#=GENOME_DIFF	1.0
#=CREATED	18:13:33 03 Jun 2025
#=PROGRAM	breseq 0.39.0 
#=COMMAND	breseq -j 8 -o /ld1/breseq_work/20250516nextseq_run_rmdup/IH111_rmdup_R1R2_ -r /ld1/E.coli_MG1655_ref/MG1655/ncbi_dataset/data/GCF_000005845.2/genomic.gbff /ld1/breseq_work/20250516nextseq_run_QC/work/test_work/seqkit_rmdup_-s/INPUT_FQ/IH111_rmdup_R1.fastq.gz /ld1/breseq_work/20250516nextseq_run_QC/work/test_work/seqkit_rmdup_-s/INPUT_FQ/IH111_rmdup_R2.fastq.gz
#=REFSEQ	/ld1/E.coli_MG1655_ref/MG1655/ncbi_dataset/data/GCF_000005845.2/genomic.gbff
#=READSEQ	/ld1/breseq_work/20250516nextseq_run_QC/work/test_work/seqkit_rmdup_-s/INPUT_FQ/IH111_rmdup_R1.fastq.gz
#=READSEQ	/ld1/breseq_work/20250516nextseq_run_QC/work/test_work/seqkit_rmdup_-s/INPUT_FQ/IH111_rmdup_R2.fastq.gz
#=CONVERTED-BASES	568200000
#=CONVERTED-READS	1894000
#=INPUT-BASES	568280700
#=INPUT-READS	1894269
#=MAPPED-BASES	552854772
#=MAPPED-READS	1845666
SNP	1	53	NC_000913	557635	T
MOB	2	159,163	NC_000913	572138	IS2	1	5
SNP	3	54	NC_000913	680015	T
SNP	4	55	NC_000913	706052	A
SNP	5	56	NC_000913	706759	A
SNP	6	57	NC_000913	708774	A
MOB	7	156,157	NC_000913	820823	IS5	-1	4
SNP	8	60	NC_000913	956539	T
SNP	9	61	NC_000913	956691	T
SNP	10	62	NC_000913	1076997	T
SNP	11	63	NC_000913	1093264	T
MOB	12	160,171	NC_000913	1105376	IS2	-1	5
SNP	13	64	NC_000913	1196220	T
SNP	14	65	NC_000913	1196232	T
SNP	15	66	NC_000913	1196245	C
SNP	16	67	NC_000913	1196247	G
SNP	17	76	NC_000913	1279000	A
SNP	18	80	NC_000913	1337394	G
DEL	19	148,174	NC_000913	1397239	10478	mediated=IS5
SNP	20	86	NC_000913	1567492	G
SNP	21	88	NC_000913	1652331	C
SNP	22	89	NC_000913	1689119	A
SNP	23	92	NC_000913	1772818	T
SNP	24	94	NC_000913	1844295	T
MOB	25	175,178	NC_000913	1859380	IS5	1	4
MOB	26	177,179	NC_000913	1909378	IS2	-1	5
SNP	27	96	NC_000913	2015789	A
SNP	28	97	NC_000913	2032423	A
MOB	29	158,183	NC_000913	2034215	IS3	1	5	ins_start=A
SNP	30	98	NC_000913	2043522	A
DEL	31	100,101	NC_000913	2173363	2
MOB	32	184,186	NC_000913	2317455	IS2	-1	5
MOB	33	180,181	NC_000913	2406780	IS1	-1	8
DEL	34	150,188	NC_000913	2558699	6790
SNP	35	110	NC_000913	2745600	G
SNP	36	111	NC_000913	2774947	A
SNP	37	112	NC_000913	2867455	A
SNP	38	117	NC_000913	3109181	G
MOB	39	185,191	NC_000913	3189075	IS5	1	4
SNP	40	123	NC_000913	3486205	A
SNP	41	124	NC_000913	3490498	G
SNP	42	125	NC_000913	3526483	A
INS	43	126	NC_000913	3560455	G
SNP	44	131	NC_000913	3948012	T
SNP	45	132	NC_000913	3954923	T
SNP	46	134	NC_000913	4123447	T
INS	47	140,141	NC_000913	4296381	GC
SNP	48	143	NC_000913	4486856	A
SNP	49	144	NC_000913	4548969	G
RA	50	.	NC_000913	58065	0	C	A	bias_e_value=0.000563529	bias_p_value=1.21407e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=185.2	fisher_strand_p_value=4.47458e-12	frequency=3.571e-01	ks_quality_p_value=1	major_base=C	major_cov=28/44	major_frequency=6.429e-01	minor_base=A	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=3.571e-01	polymorphism_score=21.1	prediction=polymorphism	ref_cov=28/44	total_cov=68/44
RA	51	.	NC_000913	85651	0	G	T	bias_e_value=21.7849	bias_p_value=4.69335e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=255.4	fisher_strand_p_value=2.92516e-07	frequency=2.609e-01	ks_quality_p_value=1	major_base=G	major_cov=42/60	major_frequency=7.391e-01	minor_base=T	minor_cov=0/36	new_cov=0/36	polymorphism_frequency=2.609e-01	polymorphism_score=13.2	prediction=polymorphism	ref_cov=42/60	total_cov=42/96
RA	52	.	NC_000913	141849	0	C	A	bias_e_value=0.00206202	bias_p_value=4.44243e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=308.4	fisher_strand_p_value=1.72291e-11	frequency=2.517e-01	ks_quality_p_value=1	major_base=C	major_cov=44/63	major_frequency=7.483e-01	minor_base=A	minor_cov=36/0	new_cov=36/0	polymorphism_frequency=2.517e-01	polymorphism_score=19.3	prediction=polymorphism	ref_cov=44/63	total_cov=80/63
RA	53	.	NC_000913	557635	0	A	T	consensus_score=398.0	frequency=1	major_base=T	major_cov=58/49	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=58/49	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=58/49
RA	54	.	NC_000913	680015	0	C	T	bias_e_value=4641650	bias_p_value=1	consensus_score=362.0	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=47/52	major_frequency=9.900e-01	minor_base=G	minor_cov=0/1	new_cov=47/52	polymorphism_frequency=9.900e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=47/53
RA	55	.	NC_000913	706052	0	C	A	bias_e_value=2767090	bias_p_value=0.596144	consensus_score=325.1	fisher_strand_p_value=0.279067	frequency=1	ks_quality_p_value=0.894734	major_base=A	major_cov=44/67	major_frequency=8.740e-01	minor_base=C	minor_cov=9/7	new_cov=44/67	polymorphism_frequency=8.740e-01	polymorphism_score=40.5	prediction=consensus	ref_cov=9/7	total_cov=53/74
RA	56	.	NC_000913	706759	0	G	A	consensus_score=290.0	frequency=1	major_base=A	major_cov=27/49	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=27/49	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=27/49
RA	57	.	NC_000913	708774	0	G	A	bias_e_value=3806580	bias_p_value=0.820092	consensus_score=336.4	fisher_strand_p_value=0.46875	frequency=1	ks_quality_p_value=0.989312	major_base=A	major_cov=51/44	major_frequency=9.896e-01	minor_base=.	minor_cov=0/1	new_cov=51/44	polymorphism_frequency=9.896e-01	polymorphism_score=-2.3	prediction=consensus	ref_cov=0/0	total_cov=51/45
RA	58	.	NC_000913	834674	0	C	A	bias_e_value=0.0469282	bias_p_value=1.01102e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=235.8	fisher_strand_p_value=4.48859e-10	frequency=2.500e-01	ks_quality_p_value=1	major_base=C	major_cov=34/53	major_frequency=7.500e-01	minor_base=A	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=2.500e-01	polymorphism_score=18.1	prediction=polymorphism	ref_cov=34/53	total_cov=63/53
RA	59	.	NC_000913	847955	0	G	A	bias_e_value=0.000222175	bias_p_value=4.78655e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=326.3	fisher_strand_p_value=1.7035e-12	frequency=2.209e-01	ks_quality_p_value=1	major_base=G	major_cov=79/55	major_frequency=7.791e-01	minor_base=A	minor_cov=0/38	new_cov=0/38	polymorphism_frequency=2.209e-01	polymorphism_score=51.1	prediction=polymorphism	ref_cov=79/55	total_cov=79/93
RA	60	.	NC_000913	956539	0	C	T	consensus_score=455.8	frequency=1	major_base=T	major_cov=72/50	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=72/50	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=72/50
RA	61	.	NC_000913	956691	0	C	T	consensus_score=442.1	frequency=1	major_base=T	major_cov=56/66	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=56/66	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=56/66
RA	62	.	NC_000913	1076997	0	C	T	consensus_score=285.1	frequency=1	major_base=T	major_cov=39/39	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=39/39	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=39/39
RA	63	.	NC_000913	1093264	0	C	T	bias_e_value=4641650	bias_p_value=1	consensus_score=764.6	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=100/106	major_frequency=9.952e-01	minor_base=G	minor_cov=0/1	new_cov=100/106	polymorphism_frequency=9.952e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=100/107
RA	64	.	NC_000913	1196220	0	C	T	consensus_score=214.2	frequency=1	major_base=T	major_cov=38/29	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=38/29	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=38/29
RA	65	.	NC_000913	1196232	0	C	T	consensus_score=183.9	frequency=1	major_base=T	major_cov=35/24	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=35/24	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=35/24
RA	66	.	NC_000913	1196245	0	T	C	consensus_score=146.0	frequency=1	major_base=C	major_cov=29/20	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=29/20	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=29/20
