#=GENOME_DIFF	1.0
#=TITLE	D22
#=CREATED	15:49:11 03 Mar 2017
#=PROGRAM	breseq 0.29.0 
#=COMMAND	breseq -j 2 -r /var/genomes/g2d_mirror/Staphylococcus_aureus_subsp_aureus_USA300_FPR3757/ASM1346v1_genomic.gbff -n D22 -o /var/www/ngs/solomon/breseq/D22 --no-junction-prediction /var/ngs/rnaseq/raw/solomon/RNAseq_USA300_Eleni/OtA1588_D22A0.5_R1_.fastq
#=REFSEQ	/var/genomes/g2d_mirror/Staphylococcus_aureus_subsp_aureus_USA300_FPR3757/ASM1346v1_genomic.gbff
#=READSEQ	/var/ngs/rnaseq/raw/solomon/RNAseq_USA300_Eleni/OtA1588_D22A0.5_R1_.fastq
#=CONVERTED-BASES	525723200
#=CONVERTED-READS	5257232
#=INPUT-BASES	525741200
#=INPUT-READS	5257412
#=MAPPED-BASES	309106754
#=MAPPED-READS	3120829
SNP	1	55	NC_007790	249	G
SNP	2	56	NC_007790	258	A
SNP	3	57	NC_007790	277	T
SNP	4	58	NC_007790	298	T
SNP	5	59	NC_007790	300	C
SNP	6	60	NC_007790	316	G
SUB	7	61,62	NC_007790	321	2	GT
SNP	8	63	NC_007790	327	A
SNP	9	64	NC_007790	336	G
SUB	10	65,66	NC_007790	339	2	TT
SNP	11	67	NC_007790	342	T
SNP	12	68	NC_007790	355	C
SNP	13	69	NC_007790	357	T
SNP	14	70	NC_007790	361	T
SNP	15	71	NC_007790	363	A
SNP	16	72	NC_007790	368	T
SUB	17	73,74	NC_007790	370	2	CG
SNP	18	85	NC_007790	717	A
SNP	19	86	NC_007790	729	C
SNP	20	87	NC_007790	744	C
SNP	21	90	NC_007790	759	C
SNP	22	92	NC_007790	781	T
SNP	23	93	NC_007790	790	C
SNP	24	95	NC_007790	837	A
SNP	25	96	NC_007790	844	G
SNP	26	97	NC_007790	849	G
SNP	27	98	NC_007790	875	C
SNP	28	99	NC_007790	898	A
SNP	29	100	NC_007790	918	G
SNP	30	101	NC_007790	945	G
SNP	31	102	NC_007790	951	A
DEL	32	104	NC_007790	1266	1	repeat_length=1	repeat_new_copies=4	repeat_ref_copies=5	repeat_seq=T
SNP	33	105	NC_007790	1276	T
SNP	34	106	NC_007790	1278	T
SNP	35	107	NC_007790	1280	T
SNP	36	109	NC_007790	1303	G
SNP	37	118	NC_007790	1451	G
SNP	38	123	NC_007790	1468	A
SUB	39	127,128	NC_007790	1478	2	TA
SNP	40	131	NC_007790	1502	T
SNP	41	132	NC_007790	1510	T
SNP	42	133	NC_007790	1572	C
SNP	43	134	NC_007790	1588	G
SNP	44	135	NC_007790	1603	A
SNP	45	136	NC_007790	1671	T
SNP	46	137	NC_007790	1694	T
SNP	47	138	NC_007790	1744	T
SNP	48	139	NC_007790	1778	A
SNP	49	140	NC_007790	1871	A
SUB	50	141,142,143	NC_007790	1954	2	TGC
SNP	51	144	NC_007790	1967	G
DEL	52	149	NC_007791	1	4439
DEL	53	150	NC_007792	1	37136
DEL	54	151	NC_007793	1	2872769
RA	55	.	NC_007790	249	0	A	G	consensus_score=69.5	frequency=1	major_base=G	major_cov=25/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=25/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=25/0
RA	56	.	NC_007790	258	0	G	A	consensus_score=91.9	frequency=1	major_base=A	major_cov=31/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=31/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=31/0
RA	57	.	NC_007790	277	0	G	T	bias_e_value=2666180	bias_p_value=0.913866	consensus_score=105.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.614783	major_base=T	major_cov=36/0	major_frequency=9.730e-01	minor_base=C	minor_cov=1/0	new_cov=36/0	polymorphism_frequency=9.730e-01	polymorphism_score=-4.8	prediction=consensus	ref_cov=0/0	total_cov=37/0
RA	58	.	NC_007790	298	0	G	T	bias_e_value=2908360	bias_p_value=0.996879	consensus_score=210.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.922047	major_base=T	major_cov=69/0	major_frequency=9.857e-01	minor_base=C	minor_cov=1/0	new_cov=69/0	polymorphism_frequency=9.857e-01	polymorphism_score=-5.0	prediction=consensus	ref_cov=0/0	total_cov=70/0
RA	59	.	NC_007790	300	0	T	C	consensus_score=199.8	frequency=1	major_base=C	major_cov=70/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=70/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=70/0
RA	60	.	NC_007790	316	0	A	G	consensus_score=216.0	frequency=1	major_base=G	major_cov=73/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=73/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=73/0
