	log10_base_likelihood=-11.0308	log10_qual_likelihood_position_model=14.7895	log10_strand_likelihood_position_model=10.3591	new_cov=10/0	polymorphism_quality=5.6	quality=5.6	quality_position_model=Inf	ref_cov=12/170	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=22/170
RA	574	.	NC_007779	3338300	0	T	.	bias_e_value=3614910	bias_p_value=0.778014	fisher_strand_p_value=1	frequency=9.109497e-03	genotype_quality=1275.4	ks_quality_p_value=0.412769	log10_base_likelihood=-7.70549	log10_qual_likelihood_position_model=2.39975	log10_strand_likelihood_position_model=0.369202	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=8.08161e-07	ref_cov=189/135	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=192/137
RA	575	.	NC_007779	3350708	0	A	C	bias_e_value=1.87456e-16	bias_p_value=4.0345e-23	fisher_strand_p_value=7.12802e-25	frequency=1.084146e-01	genotype_quality=808.8	ks_quality_p_value=1	log10_base_likelihood=-28.0206	log10_qual_likelihood_position_model=43.6077	log10_strand_likelihood_position_model=24.147	new_cov=0/58	polymorphism_quality=22.8	quality=22.8	quality_position_model=Inf	ref_cov=183/86	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=183/144
RA	576	.	NC_007779	3372446	0	T	G	bias_e_value=2201230	bias_p_value=0.473757	fisher_strand_p_value=0.171428	frequency=2.367115e-02	genotype_quality=1002.7	ks_quality_p_value=1	log10_base_likelihood=-5.73885	log10_qual_likelihood_position_model=14.8807	log10_strand_likelihood_position_model=1.16012	new_cov=10/4	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=143/141	reject=EVALUE,SURROUNDING_HOMOPOLYMER	tot_cov=153/145
RA	577	.	NC_007779	3377617	0	A	C	bias_e_value=0.236216	bias_p_value=5.08391e-08	fisher_strand_p_value=2.44055e-09	frequency=4.595852e-02	genotype_quality=952.1	ks_quality_p_value=1	log10_base_likelihood=-10.8027	log10_qual_likelihood_position_model=27.4375	log10_strand_likelihood_position_model=8.63844	new_cov=0/31	polymorphism_quality=5.4	quality=5.4	quality_position_model=Inf	ref_cov=149/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/183
RA	578	.	NC_007779	3385700	1	.	T	bias_e_value=1428280	bias_p_value=0.3074	fisher_strand_p_value=0.201365	frequency=6.711006e-03	genotype_quality=1427.5	ks_quality_p_value=0.448364	log10_base_likelihood=-8.05964	log10_qual_likelihood_position_model=1.61575	log10_strand_likelihood_position_model=0.696016	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.16248e-07	ref_cov=132/164	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=134/164
RA	579	.	NC_007779	3387541	0	G	A	bias_e_value=0.660177	bias_p_value=1.42086e-07	fisher_strand_p_value=7.19421e-09	frequency=4.373837e-02	genotype_quality=1057.2	ks_quality_p_value=1	log10_base_likelihood=-7.45004	log10_qual_likelihood_position_model=18.0328	log10_strand_likelihood_position_model=8.14302	new_cov=0/18	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=195/97	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=195/115
RA	580	.	NC_007779	3389914	0	A	C	bias_e_value=1.21446e-13	bias_p_value=2.6138e-20	fisher_strand_p_value=5.22728e-22	frequency=1.028628e-01	genotype_quality=687.0	ks_quality_p_value=1	log10_base_likelihood=-15.2214	log10_qual_likelihood_position_model=36.883	log10_strand_likelihood_position_model=21.2817	new_cov=0/54	polymorphism_quality=9.9	quality=9.9	quality_position_model=Inf	ref_cov=149/75	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/129
RA	581	.	NC_007779	3392267	0	C	A	bias_e_value=1.8628e-09	bias_p_value=4.00919e-16	fisher_strand_p_value=9.98671e-18	frequency=7.682705e-02	genotype_quality=1169.4	ks_quality_p_value=1	log10_base_likelihood=-19.5768	log10_qual_likelihood_position_model=24.9841	log10_strand_likelihood_position_model=17.0006	new_cov=37/0	polymorphism_quality=14.3	quality=14.3	quality_position_model=Inf	ref_cov=96/215	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/215
RA	582	.	NC_007779	3397405	0	A	C	bias_e_value=8.94861e-32	bias_p_value=1.92595e-38	fisher_strand_p_value=2.08507e-40	frequency=2.224503e-01	genotype_quality=557.4	ks_quality_p_value=1	log10_base_likelihood=-46.6622	log10_qual_likelihood_position_model=58.3232	log10_strand_likelihood_position_model=39.6809	new_cov=0/80	polymorphism_quality=41.6	quality=41.6	quality_position_model=Inf	ref_cov=155/37	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=155/118
RA	583	.	NC_007779	3397813	0	C	G	frequency=1	genotype_quality=1262.1	new_cov=136/160	quality=1262.1	ref_cov=0/0	tot_cov=136/160
RA	584	.	NC_007779	3404070	0	T	G	bias_e_value=1.56958e-12	bias_p_value=3.3781e-19	fisher_strand_p_value=7.12826e-21	frequency=1.628857e-01	genotype_quality=526.8	ks_quality_p_value=1	log10_base_likelihood=-31.1231	log10_qual_likelihood_position_model=38.6895	log10_strand_likelihood_position_model=20.147	new_cov=49/0	polymorphism_quality=25.9	quality=25.9	quality_position_model=Inf	ref_cov=56/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=106/125
RA	585	.	NC_007779	3407746	0	C	A	bias_e_value=2992	bias_p_value=0.000643948	fisher_strand_p_value=6.00698e-05	frequency=2.544308e-02	genotype_quality=1155.9	ks_quality_p_value=1	log10_base_likelihood=-6.07583	log10_qual_likelihood_position_model=14.0266	log10_strand_likelihood_position_model=4.22134	new_cov=12/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=Inf	ref_cov=137/179	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/179
RA	586	.	NC_007779	3407926	0	T	G	bias_e_value=6.05054e-05	bias_p_value=1.30222e-11	fisher_strand_p_value=4.42225e-13	frequency=5.773354e-02	genotype_quality=873.2	ks_quality_p_value=1	log10_base_likelihood=-8.80902	log10_qual_likelihood_position_model=30.1069	log10_strand_likelihood_position_model=12.3544	new_cov=36/0	polymorphism_quality=3.3	quality=3.3	quality_position_model=Inf	ref_cov=115/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/160
RA	587	.	NC_007779	3421203	0	T	C	bias_e_value=1.0028e-10	bias_p_value=2.15826e-17	fisher_strand_p_value=5.00303e-19	frequency=9.916973e-02	genotype_quality=732.4	ks_quality_p_value=1	log10_base_likelihood=-21.5005	log10_qual_likelihood_position_model=30.2118	log10_strand_likelihood_position_model=18.3008	new_cov=0/27	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=170/32	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=170/59
RA	588	.	NC_007779	3421217	0	C	G	bias_e_value=0.000185614	bias_p_value=3.99485e-11	fisher_strand_p_value=1.64634e-12	frequency=7.352686e-02	genotype_quality=846.6	ks_quality_p_value=0.857851	log10_base_likelihood=-13.7728	log10_qual_likelihood_position_model=28.8706	log10_strand_likelihood_position_model=11.7835	new_cov=0/24	polymorphism_quality=8.4	quality=8.4	quality_position_model=Inf	ref_cov=168/68	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=168/92
RA	589	.	NC_007779	3423128	1	.	G	bias_e_value=1683160	bias_p_value=0.362255	fisher_strand_p_value=0.211489	frequency=7.812500e-03	genotype_quality=901.4	ks_quality_p_value=0.540556	log10_base_likelihood=-8.04637	log10_qual_likelihood_position_model=1.34525	log10_strand_likelihood_position_model=0.674712	new_cov=2/0	polymorphism_quality=2.6	quality=2.6	quality_position_model=5.98724e-08	ref_cov=116/138	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=118/138
RA	590	.	NC_007779	3426978	0	A	T	bias_e_value=2406940	bias_p_value=0.518031	fisher_strand_p_value=0.247071	frequency=1.398659e-02	genotype_quality=736.9	ks_quality_p_value=0.79982	log10_base_likelihood=-6.62595	log10_qual_likelihood_position_model=2.19838	log10_strand_likelihood_position_model=0.872886	new_cov=3/0	polymorphism_quality=1.1	quality=1.1	quality_position_model=2.26296e-05	ref_cov=107/104	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=110/104
RA	591	.	NC_007779	3428694	0	A	T	bias_e_value=2515280	bias_p_value=0.541348	fisher_strand_p_value=0.247801	frequency=8.849144e-03	genotype_quality=1329.0	ks_quality_p_value=0.856829	log10_base_likelihood=-6.34213	log10_qual_likelihood_position_model=1.79714	log10_strand_likelihood_position_model=0.899241	new_cov=0/3	polymorphism_quality=0.8	quality=0.8	quality_position_model=1.81401e-05	ref_cov=168/167	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=168/170
RA	592	.	NC_007779	3441442	0	C	A	bias_e_value=19.3603	bias_p_value=4.16679e-06	fisher_strand_p_value=2.57661e-07	frequency=4.634714e-02	genotype_quality=1046.8	ks_quality_p_value=1	log10_base_likelihood=-9.13169	log10_qual_likelihood_position_model=22.0833	log10_strand_likelihood_position_model=6.88729	new_cov=24/0	polymorphism_quality=3.7	quality=3.7	quality_position_model=Inf	ref_cov=149/151	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/151
RA	593	.	NC_007779	3447052	0	T	C	bias_e_value=2.12776	bias_p_value=4.57944e-07	fisher_strand_p_value=2.47335e-08	frequency=4.860020e-02	genotype_quality=950.8	ks_quality_p_value=1	log10_base_likelihood=-5.73087	log10_qual_likelihood_position_model=17.6422	log10_strand_likelihood_position_model=7.71878	new_cov=0/25	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=152/134	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=152/159
RA	594	.	NC_007779	3447060	0	T	A	bias_e_value=4992.86	bias_p_value=0.00107458	fisher_strand_p_value=0.000105832	frequency=3.876686e-02	genotype_quality=1099.6	ks_quality_p_value=1	log10_base_likelihood=-11.0965	log10_qual_likelihood_position_model=22.8474	log10_strand_likelihood_position_model=4.09297	new_cov=0/14	polymorphism_quality=5.7	quality=5.7	quality_position_model=Inf	ref_cov=156/155	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=156/170
RA	595	.	NC_007779	3459814	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	596	.	NC_007779	3459815	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	597	.	NC_007779	3459816	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	598	.	NC_007779	3459818	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	599	.	NC_007779	3459820	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	600	.	NC_007779	3459821	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	601	.	NC_007779	3459822	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	602	.	NC_007779	3459823	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	603	.	NC_007779	3459826	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	604	.	NC_007779	3459827	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	605	.	NC_007779	3459828	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	606	.	NC_007779	3459829	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	607	.	NC_007779	3459830	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	608	.	NC_007779	3459831	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	609	.	NC_007779	3459832	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	610	.	NC_007779	3459833	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	611	.	NC_007779	3459834	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	612	.	NC_007779	3459835	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	613	.	NC_007779	3459836	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	614	.	NC_007779	3459837	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	615	.	NC_007779	3459838	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	616	.	NC_007779	3459839	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	617	.	NC_007779	3459840	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	618	.	NC_007779	3459841	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	619	.	NC_007779	3459843	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	620	.	NC_007779	3459844	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	621	.	NC_007779	3459845	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	622	.	NC_007779	3459846	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	623	.	NC_007779	3459847	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	624	.	NC_007779	3459848	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	625	.	NC_007779	3459849	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	626	.	NC_007779	3459850	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	627	.	NC_007779	3459851	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	628	.	NC_007779	3459852	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	629	.	NC_007779	3459853	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	630	.	NC_007779	3459854	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	631	.	NC_007779	3459855	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	632	.	NC_007779	3459857	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	633	.	NC_007779	3459858	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	634	.	NC_007779	3459859	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	635	.	NC_007779	3459861	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	636	.	NC_007779	3459862	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	637	.	NC_007779	3459864	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	638	.	NC_007779	3459865	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	639	.	NC_007779	3459866	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	640	.	NC_007779	3459867	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	641	.	NC_007779	3459869	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	642	.	NC_007779	3459870	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	643	.	NC_007779	3459872	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	644	.	NC_007779	3459873	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	645	.	NC_007779	3459874	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	646	.	NC_007779	3459875	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	647	.	NC_007779	3459876	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	648	.	NC_007779	3459877	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	649	.	NC_007779	3459879	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	650	.	NC_007779	3459880	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	651	.	NC_007779	3459881	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	652	.	NC_007779	3459882	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	653	.	NC_007779	3459883	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	654	.	NC_007779	3459884	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	655	.	NC_007779	3459885	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	656	.	NC_007779	3459887	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	657	.	NC_007779	3459888	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	658	.	NC_007779	3459889	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	659	.	NC_007779	3459890	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	660	.	NC_007779	3459891	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	661	.	NC_007779	3475527	0	T	G	bias_e_value=1.7784e-23	bias_p_value=3.82754e-30	fisher_strand_p_value=5.24132e-32	frequency=2.317181e-01	genotype_quality=564.8	ks_quality_p_value=1	log10_base_likelihood=-55.6158	log10_qual_likelihood_position_model=52.369	log10_strand_likelihood_position_model=31.2826	new_cov=80/1	polymorphism_quality=50.6	quality=50.6	quality_position_model=Inf	ref_cov=56/146	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=136/147
RA	662	.	NC_007779	3475533	0	C	T	bias_e_value=2.23962e-18	bias_p_value=4.82019e-25	fisher_strand_p_value=7.88845e-27	frequency=2.307076e-01	genotype_quality=669.5	ks_quality_p_value=1	log10_base_likelihood=-97.242	log10_qual_likelihood_position_model=61.0244	log10_strand_likelihood_position_model=26.103	new_cov=68/0	polymorphism_quality=92.3	quality=92.3	quality_position_model=3.82075e-12	ref_cov=73/149	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=141/149
RA	663	.	NC_007779	3478396	0	T	.	bias_e_value=1139840	bias_p_value=0.245321	fisher_strand_p_value=1	frequency=9.605408e-03	genotype_quality=1226.8	ks_quality_p_value=0.0659731	log10_base_likelihood=-7.67712	log10_qual_likelihood_position_model=2.57124	log10_strand_likelihood_position_model=0.384566	new_cov=1/2	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.3542e-06	ref_cov=138/171	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=139/173
RA	664	.	NC_007779	3481746	0	T	G	bias_e_value=4.76688e-11	bias_p_value=1.02594e-17	fisher_strand_p_value=2.33699e-19	frequency=1.224637e-01	genotype_quality=817.5	ks_quality_p_value=1	log10_base_likelihood=-24.1871	log10_qual_likelihood_position_model=38.1947	log10_strand_likelihood_position_model=18.6313	new_cov=49/0	polymorphism_quality=18.9	quality=18.9	quality_position_model=Inf	ref_cov=99/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=149/174
RA	665	.	NC_007779	3486216	0	T	G	bias_e_value=7.40568e-11	bias_p_value=1.59388e-17	fisher_strand_p_value=3.66835e-19	frequency=5.098057e-02	genotype_quality=927.0	ks_quality_p_value=1	log10_base_likelihood=-6.12509	log10_qual_likelihood_position_model=48.0456	log10_strand_likelihood_position_model=18.4355	new_cov=45/0	polymorphism_quality=0.6	quality=0.6	quality_position_model=Inf	ref_cov=101/193	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/193
RA	666	.	NC_007779	3499066	0	A	C	bias_e_value=0.00198954	bias_p_value=4.28196e-10	fisher_strand_p_value=1.65821e-11	frequency=7.200432e-02	genotype_quality=692.2	ks_quality_p_value=1	log10_base_likelihood=-20.1785	log10_qual_likelihood_position_model=22.8968	log10_strand_likelihood_position_model=10.7804	new_cov=0/18	polymorphism_quality=14.9	quality=14.9	quality_position_model=Inf	ref_cov=161/45	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/63
RA	667	.	NC_007779	3512358	0	A	.	bias_e_value=1382330	bias_p_value=0.29751	fisher_strand_p_value=0.103587	frequency=9.544373e-03	genotype_quality=1249.7	ks_quality_p_value=0.832257	log10_base_likelihood=-7.71417	log10_qual_likelihood_position_model=2.26132	log10_strand_likelihood_position_model=0.984697	new_cov=0/3	polymorphism_quality=2.2	quality=2.2	quality_position_model=2.48816e-06	ref_cov=166/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=166/148