RA	67	.	NC_000913	1196247	0	A	G	consensus_score=147.7	frequency=1	major_base=G	major_cov=29/20	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=29/20	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=29/20
RA	68	.	NC_000913	1196277	0	C	T	consensus_score=109.3	deleted=1	frequency=1	major_base=T	major_cov=24/16	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=24/16	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=24/16
RA	69	.	NC_000913	1196280	0	G	C	consensus_score=106.3	deleted=1	frequency=1	major_base=C	major_cov=24/16	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=24/16	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=24/16
RA	70	.	NC_000913	1196283	0	A	G	consensus_score=107.1	deleted=1	frequency=1	major_base=G	major_cov=24/16	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=24/16	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=24/16
RA	71	.	NC_000913	1196292	0	C	T	consensus_score=102.0	deleted=1	frequency=1	major_base=T	major_cov=23/15	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=23/15	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=23/15
RA	72	.	NC_000913	1196304	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=80.7	deleted=1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=17/15	major_frequency=9.697e-01	minor_base=C	minor_cov=1/0	new_cov=17/15	polymorphism_frequency=9.697e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=18/15
RA	73	.	NC_000913	1196316	0	T	A	consensus_score=78.1	deleted=1	frequency=1	major_base=A	major_cov=16/15	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=16/15	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=16/15
RA	74	.	NC_000913	1196325	0	A	G	consensus_score=57.7	deleted=1	frequency=1	major_base=G	major_cov=12/13	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=12/13	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=12/13
RA	75	.	NC_000913	1196352	0	C	A	consensus_score=31.6	deleted=1	frequency=1	major_base=A	major_cov=9/7	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=9/7	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=9/7
RA	76	.	NC_000913	1279000	0	C	A	consensus_score=390.7	frequency=1	major_base=A	major_cov=74/35	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=74/35	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=74/35
RA	77	.	NC_000913	1286870	0	C	A	bias_e_value=913250	bias_p_value=0.196751	consensus_reject=FREQUENCY_CUTOFF	consensus_score=191.0	fisher_strand_p_value=0.0490986	frequency=2.762e-01	ks_quality_p_value=0.99779	major_base=C	major_cov=30/46	major_frequency=7.238e-01	minor_base=A	minor_cov=18/11	new_cov=18/11	polymorphism_frequency=2.762e-01	polymorphism_score=50.8	prediction=polymorphism	ref_cov=30/46	total_cov=48/59
RA	78	.	NC_000913	1286874	0	G	A	bias_e_value=377271	bias_p_value=0.0812794	consensus_reject=FREQUENCY_CUTOFF	consensus_score=195.2	fisher_strand_p_value=0.0157867	frequency=2.642e-01	ks_quality_p_value=1	major_base=G	major_cov=29/49	major_frequency=7.358e-01	minor_base=A	minor_cov=18/10	new_cov=18/10	polymorphism_frequency=2.642e-01	polymorphism_score=56.4	prediction=polymorphism	ref_cov=29/49	total_cov=47/59
RA	79	.	NC_000913	1334966	0	A	C	bias_e_value=8.1127e-05	bias_p_value=1.7478e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=326.7	fisher_strand_p_value=5.99749e-13	frequency=2.500e-01	ks_quality_p_value=1	major_base=A	major_cov=67/74	major_frequency=7.500e-01	minor_base=C	minor_cov=47/0	new_cov=47/0	polymorphism_frequency=2.500e-01	polymorphism_score=28.3	prediction=polymorphism	ref_cov=67/74	total_cov=114/74
RA	80	.	NC_000913	1337394	0	A	G	consensus_score=521.1	frequency=1	major_base=G	major_cov=88/48	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=88/48	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=88/48
RA	81	.	NC_000913	1351463	0	C	A	bias_e_value=0.923823	bias_p_value=1.99029e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=219.3	fisher_strand_p_value=1.0262e-08	frequency=2.920e-01	ks_quality_p_value=1	major_base=C	major_cov=54/43	major_frequency=7.080e-01	minor_base=A	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=2.920e-01	polymorphism_score=13.1	prediction=polymorphism	ref_cov=54/43	total_cov=94/43
RA	82	.	NC_000913	1427992	0	G	T	bias_e_value=4.63813e-05	bias_p_value=9.99241e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=234.0	fisher_strand_p_value=3.36206e-13	frequency=3.446e-01	ks_quality_p_value=1	major_base=G	major_cov=52/45	major_frequency=6.554e-01	minor_base=T	minor_cov=0/51	new_cov=0/51	polymorphism_frequency=3.446e-01	polymorphism_score=16.3	prediction=polymorphism	ref_cov=52/45	total_cov=52/96
RA	83	.	NC_000913	1466432	0	A	G	bias_e_value=4517080	bias_p_value=0.973163	consensus_reject=FREQUENCY_CUTOFF	consensus_score=124.7	fisher_strand_p_value=0.777454	frequency=2.464e-01	ks_quality_p_value=1	major_base=A	major_cov=22/30	major_frequency=7.536e-01	minor_base=G	minor_cov=6/11	new_cov=6/11	polymorphism_frequency=2.464e-01	polymorphism_score=31.9	prediction=polymorphism	ref_cov=22/30	total_cov=29/41
RA	84	.	NC_000913	1466438	0	T	G	bias_e_value=4113530	bias_p_value=0.88622	consensus_reject=FREQUENCY_CUTOFF	consensus_score=123.4	fisher_strand_p_value=0.562636	frequency=2.143e-01	ks_quality_p_value=1	major_base=T	major_cov=24/31	major_frequency=7.857e-01	minor_base=G	minor_cov=5/10	new_cov=5/10	polymorphism_frequency=2.143e-01	polymorphism_score=23.9	prediction=polymorphism	ref_cov=24/31	total_cov=29/41
RA	85	.	NC_000913	1470627	0	C	A	bias_e_value=4.77978e-09	bias_p_value=1.02976e-15	consensus_reject=FREQUENCY_CUTOFF	consensus_score=414.2	fisher_strand_p_value=2.62844e-17	frequency=2.557e-01	ks_quality_p_value=1	major_base=C	major_cov=43/88	major_frequency=7.443e-01	minor_base=A	minor_cov=45/0	new_cov=45/0	polymorphism_frequency=2.557e-01	polymorphism_score=14.9	prediction=polymorphism	ref_cov=43/88	total_cov=88/88
RA	86	.	NC_000913	1567492	0	A	G	consensus_score=547.3	frequency=1	major_base=G	major_cov=56/83	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=56/83	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=56/83
RA	87	.	NC_000913	1577330	0	T	G	bias_e_value=0.67936	bias_p_value=1.46362e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=265.6	fisher_strand_p_value=7.42246e-09	frequency=2.222e-01	ks_quality_p_value=1	major_base=T	major_cov=52/32	major_frequency=7.778e-01	minor_base=G	minor_cov=0/24	new_cov=0/24	polymorphism_frequency=2.222e-01	polymorphism_score=11.9	prediction=polymorphism	ref_cov=52/32	total_cov=53/57
RA	88	.	NC_000913	1652331	0	T	C	consensus_score=535.0	frequency=1	major_base=C	major_cov=74/61	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=74/61	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=74/61
RA	89	.	NC_000913	1689119	0	G	A	consensus_score=383.1	frequency=1	major_base=A	major_cov=50/52	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=50/52	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=50/52
RA	90	.	NC_000913	1716740	0	G	T	bias_e_value=0.000401301	bias_p_value=8.64566e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=273.0	fisher_strand_p_value=3.14559e-12	frequency=2.615e-01	ks_quality_p_value=1	major_base=G	major_cov=61/35	major_frequency=7.385e-01	minor_base=T	minor_cov=0/34	new_cov=0/34	polymorphism_frequency=2.615e-01	polymorphism_score=12.1	prediction=polymorphism	ref_cov=61/35	total_cov=61/69
RA	91	.	NC_000913	1756353	0	C	A	bias_e_value=0.969157	bias_p_value=2.08796e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=265.7	fisher_strand_p_value=1.07937e-08	frequency=2.419e-01	ks_quality_p_value=1	major_base=C	major_cov=43/51	major_frequency=7.581e-01	minor_base=A	minor_cov=30/0	new_cov=30/0	polymorphism_frequency=2.419e-01	polymorphism_score=11.5	prediction=polymorphism	ref_cov=43/51	total_cov=73/51