RA	61	.	NC_007790	321	0	A	G	consensus_score=203.9	frequency=1	major_base=G	major_cov=73/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=73/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=73/0
RA	62	.	NC_007790	322	0	A	T	consensus_score=211.9	frequency=1	major_base=T	major_cov=73/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=73/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=73/0
RA	63	.	NC_007790	327	0	G	A	consensus_score=217.7	frequency=1	major_base=A	major_cov=73/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=73/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=73/0
RA	64	.	NC_007790	336	0	A	G	consensus_score=136.2	frequency=1	major_base=G	major_cov=48/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=48/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=48/0
RA	65	.	NC_007790	339	0	A	T	consensus_score=141.9	frequency=1	major_base=T	major_cov=48/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=48/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=48/0
RA	66	.	NC_007790	340	0	G	T	consensus_score=143.4	frequency=1	major_base=T	major_cov=48/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=48/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=48/0
RA	67	.	NC_007790	342	0	A	T	consensus_score=138.7	frequency=1	major_base=T	major_cov=48/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=48/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=48/0
RA	68	.	NC_007790	355	0	T	C	consensus_score=101.7	frequency=1	major_base=C	major_cov=39/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=39/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=39/0
RA	69	.	NC_007790	357	0	A	T	consensus_score=105.7	frequency=1	major_base=T	major_cov=39/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=39/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=39/0
RA	70	.	NC_007790	361	0	C	T	consensus_score=99.5	frequency=1	major_base=T	major_cov=37/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=37/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=37/0
RA	71	.	NC_007790	363	0	T	A	consensus_score=94.1	frequency=1	major_base=A	major_cov=37/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=37/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=37/0
RA	72	.	NC_007790	368	0	C	T	consensus_score=102.0	frequency=1	major_base=T	major_cov=36/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=36/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=36/0
RA	73	.	NC_007790	370	0	A	C	consensus_score=85.5	frequency=1	major_base=C	major_cov=36/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=36/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=36/0
RA	74	.	NC_007790	371	0	A	G	consensus_score=89.9	frequency=1	major_base=G	major_cov=36/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=36/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=36/0
RA	75	.	NC_007790	482	0	G	A	consensus_score=14.9	deleted=1	frequency=1	major_base=A	major_cov=6/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/1
RA	76	.	NC_007790	489	0	A	T	consensus_score=15.4	deleted=1	frequency=1	major_base=T	major_cov=6/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/1
RA	77	.	NC_007790	495	0	T	A	consensus_score=14.3	deleted=1	frequency=1	major_base=A	major_cov=6/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/1
RA	78	.	NC_007790	498	0	C	A	consensus_score=15.3	deleted=1	frequency=1	major_base=A	major_cov=6/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/1
RA	79	.	NC_007790	528	0	G	A	consensus_score=24.1	deleted=1	frequency=1	major_base=A	major_cov=9/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=9/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=9/1