RA	668	.	NC_007779	3518740	0	G	.	bias_e_value=4527610	bias_p_value=0.974448	fisher_strand_p_value=1	frequency=9.002686e-03	genotype_quality=1393.5	ks_quality_p_value=0.782627	log10_base_likelihood=-8.19744	log10_qual_likelihood_position_model=1.21004	log10_strand_likelihood_position_model=0.391494	new_cov=1/2	polymorphism_quality=2.7	quality=2.7	quality_position_model=1.54627e-08	ref_cov=151/179	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=152/181
RA	669	.	NC_007779	3519465	1	.	A	bias_e_value=2214910	bias_p_value=0.476702	fisher_strand_p_value=0.173505	frequency=6.005287e-03	genotype_quality=1634.4	ks_quality_p_value=0.99768	log10_base_likelihood=-7.39635	log10_qual_likelihood_position_model=2.93637	log10_strand_likelihood_position_model=0.760688	new_cov=0/2	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.59305e-05	ref_cov=194/137	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=194/139
RA	670	.	NC_007779	3519466	0	A	.	bias_e_value=1228660	bias_p_value=0.264437	fisher_strand_p_value=0.0732402	frequency=8.860588e-03	genotype_quality=1340.0	ks_quality_p_value=0.998676	log10_base_likelihood=-7.30232	log10_qual_likelihood_position_model=3.70299	log10_strand_likelihood_position_model=1.13525	new_cov=0/3	polymorphism_quality=1.8	quality=1.8	quality_position_model=0.000328229	ref_cov=196/139	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=196/142
RA	671	.	NC_007779	3520391	0	C	G	bias_e_value=3.92959e-06	bias_p_value=8.4574e-13	fisher_strand_p_value=2.6232e-14	frequency=7.849121e-02	genotype_quality=666.7	ks_quality_p_value=0.999007	log10_base_likelihood=-19.9663	log10_qual_likelihood_position_model=16.1176	log10_strand_likelihood_position_model=13.5812	new_cov=14/0	polymorphism_quality=14.7	quality=14.7	quality_position_model=Inf	ref_cov=11/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=25/151
RA	672	.	NC_007779	3535168	0	A	.	bias_e_value=2833260	bias_p_value=0.609784	fisher_strand_p_value=1	frequency=9.575844e-03	genotype_quality=1238.4	ks_quality_p_value=0.259662	log10_base_likelihood=-7.82328	log10_qual_likelihood_position_model=1.53337	log10_strand_likelihood_position_model=0.362429	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=7.57745e-08	ref_cov=186/124	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=188/125
RA	673	.	NC_007779	3543542	0	G	T	bias_e_value=0.00155504	bias_p_value=3.3468e-10	fisher_strand_p_value=1.28333e-11	frequency=7.060432e-02	genotype_quality=840.1	ks_quality_p_value=1	log10_base_likelihood=-16.0421	log10_qual_likelihood_position_model=24.0147	log10_strand_likelihood_position_model=10.8917	new_cov=0/25	polymorphism_quality=10.7	quality=10.7	quality_position_model=Inf	ref_cov=153/76	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=153/101
RA	674	.	NC_007779	3543547	0	A	C	bias_e_value=1.43439e-38	bias_p_value=3.08714e-45	fisher_strand_p_value=2.85389e-47	frequency=2.932153e-01	genotype_quality=545.1	ks_quality_p_value=1	log10_base_likelihood=-80.9643	log10_qual_likelihood_position_model=73.6636	log10_strand_likelihood_position_model=46.6618	new_cov=0/114	polymorphism_quality=76.0	quality=76.0	quality_position_model=Inf	ref_cov=160/52	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=160/166
RA	675	.	NC_007779	3560478	0	G	T	bias_e_value=50.0789	bias_p_value=1.07782e-05	fisher_strand_p_value=7.11128e-07	frequency=3.614330e-02	genotype_quality=1357.4	ks_quality_p_value=1	log10_base_likelihood=-8.13687	log10_qual_likelihood_position_model=20.9783	log10_strand_likelihood_position_model=6.27302	new_cov=0/23	polymorphism_quality=2.7	quality=2.7	quality_position_model=Inf	ref_cov=179/193	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=179/217
RA	676	.	NC_007779	3561760	1	.	T	bias_e_value=4614690	bias_p_value=0.99319	fisher_strand_p_value=1	frequency=5.698204e-03	genotype_quality=1715.7	ks_quality_p_value=0.885588	log10_base_likelihood=-7.61616	log10_qual_likelihood_position_model=2.07234	log10_strand_likelihood_position_model=0.326037	new_cov=1/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=4.12176e-07	ref_cov=217/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=218/133
RA	677	.	NC_007779	3576400	1	.	A	bias_e_value=4638010	bias_p_value=0.998209	fisher_strand_p_value=1	frequency=5.730629e-03	genotype_quality=1695.0	ks_quality_p_value=0.940756	log10_base_likelihood=-7.65125	log10_qual_likelihood_position_model=1.89351	log10_strand_likelihood_position_model=0.303224	new_cov=1/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=2.34086e-07	ref_cov=158/189	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=159/190
RA	678	.	NC_007779	3580297	0	G	T	bias_e_value=160.919	bias_p_value=3.46336e-05	fisher_strand_p_value=2.49113e-06	frequency=3.323364e-02	genotype_quality=1170.4	ks_quality_p_value=1	log10_base_likelihood=-7.42844	log10_qual_likelihood_position_model=16.4252	log10_strand_likelihood_position_model=5.74758	new_cov=0/19	polymorphism_quality=1.9	quality=1.9	quality_position_model=Inf	ref_cov=168/157	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/176
RA	679	.	NC_007779	3599471	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	680	.	NC_007779	3599472	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	681	.	NC_007779	3599473	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	682	.	NC_007779	3599474	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	683	.	NC_007779	3599476	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	684	.	NC_007779	3599477	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	685	.	NC_007779	3599478	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	686	.	NC_007779	3599479	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	687	.	NC_007779	3599481	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	688	.	NC_007779	3599482	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	689	.	NC_007779	3599483	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	690	.	NC_007779	3599484	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	691	.	NC_007779	3599487	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	692	.	NC_007779	3599488	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	693	.	NC_007779	3599490	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	694	.	NC_007779	3599491	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	695	.	NC_007779	3603950	0	A	C	bias_e_value=1.2612e-11	bias_p_value=2.71439e-18	fisher_strand_p_value=5.99728e-20	frequency=1.062684e-01	genotype_quality=725.7	ks_quality_p_value=1	log10_base_likelihood=-24.567	log10_qual_likelihood_position_model=49.7365	log10_strand_likelihood_position_model=19.2259	new_cov=1/47	polymorphism_quality=19.3	quality=19.3	quality_position_model=Inf	ref_cov=166/72	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=167/122
RA	696	.	NC_007779	3609437	1	.	G	bias_e_value=4141450	bias_p_value=0.891338	fisher_strand_p_value=0.572225	frequency=7.672310e-03	genotype_quality=1924.5	ks_quality_p_value=0.999012	log10_base_likelihood=-11.7319	log10_qual_likelihood_position_model=2.50728	log10_strand_likelihood_position_model=0.519893	new_cov=2/1	polymorphism_quality=6.3	quality=6.3	quality_position_model=1.05504e-10	ref_cov=160/228	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=162/229
RA	697	.	NC_007779	3609441	0	T	G	bias_e_value=9.59668e-19	bias_p_value=2.06543e-25	fisher_strand_p_value=3.33318e-27	frequency=6.744003e-02	genotype_quality=950.2	ks_quality_p_value=1	log10_base_likelihood=-10.6745	log10_qual_likelihood_position_model=39.1008	log10_strand_likelihood_position_model=26.4771	new_cov=57/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=87/219	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/219
RA	698	.	NC_007779	3609448	0	A	T	bias_e_value=6221.76	bias_p_value=0.00133907	fisher_strand_p_value=0.000135133	frequency=2.028275e-02	genotype_quality=1137.6	ks_quality_p_value=1	log10_base_likelihood=-5.83574	log10_qual_likelihood_position_model=11.4064	log10_strand_likelihood_position_model=3.86924	new_cov=7/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=82/221	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=89/221
RA	699	.	NC_007779	3615064	0	C	A	bias_e_value=90.6094	bias_p_value=1.95013e-05	fisher_strand_p_value=1.34334e-06	frequency=2.667046e-02	genotype_quality=1428.6	ks_quality_p_value=0.999749	log10_base_likelihood=-5.72513	log10_qual_likelihood_position_model=22.4309	log10_strand_likelihood_position_model=5.88988	new_cov=21/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=204/195	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=225/195
RA	700	.	NC_007779	3627544	1	.	T	bias_e_value=3789630	bias_p_value=0.815618	fisher_strand_p_value=0.610523	frequency=9.901047e-03	genotype_quality=1445.9	ks_quality_p_value=0.750118	log10_base_likelihood=-12.3506	log10_qual_likelihood_position_model=2.44241	log10_strand_likelihood_position_model=0.441274	new_cov=1/2	polymorphism_quality=7.0	quality=7.0	quality_position_model=1.75241e-11	ref_cov=156/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=157/146
RA	701	.	NC_007779	3646400	0	C	A	bias_e_value=10.7556	bias_p_value=2.31486e-06	fisher_strand_p_value=1.58023e-07	frequency=3.611851e-02	genotype_quality=1057.6	ks_quality_p_value=0.872092	log10_base_likelihood=-5.70149	log10_qual_likelihood_position_model=25.2122	log10_strand_likelihood_position_model=6.80128	new_cov=21/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=139/166	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/166
RA	702	.	NC_007779	3647696	1	.	A	bias_e_value=3455470	bias_p_value=0.743697	fisher_strand_p_value=0.498937	frequency=6.097794e-03	genotype_quality=1610.1	ks_quality_p_value=0.753411	log10_base_likelihood=-7.95153	log10_qual_likelihood_position_model=1.18706	log10_strand_likelihood_position_model=0.577226	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.08339e-08	ref_cov=167/159	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=169/159
RA	703	.	NC_007779	3653996	1	.	G	bias_e_value=4345630	bias_p_value=0.935283	fisher_strand_p_value=1	frequency=6.801605e-03	genotype_quality=1425.1	ks_quality_p_value=0.66252	log10_base_likelihood=-7.23597	log10_qual_likelihood_position_model=2.00682	log10_strand_likelihood_position_model=0.330989	new_cov=2/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=8.86021e-07	ref_cov=199/93	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=201/93
RA	704	.	NC_007779	3654011	0	A	C	bias_e_value=1.55515	bias_p_value=3.34705e-07	fisher_strand_p_value=1.77597e-08	frequency=2.976990e-02	genotype_quality=1069.8	ks_quality_p_value=1	log10_base_likelihood=-8.5249	log10_qual_likelihood_position_model=21.6739	log10_strand_likelihood_position_model=7.75056	new_cov=0/17	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=204/101	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=204/118
RA	705	.	NC_007779	3654011	1	.	C	bias_e_value=1834250	bias_p_value=0.394775	fisher_strand_p_value=0.138092	frequency=6.366730e-03	genotype_quality=1476.0	ks_quality_p_value=0.939787	log10_base_likelihood=-6.29648	log10_qual_likelihood_position_model=3.7372	log10_strand_likelihood_position_model=0.85983	new_cov=0/2	polymorphism_quality=0.8	quality=0.8	quality_position_model=0.00224208	ref_cov=197/115	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=197/117
RA	706	.	NC_007779	3662279	0	A	C	bias_e_value=7.39015e-12	bias_p_value=1.59054e-18	fisher_strand_p_value=3.47226e-20	frequency=8.395433e-02	genotype_quality=779.4	ks_quality_p_value=1	log10_base_likelihood=-13.0557	log10_qual_likelihood_position_model=52.477	log10_strand_likelihood_position_model=19.4594	new_cov=0/55	polymorphism_quality=7.7	quality=7.7	quality_position_model=Inf	ref_cov=158/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/154
RA	707	.	NC_007779	3673380	0	G	T	bias_e_value=380.097	bias_p_value=8.18059e-05	fisher_strand_p_value=7.40789e-06	frequency=3.490257e-02	genotype_quality=1086.7	ks_quality_p_value=0.851162	log10_base_likelihood=-7.11163	log10_qual_likelihood_position_model=25.237	log10_strand_likelihood_position_model=5.18744	new_cov=0/20	polymorphism_quality=1.6	quality=1.6	quality_position_model=Inf	ref_cov=149/172	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=149/192
RA	708	.	NC_007779	3676780	0	A	C	bias_e_value=4.01531e-08	bias_p_value=8.64188e-15	fisher_strand_p_value=2.33609e-16	frequency=9.912872e-02	genotype_quality=853.8	ks_quality_p_value=1	log10_base_likelihood=-19.1337	log10_qual_likelihood_position_model=36.5513	log10_strand_likelihood_position_model=15.6315	new_cov=0/44	polymorphism_quality=13.8	quality=13.8	quality_position_model=Inf	ref_cov=173/115	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/161
RA	709	.	NC_007779	3677212	0	C	G	bias_e_value=1020.26	bias_p_value=0.000219583	fisher_strand_p_value=1.84518e-05	frequency=2.802181e-02	genotype_quality=751.5	ks_quality_p_value=1	log10_base_likelihood=-7.61011	log10_qual_likelihood_position_model=8.78347	log10_strand_likelihood_position_model=4.73396	new_cov=0/6	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=162/28	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=162/34
RA	710	.	NC_007779	3677217	0	T	G	bias_e_value=48321.3	bias_p_value=0.0103999	fisher_strand_p_value=0.00136963	frequency=4.068089e-02	genotype_quality=545.5	ks_quality_p_value=1	log10_base_likelihood=-6.29799	log10_qual_likelihood_position_model=15.4995	log10_strand_likelihood_position_model=2.93638	new_cov=9/9	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=150/27	reject=EVALUE,SURROUNDING_HOMOPOLYMER	tot_cov=159/36
RA	711	.	NC_007779	3677219	0	A	G	bias_e_value=0.00579796	bias_p_value=1.24786e-09	fisher_strand_p_value=5.05361e-11	frequency=4.670811e-02	genotype_quality=610.8	ks_quality_p_value=0.999328	log10_base_likelihood=-6.32459	log10_qual_likelihood_position_model=14.1695	log10_strand_likelihood_position_model=10.2964	new_cov=0/12	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=163/20	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=164/33
RA	712	.	NC_007779	3683153	0	A	C	bias_e_value=410.065	bias_p_value=8.82557e-05	fisher_strand_p_value=7.68407e-06	frequency=2.920246e-02	genotype_quality=562.0	ks_quality_p_value=0.890913	log10_base_likelihood=-8.89447	log10_qual_likelihood_position_model=5.32465	log10_strand_likelihood_position_model=5.11441	new_cov=0/5	polymorphism_quality=3.4	quality=3.4	quality_position_model=Inf	ref_cov=152/13	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=152/18
RA	713	.	NC_007779	3686205	0	A	.	bias_e_value=3878440	bias_p_value=0.834732	fisher_strand_p_value=1	frequency=1.576328e-02	genotype_quality=1237.9	ks_quality_p_value=0.483322	log10_base_likelihood=-13.9348	log10_qual_likelihood_position_model=4.46747	log10_strand_likelihood_position_model=0.461854	new_cov=3/2	polymorphism_quality=8.6	quality=8.6	quality_position_model=5.19359e-11	ref_cov=178/134	reject=INDEL_HOMOPOLYMER	tot_cov=181/136
RA	714	.	NC_007779	3688841	0	T	G	bias_e_value=20.9301	bias_p_value=4.50464e-06	fisher_strand_p_value=2.79991e-07	frequency=4.179287e-02	genotype_quality=810.1	ks_quality_p_value=1	log10_base_likelihood=-5.72004	log10_qual_likelihood_position_model=22.8384	log10_strand_likelihood_position_model=6.56296	new_cov=1/14	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=152/54	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/68
RA	715	.	NC_007779	3688858	0	A	C	bias_e_value=8.09424e-21	bias_p_value=1.74207e-27	fisher_strand_p_value=2.60724e-29	frequency=1.834006e-01	genotype_quality=544.2	ks_quality_p_value=1	log10_base_likelihood=-39.874	log10_qual_likelihood_position_model=47.6192	log10_strand_likelihood_position_model=28.5838	new_cov=0/51	polymorphism_quality=34.7	quality=34.7	quality_position_model=Inf	ref_cov=149/33	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=149/84
RA	716	.	NC_007779	3693317	0	A	T	bias_e_value=1596990	bias_p_value=0.343711	fisher_strand_p_value=0.106609	frequency=1.394844e-02	genotype_quality=748.2	ks_quality_p_value=0.99351	log10_base_likelihood=-6.04396	log10_qual_likelihood_position_model=2.34965	log10_strand_likelihood_position_model=0.972208	new_cov=3/0	polymorphism_quality=0.5	quality=0.5	quality_position_model=0.000173421	ref_cov=99/112	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=102/112
RA	717	.	NC_007779	3698665	0	A	G	bias_e_value=1249430	bias_p_value=0.268906	fisher_strand_p_value=0.622409	frequency=1.025486e-02	genotype_quality=1122.9	ks_quality_p_value=0.120274	log10_base_likelihood=-5.58233	log10_qual_likelihood_position_model=2.66564	log10_strand_likelihood_position_model=0.425984	new_cov=1/2	polymorphism_quality=0.0	quality=0.0	quality_position_model=0.00030726	ref_cov=145/143	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=146/145
RA	718	.	NC_007779	3701118	0	G	T	bias_e_value=0.00144307	bias_p_value=3.10582e-10	fisher_strand_p_value=1.18739e-11	frequency=9.441662e-02	genotype_quality=843.9	ks_quality_p_value=1	log10_base_likelihood=-19.4084	log10_qual_likelihood_position_model=24.3036	log10_strand_likelihood_position_model=11.1211	new_cov=0/34	polymorphism_quality=14.1	quality=14.1	quality_position_model=Inf	ref_cov=137/105	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=137/139
RA	719	.	NC_007779	3711109	0	C	A	bias_e_value=64.2417	bias_p_value=1.38263e-05	fisher_strand_p_value=9.28589e-07	frequency=4.724932e-02	genotype_quality=798.8	ks_quality_p_value=1	log10_base_likelihood=-6.44674	log10_qual_likelihood_position_model=15.0419	log10_strand_likelihood_position_model=6.03218	new_cov=18/0	polymorphism_quality=0.9	quality=0.9	quality_position_model=Inf	ref_cov=105/133	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=124/133