RA	92	.	NC_000913	1772818	0	C	T	consensus_score=458.8	frequency=1	major_base=T	major_cov=45/81	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=45/81	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=45/81
RA	93	.	NC_000913	1812509	0	G	T	bias_e_value=5.70652e-07	bias_p_value=1.22942e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=387.7	fisher_strand_p_value=3.58837e-15	frequency=2.426e-01	ks_quality_p_value=1	major_base=G	major_cov=82/46	major_frequency=7.574e-01	minor_base=T	minor_cov=0/41	new_cov=0/41	polymorphism_frequency=2.426e-01	polymorphism_score=11.3	prediction=polymorphism	ref_cov=82/46	total_cov=82/87
RA	94	.	NC_000913	1844295	0	C	T	consensus_score=485.2	frequency=1	major_base=T	major_cov=43/90	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=43/90	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=43/90
RA	95	.	NC_000913	1922815	0	C	A	bias_e_value=5756.59	bias_p_value=0.0012402	consensus_reject=FREQUENCY_CUTOFF	consensus_score=183.6	fisher_strand_p_value=0.000124088	frequency=3.276e-01	ks_quality_p_value=1	major_base=C	major_cov=25/53	major_frequency=6.724e-01	minor_base=A	minor_cov=27/11	new_cov=27/11	polymorphism_frequency=3.276e-01	polymorphism_score=23.2	prediction=polymorphism	ref_cov=25/53	total_cov=52/64
RA	96	.	NC_000913	2015789	0	G	A	consensus_score=330.9	frequency=1	major_base=A	major_cov=41/51	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=41/51	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=41/51
RA	97	.	NC_000913	2032423	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=476.3	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=65/63	major_frequency=9.922e-01	minor_base=C	minor_cov=1/0	new_cov=65/63	polymorphism_frequency=9.922e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=66/64
RA	98	.	NC_000913	2043522	0	C	A	consensus_score=501.9	frequency=1	major_base=A	major_cov=74/67	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=74/67	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=74/67
RA	99	.	NC_000913	2159413	0	C	T	bias_e_value=892.687	bias_p_value=0.000192321	consensus_reject=FREQUENCY_CUTOFF	consensus_score=102.0	fisher_strand_p_value=1.59669e-05	frequency=2.759e-01	ks_quality_p_value=1	major_base=C	major_cov=17/25	major_frequency=7.241e-01	minor_base=T	minor_cov=16/0	new_cov=16/0	polymorphism_frequency=2.759e-01	polymorphism_score=17.2	prediction=polymorphism	ref_cov=17/25	total_cov=33/25
RA	100	.	NC_000913	2173363	0	C	.	bias_e_value=3849200	bias_p_value=0.829273	consensus_score=548.2	fisher_strand_p_value=0.490566	frequency=1	ks_quality_p_value=0.970088	major_base=.	major_cov=54/51	major_frequency=9.906e-01	minor_base=C	minor_cov=0/1	new_cov=54/51	polymorphism_frequency=9.906e-01	polymorphism_score=-1.4	prediction=consensus	ref_cov=0/1	total_cov=54/52
RA	101	.	NC_000913	2173364	0	C	.	bias_e_value=3849200	bias_p_value=0.829273	consensus_score=548.2	fisher_strand_p_value=0.490566	frequency=1	ks_quality_p_value=0.970088	major_base=.	major_cov=54/51	major_frequency=9.906e-01	minor_base=C	minor_cov=0/1	new_cov=54/51	polymorphism_frequency=9.906e-01	polymorphism_score=-1.4	prediction=consensus	ref_cov=0/1	total_cov=54/52
RA	102	.	NC_000913	2288418	0	G	T	bias_e_value=6.86669e-07	bias_p_value=1.47936e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=355.0	fisher_strand_p_value=4.34207e-15	frequency=2.781e-01	ks_quality_p_value=1	major_base=G	major_cov=73/49	major_frequency=7.219e-01	minor_base=T	minor_cov=0/47	new_cov=0/47	polymorphism_frequency=2.781e-01	polymorphism_score=18.9	prediction=polymorphism	ref_cov=73/49	total_cov=73/96
RA	103	.	NC_000913	2457177	0	T	G	bias_e_value=321.493	bias_p_value=6.92625e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.2	fisher_strand_p_value=5.26537e-06	frequency=2.133e-01	ks_quality_p_value=1	major_base=T	major_cov=36/23	major_frequency=7.867e-01	minor_base=G	minor_cov=0/16	new_cov=0/16	polymorphism_frequency=2.133e-01	polymorphism_score=13.1	prediction=polymorphism	ref_cov=36/23	total_cov=36/44
RA	104	.	NC_000913	2477264	0	T	C	bias_e_value=8.10191e-07	bias_p_value=1.74548e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=285.8	fisher_strand_p_value=5.14891e-15	frequency=2.764e-01	ks_quality_p_value=1	major_base=T	major_cov=24/65	major_frequency=7.236e-01	minor_base=C	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=2.764e-01	polymorphism_score=10.4	prediction=polymorphism	ref_cov=24/65	total_cov=59/65
RA	105	.	NC_000913	2477265	0	A	C	bias_e_value=1.78866e-15	bias_p_value=3.8535e-22	consensus_reject=FREQUENCY_CUTOFF	consensus_score=184.3	fisher_strand_p_value=7.09636e-24	frequency=3.902e-01	ks_quality_p_value=1	major_base=A	major_cov=11/64	major_frequency=6.098e-01	minor_base=C	minor_cov=48/0	new_cov=48/0	polymorphism_frequency=3.902e-01	polymorphism_score=42.9	prediction=polymorphism	ref_cov=11/64	total_cov=59/65
RA	106	.	NC_000913	2490240	0	G	T	bias_e_value=0.0033465	bias_p_value=7.20971e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=321.0	fisher_strand_p_value=2.85189e-11	frequency=2.453e-01	ks_quality_p_value=1	major_base=G	major_cov=65/55	major_frequency=7.547e-01	minor_base=T	minor_cov=0/39	new_cov=0/39	polymorphism_frequency=2.453e-01	polymorphism_score=10.2	prediction=polymorphism	ref_cov=65/55	total_cov=65/94
RA	107	.	NC_000913	2490512	0	C	A	bias_e_value=1.70633	bias_p_value=3.67613e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=297.6	fisher_strand_p_value=1.96089e-08	frequency=2.030e-01	ks_quality_p_value=1	major_base=C	major_cov=48/58	major_frequency=7.970e-01	minor_base=A	minor_cov=27/0	new_cov=27/0	polymorphism_frequency=2.030e-01	polymorphism_score=10.7	prediction=polymorphism	ref_cov=48/58	total_cov=75/58
RA	108	.	NC_000913	2611413	0	C	A	bias_e_value=0.0412522	bias_p_value=8.88739e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=226.5	fisher_strand_p_value=3.9222e-10	frequency=2.475e-01	ks_quality_p_value=1	major_base=C	major_cov=25/51	major_frequency=7.525e-01	minor_base=A	minor_cov=25/0	new_cov=25/0	polymorphism_frequency=2.475e-01	polymorphism_score=11.2	prediction=polymorphism	ref_cov=25/51	total_cov=50/51
RA	109	.	NC_000913	2704512	0	C	A	bias_e_value=0.0367653	bias_p_value=7.92073e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=203.4	fisher_strand_p_value=3.47711e-10	frequency=2.736e-01	ks_quality_p_value=1	major_base=C	major_cov=29/48	major_frequency=7.264e-01	minor_base=A	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=2.736e-01	polymorphism_score=17.0	prediction=polymorphism	ref_cov=29/48	total_cov=58/48
RA	110	.	NC_000913	2745600	0	A	G	consensus_score=422.5	frequency=1	major_base=G	major_cov=63/46	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=63/46	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=63/46
RA	111	.	NC_000913	2774947	0	G	A	bias_e_value=3810320	bias_p_value=0.820897	consensus_score=506.6	fisher_strand_p_value=0.464789	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=65/76	major_frequency=9.930e-01	minor_base=C	minor_cov=1/0	new_cov=65/76	polymorphism_frequency=9.930e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=66/76
RA	112	.	NC_000913	2867455	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=518.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=87/58	major_frequency=9.932e-01	minor_base=C	minor_cov=1/0	new_cov=87/58	polymorphism_frequency=9.932e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=88/58