RA	80	.	NC_007790	531	0	C	T	consensus_score=20.0	deleted=1	frequency=1	major_base=T	major_cov=9/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=9/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=9/0
RA	81	.	NC_007790	537	0	T	C	consensus_score=19.4	deleted=1	frequency=1	major_base=C	major_cov=9/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=9/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=9/0
RA	82	.	NC_007790	546	0	A	G	consensus_score=18.6	deleted=1	frequency=1	major_base=G	major_cov=9/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=9/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=9/0
RA	83	.	NC_007790	561	0	A	G	consensus_score=18.0	deleted=1	frequency=1	major_base=G	major_cov=9/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=9/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=9/0
RA	84	.	NC_007790	711	0	A	G	bias_e_value=450191	bias_p_value=0.154309	consensus_score=17.2	fisher_strand_p_value=0.0415629	frequency=6.452e-01	ks_quality_p_value=0.856302	major_base=G	major_cov=19/1	major_frequency=6.452e-01	minor_base=A	minor_cov=7/4	new_cov=19/1	polymorphism_frequency=6.452e-01	polymorphism_score=19.8	prediction=polymorphism	ref_cov=7/4	total_cov=26/5
RA	85	.	NC_007790	717	0	C	A	bias_e_value=2141050	bias_p_value=0.733872	consensus_score=111.6	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.365998	major_base=A	major_cov=33/6	major_frequency=9.750e-01	minor_base=C	minor_cov=1/0	new_cov=33/6	polymorphism_frequency=9.750e-01	polymorphism_score=-3.2	prediction=consensus	ref_cov=1/0	total_cov=34/6
RA	86	.	NC_007790	729	0	G	C	bias_e_value=2712410	bias_p_value=0.929714	consensus_score=135.5	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.649315	major_base=C	major_cov=43/6	major_frequency=9.800e-01	minor_base=G	minor_cov=1/0	new_cov=43/6	polymorphism_frequency=9.800e-01	polymorphism_score=-3.7	prediction=consensus	ref_cov=1/0	total_cov=44/6
RA	87	.	NC_007790	744	0	T	C	bias_e_value=2693400	bias_p_value=0.923198	consensus_score=198.8	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.634615	major_base=C	major_cov=48/27	major_frequency=9.868e-01	minor_base=T	minor_cov=1/0	new_cov=48/27	polymorphism_frequency=9.868e-01	polymorphism_score=-4.9	prediction=consensus	ref_cov=1/0	total_cov=50/27
RA	88	.	NC_007790	757	0	G	A	bias_e_value=107165	bias_p_value=0.0367321	consensus_score=214.6	fisher_strand_p_value=0.00981751	frequency=2.303e-01	ks_quality_p_value=0.611873	major_base=G	major_cov=102/15	major_frequency=7.697e-01	minor_base=A	minor_cov=23/12	new_cov=23/12	polymorphism_frequency=2.303e-01	polymorphism_score=67.4	prediction=polymorphism	ref_cov=102/15	total_cov=125/27
RA	89	.	NC_007790	758	0	A	G	bias_e_value=72977.5	bias_p_value=0.025014	consensus_score=235.4	fisher_strand_p_value=0.00981751	frequency=2.303e-01	ks_quality_p_value=0.387749	major_base=A	major_cov=102/15	major_frequency=7.697e-01	minor_base=G	minor_cov=23/12	new_cov=23/12	polymorphism_frequency=2.303e-01	polymorphism_score=62.2	prediction=polymorphism	ref_cov=102/15	total_cov=125/27
RA	90	.	NC_007790	759	0	T	C	bias_e_value=2588730	bias_p_value=0.887322	consensus_score=408.2	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.564556	major_base=C	major_cov=124/27	major_frequency=9.934e-01	minor_base=T	minor_cov=1/0	new_cov=124/27	polymorphism_frequency=9.934e-01	polymorphism_score=-5.2	prediction=consensus	ref_cov=1/0	total_cov=125/27
RA	91	.	NC_007790	762	0	T	C	bias_e_value=172652	bias_p_value=0.0591788	consensus_score=208.8	fisher_strand_p_value=0.0107277	frequency=7.632e-01	ks_quality_p_value=0.995925	major_base=C	major_cov=101/15	major_frequency=7.632e-01	minor_base=T	minor_cov=24/12	new_cov=101/15	polymorphism_frequency=7.632e-01	polymorphism_score=69.8	prediction=polymorphism	ref_cov=24/12	total_cov=125/27