RA	720	.	NC_007779	3728146	1	.	T	bias_e_value=795629	bias_p_value=0.171238	fisher_strand_p_value=0.0883775	frequency=1.197624e-02	genotype_quality=795.4	ks_quality_p_value=0.461358	log10_base_likelihood=-8.37843	log10_qual_likelihood_position_model=1.50631	log10_strand_likelihood_position_model=1.05366	new_cov=2/0	polymorphism_quality=2.9	quality=2.9	quality_position_model=9.82468e-08	ref_cov=48/117	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=50/117
RA	721	.	NC_007779	3730938	1	.	T	bias_e_value=1457890	bias_p_value=0.313773	fisher_strand_p_value=0.174419	frequency=6.644249e-03	genotype_quality=1491.2	ks_quality_p_value=0.53292	log10_base_likelihood=-7.99519	log10_qual_likelihood_position_model=1.88014	log10_strand_likelihood_position_model=0.758407	new_cov=0/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.95741e-07	ref_cov=175/124	reject=POLYMORPHISM_STRAND	tot_cov=175/126
RA	722	.	NC_007779	3731041	1	.	T	bias_e_value=4416110	bias_p_value=0.950451	fisher_strand_p_value=1	frequency=7.692337e-03	genotype_quality=1254.0	ks_quality_p_value=0.702192	log10_base_likelihood=-7.67701	log10_qual_likelihood_position_model=2.58772	log10_strand_likelihood_position_model=0.315722	new_cov=1/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.1946e-06	ref_cov=154/104	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=155/105
RA	723	.	NC_007779	3732310	0	G	T	bias_e_value=2.90777e-05	bias_p_value=6.2582e-12	fisher_strand_p_value=2.0719e-13	frequency=7.731819e-02	genotype_quality=1020.0	ks_quality_p_value=1	log10_base_likelihood=-21.5052	log10_qual_likelihood_position_model=21.4415	log10_strand_likelihood_position_model=12.6836	new_cov=0/33	polymorphism_quality=16.2	quality=16.2	quality_position_model=Inf	ref_cov=180/110	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=180/145
RA	724	.	NC_007779	3734364	1	.	A	bias_e_value=4419200	bias_p_value=0.951116	fisher_strand_p_value=1	frequency=6.944656e-03	genotype_quality=1412.0	ks_quality_p_value=0.704079	log10_base_likelihood=-7.96018	log10_qual_likelihood_position_model=1.33362	log10_strand_likelihood_position_model=0.301219	new_cov=1/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=2.94046e-08	ref_cov=134/152	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/153
RA	725	.	NC_007779	3741461	0	A	T	bias_e_value=0.863514	bias_p_value=1.85848e-07	fisher_strand_p_value=9.54682e-09	frequency=6.654644e-02	genotype_quality=1061.7	ks_quality_p_value=1	log10_base_likelihood=-25.9669	log10_qual_likelihood_position_model=27.1727	log10_strand_likelihood_position_model=8.02014	new_cov=22/0	polymorphism_quality=20.7	quality=20.7	quality_position_model=Inf	ref_cov=118/170	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=140/170
RA	726	.	NC_007779	3750122	0	C	.	bias_e_value=9585.84	bias_p_value=0.0020631	fisher_strand_p_value=0.480064	frequency=1	genotype_quality=1603.0	ks_quality_p_value=0.00045587	log10_base_likelihood=-95.0047	log10_qual_likelihood_position_model=12.8413	log10_strand_likelihood_position_model=0.903544	new_cov=164/180	polymorphism_changed_to_consensus=1	polymorphism_quality=90.1	quality=90.1	quality_position_model=9.82177e-84	ref_cov=7/12	tot_cov=171/192
RA	727	.	NC_007779	3750123	0	C	T	bias_e_value=3236670	bias_p_value=0.696607	fisher_strand_p_value=0.480064	frequency=5.221128e-02	genotype_quality=1346.2	ks_quality_p_value=0.688816	log10_base_likelihood=-40.9237	log10_qual_likelihood_position_model=10.6599	log10_strand_likelihood_position_model=0.903544	new_cov=7/12	polymorphism_quality=35.8	quality=35.8	quality_position_model=1.29075e-31	ref_cov=164/180	tot_cov=171/192
RA	728	.	NC_007779	3752138	1	.	A	bias_e_value=2627430	bias_p_value=0.565485	fisher_strand_p_value=0.514223	frequency=5.796432e-03	genotype_quality=1699.7	ks_quality_p_value=0.443924	log10_base_likelihood=-7.52605	log10_qual_likelihood_position_model=1.57359	log10_strand_likelihood_position_model=0.46153	new_cov=2/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=2.14592e-07	ref_cov=201/142	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=203/142
RA	729	.	NC_007779	3761469	0	A	C	bias_e_value=2.26935e-07	bias_p_value=4.88418e-14	fisher_strand_p_value=1.3871e-15	frequency=5.064964e-02	genotype_quality=646.6	ks_quality_p_value=1	log10_base_likelihood=-8.47178	log10_qual_likelihood_position_model=22.1597	log10_strand_likelihood_position_model=14.8579	new_cov=0/16	polymorphism_quality=3.0	quality=3.0	quality_position_model=Inf	ref_cov=172/15	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=172/31
RA	730	.	NC_007779	3762475	0	T	G	bias_e_value=1.85874e-14	bias_p_value=4.00045e-21	fisher_strand_p_value=7.70539e-23	frequency=1.593103e-01	genotype_quality=732.6	ks_quality_p_value=1	log10_base_likelihood=-48.475	log10_qual_likelihood_position_model=43.5425	log10_strand_likelihood_position_model=22.1132	new_cov=57/0	polymorphism_quality=43.4	quality=43.4	quality_position_model=Inf	ref_cov=87/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/165
RA	731	.	NC_007779	3765081	1	.	T	bias_e_value=4336470	bias_p_value=0.93331	fisher_strand_p_value=1	frequency=5.539894e-03	genotype_quality=1780.4	ks_quality_p_value=0.65777	log10_base_likelihood=-8.11046	log10_qual_likelihood_position_model=1.96521	log10_strand_likelihood_position_model=0.300095	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=9.21915e-08	ref_cov=184/175	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=185/176
RA	732	.	NC_007779	3780898	1	.	G	bias_e_value=2010740	bias_p_value=0.432759	fisher_strand_p_value=0.155921	frequency=6.825447e-03	genotype_quality=1430.1	ks_quality_p_value=0.955917	log10_base_likelihood=-7.65644	log10_qual_likelihood_position_model=1.67075	log10_strand_likelihood_position_model=0.807095	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=4.52679e-07	ref_cov=114/177	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=116/177
RA	733	.	NC_007779	3786728	1	.	G	bias_e_value=2579810	bias_p_value=0.555235	fisher_strand_p_value=0.22817	frequency=5.405426e-03	genotype_quality=1829.8	ks_quality_p_value=0.970366	log10_base_likelihood=-7.34184	log10_qual_likelihood_position_model=3.13523	log10_strand_likelihood_position_model=0.641742	new_cov=2/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=2.20765e-05	ref_cov=175/193	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=177/193
RA	734	.	NC_007779	3788380	0	G	T	bias_e_value=0.00675969	bias_p_value=1.45484e-09	fisher_strand_p_value=5.92628e-11	frequency=9.768724e-02	genotype_quality=999.1	ks_quality_p_value=1	log10_base_likelihood=-30.2856	log10_qual_likelihood_position_model=22.3065	log10_strand_likelihood_position_model=10.2593	new_cov=0/41	polymorphism_quality=25.1	quality=25.1	quality_position_model=Inf	ref_cov=139/158	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=140/199
RA	735	.	NC_007779	3812429	0	G	T	bias_e_value=0.0456544	bias_p_value=9.82589e-09	fisher_strand_p_value=4.35658e-10	frequency=7.616663e-02	genotype_quality=1045.1	ks_quality_p_value=1	log10_base_likelihood=-15.3411	log10_qual_likelihood_position_model=23.8464	log10_strand_likelihood_position_model=9.39425	new_cov=0/35	polymorphism_quality=10.0	quality=10.0	quality_position_model=Inf	ref_cov=145/152	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=145/187
RA	736	.	NC_007779	3813810	0	T	G	bias_e_value=4.56018e-17	bias_p_value=9.81457e-24	fisher_strand_p_value=1.69102e-25	frequency=8.641243e-02	genotype_quality=608.9	ks_quality_p_value=1	log10_base_likelihood=-9.51667	log10_qual_likelihood_position_model=34.1312	log10_strand_likelihood_position_model=24.7719	new_cov=38/0	polymorphism_quality=4.1	quality=4.1	quality_position_model=Inf	ref_cov=28/160	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=66/160
RA	737	.	NC_007779	3820146	0	T	G	bias_e_value=3.82608e-06	bias_p_value=8.23461e-13	fisher_strand_p_value=2.54939e-14	frequency=1.132488e-01	genotype_quality=641.4	ks_quality_p_value=1	log10_base_likelihood=-20.3538	log10_qual_likelihood_position_model=28.1273	log10_strand_likelihood_position_model=13.5936	new_cov=36/0	polymorphism_quality=15.1	quality=15.1	quality_position_model=Inf	ref_cov=79/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=115/134
RA	738	.	NC_007779	3828029	0	G	T	bias_e_value=3.31712e-10	bias_p_value=7.13922e-17	fisher_strand_p_value=1.93174e-18	frequency=1.599884e-01	genotype_quality=711.6	ks_quality_p_value=0.881743	log10_base_likelihood=-58.5119	log10_qual_likelihood_position_model=46.8955	log10_strand_likelihood_position_model=17.7141	new_cov=44/0	polymorphism_quality=53.5	quality=53.5	quality_position_model=Inf	ref_cov=73/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=117/144
RA	739	.	NC_007779	3841755	1	.	A	bias_e_value=2416760	bias_p_value=0.520144	fisher_strand_p_value=0.50307	frequency=7.326126e-03	genotype_quality=1342.2	ks_quality_p_value=0.395409	log10_base_likelihood=-7.9405	log10_qual_likelihood_position_model=1.23045	log10_strand_likelihood_position_model=0.521454	new_cov=2/0	polymorphism_quality=2.5	quality=2.5	quality_position_model=4.07024e-08	ref_cov=148/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=150/123
RA	740	.	NC_007779	3841756	0	A	.	bias_e_value=1851610	bias_p_value=0.39851	fisher_strand_p_value=1	frequency=1.090050e-02	genotype_quality=1105.1	ks_quality_p_value=0.131613	log10_base_likelihood=-7.96986	log10_qual_likelihood_position_model=1.48408	log10_strand_likelihood_position_model=0.387635	new_cov=2/1	polymorphism_quality=2.5	quality=2.5	quality_position_model=5.04749e-08	ref_cov=149/123	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=151/124
RA	741	.	NC_007779	3845596	0	G	T	bias_e_value=119.477	bias_p_value=2.57142e-05	fisher_strand_p_value=1.80789e-06	frequency=3.876877e-02	genotype_quality=952.3	ks_quality_p_value=1	log10_base_likelihood=-8.34031	log10_qual_likelihood_position_model=13.0429	log10_strand_likelihood_position_model=5.74283	new_cov=0/17	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=154/122	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/139
RA	742	.	NC_007779	3846240	0	G	C	bias_e_value=1.90133e-08	bias_p_value=4.09212e-15	fisher_strand_p_value=1.10093e-16	frequency=8.800316e-02	genotype_quality=669.9	ks_quality_p_value=0.984341	log10_base_likelihood=-27.3524	log10_qual_likelihood_position_model=15.9924	log10_strand_likelihood_position_model=15.9582	new_cov=0/19	polymorphism_quality=22.1	quality=22.1	quality_position_model=Inf	ref_cov=168/19	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=168/38
RA	743	.	NC_007779	3855255	0	C	A	bias_e_value=1.3247	bias_p_value=2.85107e-07	fisher_strand_p_value=1.50967e-08	frequency=3.756046e-02	genotype_quality=771.3	ks_quality_p_value=0.993148	log10_base_likelihood=-14.4439	log10_qual_likelihood_position_model=10.4324	log10_strand_likelihood_position_model=7.82112	new_cov=0/8	polymorphism_quality=9.1	quality=9.1	quality_position_model=Inf	ref_cov=173/16	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/24
RA	744	.	NC_007779	3859254	1	.	T	bias_e_value=44893.3	bias_p_value=0.00966209	fisher_strand_p_value=0.00143002	frequency=2.112675e-02	genotype_quality=1335.2	ks_quality_p_value=0.880008	log10_base_likelihood=-26.8015	log10_qual_likelihood_position_model=2.17129	log10_strand_likelihood_position_model=2.84466	new_cov=6/0	polymorphism_quality=21.6	quality=21.6	quality_position_model=5.61362e-24	ref_cov=91/187	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=97/187
RA	745	.	NC_007779	3859258	1	.	C	bias_e_value=156532	bias_p_value=0.0336893	fisher_strand_p_value=0.00547227	frequency=2.307510e-02	genotype_quality=1186.5	ks_quality_p_value=0.990083	log10_base_likelihood=-19.663	log10_qual_likelihood_position_model=4.93971	log10_strand_likelihood_position_model=2.26183	new_cov=4/0	polymorphism_quality=14.4	quality=14.4	quality_position_model=1.5545e-14	ref_cov=67/186	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=73/186
RA	746	.	NC_007779	3859258	2	.	C	bias_e_value=426155	bias_p_value=0.0917185	fisher_strand_p_value=0.0210812	frequency=1.162720e-02	genotype_quality=1211.6	ks_quality_p_value=0.870477	log10_base_likelihood=-11.6304	log10_qual_likelihood_position_model=3.5907	log10_strand_likelihood_position_model=1.6761	new_cov=3/0	polymorphism_quality=6.2	quality=6.2	quality_position_model=2.68492e-08	ref_cov=69/186	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=72/186
RA	747	.	NC_007779	3859263	0	T	C	bias_e_value=3.04422e-06	bias_p_value=6.55188e-13	fisher_strand_p_value=2.01372e-14	frequency=7.217836e-02	genotype_quality=786.2	ks_quality_p_value=1	log10_base_likelihood=-20.4327	log10_qual_likelihood_position_model=22.0825	log10_strand_likelihood_position_model=13.696	new_cov=21/0	polymorphism_quality=15.2	quality=15.2	quality_position_model=Inf	ref_cov=45/194	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=66/194
RA	748	.	NC_007779	3859265	0	A	C	bias_e_value=2.07394	bias_p_value=4.46361e-07	fisher_strand_p_value=2.40727e-08	frequency=7.824707e-02	genotype_quality=723.1	ks_quality_p_value=1	log10_base_likelihood=-17.7782	log10_qual_likelihood_position_model=19.1513	log10_strand_likelihood_position_model=7.65658	new_cov=21/7	polymorphism_quality=12.5	quality=12.5	quality_position_model=Inf	ref_cov=50/185	reject=FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=71/193
RA	749	.	NC_007779	3859270	0	G	C	bias_e_value=1140.49	bias_p_value=0.00024546	fisher_strand_p_value=2.08442e-05	frequency=2.599239e-02	genotype_quality=964.6	ks_quality_p_value=0.99977	log10_base_likelihood=-12.1597	log10_qual_likelihood_position_model=6.81918	log10_strand_likelihood_position_model=4.68102	new_cov=7/0	polymorphism_quality=6.8	quality=6.8	quality_position_model=0.0368641	ref_cov=49/194	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=56/194
RA	750	.	NC_007779	3859275	0	T	C	bias_e_value=97.824	bias_p_value=2.1054e-05	fisher_strand_p_value=1.45863e-06	frequency=2.898693e-02	genotype_quality=869.9	ks_quality_p_value=0.999708	log10_base_likelihood=-7.25895	log10_qual_likelihood_position_model=11.6044	log10_strand_likelihood_position_model=5.83605	new_cov=9/0	polymorphism_quality=1.8	quality=1.8	quality_position_model=Inf	ref_cov=51/193	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=60/193
RA	751	.	NC_007779	3864410	0	G	C	bias_e_value=11.3772	bias_p_value=2.44864e-06	fisher_strand_p_value=1.46296e-07	frequency=4.286385e-02	genotype_quality=884.6	ks_quality_p_value=1	log10_base_likelihood=-9.67934	log10_qual_likelihood_position_model=16.3089	log10_strand_likelihood_position_model=6.83477	new_cov=0/15	polymorphism_quality=4.2	quality=4.2	quality_position_model=Inf	ref_cov=163/80	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/96
RA	752	.	NC_007779	3873374	1	.	T	bias_e_value=2040230	bias_p_value=0.439105	fisher_strand_p_value=0.216199	frequency=1.599979e-02	genotype_quality=1792.3	ks_quality_p_value=0.704913	log10_base_likelihood=-25.8851	log10_qual_likelihood_position_model=3.98076	log10_strand_likelihood_position_model=0.9834	new_cov=1/5	polymorphism_quality=20.7	quality=20.7	quality_position_model=4.1925e-23	ref_cov=181/188	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=182/193
RA	753	.	NC_007779	3873375	0	T	.	bias_e_value=2822410	bias_p_value=0.60745	fisher_strand_p_value=0.372555	frequency=1.321888e-02	genotype_quality=1467.9	ks_quality_p_value=0.692342	log10_base_likelihood=-13.7264	log10_qual_likelihood_position_model=2.69192	log10_strand_likelihood_position_model=0.774442	new_cov=1/4	polymorphism_quality=8.4	quality=8.4	quality_position_model=2.71481e-12	ref_cov=183/190	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=184/194
RA	754	.	NC_007779	3891907	0	T	.	bias_e_value=4622400	bias_p_value=0.99485	fisher_strand_p_value=1	frequency=1.138496e-02	genotype_quality=1363.0	ks_quality_p_value=0.900241	log10_base_likelihood=-10.3402	log10_qual_likelihood_position_model=2.56606	log10_strand_likelihood_position_model=0.433245	new_cov=2/2	polymorphism_quality=4.9	quality=4.9	quality_position_model=2.64433e-09	ref_cov=192/155	reject=INDEL_HOMOPOLYMER	tot_cov=194/157
RA	755	.	NC_007779	3895373	0	T	G	bias_e_value=4.44336e-12	bias_p_value=9.56315e-19	fisher_strand_p_value=2.06427e-20	frequency=1.104159e-01	genotype_quality=592.7	ks_quality_p_value=1	log10_base_likelihood=-18.0656	log10_qual_likelihood_position_model=41.2181	log10_strand_likelihood_position_model=19.6852	new_cov=42/0	polymorphism_quality=12.8	quality=12.8	quality_position_model=Inf	ref_cov=57/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=100/150
RA	756	.	NC_007779	3898657	0	C	G	frequency=1	genotype_quality=1397.7	new_cov=174/158	quality=1397.7	ref_cov=0/0	tot_cov=174/158
RA	757	.	NC_007779	3900676	1	.	G	bias_e_value=50639.2	bias_p_value=0.0108987	fisher_strand_p_value=0.00326018	frequency=1.886749e-02	genotype_quality=1534.6	ks_quality_p_value=0.443412	log10_base_likelihood=-26.3676	log10_qual_likelihood_position_model=3.22841	log10_strand_likelihood_position_model=2.48676	new_cov=6/0	polymorphism_quality=21.1	quality=21.1	quality_position_model=7.82953e-23	ref_cov=118/194	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/194
RA	758	.	NC_007779	3900680	0	T	G	bias_e_value=3.29087e-10	bias_p_value=7.08272e-17	fisher_strand_p_value=1.6895e-18	frequency=7.540369e-02	genotype_quality=706.6	ks_quality_p_value=1	log10_base_likelihood=-25.5119	log10_qual_likelihood_position_model=24.5534	log10_strand_likelihood_position_model=17.7722	new_cov=19/0	polymorphism_quality=20.3	quality=20.3	quality_position_model=Inf	ref_cov=16/193	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=35/193
RA	759	.	NC_007779	3910746	0	C	A	bias_e_value=18.1656	bias_p_value=3.90966e-06	fisher_strand_p_value=2.4075e-07	frequency=4.239941e-02	genotype_quality=1075.0	ks_quality_p_value=1	log10_base_likelihood=-6.31014	log10_qual_likelihood_position_model=26.8805	log10_strand_likelihood_position_model=6.80756	new_cov=26/0	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=162/145	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=190/145