RA	113	.	NC_000913	2913085	0	G	T	bias_e_value=0.0513446	bias_p_value=1.10617e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=265.7	fisher_strand_p_value=4.93161e-10	frequency=2.417e-01	ks_quality_p_value=1	major_base=G	major_cov=55/36	major_frequency=7.583e-01	minor_base=T	minor_cov=0/29	new_cov=0/29	polymorphism_frequency=2.417e-01	polymorphism_score=11.4	prediction=polymorphism	ref_cov=55/36	total_cov=55/65
RA	114	.	NC_000913	2990480	0	C	A	bias_e_value=1.19743e-06	bias_p_value=2.57975e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=324.3	fisher_strand_p_value=7.70136e-15	frequency=2.749e-01	ks_quality_p_value=1	major_base=C	major_cov=51/73	major_frequency=7.251e-01	minor_base=A	minor_cov=47/0	new_cov=47/0	polymorphism_frequency=2.749e-01	polymorphism_score=18.4	prediction=polymorphism	ref_cov=51/73	total_cov=98/73
RA	115	.	NC_000913	3054886	0	G	T	bias_e_value=0.0409181	bias_p_value=8.81543e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=146.7	fisher_strand_p_value=3.88898e-10	frequency=2.907e-01	ks_quality_p_value=1	major_base=G	major_cov=15/46	major_frequency=7.093e-01	minor_base=T	minor_cov=24/1	new_cov=24/1	polymorphism_frequency=2.907e-01	polymorphism_score=23.9	prediction=polymorphism	ref_cov=15/46	total_cov=39/47
RA	116	.	NC_000913	3054894	0	G	T	bias_e_value=471.566	bias_p_value=0.000101594	consensus_reject=FREQUENCY_CUTOFF	consensus_score=143.0	fisher_strand_p_value=7.97493e-06	frequency=2.941e-01	ks_quality_p_value=1	major_base=G	major_cov=18/42	major_frequency=7.059e-01	minor_base=T	minor_cov=21/4	new_cov=21/4	polymorphism_frequency=2.941e-01	polymorphism_score=17.9	prediction=polymorphism	ref_cov=18/42	total_cov=39/46
RA	117	.	NC_000913	3109181	0	A	G	consensus_score=435.1	frequency=1	major_base=G	major_cov=46/66	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=46/66	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=46/66
RA	118	.	NC_000913	3226224	0	G	T	bias_e_value=0.00106496	bias_p_value=2.29435e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=338.4	fisher_strand_p_value=8.66726e-12	frequency=2.469e-01	ks_quality_p_value=1	major_base=G	major_cov=73/49	major_frequency=7.531e-01	minor_base=T	minor_cov=1/39	new_cov=1/39	polymorphism_frequency=2.469e-01	polymorphism_score=11.4	prediction=polymorphism	ref_cov=73/49	total_cov=74/88
RA	119	.	NC_000913	3281067	0	C	A	bias_e_value=16.3323	bias_p_value=3.51864e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=128.4	fisher_strand_p_value=2.15184e-07	frequency=2.985e-01	ks_quality_p_value=1	major_base=C	major_cov=16/31	major_frequency=7.015e-01	minor_base=A	minor_cov=20/0	new_cov=20/0	polymorphism_frequency=2.985e-01	polymorphism_score=10.2	prediction=polymorphism	ref_cov=16/31	total_cov=36/31
RA	120	.	NC_000913	3401345	0	G	T	bias_e_value=6.90634	bias_p_value=1.4879e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=259.2	fisher_strand_p_value=8.61707e-08	frequency=2.321e-01	ks_quality_p_value=1	major_base=G	major_cov=47/39	major_frequency=7.679e-01	minor_base=T	minor_cov=0/26	new_cov=0/26	polymorphism_frequency=2.321e-01	polymorphism_score=10.6	prediction=polymorphism	ref_cov=47/39	total_cov=47/65
RA	121	.	NC_000913	3420669	0	G	T	bias_e_value=0.795062	bias_p_value=1.71289e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=233.2	fisher_strand_p_value=8.76019e-09	frequency=2.677e-01	ks_quality_p_value=1	major_base=G	major_cov=47/46	major_frequency=7.323e-01	minor_base=T	minor_cov=0/34	new_cov=0/34	polymorphism_frequency=2.677e-01	polymorphism_score=13.8	prediction=polymorphism	ref_cov=47/46	total_cov=47/80
RA	122	.	NC_000913	3431396	0	C	A	bias_e_value=6.59722	bias_p_value=1.42131e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=272.8	fisher_strand_p_value=8.20828e-08	frequency=2.188e-01	ks_quality_p_value=1	major_base=C	major_cov=49/51	major_frequency=7.812e-01	minor_base=A	minor_cov=28/0	new_cov=28/0	polymorphism_frequency=2.188e-01	polymorphism_score=13.2	prediction=polymorphism	ref_cov=49/51	total_cov=77/51
RA	123	.	NC_000913	3486205	0	C	A	bias_e_value=4641650	bias_p_value=1	consensus_score=374.3	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=74/33	major_frequency=9.907e-01	minor_base=C	minor_cov=1/0	new_cov=74/33	polymorphism_frequency=9.907e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=75/33
RA	124	.	NC_000913	3490498	0	C	G	bias_e_value=4641010	bias_p_value=0.999862	consensus_score=366.4	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.983458	major_base=G	major_cov=46/53	major_frequency=9.083e-01	minor_base=C	minor_cov=5/5	new_cov=46/53	polymorphism_frequency=9.083e-01	polymorphism_score=24.3	prediction=consensus	ref_cov=5/5	total_cov=51/58
RA	125	.	NC_000913	3526483	0	G	A	consensus_score=498.1	frequency=1	major_base=A	major_cov=57/79	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=57/79	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=57/79
RA	126	.	NC_000913	3560455	1	.	G	consensus_score=524.6	frequency=1	major_base=G	major_cov=62/72	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=62/72	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=62/72
RA	127	.	NC_000913	3602706	0	C	A	bias_e_value=1215970	bias_p_value=0.261969	consensus_reject=FREQUENCY_CUTOFF	consensus_score=110.6	fisher_strand_p_value=0.0722018	frequency=2.000e-01	ks_quality_p_value=1	major_base=C	major_cov=27/25	major_frequency=8.000e-01	minor_base=A	minor_cov=3/10	new_cov=3/10	polymorphism_frequency=2.000e-01	polymorphism_score=15.2	prediction=polymorphism	ref_cov=27/25	total_cov=30/35
RA	128	.	NC_000913	3669715	0	G	T	bias_e_value=0.523666	bias_p_value=1.12819e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=264.9	fisher_strand_p_value=5.64296e-09	frequency=2.617e-01	ks_quality_p_value=1	major_base=G	major_cov=50/60	major_frequency=7.383e-01	minor_base=T	minor_cov=0/39	new_cov=0/39	polymorphism_frequency=2.617e-01	polymorphism_score=11.4	prediction=polymorphism	ref_cov=50/60	total_cov=51/99
RA	129	.	NC_000913	3741871	0	G	T	bias_e_value=0.0460339	bias_p_value=9.91756e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=229.2	fisher_strand_p_value=4.39911e-10	frequency=2.880e-01	ks_quality_p_value=1	major_base=G	major_cov=48/41	major_frequency=7.120e-01	minor_base=T	minor_cov=0/36	new_cov=0/36	polymorphism_frequency=2.880e-01	polymorphism_score=17.0	prediction=polymorphism	ref_cov=48/41	total_cov=48/77
RA	130	.	NC_000913	3911533	0	C	A	bias_e_value=3.2437e-07	bias_p_value=6.98825e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=249.0	fisher_strand_p_value=2.00565e-15	frequency=3.469e-01	ks_quality_p_value=1	major_base=C	major_cov=38/58	major_frequency=6.531e-01	minor_base=A	minor_cov=51/0	new_cov=51/0	polymorphism_frequency=3.469e-01	polymorphism_score=17.0	prediction=polymorphism	ref_cov=38/58	total_cov=89/58
RA	131	.	NC_000913	3948012	0	G	T	consensus_score=460.5	frequency=1	major_base=T	major_cov=55/69	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=55/69	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=55/69
RA	132	.	NC_000913	3954923	0	C	T	consensus_score=343.0	frequency=1	major_base=T	major_cov=56/38	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=56/38	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=56/38
RA	133	.	NC_000913	4096422	0	C	A	bias_e_value=1.30374	bias_p_value=2.80878e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=239.9	fisher_strand_p_value=1.47586e-08	frequency=2.212e-01	ks_quality_p_value=1	major_base=C	major_cov=36/52	major_frequency=7.788e-01	minor_base=A	minor_cov=25/0	new_cov=25/0	polymorphism_frequency=2.212e-01	polymorphism_score=12.1	prediction=polymorphism	ref_cov=36/52	total_cov=61/52