RA	92	.	NC_007790	781	0	G	T	bias_e_value=51722.3	bias_p_value=0.0177285	consensus_score=599.0	fisher_strand_p_value=0.00254458	frequency=1	ks_quality_p_value=0.998888	major_base=T	major_cov=209/31	major_frequency=8.664e-01	minor_base=A	minor_cov=24/13	new_cov=209/31	polymorphism_frequency=8.664e-01	polymorphism_score=74.3	prediction=consensus	ref_cov=2/0	total_cov=235/44
RA	93	.	NC_007790	790	0	T	C	bias_e_value=2908670	bias_p_value=0.996986	consensus_score=776.7	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.923366	major_base=C	major_cov=251/44	major_frequency=9.966e-01	minor_base=T	minor_cov=1/0	new_cov=251/44	polymorphism_frequency=9.966e-01	polymorphism_score=-6.3	prediction=consensus	ref_cov=1/0	total_cov=252/44
RA	94	.	NC_007790	794	0	A	.	bias_e_value=2040030	bias_p_value=0.699248	consensus_score=463.8	fisher_strand_p_value=0.343848	frequency=7.562e-01	ks_quality_p_value=0.968655	major_base=.	major_cov=215/30	major_frequency=7.562e-01	minor_base=A	minor_cov=66/13	new_cov=215/30	polymorphism_frequency=7.562e-01	polymorphism_score=309.6	prediction=polymorphism	ref_cov=66/13	total_cov=282/43
RA	95	.	NC_007790	837	0	G	A	bias_e_value=2.97045	bias_p_value=1.01816e-06	consensus_score=1488.2	fisher_strand_p_value=0.193681	frequency=1	ks_quality_p_value=2.97514e-07	major_base=A	major_cov=573/25	major_frequency=9.047e-01	minor_base=G	minor_cov=58/5	new_cov=573/25	polymorphism_frequency=9.047e-01	polymorphism_score=96.2	prediction=consensus	ref_cov=58/5	total_cov=631/30
RA	96	.	NC_007790	844	0	C	G	bias_e_value=10101.3	bias_p_value=0.00346235	consensus_score=1562.7	fisher_strand_p_value=0.520517	frequency=1	ks_quality_p_value=0.000751972	major_base=G	major_cov=543/26	major_frequency=9.032e-01	minor_base=C	minor_cov=57/4	new_cov=543/26	polymorphism_frequency=9.032e-01	polymorphism_score=159.8	prediction=consensus	ref_cov=57/4	total_cov=600/30
RA	97	.	NC_007790	849	0	A	G	consensus_score=1651.5	frequency=1	major_base=G	major_cov=571/30	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=571/30	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=571/30
RA	98	.	NC_007790	875	0	T	C	bias_e_value=0.0331085	bias_p_value=1.13484e-08	consensus_score=1066.6	fisher_strand_p_value=0.514467	frequency=1	ks_quality_p_value=9.84604e-10	major_base=C	major_cov=457/21	major_frequency=8.852e-01	minor_base=T	minor_cov=58/4	new_cov=457/21	polymorphism_frequency=8.852e-01	polymorphism_score=97.0	prediction=consensus	ref_cov=58/4	total_cov=515/25
RA	99	.	NC_007790	898	0	G	A	consensus_score=750.9	frequency=1	major_base=A	major_cov=234/15	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=234/15	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=234/15
RA	100	.	NC_007790	918	0	A	G	bias_e_value=1839270	bias_p_value=0.630435	consensus_score=414.5	fisher_strand_p_value=0.380872	frequency=1	ks_quality_p_value=0.72287	major_base=G	major_cov=157/4	major_frequency=9.096e-01	minor_base=A	minor_cov=15/1	new_cov=157/4	polymorphism_frequency=9.096e-01	polymorphism_score=18.1	prediction=consensus	ref_cov=15/1	total_cov=173/5
RA	101	.	NC_007790	945	0	A	G	bias_e_value=629117	bias_p_value=0.215638	consensus_score=305.2	fisher_strand_p_value=0.133703	frequency=1	ks_quality_p_value=0.414237	major_base=G	major_cov=108/3	major_frequency=9.652e-01	minor_base=A	minor_cov=3/1	new_cov=108/3	polymorphism_frequency=9.652e-01	polymorphism_score=-1.3	prediction=consensus	ref_cov=3/1	total_cov=111/4
RA	102	.	NC_007790	951	0	C	A	consensus_score=297.0	frequency=1	major_base=A	major_cov=108/2	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=108/2	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=108/2