RA	760	.	NC_007779	3927488	1	.	A	bias_e_value=4250310	bias_p_value=0.914768	fisher_strand_p_value=1	frequency=7.781982e-03	genotype_quality=1241.2	ks_quality_p_value=0.616642	log10_base_likelihood=-8.10185	log10_qual_likelihood_position_model=1.47417	log10_strand_likelihood_position_model=0.299343	new_cov=1/1	polymorphism_quality=2.6	quality=2.6	quality_position_model=2.91961e-08	ref_cov=127/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=128/129
RA	761	.	NC_007779	3930443	0	T	G	bias_e_value=1.15406e-16	bias_p_value=2.48382e-23	fisher_strand_p_value=4.35037e-25	frequency=9.661055e-02	genotype_quality=532.2	ks_quality_p_value=1	log10_base_likelihood=-10.6382	log10_qual_likelihood_position_model=34.2862	log10_strand_likelihood_position_model=24.3615	new_cov=35/0	polymorphism_quality=5.2	quality=5.2	quality_position_model=Inf	ref_cov=20/144	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=56/144
RA	762	.	NC_007779	3933153	0	G	T	bias_e_value=2.02745	bias_p_value=4.36356e-07	fisher_strand_p_value=2.35627e-08	frequency=5.821943e-02	genotype_quality=959.7	ks_quality_p_value=0.997456	log10_base_likelihood=-12.3263	log10_qual_likelihood_position_model=21.8697	log10_strand_likelihood_position_model=7.73196	new_cov=0/25	polymorphism_quality=6.9	quality=6.9	quality_position_model=Inf	ref_cov=143/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/151
RA	763	.	NC_007779	3952095	1	.	G	bias_e_value=12797.6	bias_p_value=0.00275435	fisher_strand_p_value=0.000563749	frequency=3.535366e-02	genotype_quality=909.3	ks_quality_p_value=0.536711	log10_base_likelihood=-31.9763	log10_qual_likelihood_position_model=2.88801	log10_strand_likelihood_position_model=3.24891	new_cov=7/0	polymorphism_quality=26.8	quality=26.8	quality_position_model=4.56044e-28	ref_cov=63/128	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,INDEL_HOMOPOLYMER	tot_cov=70/128
RA	764	.	NC_007779	3958620	0	C	.	bias_e_value=4337540	bias_p_value=0.933542	fisher_strand_p_value=1	frequency=1.008987e-02	genotype_quality=1222.0	ks_quality_p_value=0.658324	log10_base_likelihood=-7.80012	log10_qual_likelihood_position_model=2.24015	log10_strand_likelihood_position_model=0.390074	new_cov=1/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=4.62197e-07	ref_cov=134/160	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=135/162
RA	765	.	NC_007779	3968717	0	A	.	bias_e_value=3770550	bias_p_value=0.811511	fisher_strand_p_value=0.558022	frequency=9.543419e-03	genotype_quality=1266.1	ks_quality_p_value=0.811337	log10_base_likelihood=-7.55839	log10_qual_likelihood_position_model=3.24908	log10_strand_likelihood_position_model=0.582397	new_cov=2/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.48985e-05	ref_cov=115/196	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=117/197
RA	766	.	NC_007779	3977705	0	A	C	bias_e_value=0.00449532	bias_p_value=9.67498e-10	fisher_strand_p_value=3.874e-11	frequency=6.096458e-02	genotype_quality=639.2	ks_quality_p_value=1	log10_base_likelihood=-8.39472	log10_qual_likelihood_position_model=22.7757	log10_strand_likelihood_position_model=10.4118	new_cov=0/30	polymorphism_quality=2.9	quality=2.9	quality_position_model=Inf	ref_cov=126/88	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=126/118
RA	767	.	NC_007779	3981333	0	A	.	bias_e_value=4109360	bias_p_value=0.88443	fisher_strand_p_value=0.599184	frequency=1.097775e-02	genotype_quality=1090.9	ks_quality_p_value=0.933833	log10_base_likelihood=-7.72166	log10_qual_likelihood_position_model=1.56525	log10_strand_likelihood_position_model=0.458052	new_cov=2/1	polymorphism_quality=2.2	quality=2.2	quality_position_model=1.30816e-07	ref_cov=125/145	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=127/146
RA	768	.	NC_007779	3985138	0	T	G	bias_e_value=1.72209e-05	bias_p_value=3.70635e-12	fisher_strand_p_value=1.20544e-13	frequency=8.764505e-02	genotype_quality=692.4	ks_quality_p_value=1	log10_base_likelihood=-10.6724	log10_qual_likelihood_position_model=30.2364	log10_strand_likelihood_position_model=12.9792	new_cov=44/0	polymorphism_quality=5.3	quality=5.3	quality_position_model=Inf	ref_cov=107/125	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=153/125
RA	769	.	NC_007779	3986830	0	T	.	bias_e_value=3938940	bias_p_value=0.847753	fisher_strand_p_value=1	frequency=1.135349e-02	genotype_quality=1046.7	ks_quality_p_value=0.501705	log10_base_likelihood=-7.86613	log10_qual_likelihood_position_model=2.24326	log10_strand_likelihood_position_model=0.421043	new_cov=2/1	polymorphism_quality=2.4	quality=2.4	quality_position_model=4.2821e-07	ref_cov=131/130	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=133/131
RA	770	.	NC_007779	4000222	0	C	G	bias_e_value=10.4025	bias_p_value=2.23886e-06	fisher_strand_p_value=1.4141e-07	frequency=4.397869e-02	genotype_quality=1108.0	ks_quality_p_value=0.94056	log10_base_likelihood=-10.8698	log10_qual_likelihood_position_model=22.2976	log10_strand_likelihood_position_model=6.84952	new_cov=0/21	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=180/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=181/171
RA	771	.	NC_007779	4009388	1	.	A	bias_e_value=879028	bias_p_value=0.189188	fisher_strand_p_value=0.498893	frequency=5.037308e-03	genotype_quality=1960.8	ks_quality_p_value=0.0932138	log10_base_likelihood=-7.525	log10_qual_likelihood_position_model=1.27366	log10_strand_likelihood_position_model=0.587938	new_cov=2/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=1.42188e-07	ref_cov=200/195	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=202/195
RA	772	.	NC_007779	4009807	0	T	G	bias_e_value=7181.4	bias_p_value=0.00154561	fisher_strand_p_value=0.000158531	frequency=1.751614e-02	genotype_quality=604.5	ks_quality_p_value=1	log10_base_likelihood=-5.61508	log10_qual_likelihood_position_model=4.82876	log10_strand_likelihood_position_model=3.79989	new_cov=4/0	polymorphism_quality=0.1	quality=0.1	quality_position_model=Inf	ref_cov=17/154	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=21/154
RA	773	.	NC_007779	4010407	0	C	A	bias_e_value=61.9007	bias_p_value=1.33225e-05	fisher_strand_p_value=9.05861e-07	frequency=3.907871e-02	genotype_quality=841.5	ks_quality_p_value=0.985103	log10_base_likelihood=-10.3546	log10_qual_likelihood_position_model=15.1443	log10_strand_likelihood_position_model=6.04294	new_cov=0/12	polymorphism_quality=4.9	quality=4.9	quality_position_model=Inf	ref_cov=165/69	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=166/81
RA	774	.	NC_007779	4023064	1	.	G	bias_e_value=503652	bias_p_value=0.108398	fisher_strand_p_value=0.0604605	frequency=2.040768e-02	genotype_quality=1171.5	ks_quality_p_value=0.374444	log10_base_likelihood=-22.0057	log10_qual_likelihood_position_model=2.13305	log10_strand_likelihood_position_model=1.46103	new_cov=5/0	polymorphism_quality=16.7	quality=16.7	quality_position_model=1.44196e-20	ref_cov=121/119	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=126/119
RA	775	.	NC_007779	4029622	1	.	G	bias_e_value=740306	bias_p_value=0.159331	fisher_strand_p_value=0.0371326	frequency=1.261711e-02	genotype_quality=1526.7	ks_quality_p_value=0.999275	log10_base_likelihood=-15.1981	log10_qual_likelihood_position_model=3.21091	log10_strand_likelihood_position_model=1.43024	new_cov=4/0	polymorphism_quality=9.9	quality=9.9	quality_position_model=1.35169e-12	ref_cov=136/177	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=140/177
RA	776	.	NC_007779	4029633	0	T	G	bias_e_value=2.88749e-08	bias_p_value=6.21456e-15	fisher_strand_p_value=1.66469e-16	frequency=6.622696e-02	genotype_quality=704.2	ks_quality_p_value=1	log10_base_likelihood=-10.0553	log10_qual_likelihood_position_model=24.6742	log10_strand_likelihood_position_model=15.7787	new_cov=20/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=25/180	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=45/180
RA	777	.	NC_007779	4031691	1	.	T	bias_e_value=121148	bias_p_value=0.026074	fisher_strand_p_value=0.00559689	frequency=1.826477e-02	genotype_quality=1033.2	ks_quality_p_value=0.714298	log10_base_likelihood=-17.2807	log10_qual_likelihood_position_model=3.26459	log10_strand_likelihood_position_model=2.25205	new_cov=4/0	polymorphism_quality=12.0	quality=12.0	quality_position_model=7.96333e-14	ref_cov=57/158	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=61/158
RA	778	.	NC_007779	4031696	0	C	T	bias_e_value=0.429479	bias_p_value=9.24341e-08	fisher_strand_p_value=4.57536e-09	frequency=3.683853e-02	genotype_quality=803.5	ks_quality_p_value=1	log10_base_likelihood=-5.88387	log10_qual_likelihood_position_model=14.0448	log10_strand_likelihood_position_model=8.33957	new_cov=11/0	polymorphism_quality=0.3	quality=0.3	quality_position_model=Inf	ref_cov=32/179	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=44/179
RA	779	.	NC_007779	4037745	0	G	T	bias_e_value=17.0818	bias_p_value=3.67641e-06	fisher_strand_p_value=2.25477e-07	frequency=4.712296e-02	genotype_quality=1043.0	ks_quality_p_value=1	log10_base_likelihood=-11.1805	log10_qual_likelihood_position_model=16.963	log10_strand_likelihood_position_model=6.86267	new_cov=0/22	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=159/140	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=159/162
RA	780	.	NC_007779	4037805	0	G	T	bias_e_value=0.740058	bias_p_value=1.59278e-07	fisher_strand_p_value=8.11414e-09	frequency=4.269123e-02	genotype_quality=1151.8	ks_quality_p_value=1	log10_base_likelihood=-5.9418	log10_qual_likelihood_position_model=22.8333	log10_strand_likelihood_position_model=8.13728	new_cov=0/27	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=168/154	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=168/181
RA	781	.	NC_007779	4043703	0	C	A	bias_e_value=0.0129305	bias_p_value=2.78295e-09	fisher_strand_p_value=1.16576e-10	frequency=5.342627e-02	genotype_quality=1190.5	ks_quality_p_value=1	log10_base_likelihood=-16.1196	log10_qual_likelihood_position_model=20.1036	log10_strand_likelihood_position_model=10.1312	new_cov=32/0	polymorphism_quality=10.8	quality=10.8	quality_position_model=Inf	ref_cov=160/189	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=193/190
RA	782	.	NC_007779	4055100	0	G	T	bias_e_value=4.26372e-16	bias_p_value=9.17654e-23	fisher_strand_p_value=2.25837e-24	frequency=1.255417e-01	genotype_quality=906.3	ks_quality_p_value=0.72867	log10_base_likelihood=-47.385	log10_qual_likelihood_position_model=45.7532	log10_strand_likelihood_position_model=23.6462	new_cov=40/0	polymorphism_quality=42.3	quality=42.3	quality_position_model=Inf	ref_cov=50/201	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=90/201
RA	783	.	NC_007779	4055329	0	T	G	bias_e_value=6.81185e-28	bias_p_value=1.46607e-34	fisher_strand_p_value=1.75939e-36	frequency=1.654253e-01	genotype_quality=580.1	ks_quality_p_value=1	log10_base_likelihood=-39.4366	log10_qual_likelihood_position_model=46.6064	log10_strand_likelihood_position_model=35.7552	new_cov=44/1	polymorphism_quality=34.3	quality=34.3	quality_position_model=Inf	ref_cov=10/177	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=54/178
RA	784	.	NC_007779	4059484	1	.	T	bias_e_value=1736000	bias_p_value=0.373627	fisher_strand_p_value=0.23287	frequency=7.326126e-03	genotype_quality=1317.0	ks_quality_p_value=0.513681	log10_base_likelihood=-7.90085	log10_qual_likelihood_position_model=1.82934	log10_strand_likelihood_position_model=0.632886	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=2.43139e-07	ref_cov=130/141	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=132/141
RA	785	.	NC_007779	4062114	0	T	G	bias_e_value=2.74146e-27	bias_p_value=5.90026e-34	fisher_strand_p_value=7.20259e-36	frequency=1.535811e-01	genotype_quality=611.6	ks_quality_p_value=1	log10_base_likelihood=-24.8359	log10_qual_likelihood_position_model=49.5227	log10_strand_likelihood_position_model=35.1434	new_cov=53/1	polymorphism_quality=19.6	quality=19.6	quality_position_model=Inf	ref_cov=20/172	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/173
RA	786	.	NC_007779	4064463	0	G	T	bias_e_value=26.7114	bias_p_value=5.74892e-06	fisher_strand_p_value=3.63205e-07	frequency=5.746412e-02	genotype_quality=877.1	ks_quality_p_value=1	log10_base_likelihood=-11.2559	log10_qual_likelihood_position_model=16.6817	log10_strand_likelihood_position_model=6.47258	new_cov=0/22	polymorphism_quality=5.8	quality=5.8	quality_position_model=Inf	ref_cov=133/126	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/148
RA	787	.	NC_007779	4065564	0	C	G	bias_e_value=2776.83	bias_p_value=0.00059764	fisher_strand_p_value=5.53254e-05	frequency=3.126049e-02	genotype_quality=894.2	ks_quality_p_value=1	log10_base_likelihood=-5.59379	log10_qual_likelihood_position_model=9.38582	log10_strand_likelihood_position_model=4.25708	new_cov=11/0	polymorphism_quality=0.0	quality=0.0	quality_position_model=Inf	ref_cov=97/148	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=108/148
RA	788	.	NC_007779	4074542	0	C	A	bias_e_value=0.00158065	bias_p_value=3.40193e-10	fisher_strand_p_value=1.30639e-11	frequency=7.301807e-02	genotype_quality=775.8	ks_quality_p_value=0.99918	log10_base_likelihood=-17.3492	log10_qual_likelihood_position_model=22.222	log10_strand_likelihood_position_model=10.8839	new_cov=0/19	polymorphism_quality=12.0	quality=12.0	quality_position_model=Inf	ref_cov=158/48	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=158/67
RA	789	.	NC_007779	4076934	0	A	C	bias_e_value=1.56005e-14	bias_p_value=3.3576e-21	fisher_strand_p_value=6.44501e-23	frequency=1.405382e-01	genotype_quality=717.5	ks_quality_p_value=1	log10_base_likelihood=-28.7801	log10_qual_likelihood_position_model=40.1754	log10_strand_likelihood_position_model=22.1908	new_cov=0/51	polymorphism_quality=23.6	quality=23.6	quality_position_model=Inf	ref_cov=168/73	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=168/125
RA	790	.	NC_007779	4078140	0	C	G	bias_e_value=0.000146366	bias_p_value=3.15013e-11	fisher_strand_p_value=1.10407e-12	frequency=6.351995e-02	genotype_quality=836.0	ks_quality_p_value=1	log10_base_likelihood=-9.80878	log10_qual_likelihood_position_model=23.4613	log10_strand_likelihood_position_model=11.957	new_cov=21/0	polymorphism_quality=4.4	quality=4.4	quality_position_model=Inf	ref_cov=51/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=72/167
RA	791	.	NC_007779	4084209	0	A	G	bias_e_value=1.37193e-10	bias_p_value=2.95271e-17	fisher_strand_p_value=6.89592e-19	frequency=1.020613e-01	genotype_quality=852.9	ks_quality_p_value=1	log10_base_likelihood=-16.4954	log10_qual_likelihood_position_model=27.1067	log10_strand_likelihood_position_model=18.1614	new_cov=40/0	polymorphism_quality=11.2	quality=11.2	quality_position_model=Inf	ref_cov=78/180	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=118/180
RA	792	.	NC_007779	4090749	0	A	T	frequency=1	genotype_quality=1354.5	new_cov=170/175	quality=1354.5	ref_cov=0/0	tot_cov=171/175
RA	793	.	NC_007779	4098730	0	G	T	bias_e_value=0.151862	bias_p_value=3.26844e-08	fisher_strand_p_value=1.53574e-09	frequency=5.582094e-02	genotype_quality=969.8	ks_quality_p_value=0.999417	log10_base_likelihood=-9.10096	log10_qual_likelihood_position_model=22.3402	log10_strand_likelihood_position_model=8.81368	new_cov=0/27	polymorphism_quality=3.6	quality=3.6	quality_position_model=Inf	ref_cov=161/130	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/157
RA	794	.	NC_007779	4115400	1	.	C	bias_e_value=949755	bias_p_value=0.20441	fisher_strand_p_value=0.0534451	frequency=1.110172e-02	genotype_quality=855.3	ks_quality_p_value=0.964563	log10_base_likelihood=-5.75766	log10_qual_likelihood_position_model=3.42894	log10_strand_likelihood_position_model=1.27209	new_cov=0/2	polymorphism_quality=0.2	quality=0.2	quality_position_model=0.0120622	ref_cov=138/40	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=138/42
RA	795	.	NC_007779	4128669	1	.	T	bias_e_value=1738940	bias_p_value=0.37426	fisher_strand_p_value=1	frequency=8.287430e-03	genotype_quality=1740.1	ks_quality_p_value=0.119919	log10_base_likelihood=-11.819	log10_qual_likelihood_position_model=2.58563	log10_strand_likelihood_position_model=0.379614	new_cov=1/2	polymorphism_quality=6.4	quality=6.4	quality_position_model=7.42536e-11	ref_cov=157/202	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=158/204
RA	796	.	NC_007779	4147012	0	A	C	bias_e_value=8.07963e-06	bias_p_value=1.73893e-12	fisher_strand_p_value=5.51539e-14	frequency=9.559441e-02	genotype_quality=893.2	ks_quality_p_value=1	log10_base_likelihood=-23.9656	log10_qual_likelihood_position_model=34.2055	log10_strand_likelihood_position_model=13.4105	new_cov=0/41	polymorphism_quality=18.7	quality=18.7	quality_position_model=Inf	ref_cov=161/123	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=161/164
RA	797	.	NC_007779	4148399	0	A	C	bias_e_value=3.36982e-20	bias_p_value=7.25265e-27	fisher_strand_p_value=1.1095e-28	frequency=1.190619e-01	genotype_quality=757.3	ks_quality_p_value=1	log10_base_likelihood=-23.4993	log10_qual_likelihood_position_model=46.4484	log10_strand_likelihood_position_model=27.9549	new_cov=0/57	polymorphism_quality=18.2	quality=18.2	quality_position_model=Inf	ref_cov=182/60	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=182/117
RA	798	.	NC_007779	4148399	1	.	C	bias_e_value=217104	bias_p_value=0.0467258	fisher_strand_p_value=0.00802057	frequency=1.686668e-02	genotype_quality=1347.6	ks_quality_p_value=1	log10_base_likelihood=-11.9628	log10_qual_likelihood_position_model=4.72759	log10_strand_likelihood_position_model=2.09579	new_cov=0/5	polymorphism_quality=6.6	quality=6.6	quality_position_model=4.97169e-07	ref_cov=182/109	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=182/114