RA	134	.	NC_000913	4123447	0	G	T	bias_e_value=3917530	bias_p_value=0.843994	consensus_score=489.5	fisher_strand_p_value=0.496299	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=65/65	major_frequency=9.848e-01	minor_base=G	minor_cov=0/2	new_cov=65/65	polymorphism_frequency=9.848e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/2	total_cov=65/67
RA	135	.	NC_000913	4136467	0	A	C	bias_e_value=4.11291	bias_p_value=8.86088e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=143.2	fisher_strand_p_value=4.97339e-08	frequency=3.125e-01	ks_quality_p_value=1	major_base=A	major_cov=22/33	major_frequency=6.875e-01	minor_base=C	minor_cov=25/0	new_cov=25/0	polymorphism_frequency=3.125e-01	polymorphism_score=19.5	prediction=polymorphism	ref_cov=22/33	total_cov=49/33
RA	136	.	NC_000913	4213310	0	G	T	bias_e_value=0.00618557	bias_p_value=1.33262e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=258.4	fisher_strand_p_value=5.40826e-11	frequency=2.766e-01	ks_quality_p_value=1	major_base=G	major_cov=55/47	major_frequency=7.234e-01	minor_base=T	minor_cov=0/39	new_cov=0/39	polymorphism_frequency=2.766e-01	polymorphism_score=12.5	prediction=polymorphism	ref_cov=55/47	total_cov=55/86
RA	137	.	NC_000913	4296190	0	A	G	bias_e_value=1960140	bias_p_value=0.422294	consensus_reject=FREQUENCY_CUTOFF	consensus_score=76.5	fisher_strand_p_value=0.170622	frequency=2.200e-01	ks_quality_p_value=0.841642	major_base=A	major_cov=17/22	major_frequency=7.800e-01	minor_base=G	minor_cov=8/3	new_cov=8/3	polymorphism_frequency=2.200e-01	polymorphism_score=23.9	prediction=polymorphism	ref_cov=17/22	total_cov=25/25
RA	138	.	NC_000913	4296191	0	A	C	bias_e_value=111092	bias_p_value=0.0239337	consensus_reject=FREQUENCY_CUTOFF	consensus_score=56.9	fisher_strand_p_value=0.00361372	frequency=2.857e-01	ks_quality_p_value=1	major_base=A	major_cov=13/22	major_frequency=7.143e-01	minor_base=C	minor_cov=12/2	new_cov=12/2	polymorphism_frequency=2.857e-01	polymorphism_score=28.9	prediction=polymorphism	ref_cov=13/22	total_cov=25/25
RA	139	.	NC_000913	4296268	0	T	C	bias_e_value=4268190	bias_p_value=0.919541	consensus_reject=FREQUENCY_CUTOFF	consensus_score=107.9	fisher_strand_p_value=0.744862	frequency=2.321e-01	ks_quality_p_value=0.841342	major_base=T	major_cov=29/14	major_frequency=7.679e-01	minor_base=C	minor_cov=8/5	new_cov=8/5	polymorphism_frequency=2.321e-01	polymorphism_score=30.6	prediction=polymorphism	ref_cov=29/14	total_cov=38/19
RA	140	.	NC_000913	4296380	1	.	C	bias_e_value=4641650	bias_p_value=1	consensus_score=269.8	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=C	major_cov=53/22	major_frequency=9.615e-01	minor_base=.	minor_cov=2/1	new_cov=53/22	polymorphism_frequency=9.615e-01	polymorphism_score=2.5	prediction=consensus	ref_cov=2/1	total_cov=55/23
RA	141	.	NC_000913	4296380	2	.	G	bias_e_value=4641650	bias_p_value=1	consensus_score=269.9	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=53/21	major_frequency=9.610e-01	minor_base=.	minor_cov=2/1	new_cov=53/21	polymorphism_frequency=9.610e-01	polymorphism_score=2.2	prediction=consensus	ref_cov=2/1	total_cov=55/23
RA	142	.	NC_000913	4360965	0	C	A	bias_e_value=4.57067e-09	bias_p_value=9.84707e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=334.5	fisher_strand_p_value=2.51051e-17	frequency=2.745e-01	ks_quality_p_value=1	major_base=C	major_cov=33/78	major_frequency=7.255e-01	minor_base=A	minor_cov=42/0	new_cov=42/0	polymorphism_frequency=2.745e-01	polymorphism_score=23.5	prediction=polymorphism	ref_cov=33/78	total_cov=75/79
RA	143	.	NC_000913	4486856	0	C	A	consensus_score=332.0	frequency=1	major_base=A	major_cov=40/54	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=40/54	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=40/54
RA	144	.	NC_000913	4548969	0	C	G	consensus_score=471.6	frequency=1	major_base=G	major_cov=80/42	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=80/42	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=80/42
RA	145	.	NC_000913	4618146	0	G	T	bias_e_value=1.83268	bias_p_value=3.94834e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=246.0	fisher_strand_p_value=2.1146e-08	frequency=2.258e-01	ks_quality_p_value=1	major_base=G	major_cov=52/44	major_frequency=7.742e-01	minor_base=T	minor_cov=0/28	new_cov=0/28	polymorphism_frequency=2.258e-01	polymorphism_score=10.0	prediction=polymorphism	ref_cov=52/44	total_cov=52/72
MC	146	.	NC_000913	253488	258675	0	767	left_inside_cov=0	left_outside_cov=122	right_inside_cov=0	right_outside_cov=112
MC	147	.	NC_000913	1196266	1211459	0	0	left_inside_cov=42	left_outside_cov=45	right_inside_cov=42	right_outside_cov=45
MC	148	.	NC_000913	1396259	1407716	984	0	left_inside_cov=43	left_outside_cov=44	right_inside_cov=0	right_outside_cov=154
MC	149	.	NC_000913	1978495	1979270	0	0	left_inside_cov=0	left_outside_cov=142	right_inside_cov=0	right_outside_cov=158
MC	150	.	NC_000913	2558699	2565488	0	0	left_inside_cov=0	left_outside_cov=92	right_inside_cov=1	right_outside_cov=93
MC	151	.	NC_000913	2755515	2755726	0	0	left_inside_cov=42	left_outside_cov=46	right_inside_cov=42	right_outside_cov=44
MC	152	.	NC_000913	3423760	3424490	730	0	left_inside_cov=42	left_outside_cov=44	right_inside_cov=42	right_outside_cov=44
JC	153	.	NC_000913	1	1	NC_000913	4641652	-1	0	alignment_overlap=0	coverage_minus=85	coverage_plus=64	flanking_left=300	flanking_right=300	frequency=1	ignore=CIRCULAR_CHROMOSOME	junction_possible_overlap_registers=299	key=NC_000913__1__1__NC_000913__4641652__-1__0____300__300__0__0	max_left=297	max_left_minus=297	max_left_plus=245	max_min_left=149	max_min_left_minus=149	max_min_left_plus=148	max_min_right=147	max_min_right_minus=147	max_min_right_plus=144	max_pos_hash_score=598	max_right=288	max_right_minus=288	max_right_plus=284	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.24	new_junction_read_count=149	polymorphism_frequency=1.000e+00	pos_hash_score=87	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=299	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=299	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=149
JC	154	.	NC_000913	253487	-1	NC_000913	391709	1	0	alignment_overlap=1	coverage_minus=53	coverage_plus=59	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=298	key=NC_000913__253488__-1__NC_000913__391709__1__1____300__300__0__1	max_left=298	max_left_minus=298	max_left_plus=298	max_min_left=140	max_min_left_minus=129	max_min_left_plus=140	max_min_right=148	max_min_right_minus=119	max_min_right_plus=148	max_pos_hash_score=596	max_right=297	max_right_minus=296	max_right_plus=297	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=0.98	new_junction_read_count=117	polymorphism_frequency=1.000e+00	pos_hash_score=90	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=298	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=1	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=112
JC	155	.	NC_000913	258676	1	NC_000913	392966	-1	-17	alignment_overlap=-17	coverage_minus=51	coverage_plus=50	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=282	key=NC_000913__258676__1__NC_000913__392966__-1__-17__CGAATATACGGGCCTAG__300__300__0__1	max_left=280	max_left_minus=279	max_left_plus=280	max_min_left=141	max_min_left_minus=138	max_min_left_plus=141	max_min_right=140	max_min_right_minus=137	max_min_right_plus=140	max_pos_hash_score=564	max_right=278	max_right_minus=270	max_right_plus=278	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=0.94	new_junction_read_count=107	polymorphism_frequency=1.000e+00	pos_hash_score=76	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=299	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=101	unique_read_sequence=CGAATATACGGGCCTAG