RA	103	.	NC_007790	1236	0	T	C	consensus_score=10.8	deleted=1	frequency=1	major_base=C	major_cov=5/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=5/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=5/1
RA	104	.	NC_007790	1262	0	T	.	bias_e_value=1801200	bias_p_value=0.617386	consensus_score=42.4	fisher_strand_p_value=0.426471	frequency=1	ks_quality_p_value=0.62219	major_base=.	major_cov=3/12	major_frequency=8.824e-01	minor_base=T	minor_cov=1/1	new_cov=3/12	polymorphism_frequency=8.824e-01	polymorphism_score=2.1	prediction=consensus	ref_cov=1/1	total_cov=4/13
RA	105	.	NC_007790	1276	0	C	T	bias_e_value=2249020	bias_p_value=0.770882	consensus_score=44.0	fisher_strand_p_value=0.447368	frequency=1	ks_quality_p_value=0.904837	major_base=T	major_cov=4/14	major_frequency=9.000e-01	minor_base=C	minor_cov=1/1	new_cov=4/14	polymorphism_frequency=9.000e-01	polymorphism_score=-2.6	prediction=consensus	ref_cov=1/1	total_cov=5/15
RA	106	.	NC_007790	1278	0	C	T	bias_e_value=2165710	bias_p_value=0.742325	consensus_score=43.7	fisher_strand_p_value=0.447368	frequency=1	ks_quality_p_value=0.837128	major_base=T	major_cov=4/14	major_frequency=9.000e-01	minor_base=C	minor_cov=1/1	new_cov=4/14	polymorphism_frequency=9.000e-01	polymorphism_score=-2.2	prediction=consensus	ref_cov=1/1	total_cov=5/15
RA	107	.	NC_007790	1280	0	C	T	bias_e_value=2308150	bias_p_value=0.791147	consensus_score=43.6	fisher_strand_p_value=0.447368	frequency=1	ks_quality_p_value=0.956529	major_base=T	major_cov=4/14	major_frequency=9.000e-01	minor_base=C	minor_cov=1/1	new_cov=4/14	polymorphism_frequency=9.000e-01	polymorphism_score=-2.4	prediction=consensus	ref_cov=1/1	total_cov=5/15
RA	108	.	NC_007790	1301	1	.	G	bias_e_value=1991410	bias_p_value=0.682582	consensus_score=52.7	fisher_strand_p_value=1	frequency=7.857e-01	ks_quality_p_value=0.318217	major_base=G	major_cov=6/16	major_frequency=7.857e-01	minor_base=.	minor_cov=2/4	new_cov=6/16	polymorphism_frequency=7.857e-01	polymorphism_score=17.8	prediction=polymorphism	ref_cov=2/4	total_cov=8/20
RA	109	.	NC_007790	1303	0	T	G	consensus_score=75.7	frequency=1	major_base=G	major_cov=8/20	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=8/20	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=8/20
RA	110	.	NC_007790	1330	0	T	C	bias_e_value=2307250	bias_p_value=0.790838	consensus_score=31.4	fisher_strand_p_value=0.579896	frequency=7.407e-01	ks_quality_p_value=0.737299	major_base=C	major_cov=3/17	major_frequency=7.407e-01	minor_base=T	minor_cov=2/5	new_cov=3/17	polymorphism_frequency=7.407e-01	polymorphism_score=10.0	prediction=polymorphism	ref_cov=2/5	total_cov=5/22
RA	111	.	NC_007790	1352	0	G	A	bias_e_value=339087	bias_p_value=0.116226	consensus_score=58.9	fisher_strand_p_value=1	frequency=2.391e-01	ks_quality_p_value=0.0247305	major_base=G	major_cov=16/19	major_frequency=7.609e-01	minor_base=A	minor_cov=5/6	new_cov=5/6	polymorphism_frequency=2.391e-01	polymorphism_score=17.6	prediction=polymorphism	ref_cov=16/19	total_cov=21/25
RA	112	.	NC_007790	1357	1	.	T	bias_e_value=1832300	bias_p_value=0.628045	consensus_score=20.7	fisher_strand_p_value=0.310073	frequency=3.611e-01	ks_quality_p_value=0.881964	major_base=.	major_cov=15/8	major_frequency=6.389e-01	minor_base=T	minor_cov=6/7	new_cov=6/7	polymorphism_frequency=3.611e-01	polymorphism_score=50.9	prediction=polymorphism	ref_cov=15/8	total_cov=21/15
RA	113	.	NC_007790	1361	0	A	C	bias_e_value=1912480	bias_p_value=0.655526	consensus_score=50.2	fisher_strand_p_value=0.708599	frequency=2.778e-01	ks_quality_p_value=0.416773	major_base=A	major_cov=16/10	major_frequency=7.222e-01	minor_base=C	minor_cov=5/5	new_cov=5/5	polymorphism_frequency=2.778e-01	polymorphism_score=25.3	prediction=polymorphism	ref_cov=16/10	total_cov=21/15