RA	799	.	NC_007779	4157323	0	C	A	bias_e_value=1947.06	bias_p_value=0.000419052	fisher_strand_p_value=4.13628e-05	frequency=4.045773e-02	genotype_quality=831.5	ks_quality_p_value=0.905149	log10_base_likelihood=-6.78842	log10_qual_likelihood_position_model=18.6204	log10_strand_likelihood_position_model=4.40389	new_cov=16/0	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=125/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=146/118
RA	800	.	NC_007779	4165991	0	A	C	frequency=1	genotype_quality=1467.0	new_cov=185/161	quality=1467.0	ref_cov=0/0	tot_cov=186/161
RA	801	.	NC_007779	4174730	0	T	.	bias_e_value=3440600	bias_p_value=0.740498	fisher_strand_p_value=0.62197	frequency=1.605320e-02	genotype_quality=975.1	ks_quality_p_value=0.599144	log10_base_likelihood=-10.9576	log10_qual_likelihood_position_model=2.02428	log10_strand_likelihood_position_model=0.598565	new_cov=1/3	polymorphism_quality=5.5	quality=5.5	quality_position_model=2.52488e-10	ref_cov=123/122	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=124/125
RA	802	.	NC_007779	4190480	0	A	C	bias_e_value=0.000388987	bias_p_value=8.37191e-11	fisher_strand_p_value=3.04427e-12	frequency=5.181217e-02	genotype_quality=851.3	ks_quality_p_value=0.99935	log10_base_likelihood=-6.35719	log10_qual_likelihood_position_model=24.8646	log10_strand_likelihood_position_model=11.5165	new_cov=0/24	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=182/78	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=182/103
RA	803	.	NC_007779	4197133	1	.	G	bias_e_value=2545560	bias_p_value=0.547865	fisher_strand_p_value=0.231681	frequency=7.843018e-03	genotype_quality=1252.1	ks_quality_p_value=0.93471	log10_base_likelihood=-7.66767	log10_qual_likelihood_position_model=1.9445	log10_strand_likelihood_position_model=0.635109	new_cov=2/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=5.62186e-07	ref_cov=121/132	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=123/132
RA	804	.	NC_007779	4197139	0	T	G	bias_e_value=9.66972e-05	bias_p_value=2.08115e-11	fisher_strand_p_value=7.18593e-13	frequency=8.154583e-02	genotype_quality=513.3	ks_quality_p_value=1	log10_base_likelihood=-21.2531	log10_qual_likelihood_position_model=18.3049	log10_strand_likelihood_position_model=12.1435	new_cov=16/0	polymorphism_quality=16.0	quality=16.0	quality_position_model=Inf	ref_cov=20/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=36/134
RA	805	.	NC_007779	4200494	0	T	G	bias_e_value=0.00316536	bias_p_value=6.81261e-10	fisher_strand_p_value=2.68854e-11	frequency=7.314205e-02	genotype_quality=662.1	ks_quality_p_value=1	log10_base_likelihood=-8.26155	log10_qual_likelihood_position_model=27.853	log10_strand_likelihood_position_model=10.5705	new_cov=28/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=82/133	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=110/133
RA	806	.	NC_007779	4207565	0	C	A	bias_e_value=599.214	bias_p_value=0.000128965	fisher_strand_p_value=1.03336e-05	frequency=4.236221e-02	genotype_quality=811.0	ks_quality_p_value=1	log10_base_likelihood=-6.96019	log10_qual_likelihood_position_model=15.7583	log10_strand_likelihood_position_model=5.092	new_cov=17/0	polymorphism_quality=1.4	quality=1.4	quality_position_model=Inf	ref_cov=115/123	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/123
RA	807	.	NC_007779	4211222	0	C	A	bias_e_value=333.056	bias_p_value=7.16815e-05	fisher_strand_p_value=5.4647e-06	frequency=3.322887e-02	genotype_quality=1158.3	ks_quality_p_value=1	log10_base_likelihood=-8.56126	log10_qual_likelihood_position_model=11.8331	log10_strand_likelihood_position_model=5.26243	new_cov=16/0	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=147/176	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=163/176
RA	808	.	NC_007779	4211657	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	809	.	NC_007779	4211658	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	810	.	NC_007779	4211659	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	811	.	NC_007779	4211662	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	812	.	NC_007779	4211664	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	813	.	NC_007779	4211665	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	814	.	NC_007779	4211666	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	815	.	NC_007779	4211667	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	816	.	NC_007779	4211668	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	817	.	NC_007779	4211670	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	818	.	NC_007779	4211671	0	C	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	819	.	NC_007779	4211673	0	T	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	820	.	NC_007779	4211674	0	G	A	frequency=1	genotype_quality=-0.5	new_cov=0/0	quality=-0.5	ref_cov=1/0	reject=EVALUE	tot_cov=1/0
RA	821	.	NC_007779	4219520	0	C	A	bias_e_value=159.811	bias_p_value=3.43951e-05	fisher_strand_p_value=2.52944e-06	frequency=4.125023e-02	genotype_quality=992.9	ks_quality_p_value=0.977546	log10_base_likelihood=-8.23237	log10_qual_likelihood_position_model=18.8968	log10_strand_likelihood_position_model=5.69534	new_cov=19/0	polymorphism_quality=2.8	quality=2.8	quality_position_model=Inf	ref_cov=134/143	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=154/143
RA	822	.	NC_007779	4220019	0	A	C	bias_e_value=5.43358e-07	bias_p_value=1.16943e-13	fisher_strand_p_value=3.40817e-15	frequency=1.146226e-01	genotype_quality=627.1	ks_quality_p_value=1	log10_base_likelihood=-15.2354	log10_qual_likelihood_position_model=49.9118	log10_strand_likelihood_position_model=14.5621	new_cov=0/51	polymorphism_quality=9.9	quality=9.9	quality_position_model=Inf	ref_cov=115/99	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=115/150
RA	823	.	NC_007779	4226513	0	C	A	bias_e_value=0.0733921	bias_p_value=1.57957e-08	fisher_strand_p_value=7.16125e-10	frequency=6.057978e-02	genotype_quality=1036.2	ks_quality_p_value=1	log10_base_likelihood=-14.0742	log10_qual_likelihood_position_model=20.0625	log10_strand_likelihood_position_model=9.14501	new_cov=27/0	polymorphism_quality=8.7	quality=8.7	quality_position_model=Inf	ref_cov=126/165	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=153/165
RA	824	.	NC_007779	4227183	0	T	G	bias_e_value=1.54058e-22	bias_p_value=3.31569e-29	fisher_strand_p_value=4.68075e-31	frequency=1.133747e-01	genotype_quality=822.6	ks_quality_p_value=1	log10_base_likelihood=-25.9481	log10_qual_likelihood_position_model=45.497	log10_strand_likelihood_position_model=30.3297	new_cov=58/0	polymorphism_quality=20.7	quality=20.7	quality_position_model=Inf	ref_cov=60/204	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=118/204
RA	825	.	NC_007779	4244592	0	G	C	bias_e_value=0.222401	bias_p_value=4.7866e-08	fisher_strand_p_value=2.29086e-09	frequency=3.653431e-02	genotype_quality=670.2	ks_quality_p_value=1	log10_base_likelihood=-9.41042	log10_qual_likelihood_position_model=8.37621	log10_strand_likelihood_position_model=8.64	new_cov=0/7	polymorphism_quality=4.0	quality=4.0	quality_position_model=Inf	ref_cov=158/6	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=158/13
RA	826	.	NC_007779	4294403	0	C	G	bias_e_value=0.750274	bias_p_value=1.61477e-07	fisher_strand_p_value=8.23222e-09	frequency=4.558372e-02	genotype_quality=1084.3	ks_quality_p_value=1	log10_base_likelihood=-8.68228	log10_qual_likelihood_position_model=17.4091	log10_strand_likelihood_position_model=8.08448	new_cov=20/0	polymorphism_quality=3.2	quality=3.2	quality_position_model=Inf	ref_cov=114/191	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=134/191
RA	827	.	NC_007779	4296690	0	G	.	bias_e_value=4274100	bias_p_value=0.919888	fisher_strand_p_value=1	frequency=1.245403e-02	genotype_quality=1334.7	ks_quality_p_value=0.627426	log10_base_likelihood=-11.2353	log10_qual_likelihood_position_model=1.81183	log10_strand_likelihood_position_model=0.425161	new_cov=2/2	polymorphism_quality=5.8	quality=5.8	quality_position_model=5.28197e-11	ref_cov=166/151	reject=INDEL_HOMOPOLYMER	tot_cov=168/153
RA	828	.	NC_007779	4304641	0	T	G	bias_e_value=3.29024e-15	bias_p_value=7.08138e-22	fisher_strand_p_value=1.31912e-23	frequency=1.003690e-01	genotype_quality=574.3	ks_quality_p_value=1	log10_base_likelihood=-13.5557	log10_qual_likelihood_position_model=34.4272	log10_strand_likelihood_position_model=22.8797	new_cov=38/0	polymorphism_quality=8.2	quality=8.2	quality_position_model=Inf	ref_cov=32/150	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=70/150
RA	829	.	NC_007779	4309615	0	C	G	bias_e_value=3.11527	bias_p_value=6.70479e-07	fisher_strand_p_value=3.70491e-08	frequency=6.781149e-02	genotype_quality=717.8	ks_quality_p_value=0.999183	log10_base_likelihood=-13.2803	log10_qual_likelihood_position_model=20.2524	log10_strand_likelihood_position_model=7.43122	new_cov=18/0	polymorphism_quality=7.9	quality=7.9	quality_position_model=Inf	ref_cov=72/129	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=90/129
RA	830	.	NC_007779	4312218	0	T	G	bias_e_value=9.71037e-06	bias_p_value=2.0899e-12	fisher_strand_p_value=6.66874e-14	frequency=5.750418e-02	genotype_quality=918.1	ks_quality_p_value=1	log10_base_likelihood=-10.9291	log10_qual_likelihood_position_model=37.3099	log10_strand_likelihood_position_model=13.176	new_cov=35/0	polymorphism_quality=5.5	quality=5.5	quality_position_model=Inf	ref_cov=108/173	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=143/173
RA	831	.	NC_007779	4318992	0	T	G	bias_e_value=0.978957	bias_p_value=2.10695e-07	fisher_strand_p_value=1.08972e-08	frequency=2.614880e-02	genotype_quality=789.3	ks_quality_p_value=1	log10_base_likelihood=-6.22687	log10_qual_likelihood_position_model=11.854	log10_strand_likelihood_position_model=7.9674	new_cov=2/8	polymorphism_quality=0.7	quality=0.7	quality_position_model=Inf	ref_cov=224/11	reject=EVALUE,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=227/19
RA	832	.	NC_007779	4318994	0	A	G	bias_e_value=0.00682838	bias_p_value=1.46963e-09	fisher_strand_p_value=5.98907e-11	frequency=3.727818e-02	genotype_quality=820.2	ks_quality_p_value=1	log10_base_likelihood=-12.0768	log10_qual_likelihood_position_model=15.8219	log10_strand_likelihood_position_model=10.2244	new_cov=1/9	polymorphism_quality=6.7	quality=6.7	quality_position_model=Inf	ref_cov=227/9	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=229/18
RA	833	.	NC_007779	4318999	1	.	C	bias_e_value=148024	bias_p_value=0.0318583	fisher_strand_p_value=0.00507538	frequency=1.282215e-02	genotype_quality=1110.2	ks_quality_p_value=0.998801	log10_base_likelihood=-7.78866	log10_qual_likelihood_position_model=2.98091	log10_strand_likelihood_position_model=2.29453	new_cov=0/2	polymorphism_quality=2.3	quality=2.3	quality_position_model=0.000290588	ref_cov=215/15	reject=POLYMORPHISM_STRAND	tot_cov=215/18
RA	834	.	NC_007779	4321435	0	G	C	bias_e_value=0.849629	bias_p_value=1.8286e-07	fisher_strand_p_value=9.42186e-09	frequency=3.747463e-02	genotype_quality=717.1	ks_quality_p_value=0.996096	log10_base_likelihood=-12.6507	log10_qual_likelihood_position_model=7.39765	log10_strand_likelihood_position_model=8.02586	new_cov=7/0	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=9/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=16/167
RA	835	.	NC_007779	4337469	0	A	C	bias_e_value=3.59885e-19	bias_p_value=7.74557e-26	fisher_strand_p_value=1.23018e-27	frequency=1.446505e-01	genotype_quality=589.6	ks_quality_p_value=1	log10_base_likelihood=-29.7258	log10_qual_likelihood_position_model=35.7912	log10_strand_likelihood_position_model=26.91	new_cov=0/41	polymorphism_quality=24.5	quality=24.5	quality_position_model=Inf	ref_cov=163/27	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=163/68
RA	836	.	NC_007779	4346787	0	A	C	bias_e_value=0.0901763	bias_p_value=1.94081e-08	fisher_strand_p_value=8.88592e-10	frequency=5.757713e-02	genotype_quality=778.8	ks_quality_p_value=1	log10_base_likelihood=-10.2591	log10_qual_likelihood_position_model=31.7283	log10_strand_likelihood_position_model=9.0742	new_cov=0/32	polymorphism_quality=4.8	quality=4.8	quality_position_model=Inf	ref_cov=129/124	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/156
RA	837	.	NC_007779	4348529	0	T	G	bias_e_value=3.63266e-16	bias_p_value=7.81834e-23	fisher_strand_p_value=1.39795e-24	frequency=1.277905e-01	genotype_quality=587.6	ks_quality_p_value=1	log10_base_likelihood=-26.3398	log10_qual_likelihood_position_model=39.4025	log10_strand_likelihood_position_model=23.8545	new_cov=40/0	polymorphism_quality=21.1	quality=21.1	quality_position_model=Inf	ref_cov=34/156	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=75/156
RA	838	.	NC_007779	4371271	0	A	.	frequency=1	genotype_quality=1147.5	new_cov=123/106	quality=1147.5	ref_cov=0/0	tot_cov=123/106
RA	839	.	NC_007779	4371272	0	A	.	frequency=1	genotype_quality=1147.5	new_cov=123/106	quality=1147.5	ref_cov=0/0	tot_cov=123/106
RA	840	.	NC_007779	4372630	0	T	.	bias_e_value=4115610	bias_p_value=0.885776	fisher_strand_p_value=0.611919	frequency=1.066589e-02	genotype_quality=1119.1	ks_quality_p_value=0.918199	log10_base_likelihood=-7.8107	log10_qual_likelihood_position_model=2.58468	log10_strand_likelihood_position_model=0.439107	new_cov=2/1	polymorphism_quality=2.3	quality=2.3	quality_position_model=1.15694e-06	ref_cov=134/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=136/145
RA	841	.	NC_007779	4392814	0	G	T	bias_e_value=126.022	bias_p_value=2.71228e-05	fisher_strand_p_value=1.91464e-06	frequency=4.279804e-02	genotype_quality=995.2	ks_quality_p_value=1	log10_base_likelihood=-7.6194	log10_qual_likelihood_position_model=16.2596	log10_strand_likelihood_position_model=5.71791	new_cov=0/18	polymorphism_quality=2.1	quality=2.1	quality_position_model=Inf	ref_cov=147/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=147/145
RA	842	.	NC_007779	4396933	1	.	A	bias_e_value=2015680	bias_p_value=0.433823	fisher_strand_p_value=0.49874	frequency=5.390167e-03	genotype_quality=1818.8	ks_quality_p_value=0.299971	log10_base_likelihood=-7.46277	log10_qual_likelihood_position_model=1.44773	log10_strand_likelihood_position_model=0.591576	new_cov=2/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=2.52107e-07	ref_cov=186/183	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=188/183
RA	843	.	NC_007779	4414725	0	T	.	bias_e_value=3972640	bias_p_value=0.855006	fisher_strand_p_value=1	frequency=1.711273e-02	genotype_quality=1105.2	ks_quality_p_value=0.512384	log10_base_likelihood=-13.9311	log10_qual_likelihood_position_model=3.22182	log10_strand_likelihood_position_model=0.466066	new_cov=2/3	polymorphism_quality=8.6	quality=8.6	quality_position_model=2.82428e-12	ref_cov=102/184	reject=INDEL_HOMOPOLYMER	tot_cov=104/188
RA	844	.	NC_007779	4419586	0	T	G	bias_e_value=8.59357e-13	bias_p_value=1.84954e-19	fisher_strand_p_value=3.85276e-21	frequency=1.855626e-01	genotype_quality=563.4	ks_quality_p_value=1	log10_base_likelihood=-41.1834	log10_qual_likelihood_position_model=39.5665	log10_strand_likelihood_position_model=20.4142	new_cov=56/0	polymorphism_quality=36.1	quality=36.1	quality_position_model=Inf	ref_cov=73/131	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=129/131
RA	845	.	NC_007779	4423038	0	C	G	bias_e_value=1.01431e-05	bias_p_value=2.18302e-12	fisher_strand_p_value=6.97592e-14	frequency=7.214737e-02	genotype_quality=791.6	ks_quality_p_value=1	log10_base_likelihood=-13.3663	log10_qual_likelihood_position_model=20.5387	log10_strand_likelihood_position_model=13.1564	new_cov=20/0	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=37/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=57/167
RA	846	.	NC_007779	4429120	0	G	T	bias_e_value=0.000141108	bias_p_value=3.03698e-11	fisher_strand_p_value=1.35846e-12	frequency=5.122328e-02	genotype_quality=1087.1	ks_quality_p_value=0.7825	log10_base_likelihood=-8.02405	log10_qual_likelihood_position_model=39.3957	log10_strand_likelihood_position_model=11.867	new_cov=0/33	polymorphism_quality=2.5	quality=2.5	quality_position_model=Inf	ref_cov=185/127	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=185/161
RA	847	.	NC_007779	4444139	0	A	.	bias_e_value=4344420	bias_p_value=0.935021	fisher_strand_p_value=1	frequency=7.905960e-03	genotype_quality=1484.0	ks_quality_p_value=0.661886	log10_base_likelihood=-7.50499	log10_qual_likelihood_position_model=2.24743	log10_strand_likelihood_position_model=0.374923	new_cov=2/1	polymorphism_quality=2.0	quality=2.0	quality_position_model=9.19623e-07	ref_cov=215/161	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=217/162
RA	848	.	NC_007779	4477098	1	.	A	bias_e_value=4627180	bias_p_value=0.995878	fisher_strand_p_value=1	frequency=7.091522e-03	genotype_quality=1364.6	ks_quality_p_value=0.910585	log10_base_likelihood=-7.59168	log10_qual_likelihood_position_model=2.68944	log10_strand_likelihood_position_model=0.319606	new_cov=1/1	polymorphism_quality=2.1	quality=2.1	quality_position_model=1.88946e-06	ref_cov=170/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=171/111
RA	849	.	NC_007779	4483915	0	G	T	bias_e_value=51.2934	bias_p_value=1.10396e-05	fisher_strand_p_value=7.35879e-07	frequency=3.371716e-02	genotype_quality=1212.0	ks_quality_p_value=0.991482	log10_base_likelihood=-6.3035	log10_qual_likelihood_position_model=17.454	log10_strand_likelihood_position_model=6.19655	new_cov=0/21	polymorphism_quality=0.8	quality=0.8	quality_position_model=Inf	ref_cov=173/167	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=173/188
RA	850	.	NC_007779	4486358	0	G	T	bias_e_value=5101.58	bias_p_value=0.00109798	fisher_strand_p_value=0.000109265	frequency=4.078579e-02	genotype_quality=680.2	ks_quality_p_value=0.992008	log10_base_likelihood=-7.16809	log10_qual_likelihood_position_model=12.5984	log10_strand_likelihood_position_model=3.96152	new_cov=9/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=Inf	ref_cov=64/121	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=73/121