JC	156	.	NC_000913	273955	1	NC_000913	820826	-1	0	alignment_overlap=0	coverage_minus=91	coverage_plus=74	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__273955__1__NC_000913__820826__-1__0____300__300__1__0	max_left=285	max_left_minus=285	max_left_plus=269	max_min_left=148	max_min_left_minus=146	max_min_left_plus=148	max_min_right=150	max_min_right_minus=138	max_min_right_plus=150	max_pos_hash_score=598	max_right=298	max_right_minus=298	max_right_plus=293	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.41	new_junction_read_count=169	polymorphism_frequency=1.000e+00	pos_hash_score=96	prediction=consensus	read_count_offset=4	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=295	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=165
JC	157	.	NC_000913	275149	-1	NC_000913	820823	1	0	alignment_overlap=0	coverage_minus=65	coverage_plus=42	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__275149__-1__NC_000913__820823__1__0____300__300__1__0	max_left=294	max_left_minus=294	max_left_plus=267	max_min_left=147	max_min_left_minus=130	max_min_left_plus=147	max_min_right=149	max_min_right_minus=149	max_min_right_plus=126	max_pos_hash_score=598	max_right=297	max_right_minus=297	max_right_plus=289	neg_log10_pos_hash_p_value=0.3	new_junction_coverage=0.92	new_junction_read_count=111	polymorphism_frequency=1.000e+00	pos_hash_score=74	prediction=consensus	read_count_offset=4	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=295	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=107
JC	158	.	NC_000913	315229	1	NC_000913	2034219	-1	-1	alignment_overlap=-1	coverage_minus=69	coverage_plus=48	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=298	key=NC_000913__315229__1__NC_000913__2034219__-1__-1__T__300__300__0__0	max_left=293	max_left_minus=286	max_left_plus=293	max_min_left=149	max_min_left_minus=149	max_min_left_plus=147	max_min_right=148	max_min_right_minus=137	max_min_right_plus=148	max_pos_hash_score=596	max_right=293	max_right_minus=292	max_right_plus=293	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.01	new_junction_read_count=121	polymorphism_frequency=1.000e+00	pos_hash_score=82	prediction=consensus	read_count_offset=5	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=117	unique_read_sequence=T
JC	159	.	NC_000913	381260	1	NC_000913	572142	-1	0	alignment_overlap=0	coverage_minus=60	coverage_plus=60	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__381260__1__NC_000913__572142__-1__0____300__300__1__0	max_left=292	max_left_minus=289	max_left_plus=292	max_min_left=147	max_min_left_minus=147	max_min_left_plus=141	max_min_right=147	max_min_right_minus=132	max_min_right_plus=147	max_pos_hash_score=598	max_right=299	max_right_minus=299	max_right_plus=290	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.01	new_junction_read_count=122	polymorphism_frequency=1.000e+00	pos_hash_score=84	prediction=consensus	read_count_offset=5	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=120
JC	160	.	NC_000913	381260	1	NC_000913	1105376	1	0	alignment_overlap=1	coverage_minus=90	coverage_plus=53	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=298	key=NC_000913__381260__1__NC_000913__1105375__1__1____300__300__1__0	max_left=295	max_left_minus=291	max_left_plus=295	max_min_left=144	max_min_left_minus=144	max_min_left_plus=138	max_min_right=137	max_min_right_minus=137	max_min_right_plus=132	max_pos_hash_score=596	max_right=297	max_right_minus=295	max_right_plus=297	neg_log10_pos_hash_p_value=0.3	new_junction_coverage=1.20	new_junction_read_count=144	polymorphism_frequency=1.000e+00	pos_hash_score=75	prediction=consensus	read_count_offset=5	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=1	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=293	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=143
JC	161	.	NC_000913	391883	1	NC_000913	392966	-1	0	alignment_overlap=0	coverage_minus=58	coverage_plus=31	flanking_left=300	flanking_right=300	frequency=NA	junction_possible_overlap_registers=299	key=NC_000913__391883__1__NC_000913__392966__-1__0____300__300__1__1	max_left=295	max_left_minus=295	max_left_plus=284	max_min_left=149	max_min_left_minus=149	max_min_left_plus=143	max_min_right=150	max_min_right_minus=150	max_min_right_plus=150	max_pos_hash_score=598	max_right=296	max_right_minus=296	max_right_plus=279	neg_log10_pos_hash_p_value=0.4	new_junction_coverage=0.74	new_junction_read_count=89	polymorphism_frequency=NA	pos_hash_score=68	prediction=unknown	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=89
JC	162	.	NC_000913	567858	1	NC_000913	568034	-1	0	alignment_overlap=1	coverage_minus=58	coverage_plus=65	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=298	key=NC_000913__567857__1__NC_000913__568034__-1__1____300__300__0__1	max_left=298	max_left_minus=297	max_left_plus=298	max_min_left=148	max_min_left_minus=148	max_min_left_plus=129	max_min_right=149	max_min_right_minus=149	max_min_right_plus=140	max_pos_hash_score=596	max_right=297	max_right_minus=292	max_right_plus=297	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.04	new_junction_read_count=125	polymorphism_frequency=8.803e-01	pos_hash_score=84	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.14	side_1_overlap=0	side_1_possible_overlap_registers=298	side_1_read_count=17	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=1	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=123
JC	163	.	NC_000913	572138	1	NC_000913	1467910	1	0	alignment_overlap=0	coverage_minus=52	coverage_plus=87	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__572138__1__NC_000913__1467910__1__0____300__300__0__1	max_left=299	max_left_minus=299	max_left_plus=298	max_min_left=143	max_min_left_minus=143	max_min_left_plus=130	max_min_right=141	max_min_right_minus=133	max_min_right_plus=141	max_pos_hash_score=598	max_right=294	max_right_minus=267	max_right_plus=294	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.17	new_junction_read_count=141	polymorphism_frequency=1.000e+00	pos_hash_score=79	prediction=consensus	read_count_offset=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=294	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=139
JC	164	.	NC_000913	696741	-1	NC_000913	697135	1	0	alignment_overlap=78	coverage_minus=4	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.177e-01	junction_possible_overlap_registers=221	key=NC_000913__696741__-1__NC_000913__697057__1__78____300__300__0__0	max_left=182	max_left_minus=182	max_left_plus=152	max_min_left=86	max_min_left_minus=73	max_min_left_plus=86	max_min_right=79	max_min_right_minus=79	max_min_right_plus=55	max_pos_hash_score=442	max_right=179	max_right_minus=141	max_right_plus=179	neg_log10_pos_hash_p_value=6.9	new_junction_coverage=0.09	new_junction_read_count=8	polymorphism_frequency=1.177e-01	pos_hash_score=8	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.64	side_1_overlap=78	side_1_possible_overlap_registers=299	side_1_read_count=77	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.71	side_2_overlap=0	side_2_possible_overlap_registers=221	side_2_read_count=63	side_2_redundant=0	total_non_overlap_reads=8
JC	165	.	NC_000913	732239	-1	NC_000913	3622029	1	0	alignment_overlap=12	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=7.685e-02	junction_possible_overlap_registers=287	key=NC_000913__732239__-1__NC_000913__3622017__1__12____300__300__0__0	max_left=157	max_left_minus=157	max_left_plus=53	max_min_left=120	max_min_left_minus=120	max_min_left_plus=53	max_min_right=131	max_min_right_minus=131	max_min_right_plus=0	max_pos_hash_score=574	max_right=235	max_right_minus=168	max_right_plus=235	neg_log10_pos_hash_p_value=11.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=7.685e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.61	side_1_overlap=12	side_1_possible_overlap_registers=299	side_1_read_count=73	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=0	side_2_possible_overlap_registers=287	side_2_read_count=2	side_2_redundant=0	total_non_overlap_reads=3