RA	114	.	NC_007790	1366	0	T	A	bias_e_value=1566310	bias_p_value=0.536873	consensus_score=-3.8	fisher_strand_p_value=0.226195	frequency=5.000e-01	ks_quality_p_value=0.925961	major_base=T	major_cov=10/3	major_frequency=5.000e-01	minor_base=A	minor_cov=6/7	new_cov=6/7	polymorphism_frequency=5.000e-01	polymorphism_score=33.5	prediction=polymorphism	ref_cov=10/3	total_cov=21/15
RA	115	.	NC_007790	1373	0	C	T	bias_e_value=351987	bias_p_value=0.120648	consensus_score=3.4	fisher_strand_p_value=0.045516	frequency=5.250e-01	ks_quality_p_value=0.569765	major_base=T	major_cov=11/10	major_frequency=5.250e-01	minor_base=C	minor_cov=16/3	new_cov=11/10	polymorphism_frequency=5.250e-01	polymorphism_score=37.5	prediction=polymorphism	ref_cov=16/3	total_cov=27/14
RA	116	.	NC_007790	1406	0	C	G	bias_e_value=82956.4	bias_p_value=0.0284344	consensus_score=87.3	fisher_strand_p_value=0.00442938	frequency=2.963e-01	ks_quality_p_value=1	major_base=C	major_cov=35/3	major_frequency=7.037e-01	minor_base=G	minor_cov=9/7	new_cov=9/7	polymorphism_frequency=2.963e-01	polymorphism_score=43.2	prediction=polymorphism	ref_cov=35/3	total_cov=44/10
RA	117	.	NC_007790	1414	0	T	G	bias_e_value=900523	bias_p_value=0.308666	consensus_score=69.8	fisher_strand_p_value=0.0908116	frequency=3.091e-01	ks_quality_p_value=1	major_base=T	major_cov=35/3	major_frequency=6.909e-01	minor_base=G	minor_cov=12/5	new_cov=12/5	polymorphism_frequency=3.091e-01	polymorphism_score=49.0	prediction=polymorphism	ref_cov=35/3	total_cov=47/8
RA	118	.	NC_007790	1451	0	T	G	bias_e_value=2074000	bias_p_value=0.710891	consensus_score=96.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.343817	major_base=G	major_cov=33/1	major_frequency=8.500e-01	minor_base=T	minor_cov=6/0	new_cov=33/1	polymorphism_frequency=8.500e-01	polymorphism_score=10.7	prediction=consensus	ref_cov=6/0	total_cov=39/1
RA	119	.	NC_007790	1461	0	T	.	bias_e_value=2912340	bias_p_value=0.998243	consensus_score=21.6	fisher_strand_p_value=1	frequency=5.161e-01	ks_quality_p_value=0.941309	major_base=.	major_cov=15/1	major_frequency=5.161e-01	minor_base=T	minor_cov=15/0	new_cov=15/1	polymorphism_frequency=5.161e-01	polymorphism_score=68.3	prediction=polymorphism	ref_cov=15/0	total_cov=36/1
RA	120	.	NC_007790	1462	0	T	A	bias_e_value=2915690	bias_p_value=0.99939	consensus_score=31.7	fisher_strand_p_value=1	frequency=3.889e-01	ks_quality_p_value=0.965264	major_base=T	major_cov=21/1	major_frequency=6.111e-01	minor_base=A	minor_cov=14/0	new_cov=14/0	polymorphism_frequency=3.889e-01	polymorphism_score=31.1	prediction=polymorphism	ref_cov=21/1	total_cov=36/1
RA	121	.	NC_007790	1463	0	A	G	bias_e_value=2915410	bias_p_value=0.999293	consensus_score=18.6	fisher_strand_p_value=1	frequency=4.000e-01	ks_quality_p_value=0.962621	major_base=A	major_cov=20/1	major_frequency=6.000e-01	minor_base=G	minor_cov=14/0	new_cov=14/0	polymorphism_frequency=4.000e-01	polymorphism_score=25.8	prediction=polymorphism	ref_cov=20/1	total_cov=35/1
RA	122	.	NC_007790	1464	0	A	G	bias_e_value=350646	bias_p_value=0.120189	consensus_score=-1.0	fisher_strand_p_value=0.472222	frequency=4.722e-01	ks_quality_p_value=0.0546516	major_base=A	major_cov=19/0	major_frequency=5.278e-01	minor_base=G	minor_cov=16/1	new_cov=16/1	polymorphism_frequency=4.722e-01	polymorphism_score=34.1	prediction=polymorphism	ref_cov=19/0	total_cov=35/1
RA	123	.	NC_007790	1468	0	C	A	bias_e_value=2271150	bias_p_value=0.778464	consensus_score=62.6	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.413277	major_base=A	major_cov=21/1	major_frequency=8.800e-01	minor_base=.	minor_cov=3/0	new_cov=21/1	polymorphism_frequency=8.800e-01	polymorphism_score=3.1	prediction=consensus	ref_cov=0/0	total_cov=24/1