RA	851	.	NC_007779	4509629	1	.	T	bias_e_value=2875280	bias_p_value=0.618828	fisher_strand_p_value=1	frequency=1.102924e-02	genotype_quality=1326.6	ks_quality_p_value=0.266434	log10_base_likelihood=-12.3502	log10_qual_likelihood_position_model=1.49973	log10_strand_likelihood_position_model=0.386143	new_cov=1/2	polymorphism_quality=7.0	quality=7.0	quality_position_model=1.68008e-12	ref_cov=121/148	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=122/150
RA	852	.	NC_007779	4514698	0	A	G	bias_e_value=4632190	bias_p_value=0.996956	fisher_strand_p_value=1	frequency=1.191235e-02	genotype_quality=1387.7	ks_quality_p_value=0.923001	log10_base_likelihood=-7.95605	log10_qual_likelihood_position_model=4.07524	log10_strand_likelihood_position_model=0.476682	new_cov=3/2	polymorphism_quality=2.5	quality=2.5	quality_position_model=3.26375e-05	ref_cov=190/165	tot_cov=193/167
RA	853	.	NC_007779	4515413	0	T	G	bias_e_value=1.64003e-12	bias_p_value=3.52974e-19	fisher_strand_p_value=7.4553e-21	frequency=5.716276e-02	genotype_quality=781.8	ks_quality_p_value=1	log10_base_likelihood=-5.92548	log10_qual_likelihood_position_model=35.2389	log10_strand_likelihood_position_model=20.1275	new_cov=36/0	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=53/185	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=89/185
RA	854	.	NC_007779	4515952	0	G	T	bias_e_value=12.9366	bias_p_value=2.78425e-06	fisher_strand_p_value=1.67716e-07	frequency=3.969479e-02	genotype_quality=1128.8	ks_quality_p_value=1	log10_base_likelihood=-5.97307	log10_qual_likelihood_position_model=30.3995	log10_strand_likelihood_position_model=6.90079	new_cov=0/30	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=151/201	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/231
RA	855	.	NC_007779	4540870	0	T	G	bias_e_value=2.29294e-31	bias_p_value=4.93495e-38	fisher_strand_p_value=5.39827e-40	frequency=1.874294e-01	genotype_quality=574.0	ks_quality_p_value=1	log10_base_likelihood=-34.1425	log10_qual_likelihood_position_model=50.9088	log10_strand_likelihood_position_model=39.2677	new_cov=65/0	polymorphism_quality=29.0	quality=29.0	quality_position_model=Inf	ref_cov=26/166	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=91/167
RA	856	.	NC_007779	4540877	0	A	T	bias_e_value=3.48125e-14	bias_p_value=7.49248e-21	fisher_strand_p_value=1.46116e-22	frequency=1.374459e-01	genotype_quality=788.9	ks_quality_p_value=1	log10_base_likelihood=-37.329	log10_qual_likelihood_position_model=31.2383	log10_strand_likelihood_position_model=21.8353	new_cov=34/0	polymorphism_quality=32.2	quality=32.2	quality_position_model=Inf	ref_cov=33/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=67/167
RA	857	.	NC_007779	4541066	0	C	G	bias_e_value=4.47913	bias_p_value=9.64014e-07	fisher_strand_p_value=5.45875e-08	frequency=6.984282e-02	genotype_quality=609.6	ks_quality_p_value=0.996204	log10_base_likelihood=-12.6576	log10_qual_likelihood_position_model=16.2036	log10_strand_likelihood_position_model=7.26291	new_cov=0/13	polymorphism_quality=7.3	quality=7.3	quality_position_model=Inf	ref_cov=120/39	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=121/53
RA	858	.	NC_007779	4542789	0	A	C	bias_e_value=8.73731e-06	bias_p_value=1.88047e-12	fisher_strand_p_value=5.97967e-14	frequency=9.157276e-02	genotype_quality=702.8	ks_quality_p_value=1	log10_base_likelihood=-13.3692	log10_qual_likelihood_position_model=29.5138	log10_strand_likelihood_position_model=13.2233	new_cov=0/33	polymorphism_quality=8.0	quality=8.0	quality_position_model=Inf	ref_cov=143/78	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=143/111
RA	859	.	NC_007779	4546535	0	T	A	frequency=1	genotype_quality=990.6	new_cov=145/100	quality=990.6	ref_cov=0/0	tot_cov=145/100
RA	860	.	NC_007779	4554527	1	.	C	bias_e_value=1366350	bias_p_value=0.29407	fisher_strand_p_value=0.0935441	frequency=8.657455e-03	genotype_quality=1066.8	ks_quality_p_value=0.906651	log10_base_likelihood=-7.21406	log10_qual_likelihood_position_model=3.16904	log10_strand_likelihood_position_model=1.02898	new_cov=2/0	polymorphism_quality=1.7	quality=1.7	quality_position_model=8.42142e-05	ref_cov=69/160	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=71/160
RA	861	.	NC_007779	4554532	0	T	C	bias_e_value=5.45401	bias_p_value=1.17383e-06	fisher_strand_p_value=6.71336e-08	frequency=4.339695e-02	genotype_quality=679.1	ks_quality_p_value=0.998088	log10_base_likelihood=-11.521	log10_qual_likelihood_position_model=10.4858	log10_strand_likelihood_position_model=7.17306	new_cov=11/0	polymorphism_quality=6.1	quality=6.1	quality_position_model=Inf	ref_cov=42/167	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=53/167
RA	862	.	NC_007779	4555389	0	C	A	bias_e_value=1715.77	bias_p_value=0.000369274	fisher_strand_p_value=3.42358e-05	frequency=2.708626e-02	genotype_quality=1016.2	ks_quality_p_value=0.951874	log10_base_likelihood=-5.73549	log10_qual_likelihood_position_model=19.1365	log10_strand_likelihood_position_model=4.46552	new_cov=14/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=130/149	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=144/149
RA	863	.	NC_007779	4557828	0	A	.	bias_e_value=4581410	bias_p_value=0.986026	fisher_strand_p_value=1	frequency=1.431656e-02	genotype_quality=1358.1	ks_quality_p_value=0.837551	log10_base_likelihood=-13.587	log10_qual_likelihood_position_model=2.91749	log10_strand_likelihood_position_model=0.474333	new_cov=3/2	polymorphism_quality=8.2	quality=8.2	quality_position_model=3.16173e-12	ref_cov=185/158	reject=INDEL_HOMOPOLYMER	tot_cov=188/161
RA	864	.	NC_007779	4559786	0	C	A	bias_e_value=63.8976	bias_p_value=1.37523e-05	fisher_strand_p_value=9.23259e-07	frequency=3.970337e-02	genotype_quality=906.6	ks_quality_p_value=1	log10_base_likelihood=-5.75499	log10_qual_likelihood_position_model=20.1684	log10_strand_likelihood_position_model=6.05602	new_cov=21/0	polymorphism_quality=0.2	quality=0.2	quality_position_model=Inf	ref_cov=125/128	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=146/129
RA	865	.	NC_007779	4561440	1	.	T	bias_e_value=1342660	bias_p_value=0.288972	fisher_strand_p_value=0.124784	frequency=7.017136e-03	genotype_quality=1384.8	ks_quality_p_value=0.663194	log10_base_likelihood=-8.07398	log10_qual_likelihood_position_model=1.41961	log10_strand_likelihood_position_model=0.903842	new_cov=0/2	polymorphism_quality=2.6	quality=2.6	quality_position_model=1.15516e-07	ref_cov=184/99	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=184/101
RA	866	.	NC_007779	4573184	0	T	G	bias_e_value=2.57727e-19	bias_p_value=5.5469e-26	fisher_strand_p_value=8.76261e-28	frequency=1.021523e-01	genotype_quality=765.3	ks_quality_p_value=1	log10_base_likelihood=-10.0366	log10_qual_likelihood_position_model=43.635	log10_strand_likelihood_position_model=27.0574	new_cov=74/0	polymorphism_quality=4.6	quality=4.6	quality_position_model=Inf	ref_cov=93/169	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=171/169
RA	867	.	NC_007779	4578176	0	A	G	bias_e_value=0.00667623	bias_p_value=1.43688e-09	fisher_strand_p_value=5.85002e-11	frequency=4.927731e-02	genotype_quality=777.8	ks_quality_p_value=1	log10_base_likelihood=-6.5665	log10_qual_likelihood_position_model=17.9404	log10_strand_likelihood_position_model=10.2328	new_cov=14/0	polymorphism_quality=1.0	quality=1.0	quality_position_model=Inf	ref_cov=32/172	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=46/172
RA	868	.	NC_007779	4581670	0	C	A	bias_e_value=0.294267	bias_p_value=6.33333e-08	fisher_strand_p_value=3.17392e-09	frequency=4.578686e-02	genotype_quality=962.5	ks_quality_p_value=0.968647	log10_base_likelihood=-8.53032	log10_qual_likelihood_position_model=22.116	log10_strand_likelihood_position_model=8.4984	new_cov=0/17	polymorphism_quality=3.1	quality=3.1	quality_position_model=Inf	ref_cov=179/74	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=179/91
RA	869	.	NC_007779	4584556	0	C	A	bias_e_value=15.9877	bias_p_value=3.44093e-06	fisher_strand_p_value=2.1433e-07	frequency=6.155205e-02	genotype_quality=964.4	ks_quality_p_value=0.980387	log10_base_likelihood=-18.1054	log10_qual_likelihood_position_model=20.3497	log10_strand_likelihood_position_model=6.85192	new_cov=22/0	polymorphism_quality=12.8	quality=12.8	quality_position_model=Inf	ref_cov=127/145	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=151/145
RA	870	.	NC_007779	4584731	0	G	T	bias_e_value=0.609882	bias_p_value=1.31261e-07	fisher_strand_p_value=6.61816e-09	frequency=3.600693e-02	genotype_quality=986.1	ks_quality_p_value=1	log10_base_likelihood=-6.79591	log10_qual_likelihood_position_model=15.1001	log10_strand_likelihood_position_model=8.17926	new_cov=0/18	polymorphism_quality=1.3	quality=1.3	quality_position_model=Inf	ref_cov=189/93	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=189/115
RA	871	.	NC_007779	4585127	1	.	A	bias_e_value=4646330	bias_p_value=1	fisher_strand_p_value=1	frequency=6.531715e-03	genotype_quality=1503.3	ks_quality_p_value=1	log10_base_likelihood=-6.42677	log10_qual_likelihood_position_model=2.83648	log10_strand_likelihood_position_model=0.299775	new_cov=1/1	polymorphism_quality=0.9	quality=0.9	quality_position_model=4.305e-05	ref_cov=155/149	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/150
RA	872	.	NC_007779	4597497	0	G	T	bias_e_value=3482130	bias_p_value=0.749436	fisher_strand_p_value=0.57713	frequency=1.356030e-02	genotype_quality=867.1	ks_quality_p_value=0.661578	log10_base_likelihood=-6.08001	log10_qual_likelihood_position_model=2.5952	log10_strand_likelihood_position_model=0.502221	new_cov=2/1	polymorphism_quality=0.5	quality=0.5	quality_position_model=9.14109e-05	ref_cov=92/125	reject=EVALUE,POLYMORPHISM_STRAND	tot_cov=94/126
RA	873	.	NC_007779	4598763	0	A	C	bias_e_value=66.4792	bias_p_value=1.43079e-05	fisher_strand_p_value=9.63306e-07	frequency=4.070950e-02	genotype_quality=808.7	ks_quality_p_value=1	log10_base_likelihood=-5.99224	log10_qual_likelihood_position_model=20.5475	log10_strand_likelihood_position_model=6.17802	new_cov=0/20	polymorphism_quality=0.4	quality=0.4	quality_position_model=Inf	ref_cov=133/118	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=133/139
RA	874	.	NC_007779	4599760	0	C	A	bias_e_value=20.3856	bias_p_value=4.38747e-06	fisher_strand_p_value=2.72233e-07	frequency=3.144264e-02	genotype_quality=1157.5	ks_quality_p_value=1	log10_base_likelihood=-7.06061	log10_qual_likelihood_position_model=17.0364	log10_strand_likelihood_position_model=6.56506	new_cov=17/0	polymorphism_quality=1.5	quality=1.5	quality_position_model=Inf	ref_cov=123/189	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=141/189
RA	875	.	NC_007779	4610766	1	.	G	bias_e_value=3518870	bias_p_value=0.757345	fisher_strand_p_value=0.537317	frequency=6.557465e-03	genotype_quality=1446.9	ks_quality_p_value=0.726061	log10_base_likelihood=-7.89371	log10_qual_likelihood_position_model=1.53006	log10_strand_likelihood_position_model=0.389337	new_cov=2/0	polymorphism_quality=2.4	quality=2.4	quality_position_model=6.77773e-08	ref_cov=193/110	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=195/110
RA	876	.	NC_007779	4610781	0	A	C	bias_e_value=1.14844e-06	bias_p_value=2.4717e-13	fisher_strand_p_value=7.36909e-15	frequency=6.805182e-02	genotype_quality=1011.9	ks_quality_p_value=1	log10_base_likelihood=-20.7612	log10_qual_likelihood_position_model=39.3139	log10_strand_likelihood_position_model=14.1387	new_cov=1/39	polymorphism_quality=15.5	quality=15.5	quality_position_model=Inf	ref_cov=198/113	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=199/152
RA	877	.	NC_007779	4610781	1	.	C	bias_e_value=1251220	bias_p_value=0.269291	fisher_strand_p_value=0.0820397	frequency=8.895874e-03	genotype_quality=1494.3	ks_quality_p_value=0.91429	log10_base_likelihood=-9.72255	log10_qual_likelihood_position_model=5.72168	log10_strand_likelihood_position_model=1.08598	new_cov=0/3	polymorphism_quality=4.3	quality=4.3	quality_position_model=0.000107928	ref_cov=190/144	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=190/147
RA	878	.	NC_007779	4610887	1	.	G	bias_e_value=4646130	bias_p_value=0.999957	fisher_strand_p_value=1	frequency=6.848335e-03	genotype_quality=1419.3	ks_quality_p_value=0.990784	log10_base_likelihood=-7.37725	log10_qual_likelihood_position_model=2.31018	log10_strand_likelihood_position_model=0.301582	new_cov=1/1	polymorphism_quality=1.9	quality=1.9	quality_position_model=1.21798e-06	ref_cov=155/135	reject=EVALUE,POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=156/136
RA	879	.	NC_007779	4615146	0	T	G	bias_e_value=225.211	bias_p_value=4.84706e-05	fisher_strand_p_value=3.62229e-06	frequency=3.270721e-02	genotype_quality=488.8	ks_quality_p_value=0.988257	log10_base_likelihood=-7.69507	log10_qual_likelihood_position_model=5.36227	log10_strand_likelihood_position_model=5.44102	new_cov=5/0	polymorphism_quality=2.2	quality=2.2	quality_position_model=Inf	ref_cov=9/134	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=14/134
RA	880	.	NC_007779	4635770	0	G	T	bias_e_value=1293.73	bias_p_value=0.000278442	fisher_strand_p_value=2.39194e-05	frequency=3.635406e-02	genotype_quality=837.5	ks_quality_p_value=1	log10_base_likelihood=-6.59204	log10_qual_likelihood_position_model=10.9438	log10_strand_likelihood_position_model=4.73	new_cov=0/18	polymorphism_quality=1.1	quality=1.1	quality_position_model=Inf	ref_cov=130/147	reject=EVALUE,POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE	tot_cov=130/165
RA	881	.	NC_007779	4636467	1	.	G	bias_e_value=1727960	bias_p_value=0.371897	fisher_strand_p_value=0.12331	frequency=7.117271e-03	genotype_quality=1371.2	ks_quality_p_value=0.963489	log10_base_likelihood=-7.50628	log10_qual_likelihood_position_model=2.49446	log10_strand_likelihood_position_model=0.909003	new_cov=2/0	polymorphism_quality=2.0	quality=2.0	quality_position_model=6.00093e-06	ref_cov=97/182	reject=POLYMORPHISM_STRAND	tot_cov=99/182
RA	882	.	NC_007779	4636470	0	C	G	bias_e_value=8.21514e-19	bias_p_value=1.76809e-25	fisher_strand_p_value=2.84608e-27	frequency=1.477218e-01	genotype_quality=812.9	ks_quality_p_value=1	log10_base_likelihood=-51.0367	log10_qual_likelihood_position_model=31.8981	log10_strand_likelihood_position_model=26.5458	new_cov=40/0	polymorphism_quality=46.0	quality=46.0	quality_position_model=Inf	ref_cov=31/180	reject=POLYMORPHISM_STRAND,FISHER_STRAND_P_VALUE,SURROUNDING_HOMOPOLYMER	tot_cov=71/180
RA	883	.	NC_007779	4642414	1	.	A	bias_e_value=3575590	bias_p_value=0.769551	fisher_strand_p_value=1	frequency=1.865673e-02	genotype_quality=1252.4	ks_quality_p_value=0.403327	log10_base_likelihood=-21.7988	log10_qual_likelihood_position_model=3.34801	log10_strand_likelihood_position_model=0.471149	new_cov=2/3	polymorphism_quality=16.5	quality=16.5	quality_position_model=3.94433e-20	ref_cov=120/143	reject=INDEL_HOMOPOLYMER	tot_cov=122/146
RA	884	.	NC_007779	4644244	1	.	T	bias_e_value=2584400	bias_p_value=0.556224	fisher_strand_p_value=0.271828	frequency=9.614944e-03	genotype_quality=1487.0	ks_quality_p_value=0.816929	log10_base_likelihood=-11.6961	log10_qual_likelihood_position_model=2.58392	log10_strand_likelihood_position_model=0.690936	new_cov=3/0	polymorphism_quality=6.3	quality=6.3	quality_position_model=2.05879e-10	ref_cov=181/128	reject=POLYMORPHISM_STRAND,INDEL_HOMOPOLYMER	tot_cov=184/128
MC	885	.	NC_007779	274733	371972	0	0	left_inside_cov=0	left_outside_cov=312	right_inside_cov=4	right_outside_cov=314
MC	886	.	NC_007779	654214	655412	1197	0	left_inside_cov=1	left_outside_cov=339	right_inside_cov=0	right_outside_cov=338
MC	887	.	NC_007779	1288322	1288504	90	45	left_inside_cov=197	left_outside_cov=199	right_inside_cov=195	right_outside_cov=200
MC	888	.	NC_007779	1301041	1302376	1327	0	left_inside_cov=0	left_outside_cov=323	right_inside_cov=0	right_outside_cov=316
MC	889	.	NC_007779	1413639	1436698	0	0	left_inside_cov=0	left_outside_cov=384	right_inside_cov=2	right_outside_cov=388
MC	890	.	NC_007779	2176983	2178208	1194	0	left_inside_cov=0	left_outside_cov=391	right_inside_cov=0	right_outside_cov=414
MC	891	.	NC_007779	2320794	2322129	1328	0	left_inside_cov=0	left_outside_cov=281	right_inside_cov=1	right_outside_cov=283
MC	892	.	NC_007779	3128845	3147473	1157	0	left_inside_cov=196	left_outside_cov=202	right_inside_cov=0	right_outside_cov=570
MC	893	.	NC_007779	3261134	3262337	1198	0	left_inside_cov=1	left_outside_cov=366	right_inside_cov=0	right_outside_cov=267
MC	894	.	NC_007779	3742936	3744271	1325	0	left_inside_cov=0	left_outside_cov=395	right_inside_cov=1	right_outside_cov=391
MC	895	.	NC_007779	3958123	3958156	0	0	left_inside_cov=0	left_outside_cov=340	right_inside_cov=1	right_outside_cov=338
JC	896	.	NC_007779	1	1	NC_007779	4646332	-1	0	alignment_overlap=0	circular_chromosome=1	coverage_minus=164	coverage_plus=177	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=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=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=1.14	new_junction_frequency=1.000000e+00	new_junction_read_count=341	pos_hash_score=142	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=341
JC	897	.	NC_007779	274732	-1	NC_007779	371973	1	0	alignment_overlap=8	coverage_minus=128	coverage_plus=119	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=80	key=NC_007779__274732__-1__NC_007779__371965__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=86	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=46	max_min_right_minus=46	max_min_right_plus=46	max_pos_hash_score=160	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=245	pos_hash_score=124	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=2	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=80	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=247