JC	166	.	NC_000913	732239	-1	NC_000913	3765020	1	0	alignment_overlap=12	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=7.401e-02	junction_possible_overlap_registers=287	key=NC_000913__732239__-1__NC_000913__3765008__1__12____300__300__0__0	max_left=157	max_left_minus=157	max_left_plus=53	max_min_left=120	max_min_left_minus=120	max_min_left_plus=53	max_min_right=131	max_min_right_minus=131	max_min_right_plus=0	max_pos_hash_score=574	max_right=235	max_right_minus=168	max_right_plus=235	neg_log10_pos_hash_p_value=11.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=7.401e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.61	side_1_overlap=12	side_1_possible_overlap_registers=299	side_1_read_count=73	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.04	side_2_overlap=0	side_2_possible_overlap_registers=287	side_2_read_count=5	side_2_redundant=0	total_non_overlap_reads=3
JC	167	.	NC_000913	780629	-1	NC_000913	780919	1	0	alignment_overlap=76	coverage_minus=5	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=1.134e-01	junction_possible_overlap_registers=223	key=NC_000913__780629__-1__NC_000913__780843__1__76____300__300__0__0	max_left=187	max_left_minus=151	max_left_plus=187	max_min_left=105	max_min_left_minus=105	max_min_left_plus=91	max_min_right=84	max_min_right_minus=84	max_min_right_plus=37	max_pos_hash_score=446	max_right=189	max_right_minus=155	max_right_plus=189	neg_log10_pos_hash_p_value=5.8	new_junction_coverage=0.12	new_junction_read_count=11	polymorphism_frequency=1.134e-01	pos_hash_score=11	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.05	side_1_overlap=76	side_1_possible_overlap_registers=299	side_1_read_count=126	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.87	side_2_overlap=0	side_2_possible_overlap_registers=223	side_2_read_count=78	side_2_redundant=0	total_non_overlap_reads=11
JC	168	.	NC_000913	781222	-1	NC_000913	781653	1	0	alignment_overlap=76	coverage_minus=7	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.493e-01	junction_possible_overlap_registers=223	key=NC_000913__781222__-1__NC_000913__781577__1__76____300__300__0__0	max_left=210	max_left_minus=210	max_left_plus=179	max_min_left=70	max_min_left_minus=17	max_min_left_plus=70	max_min_right=81	max_min_right_minus=81	max_min_right_plus=45	max_pos_hash_score=446	max_right=222	max_right_minus=207	max_right_plus=222	neg_log10_pos_hash_p_value=5.8	new_junction_coverage=0.13	new_junction_read_count=12	polymorphism_frequency=1.493e-01	pos_hash_score=11	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.60	side_1_overlap=76	side_1_possible_overlap_registers=299	side_1_read_count=72	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.93	side_2_overlap=0	side_2_possible_overlap_registers=223	side_2_read_count=83	side_2_redundant=0	total_non_overlap_reads=12
JC	169	.	NC_000913	781322	-1	NC_000913	781811	1	0	alignment_overlap=39	coverage_minus=3	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=7.135e-02	junction_possible_overlap_registers=260	key=NC_000913__781322__-1__NC_000913__781772__1__39____300__300__0__0	max_left=256	max_left_minus=256	max_left_plus=241	max_min_left=125	max_min_left_minus=125	max_min_left_plus=119	max_min_right=88	max_min_right_minus=73	max_min_right_plus=88	max_pos_hash_score=520	max_right=142	max_right_minus=136	max_right_plus=142	neg_log10_pos_hash_p_value=8.9	new_junction_coverage=0.06	new_junction_read_count=6	polymorphism_frequency=7.135e-02	pos_hash_score=6	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.50	side_1_overlap=39	side_1_possible_overlap_registers=299	side_1_read_count=60	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.99	side_2_overlap=0	side_2_possible_overlap_registers=260	side_2_read_count=104	side_2_redundant=0	total_non_overlap_reads=6
JC	170	.	NC_000913	781543	-1	NC_000913	781809	1	0	alignment_overlap=24	coverage_minus=2	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=5.273e-02	junction_possible_overlap_registers=275	key=NC_000913__781543__-1__NC_000913__781785__1__24____300__300__0__0	max_left=191	max_left_minus=191	max_left_plus=181	max_min_left=75	max_min_left_minus=75	max_min_left_plus=43	max_min_right=107	max_min_right_minus=85	max_min_right_plus=107	max_pos_hash_score=550	max_right=233	max_right_minus=201	max_right_plus=233	neg_log10_pos_hash_p_value=9.8	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=5.273e-02	pos_hash_score=5	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.66	side_1_overlap=24	side_1_possible_overlap_registers=299	side_1_read_count=79	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.97	side_2_overlap=0	side_2_possible_overlap_registers=275	side_2_read_count=107	side_2_redundant=0	total_non_overlap_reads=5
JC	171	.	NC_000913	1105380	-1	NC_000913	1467910	1	0	alignment_overlap=0	coverage_minus=42	coverage_plus=96	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1105380__-1__NC_000913__1467910__1__0____300__300__0__1	max_left=296	max_left_minus=289	max_left_plus=296	max_min_left=146	max_min_left_minus=146	max_min_left_plus=146	max_min_right=150	max_min_right_minus=150	max_min_right_plus=147	max_pos_hash_score=598	max_right=293	max_right_minus=290	max_right_plus=293	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.19	new_junction_read_count=143	polymorphism_frequency=9.929e-01	pos_hash_score=85	prediction=consensus	read_count_offset=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=0	side_1_possible_overlap_registers=294	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=138
JC	172	.	NC_000913	1286906	-1	NC_000913	1287557	1	0	alignment_overlap=20	coverage_minus=8	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=1.642e-01	junction_possible_overlap_registers=279	key=NC_000913__1286906__-1__NC_000913__1287537__1__20____300__300__0__0	max_left=274	max_left_minus=270	max_left_plus=274	max_min_left=4	max_min_left_minus=0	max_min_left_plus=4	max_min_right=61	max_min_right_minus=61	max_min_right_plus=49	max_pos_hash_score=558	max_right=276	max_right_minus=61	max_right_plus=276	neg_log10_pos_hash_p_value=7.2	new_junction_coverage=0.12	new_junction_read_count=14	polymorphism_frequency=1.642e-01	pos_hash_score=11	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.68	side_1_overlap=20	side_1_possible_overlap_registers=299	side_1_read_count=82	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.59	side_2_overlap=0	side_2_possible_overlap_registers=279	side_2_read_count=66	side_2_redundant=0	total_non_overlap_reads=14
JC	173	.	NC_000913	1287329	-1	NC_000913	1287624	1	0	alignment_overlap=87	coverage_minus=5	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.484e-01	junction_possible_overlap_registers=212	key=NC_000913__1287329__-1__NC_000913__1287537__1__87____300__300__0__0	max_left=201	max_left_minus=201	max_left_plus=180	max_min_left=74	max_min_left_minus=74	max_min_left_plus=54	max_min_right=78	max_min_right_minus=50	max_min_right_plus=78	max_pos_hash_score=424	max_right=209	max_right_minus=140	max_right_plus=209	neg_log10_pos_hash_p_value=6.3	new_junction_coverage=0.12	new_junction_read_count=10	polymorphism_frequency=1.484e-01	pos_hash_score=9	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.75	side_1_overlap=87	side_1_possible_overlap_registers=299	side_1_read_count=90	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.60	side_2_overlap=0	side_2_possible_overlap_registers=212	side_2_read_count=51	side_2_redundant=0	total_non_overlap_reads=10