RA	124	.	NC_007790	1469	0	C	A	bias_e_value=1893370	bias_p_value=0.648976	consensus_score=48.9	fisher_strand_p_value=1	frequency=2.400e-01	ks_quality_p_value=0.289994	major_base=C	major_cov=18/1	major_frequency=7.600e-01	minor_base=A	minor_cov=6/0	new_cov=6/0	polymorphism_frequency=2.400e-01	polymorphism_score=11.8	prediction=polymorphism	ref_cov=18/1	total_cov=24/1
RA	125	.	NC_007790	1474	0	T	A	bias_e_value=2910610	bias_p_value=0.99765	consensus_score=39.8	fisher_strand_p_value=1	frequency=7.600e-01	ks_quality_p_value=0.93223	major_base=A	major_cov=18/1	major_frequency=7.600e-01	minor_base=T	minor_cov=6/0	new_cov=18/1	polymorphism_frequency=7.600e-01	polymorphism_score=11.6	prediction=polymorphism	ref_cov=6/0	total_cov=24/1
RA	126	.	NC_007790	1476	1	.	T	bias_e_value=1340980	bias_p_value=0.459638	consensus_score=43.7	fisher_strand_p_value=0.210526	frequency=7.895e-01	ks_quality_p_value=0.776754	major_base=T	major_cov=15/0	major_frequency=7.895e-01	minor_base=.	minor_cov=3/1	new_cov=15/0	polymorphism_frequency=7.895e-01	polymorphism_score=7.0	prediction=polymorphism	ref_cov=3/1	total_cov=18/1
RA	127	.	NC_007790	1478	0	A	T	consensus_score=52.7	frequency=1	major_base=T	major_cov=18/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=18/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=18/1
RA	128	.	NC_007790	1479	0	C	A	bias_e_value=923788	bias_p_value=0.31664	consensus_score=45.3	fisher_strand_p_value=0.105263	frequency=1	ks_quality_p_value=0.894532	major_base=A	major_cov=17/0	major_frequency=8.947e-01	minor_base=T	minor_cov=1/1	new_cov=17/0	polymorphism_frequency=8.947e-01	polymorphism_score=-0.3	prediction=consensus	ref_cov=0/0	total_cov=18/1
RA	129	.	NC_007790	1482	0	C	T	bias_e_value=2082270	bias_p_value=0.713724	consensus_score=11.0	fisher_strand_p_value=0.368421	frequency=6.316e-01	ks_quality_p_value=0.940444	major_base=T	major_cov=12/0	major_frequency=6.316e-01	minor_base=C	minor_cov=6/1	new_cov=12/0	polymorphism_frequency=6.316e-01	polymorphism_score=9.7	prediction=polymorphism	ref_cov=6/1	total_cov=18/1
RA	130	.	NC_007790	1488	0	C	T	bias_e_value=2914140	bias_p_value=0.998857	consensus_score=16.6	fisher_strand_p_value=1	frequency=6.842e-01	ks_quality_p_value=0.952578	major_base=T	major_cov=12/1	major_frequency=6.842e-01	minor_base=C	minor_cov=6/0	new_cov=12/1	polymorphism_frequency=6.842e-01	polymorphism_score=6.4	prediction=polymorphism	ref_cov=6/0	total_cov=18/1
RA	131	.	NC_007790	1502	0	C	T	bias_e_value=2917470	bias_p_value=1	consensus_score=17.6	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=8/1	major_frequency=9.000e-01	minor_base=C	minor_cov=1/0	new_cov=8/1	polymorphism_frequency=9.000e-01	polymorphism_score=-4.3	prediction=consensus	ref_cov=1/0	total_cov=9/1
RA	132	.	NC_007790	1510	0	C	T	bias_e_value=1896430	bias_p_value=0.650024	consensus_score=22.2	fisher_strand_p_value=0.333333	frequency=1	ks_quality_p_value=0.872525	major_base=T	major_cov=8/3	major_frequency=9.167e-01	minor_base=C	minor_cov=0/1	new_cov=8/3	polymorphism_frequency=9.167e-01	polymorphism_score=-4.6	prediction=consensus	ref_cov=0/1	total_cov=8/4
RA	133	.	NC_007790	1572	0	G	C	bias_e_value=1287400	bias_p_value=0.441273	consensus_score=14.4	fisher_strand_p_value=0.375	frequency=1	ks_quality_p_value=0.409484	major_base=C	major_cov=5/2	major_frequency=8.750e-01	minor_base=G	minor_cov=0/1	new_cov=5/2	polymorphism_frequency=8.750e-01	polymorphism_score=-2.6	prediction=consensus	ref_cov=0/1	total_cov=5/3
RA	134	.	NC_007790	1588	0	A	G	bias_e_value=2014120	bias_p_value=0.690366	consensus_score=11.4	fisher_strand_p_value=0.375	frequency=1	ks_quality_p_value=0.866878	major_base=G	major_cov=5/2	major_frequency=8.750e-01	minor_base=A	minor_cov=0/1	new_cov=5/2	polymorphism_frequency=8.750e-01	polymorphism_score=-3.9	prediction=consensus	ref_cov=0/1	total_cov=5/3