JC	898	.	NC_007779	289856	1	NC_007779	2176982	-1	-33	alignment_overlap=-33	coverage_minus=123	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=57	key=NC_007779__289856__1__NC_007779__2176982__-1__-33__CTATTGCAATACCGCATTGTGAGGCGATTCATG__101__101__1__0	max_left=62	max_left_minus=62	max_left_plus=62	max_min_left=33	max_min_left_minus=33	max_min_left_plus=33	max_min_right=34	max_min_right_minus=34	max_min_right_plus=34	max_pos_hash_score=114	max_right=62	max_right_minus=62	max_right_plus=61	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.31	new_junction_frequency=1.000000e+00	new_junction_read_count=248	pos_hash_score=100	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=247	unique_read_sequence=CTATTGCAATACCGCATTGTGAGGCGATTCATG
JC	899	.	NC_007779	380484	1	NC_007779	381407	-1	0	alignment_overlap=0	coverage_minus=120	coverage_plus=105	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=92	max_left_minus=90	max_left_plus=92	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.76	new_junction_frequency=NA	new_junction_read_count=226	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=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=225
JC	900	.	NC_007779	381401	1	NC_007779	381812	-1	0	alignment_overlap=2	coverage_minus=112	coverage_plus=127	flanking_left=101	flanking_right=101	frequency=NA	junction_possible_overlap_registers=88	key=NC_007779__381401__1__NC_007779__381814__-1__2____101__101__1__1	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=48	max_min_left_plus=49	max_min_right=49	max_min_right_minus=48	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=NA	new_junction_read_count=240	pos_hash_score=126	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=239
JC	901	.	NC_007779	608570	-1	NC_007779	1305025	1	0	alignment_overlap=3	coverage_minus=116	coverage_plus=159	flanking_left=101	flanking_right=101	frequency=9.728401e-01	junction_possible_overlap_registers=87	key=NC_007779__608573__-1__NC_007779__1305025__1__3____101__101__1__0	max_left=92	max_left_minus=91	max_left_plus=92	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=174	max_right=92	max_right_minus=92	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=9.728401e-01	new_junction_read_count=277	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=0.03	side_2_overlap=3	side_2_possible_overlap_registers=90	side_2_read_count=8	side_2_redundant=0	total_non_overlap_reads=275
JC	902	.	NC_007779	654213	-1	NC_007779	655413	1	0	alignment_overlap=5	coverage_minus=140	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=85	key=NC_007779__654213__-1__NC_007779__655408__1__5____101__101__0__0	max_left=90	max_left_minus=90	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=46	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	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=0.97	new_junction_frequency=1.000000e+00	new_junction_read_count=274	pos_hash_score=133	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=272
JC	903	.	NC_007779	1209367	1	NC_007779	1211196	1	0	alignment_overlap=16	coverage_minus=23	coverage_plus=36	flanking_left=101	flanking_right=101	frequency=2.853765e-01	junction_possible_overlap_registers=74	key=NC_007779__1209367__1__NC_007779__1211180__1__16____101__101__0__0	max_left=78	max_left_minus=78	max_left_plus=73	max_min_left=40	max_min_left_minus=39	max_min_left_plus=40	max_min_right=40	max_min_right_minus=39	max_min_right_plus=40	max_pos_hash_score=148	max_right=79	max_right_minus=76	max_right_plus=79	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.24	new_junction_frequency=2.853765e-01	new_junction_read_count=59	pos_hash_score=52	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=166	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.65	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=159	side_2_redundant=0	total_non_overlap_reads=59
JC	904	.	NC_007779	1209382	-1	NC_007779	1211179	-1	0	alignment_overlap=16	coverage_minus=27	coverage_plus=19	flanking_left=101	flanking_right=101	frequency=2.389472e-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=75	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=40	max_min_right_plus=39	max_pos_hash_score=148	max_right=78	max_right_minus=73	max_right_plus=78	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.19	new_junction_frequency=2.389472e-01	new_junction_read_count=46	pos_hash_score=40	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.55	side_1_overlap=16	side_1_possible_overlap_registers=90	side_1_read_count=163	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.65	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=159	side_2_redundant=0	total_non_overlap_reads=46
JC	905	.	NC_007779	1221489	1	NC_007779	1301041	1	0	alignment_overlap=2	coverage_minus=90	coverage_plus=124	flanking_left=101	flanking_right=101	frequency=9.735577e-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=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=86	max_right_minus=84	max_right_plus=86	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.74	new_junction_frequency=9.735577e-01	new_junction_read_count=216	pos_hash_score=109	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=6	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=214
JC	906	.	NC_007779	1221495	-1	NC_007779	1302369	-1	0	alignment_overlap=0	coverage_minus=125	coverage_plus=101	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=48	max_min_right_plus=50	max_pos_hash_score=180	max_right=92	max_right_minus=92	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.76	new_junction_frequency=1.000000e+00	new_junction_read_count=226	pos_hash_score=125	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	907	.	NC_007779	1298932	-1	NC_007779	1298936	1	0	alignment_overlap=0	coverage_minus=2	coverage_plus=1	flanking_left=101	flanking_right=101	frequency=9.421961e-02	junction_possible_overlap_registers=90	key=NC_007779__1298932__-1__NC_007779__1298936__1__0____101__101__0__0	max_left=43	max_left_minus=33	max_left_plus=43	max_min_left=43	max_min_left_minus=33	max_min_left_plus=43	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=158	max_right=92	max_right_minus=92	max_right_plus=58	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.10	new_junction_frequency=9.421961e-02	new_junction_read_count=30	pos_hash_score=3	side_1_annotate_key=gene	side_1_continuation=11	side_1_coverage=0.95	side_1_overlap=0	side_1_possible_overlap_registers=79	side_1_read_count=250	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.98	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=292	side_2_redundant=0	total_non_overlap_reads=3
JC	908	.	NC_007779	1301040	-1	NC_007779	1302377	1	0	alignment_overlap=7	coverage_minus=134	coverage_plus=134	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=45	max_min_left_plus=46	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=166	max_right=88	max_right_minus=88	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=1.000000e+00	new_junction_read_count=268	pos_hash_score=130	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=268
JC	909	.	NC_007779	1301041	1	NC_007779	1302373	-1	0	alignment_overlap=2	coverage_minus=4	coverage_plus=2	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=88	key=NC_007779__1301039__1__NC_007779__1302373__-1__2____101__101__1__0	max_left=84	max_left_minus=70	max_left_plus=84	max_min_left=25	max_min_left_minus=25	max_min_left_plus=10	max_min_right=40	max_min_right_minus=40	max_min_right_plus=15	max_pos_hash_score=176	max_right=90	max_right_minus=75	max_right_plus=90	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.02	new_junction_frequency=1.000000e+00	new_junction_read_count=6	pos_hash_score=6	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=2	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=6
JC	910	.	NC_007779	1305037	-1	NC_007779	2519723	1	0	alignment_overlap=4	coverage_minus=111	coverage_plus=136	flanking_left=101	flanking_right=101	frequency=9.348978e-01	junction_possible_overlap_registers=86	key=NC_007779__1305037__-1__NC_007779__2519719__1__4____101__101__0__1	max_left=91	max_left_minus=90	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.86	new_junction_frequency=9.348978e-01	new_junction_read_count=247	pos_hash_score=121	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.06	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=18	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=247
JC	911	.	NC_007779	1397758	1	NC_007779	1672777	1	0	alignment_overlap=0	coverage_minus=142	coverage_plus=136	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=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.94	new_junction_frequency=1.000000e+00	new_junction_read_count=280	pos_hash_score=135	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=278
JC	912	.	NC_007779	1413638	-1	NC_007779	1436699	1	0	alignment_overlap=26	coverage_minus=132	coverage_plus=114	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=68	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=36	max_min_right_plus=37	max_pos_hash_score=128	max_right=69	max_right_minus=69	max_right_plus=67	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.16	new_junction_frequency=1.000000e+00	new_junction_read_count=247	pos_hash_score=105	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=246
JC	913	.	NC_007779	1672780	-1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=130	coverage_plus=136	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1672780__-1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=87	max_right_minus=84	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.89	new_junction_frequency=1.000000e+00	new_junction_read_count=266	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=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=266
JC	914	.	NC_007779	1907280	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=125	coverage_plus=119	flanking_left=101	flanking_right=101	frequency=9.534884e-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=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=93	max_right_minus=86	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.82	new_junction_frequency=9.534884e-01	new_junction_read_count=246	pos_hash_score=121	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=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=244
JC	915	.	NC_007779	1907288	-1	NC_007779	2411458	1	0	alignment_overlap=0	coverage_minus=129	coverage_plus=161	flanking_left=101	flanking_right=101	frequency=9.635762e-01	junction_possible_overlap_registers=90	key=NC_007779__1907288__-1__NC_007779__2411458__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=9.635762e-01	new_junction_read_count=291	pos_hash_score=138	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.04	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=11	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=290
JC	916	.	NC_007779	1980067	-1	NC_007779	3261129	1	-20	alignment_overlap=-20	coverage_minus=10	coverage_plus=0	flanking_left=101	flanking_right=101	frequency=1.313869e-01	junction_possible_overlap_registers=70	key=NC_007779__1980067__-1__NC_007779__3261129__1__-20__AGTATGACTTATACATTTAT__101__101__0__1	max_left=65	max_left_minus=65	max_left_plus=0	max_min_left=39	max_min_left_minus=39	max_min_left_plus=0	max_min_right=40	max_min_right_minus=40	max_min_right_plus=0	max_pos_hash_score=140	max_right=71	max_right_minus=71	max_right_plus=0	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.04	new_junction_frequency=1.313869e-01	new_junction_read_count=10	pos_hash_score=8	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.28	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=85	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=10	unique_read_sequence=AGTATGACTTATACATTTAT
JC	917	.	NC_007779	1980091	1	NC_007779	1980209	1	0	alignment_overlap=0	coverage_minus=133	coverage_plus=59	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__1980091__1__NC_007779__1980209__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=38	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.69	new_junction_frequency=1.000000e+00	new_junction_read_count=205	pos_hash_score=95	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=192
JC	918	.	NC_007779	1980095	-1	NC_007779	2176984	1	0	alignment_overlap=1	coverage_minus=166	coverage_plus=135	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=93	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.04	new_junction_frequency=1.000000e+00	new_junction_read_count=308	pos_hash_score=139	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=301
JC	919	.	NC_007779	2178209	1	NC_007779	2412225	-1	0	alignment_overlap=0	coverage_minus=131	coverage_plus=161	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=94	max_left_minus=94	max_left_plus=93	max_min_left=50	max_min_left_minus=50	max_min_left_plus=48	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=294	pos_hash_score=139	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=292
JC	920	.	NC_007779	2320793	-1	NC_007779	2322130	1	0	alignment_overlap=5	coverage_minus=106	coverage_plus=125	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=85	key=NC_007779__2320793__-1__NC_007779__2322125__1__5____101__101__0__0	max_left=90	max_left_minus=90	max_left_plus=90	max_min_left=47	max_min_left_minus=47	max_min_left_plus=46	max_min_right=48	max_min_right_minus=48	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=88	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.84	new_junction_frequency=1.000000e+00	new_junction_read_count=238	pos_hash_score=123	side_1_annotate_key=gene	side_1_continuation=1	side_1_coverage=0.00	side_1_overlap=5	side_1_possible_overlap_registers=89	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=231
JC	921	.	NC_007779	2320794	1	NC_007779	2589834	-1	0	alignment_overlap=0	coverage_minus=81	coverage_plus=210	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=89	max_left_minus=83	max_left_plus=89	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=292	pos_hash_score=124	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=291
JC	922	.	NC_007779	2322124	-1	NC_007779	2589830	1	0	alignment_overlap=0	coverage_minus=143	coverage_plus=221	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__2322124__-1__NC_007779__2589830__1__0____101__101__1__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.22	new_junction_frequency=1.000000e+00	new_junction_read_count=366	pos_hash_score=146	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=364
JC	923	.	NC_007779	2411458	1	NC_007779	2985055	-1	0	alignment_overlap=0	coverage_minus=123	coverage_plus=163	flanking_left=101	flanking_right=101	frequency=9.694915e-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=92	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.96	new_junction_frequency=9.694915e-01	new_junction_read_count=286	pos_hash_score=141	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.03	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=9	side_2_redundant=0	total_non_overlap_reads=286
JC	924	.	NC_007779	2412225	-1	NC_007779	2985047	1	0	alignment_overlap=0	coverage_minus=95	coverage_plus=114	flanking_left=101	flanking_right=101	frequency=9.500000e-01	junction_possible_overlap_registers=90	key=NC_007779__2412225__-1__NC_007779__2985047__1__0____101__101__1__0	max_left=89	max_left_minus=86	max_left_plus=89	max_min_left=50	max_min_left_minus=50	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=94	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.70	new_junction_frequency=9.500000e-01	new_junction_read_count=209	pos_hash_score=116	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.04	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=11	side_2_redundant=0	total_non_overlap_reads=209
JC	925	.	NC_007779	2865229	1	NC_007779	2865274	-1	0	alignment_overlap=4	coverage_minus=130	coverage_plus=133	flanking_left=101	flanking_right=101	frequency=6.640953e-01	junction_possible_overlap_registers=86	key=NC_007779__2865229__1__NC_007779__2865278__-1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=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=0.92	new_junction_frequency=6.640953e-01	new_junction_read_count=264	pos_hash_score=129	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.52	side_1_overlap=4	side_1_possible_overlap_registers=90	side_1_read_count=156	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.41	side_2_overlap=0	side_2_possible_overlap_registers=86	side_2_read_count=118	side_2_redundant=0	total_non_overlap_reads=263
JC	926	.	NC_007779	3147474	1	NC_007779	3262328	-1	0	alignment_overlap=0	coverage_minus=200	coverage_plus=194	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3147474__1__NC_007779__3262328__-1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.32	new_junction_frequency=1.000000e+00	new_junction_read_count=394	pos_hash_score=153	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=394
JC	927	.	NC_007779	3186081	-1	NC_007779	3512753	1	0	alignment_overlap=1	coverage_minus=176	coverage_plus=146	flanking_left=101	flanking_right=101	frequency=9.848768e-01	junction_possible_overlap_registers=89	key=NC_007779__3186082__-1__NC_007779__3512753__1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.09	new_junction_frequency=9.848768e-01	new_junction_read_count=322	pos_hash_score=149	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=1	side_2_possible_overlap_registers=90	side_2_read_count=5	side_2_redundant=0	total_non_overlap_reads=322
JC	928	.	NC_007779	3261133	-1	NC_007779	3748109	-1	-6	alignment_overlap=-6	coverage_minus=196	coverage_plus=134	flanking_left=101	flanking_right=101	frequency=9.971882e-01	junction_possible_overlap_registers=84	key=NC_007779__3261133__-1__NC_007779__3748109__-1__-6__CTTTGC__101__101__0__1	max_left=89	max_left_minus=89	max_left_plus=89	max_min_left=47	max_min_left_minus=47	max_min_left_plus=46	max_min_right=47	max_min_right_minus=47	max_min_right_plus=47	max_pos_hash_score=168	max_right=89	max_right_minus=89	max_right_plus=89	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.19	new_junction_frequency=9.971882e-01	new_junction_read_count=331	pos_hash_score=143	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=330	unique_read_sequence=CTTTGC
JC	929	.	NC_007779	3261134	1	NC_007779	3265774	1	0	alignment_overlap=0	coverage_minus=137	coverage_plus=164	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3261134__1__NC_007779__3265774__1__0____101__101__1__0	max_left=95	max_left_minus=94	max_left_plus=95	max_min_left=50	max_min_left_minus=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=303	pos_hash_score=140	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=301
JC	930	.	NC_007779	3261135	1	NC_007779	3262338	1	0	alignment_overlap=1	coverage_minus=115	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3261134__1__NC_007779__3262338__1__1____101__101__1__0	max_left=84	max_left_minus=84	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=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=0.84	new_junction_frequency=1.000000e+00	new_junction_read_count=248	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=1	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=247
JC	931	.	NC_007779	3265777	-1	NC_007779	3365411	1	0	alignment_overlap=0	coverage_minus=213	coverage_plus=140	flanking_left=101	flanking_right=101	frequency=9.971910e-01	junction_possible_overlap_registers=90	key=NC_007779__3265777__-1__NC_007779__3365411__1__0____101__101__0__1	max_left=95	max_left_minus=95	max_left_plus=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=50	max_pos_hash_score=180	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.19	new_junction_frequency=9.971910e-01	new_junction_read_count=355	pos_hash_score=146	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=90	side_1_read_count=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=353
JC	932	.	NC_007779	3512759	-1	NC_007779	3744262	-1	0	alignment_overlap=1	coverage_minus=107	coverage_plus=161	flanking_left=101	flanking_right=101	frequency=9.783402e-01	junction_possible_overlap_registers=89	key=NC_007779__3512759__-1__NC_007779__3744263__-1__1____101__101__0__1	max_left=94	max_left_minus=93	max_left_plus=94	max_min_left=49	max_min_left_minus=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=84	max_right_minus=84	max_right_plus=83	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=9.783402e-01	new_junction_read_count=268	pos_hash_score=129	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=6	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=268
JC	933	.	NC_007779	3742935	-1	NC_007779	3744272	1	0	alignment_overlap=8	coverage_minus=176	coverage_plus=141	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=82	key=NC_007779__3742935__-1__NC_007779__3744264__1__8____101__101__0__0	max_left=87	max_left_minus=87	max_left_plus=87	max_min_left=46	max_min_left_minus=45	max_min_left_plus=46	max_min_right=46	max_min_right_minus=46	max_min_right_plus=46	max_pos_hash_score=164	max_right=87	max_right_minus=87	max_right_plus=87	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=318	pos_hash_score=138	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=317
JC	934	.	NC_007779	3744263	-1	NC_007779	3903274	1	0	alignment_overlap=0	coverage_minus=159	coverage_plus=113	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__3744263__-1__NC_007779__3903274__1__0____101__101__1__0	max_left=90	max_left_minus=90	max_left_plus=88	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=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=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=274	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=272
JC	935	.	NC_007779	3746910	-1	NC_007779	3748110	1	0	alignment_overlap=4	coverage_minus=127	coverage_plus=132	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3746910__-1__NC_007779__3748106__1__4____101__101__0__0	max_left=91	max_left_minus=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=47	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.91	new_junction_frequency=1.000000e+00	new_junction_read_count=260	pos_hash_score=133	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=259
JC	936	.	NC_007779	3746911	1	NC_007779	3748646	-1	0	alignment_overlap=0	coverage_minus=162	coverage_plus=125	flanking_left=101	flanking_right=101	frequency=9.967213e-01	junction_possible_overlap_registers=90	key=NC_007779__3746911__1__NC_007779__3748646__-1__0____101__101__1__0	max_left=92	max_left_minus=92	max_left_plus=92	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.02	new_junction_frequency=9.967213e-01	new_junction_read_count=304	pos_hash_score=134	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=1	side_2_redundant=0	total_non_overlap_reads=287
JC	937	.	NC_007779	3748105	-1	NC_007779	3748643	1	0	alignment_overlap=0	coverage_minus=157	coverage_plus=151	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=93	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.03	new_junction_frequency=1.000000e+00	new_junction_read_count=309	pos_hash_score=151	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=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=308
JC	938	.	NC_007779	3750590	-1	NC_007779	3751790	1	0	alignment_overlap=4	coverage_minus=168	coverage_plus=165	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__3750590__-1__NC_007779__3751786__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=48	max_min_right_minus=48	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.17	new_junction_frequency=1.000000e+00	new_junction_read_count=335	pos_hash_score=151	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=333
JC	939	.	NC_007779	3903279	-1	NC_007779	4504190	-1	0	alignment_overlap=1	coverage_minus=132	coverage_plus=152	flanking_left=101	flanking_right=101	frequency=9.864049e-01	junction_possible_overlap_registers=89	key=NC_007779__3903279__-1__NC_007779__4504191__-1__1____101__101__0__1	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=48	max_min_left_minus=48	max_min_left_plus=48	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=178	max_right=94	max_right_minus=94	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.97	new_junction_frequency=9.864049e-01	new_junction_read_count=287	pos_hash_score=141	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=1	side_1_possible_overlap_registers=90	side_1_read_count=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=284
JC	940	.	NC_007779	3958122	-1	NC_007779	3958157	1	0	alignment_overlap=2	coverage_minus=143	coverage_plus=149	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=88	key=NC_007779__3958122__-1__NC_007779__3958155__1__2____101__101__0__0	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=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=1.00	new_junction_frequency=1.000000e+00	new_junction_read_count=292	pos_hash_score=139	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=2	side_1_possible_overlap_registers=90	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=88	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=292
JC	941	.	NC_007779	3987186	1	NC_007779	4009203	-1	0	alignment_overlap=1	coverage_minus=169	coverage_plus=155	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=89	key=NC_007779__3987185__1__NC_007779__4009203__-1__1____101__101__1__0	max_left=94	max_left_minus=94	max_left_plus=94	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=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=1.10	new_junction_frequency=1.000000e+00	new_junction_read_count=325	pos_hash_score=150	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=324
JC	942	.	NC_007779	3988379	-1	NC_007779	4009199	1	0	alignment_overlap=0	coverage_minus=176	coverage_plus=175	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=49	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=94	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.18	new_junction_frequency=1.000000e+00	new_junction_read_count=352	pos_hash_score=159	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=351
JC	943	.	NC_007779	4310362	-1	NC_007779	4311562	1	0	alignment_overlap=4	coverage_minus=166	coverage_plus=200	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=86	key=NC_007779__4310362__-1__NC_007779__4311558__1__4____101__101__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=48	max_min_left_minus=48	max_min_left_plus=47	max_min_right=48	max_min_right_minus=47	max_min_right_plus=48	max_pos_hash_score=172	max_right=91	max_right_minus=91	max_right_plus=91	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.28	new_junction_frequency=1.000000e+00	new_junction_read_count=366	pos_hash_score=149	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=366
JC	944	.	NC_007779	4310363	1	NC_007779	4353540	1	0	alignment_overlap=0	coverage_minus=129	coverage_plus=140	flanking_left=101	flanking_right=101	frequency=1.000000e+00	junction_possible_overlap_registers=90	key=NC_007779__4310363__1__NC_007779__4353540__1__0____101__101__1__0	max_left=94	max_left_minus=93	max_left_plus=94	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=49	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.92	new_junction_frequency=1.000000e+00	new_junction_read_count=274	pos_hash_score=135	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=269
JC	945	.	NC_007779	4311557	-1	NC_007779	4353543	-1	0	alignment_overlap=0	coverage_minus=141	coverage_plus=145	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=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=47	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.98	new_junction_frequency=1.000000e+00	new_junction_read_count=293	pos_hash_score=137	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=90	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=286
JC	946	.	NC_007779	4355060	1	NC_007779	4502861	1	0	alignment_overlap=0	coverage_minus=150	coverage_plus=150	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=94	max_left_plus=95	max_min_left=50	max_min_left_minus=50	max_min_left_plus=50	max_min_right=50	max_min_right_minus=50	max_min_right_plus=50	max_pos_hash_score=180	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=NT	new_junction_coverage=1.01	new_junction_frequency=1.000000e+00	new_junction_read_count=302	pos_hash_score=142	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=300
JC	947	.	NC_007779	4355066	-1	NC_007779	4504189	-1	0	alignment_overlap=2	coverage_minus=132	coverage_plus=128	flanking_left=101	flanking_right=101	frequency=9.962819e-01	junction_possible_overlap_registers=88	key=NC_007779__4355066__-1__NC_007779__4504191__-1__2____101__101__0__1	max_left=93	max_left_minus=93	max_left_plus=93	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=49	max_min_right_minus=49	max_min_right_plus=49	max_pos_hash_score=176	max_right=93	max_right_minus=93	max_right_plus=93	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.90	new_junction_frequency=9.962819e-01	new_junction_read_count=262	pos_hash_score=135	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=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=260
JC	948	.	NC_007779	4547362	1	NC_007779	4547676	1	0	alignment_overlap=9	coverage_minus=14	coverage_plus=10	flanking_left=101	flanking_right=101	frequency=1.106756e-01	junction_possible_overlap_registers=81	key=NC_007779__4547362__1__NC_007779__4547667__1__9____101__101__0__0	max_left=86	max_left_minus=86	max_left_plus=86	max_min_left=44	max_min_left_minus=44	max_min_left_plus=23	max_min_right=36	max_min_right_minus=31	max_min_right_plus=36	max_pos_hash_score=162	max_right=86	max_right_minus=86	max_right_plus=75	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.09	new_junction_frequency=1.106756e-01	new_junction_read_count=24	pos_hash_score=21	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.65	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=193	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.79	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=212	side_2_redundant=0	total_non_overlap_reads=24
JC	949	.	NC_007779	4547370	-1	NC_007779	4547666	-1	0	alignment_overlap=9	coverage_minus=17	coverage_plus=17	flanking_left=101	flanking_right=101	frequency=1.501767e-01	junction_possible_overlap_registers=81	key=NC_007779__4547370__-1__NC_007779__4547675__-1__9____101__101__0__0	max_left=74	max_left_minus=73	max_left_plus=74	max_min_left=45	max_min_left_minus=45	max_min_left_plus=41	max_min_right=45	max_min_right_minus=45	max_min_right_plus=39	max_pos_hash_score=162	max_right=79	max_right_minus=77	max_right_plus=79	neg_log10_pos_hash_p_value=NT	new_junction_coverage=0.13	new_junction_frequency=1.501767e-01	new_junction_read_count=34	pos_hash_score=32	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.64	side_1_overlap=9	side_1_possible_overlap_registers=90	side_1_read_count=192	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.79	side_2_overlap=0	side_2_possible_overlap_registers=81	side_2_read_count=212	side_2_redundant=0	total_non_overlap_reads=34
UN	950	.	NC_007779	15482	16634
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UN	954	.	NC_007779	224987	225488
UN	955	.	NC_007779	225834	225923
UN	956	.	NC_007779	226121	226202
UN	957	.	NC_007779	226396	226505
UN	958	.	NC_007779	226701	226870
UN	959	.	NC_007779	227085	228591
UN	960	.	NC_007779	228787	228911
UN	961	.	NC_007779	269859	270420
UN	962	.	NC_007779	270706	270710
UN	963	.	NC_007779	273277	274275
UN	964	.	NC_007779	274733	371972
UN	965	.	NC_007779	380574	381723
UN	966	.	NC_007779	391029	392101
UN	967	.	NC_007779	525193	525848
UN	968	.	NC_007779	566089	567161
UN	969	.	NC_007779	573903	574918
UN	970	.	NC_007779	580439	580490
UN	971	.	NC_007779	607325	608476
UN	972	.	NC_007779	654214	655412
UN	973	.	NC_007779	688367	689375
UN	974	.	NC_007779	730322	730466
UN	975	.	NC_007779	730827	730860
UN	976	.	NC_007779	732510	732613
UN	977	.	NC_007779	733124	733151
UN	978	.	NC_007779	734995	735022
UN	979	.	NC_007779	1050344	1050399
UN	980	.	NC_007779	1050560	1050730
UN	981	.	NC_007779	1094763	1095829
UN	982	.	NC_007779	1105719	1106860
UN	983	.	NC_007779	1270767	1270800
UN	984	.	NC_007779	1271838	1271869
UN	985	.	NC_007779	1288372	1288460
UN	986	.	NC_007779	1301041	1302316
UN	987	.	NC_007779	1302319	1302320
UN	988	.	NC_007779	1302322	1302326
UN	989	.	NC_007779	1302329	1302332
UN	990	.	NC_007779	1302370	1302371
UN	991	.	NC_007779	1302374	1302376
UN	992	.	NC_007779	1397851	1398859
UN	993	.	NC_007779	1413639	1436698
UN	994	.	NC_007779	1469721	1470864
UN	995	.	NC_007779	1471108	1472133
UN	996	.	NC_007779	1530138	1530792
UN	997	.	NC_007779	1533980	1534024
UN	998	.	NC_007779	1572480	1572486
UN	999	.	NC_007779	1572677	1572963
UN	1000	.	NC_007779	1573217	1573420
UN	1001	.	NC_007779	1634762	1634840
UN	1002	.	NC_007779	1635034	1635247
UN	1003	.	NC_007779	1635440	1635540
UN	1004	.	NC_007779	1635910	1636255
UN	1005	.	NC_007779	1636451	1636638
UN	1006	.	NC_007779	1637648	1637700
UN	1007	.	NC_007779	1652655	1653165
UN	1008	.	NC_007779	1980303	1981333
UN	1009	.	NC_007779	2068409	2068502
UN	1010	.	NC_007779	2068701	2068747
UN	1011	.	NC_007779	2068961	2069339
UN	1012	.	NC_007779	2071175	2072318
UN	1013	.	NC_007779	2103980	2104987
UN	1014	.	NC_007779	2172403	2173467
UN	1015	.	NC_007779	2176983	2178208
UN	1016	.	NC_007779	2292347	2293348
UN	1017	.	NC_007779	2308005	2308023
UN	1018	.	NC_007779	2308231	2308249
UN	1019	.	NC_007779	2320794	2322129
UN	1020	.	NC_007779	2411554	2412126
UN	1021	.	NC_007779	2519814	2520966
UN	1022	.	NC_007779	2724816	2727806
UN	1023	.	NC_007779	2728091	2728121
UN	1024	.	NC_007779	2728320	2729507
UN	1025	.	NC_007779	2729833	2729930
UN	1026	.	NC_007779	2995113	2996255
UN	1027	.	NC_007779	3128895	3147473
UN	1028	.	NC_007779	3184842	3185985
UN	1029	.	NC_007779	3261134	3262337
UN	1030	.	NC_007779	3365504	3366515
UN	1031	.	NC_007779	3423612	3424407
UN	1032	.	NC_007779	3424605	3426561
UN	1033	.	NC_007779	3426758	3426847
UN	1034	.	NC_007779	3427044	3428592
UN	1035	.	NC_007779	3459669	3460046
UN	1036	.	NC_007779	3460237	3460349
UN	1037	.	NC_007779	3465132	3468011
UN	1038	.	NC_007779	3468300	3468330
UN	1039	.	NC_007779	3468559	3470290
UN	1040	.	NC_007779	3596172	3597191
UN	1041	.	NC_007779	3597394	3597855
UN	1042	.	NC_007779	3598088	3598748
UN	1043	.	NC_007779	3598944	3599186
UN	1044	.	NC_007779	3599298	3599491
UN	1045	.	NC_007779	3599687	3600848
UN	1046	.	NC_007779	3601046	3601421
UN	1047	.	NC_007779	3689826	3689895
UN	1048	.	NC_007779	3690159	3690355
UN	1049	.	NC_007779	3690552	3690667
UN	1050	.	NC_007779	3690874	3691015
UN	1051	.	NC_007779	3691208	3692523
UN	1052	.	NC_007779	3692789	3693001
UN	1053	.	NC_007779	3693048	3693048
UN	1054	.	NC_007779	3693072	3693072
UN	1055	.	NC_007779	3693099	3693186
UN	1056	.	NC_007779	3693383	3694550
UN	1057	.	NC_007779	3694746	3694927
UN	1058	.	NC_007779	3694930	3694931
UN	1059	.	NC_007779	3742936	3744271
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UN	1062	.	NC_007779	3874863	3874904
UN	1063	.	NC_007779	3875220	3875220
UN	1064	.	NC_007779	3875223	3876241
UN	1065	.	NC_007779	3876438	3878053
UN	1066	.	NC_007779	3958123	3958156
UN	1067	.	NC_007779	3973174	3973377
UN	1068	.	NC_007779	3973631	3973913
UN	1069	.	NC_007779	3974108	3974114
UN	1070	.	NC_007779	3987277	3988288
UN	1071	.	NC_007779	4015543	4015587
UN	1072	.	NC_007779	4017854	4017897
UN	1073	.	NC_007779	4018214	4019232
UN	1074	.	NC_007779	4019430	4021044
UN	1075	.	NC_007779	4056314	4056889
UN	1076	.	NC_007779	4169476	4169587
UN	1077	.	NC_007779	4169782	4170155
UN	1078	.	NC_007779	4211520	4211762
UN	1079	.	NC_007779	4211960	4213506
UN	1080	.	NC_007779	4213667	4215789
UN	1081	.	NC_007779	4215987	4216658
UN	1082	.	NC_007779	4299523	4299550
UN	1083	.	NC_007779	4299747	4299777
UN	1084	.	NC_007779	4310363	4311561
UN	1085	.	NC_007779	4502953	4504094
UN	1086	.	NC_007779	4512231	4513265