RA	135	.	NC_007790	1603	0	G	A	consensus_score=47.0	frequency=1	major_base=A	major_cov=16/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=16/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=16/1
RA	136	.	NC_007790	1671	0	G	T	consensus_score=61.1	frequency=1	major_base=T	major_cov=21/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=21/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=21/1
RA	137	.	NC_007790	1694	0	C	T	consensus_score=30.8	frequency=1	major_base=T	major_cov=12/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=12/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=12/0
RA	138	.	NC_007790	1744	0	A	T	consensus_score=174.8	frequency=1	major_base=T	major_cov=56/3	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=56/3	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=56/3
RA	139	.	NC_007790	1778	0	G	A	consensus_score=186.9	frequency=1	major_base=A	major_cov=61/5	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=61/5	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=61/5
RA	140	.	NC_007790	1871	0	C	A	consensus_score=135.3	frequency=1	major_base=A	major_cov=38/10	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=38/10	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=38/10
RA	141	.	NC_007790	1953	1	.	T	bias_e_value=218380	bias_p_value=0.0748524	consensus_score=69.3	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.014256	major_base=T	major_cov=22/2	major_frequency=8.276e-01	minor_base=.	minor_cov=5/0	new_cov=22/2	polymorphism_frequency=8.276e-01	polymorphism_score=9.0	prediction=consensus	ref_cov=5/0	total_cov=27/2
RA	142	.	NC_007790	1954	0	A	G	bias_e_value=1972700	bias_p_value=0.67617	consensus_score=45.0	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.312659	major_base=G	major_cov=21/2	major_frequency=8.519e-01	minor_base=A	minor_cov=4/0	new_cov=21/2	polymorphism_frequency=8.519e-01	polymorphism_score=1.7	prediction=consensus	ref_cov=4/0	total_cov=27/2
RA	143	.	NC_007790	1955	0	T	C	bias_e_value=1289730	bias_p_value=0.442072	consensus_score=51.6	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.153983	major_base=C	major_cov=24/2	major_frequency=8.966e-01	minor_base=T	minor_cov=3/0	new_cov=24/2	polymorphism_frequency=8.966e-01	polymorphism_score=-0.1	prediction=consensus	ref_cov=3/0	total_cov=27/2
RA	144	.	NC_007790	1967	0	C	G	bias_e_value=1155120	bias_p_value=0.395931	consensus_score=54.3	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.130344	major_base=G	major_cov=20/2	major_frequency=8.800e-01	minor_base=C	minor_cov=3/0	new_cov=20/2	polymorphism_frequency=8.800e-01	polymorphism_score=2.7	prediction=consensus	ref_cov=3/0	total_cov=23/2
MC	145	.	NC_007790	101	241	0	0	left_inside_cov=9	left_outside_cov=13	right_inside_cov=0	right_outside_cov=24
MC	146	.	NC_007790	378	704	0	0	left_inside_cov=4	left_outside_cov=36	right_inside_cov=11	right_outside_cov=13
MC	147	.	NC_007790	983	1253	0	0	left_inside_cov=8	left_outside_cov=12	right_inside_cov=7	right_outside_cov=13
MC	148	.	NC_007790	1983	3125	0	0	left_inside_cov=10	left_outside_cov=14	right_inside_cov=0	right_outside_cov=NA
MC	149	.	NC_007791	1	4439	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
MC	150	.	NC_007792	1	37136	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
MC	151	.	NC_007793	1	2872769	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
UN	152	.	NC_007790	1	1
UN	153	.	NC_007790	109	243
UN	154	.	NC_007790	377	474
UN	155	.	NC_007790	493	493
UN	156	.	NC_007790	568	704
UN	157	.	NC_007790	987	1141
UN	158	.	NC_007790	1144	1227
UN	159	.	NC_007790	1230	1230
UN	160	.	NC_007790	1244	1244
UN	161	.	NC_007790	1248	1248
UN	162	.	NC_007790	1366	1366
UN	163	.	NC_007790	1373	1373
UN	164	.	NC_007790	1464	1464
UN	165	.	NC_007790	1518	1548
UN	166	.	NC_007790	1983	1983
UN	167	.	NC_007790	2006	2006
UN	168	.	NC_007790	2022	3125