JC	174	.	NC_000913	1397238	-1	NC_000913	1407717	1	0	alignment_overlap=0	coverage_minus=89	coverage_plus=59	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1397238__-1__NC_000913__1407717__1__0____300__300__1__0	max_left=295	max_left_minus=295	max_left_plus=295	max_min_left=146	max_min_left_minus=139	max_min_left_plus=146	max_min_right=148	max_min_right_minus=148	max_min_right_plus=145	max_pos_hash_score=598	max_right=298	max_right_minus=298	max_right_plus=295	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.27	new_junction_read_count=153	polymorphism_frequency=1.000e+00	pos_hash_score=79	prediction=consensus	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=299	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=148
JC	175	.	NC_000913	1397238	-1	NC_000913	1859380	1	0	alignment_overlap=0	coverage_minus=43	coverage_plus=59	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1397238__-1__NC_000913__1859380__1__0____300__300__1__0	max_left=294	max_left_minus=286	max_left_plus=294	max_min_left=139	max_min_left_minus=139	max_min_left_plus=135	max_min_right=145	max_min_right_minus=143	max_min_right_plus=145	max_pos_hash_score=598	max_right=298	max_right_minus=298	max_right_plus=291	neg_log10_pos_hash_p_value=0.4	new_junction_coverage=0.88	new_junction_read_count=106	polymorphism_frequency=1.000e+00	pos_hash_score=69	prediction=consensus	read_count_offset=4	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=295	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=102
JC	176	.	NC_000913	1397238	-1	NC_000913	1978494	-1	0	alignment_overlap=0	coverage_minus=68	coverage_plus=72	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1397238__-1__NC_000913__1978494__-1__0____300__300__1__0	max_left=295	max_left_minus=291	max_left_plus=295	max_min_left=143	max_min_left_minus=132	max_min_left_plus=143	max_min_right=138	max_min_right_minus=138	max_min_right_plus=138	max_pos_hash_score=598	max_right=296	max_right_minus=296	max_right_plus=289	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.17	new_junction_read_count=141	polymorphism_frequency=1.000e+00	pos_hash_score=85	prediction=consensus	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=299	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=140
JC	177	.	NC_000913	1651548	-1	NC_000913	1909382	-1	0	alignment_overlap=0	coverage_minus=86	coverage_plus=47	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1651548__-1__NC_000913__1909382__-1__0____300__300__1__0	max_left=296	max_left_minus=293	max_left_plus=296	max_min_left=149	max_min_left_minus=149	max_min_left_plus=140	max_min_right=148	max_min_right_minus=141	max_min_right_plus=148	max_pos_hash_score=598	max_right=295	max_right_minus=295	max_right_plus=294	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.13	new_junction_read_count=136	polymorphism_frequency=9.926e-01	pos_hash_score=78	prediction=consensus	read_count_offset=5	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.01	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=1	side_2_redundant=0	total_non_overlap_reads=133
JC	178	.	NC_000913	1859383	-1	NC_000913	2102943	-1	0	alignment_overlap=0	coverage_minus=52	coverage_plus=84	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1859383__-1__NC_000913__2102943__-1__0____300__300__0__1	max_left=296	max_left_minus=296	max_left_plus=296	max_min_left=149	max_min_left_minus=149	max_min_left_plus=139	max_min_right=146	max_min_right_minus=145	max_min_right_plus=146	max_pos_hash_score=598	max_right=289	max_right_minus=289	max_right_plus=288	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.17	new_junction_read_count=141	polymorphism_frequency=1.000e+00	pos_hash_score=82	prediction=consensus	read_count_offset=4	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=295	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=136
JC	179	.	NC_000913	1909378	1	NC_000913	2070271	-1	0	alignment_overlap=1	coverage_minus=64	coverage_plus=45	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=298	key=NC_000913__1909377__1__NC_000913__2070271__-1__1____300__300__0__1	max_left=297	max_left_minus=297	max_left_plus=295	max_min_left=144	max_min_left_minus=144	max_min_left_plus=142	max_min_right=142	max_min_right_minus=142	max_min_right_plus=136	max_pos_hash_score=596	max_right=296	max_right_minus=296	max_right_plus=262	neg_log10_pos_hash_p_value=0.4	new_junction_coverage=0.92	new_junction_read_count=110	polymorphism_frequency=1.000e+00	pos_hash_score=70	prediction=consensus	read_count_offset=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=293	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=1	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=109
JC	180	.	NC_000913	1978503	1	NC_000913	2406787	-1	0	alignment_overlap=1	coverage_minus=70	coverage_plus=54	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=298	key=NC_000913__1978503__1__NC_000913__2406788__-1__1____300__300__1__0	max_left=289	max_left_minus=285	max_left_plus=289	max_min_left=148	max_min_left_minus=139	max_min_left_plus=148	max_min_right=149	max_min_right_minus=149	max_min_right_plus=128	max_pos_hash_score=596	max_right=297	max_right_minus=285	max_right_plus=297	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.06	new_junction_read_count=127	polymorphism_frequency=1.000e+00	pos_hash_score=83	prediction=consensus	read_count_offset=8	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=1	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=290	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=124
JC	181	.	NC_000913	1979270	-1	NC_000913	2406780	1	0	alignment_overlap=0	coverage_minus=53	coverage_plus=60	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1979270__-1__NC_000913__2406780__1__0____300__300__1__0	max_left=284	max_left_minus=284	max_left_plus=278	max_min_left=149	max_min_left_minus=148	max_min_left_plus=149	max_min_right=149	max_min_right_minus=147	max_min_right_plus=149	max_pos_hash_score=598	max_right=298	max_right_minus=298	max_right_plus=292	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=0.96	new_junction_read_count=115	polymorphism_frequency=1.000e+00	pos_hash_score=89	prediction=consensus	read_count_offset=8	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=291	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=113
JC	182	.	NC_000913	1979271	1	NC_000913	2102947	-1	0	alignment_overlap=0	coverage_minus=53	coverage_plus=102	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__1979271__1__NC_000913__2102947__-1__0____300__300__0__1	max_left=299	max_left_minus=294	max_left_plus=299	max_min_left=145	max_min_left_minus=145	max_min_left_plus=135	max_min_right=150	max_min_right_minus=146	max_min_right_plus=150	max_pos_hash_score=598	max_right=298	max_right_minus=286	max_right_plus=298	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.31	new_junction_read_count=158	polymorphism_frequency=1.000e+00	pos_hash_score=96	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=299	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=155
JC	183	.	NC_000913	2034215	1	NC_000913	2171428	-1	0	alignment_overlap=0	coverage_minus=61	coverage_plus=58	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__2034215__1__NC_000913__2171428__-1__0____300__300__0__1	max_left=298	max_left_minus=293	max_left_plus=298	max_min_left=146	max_min_left_minus=146	max_min_left_plus=140	max_min_right=148	max_min_right_minus=148	max_min_right_plus=147	max_pos_hash_score=598	max_right=296	max_right_minus=296	max_right_plus=289	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.01	new_junction_read_count=121	polymorphism_frequency=1.000e+00	pos_hash_score=77	prediction=consensus	read_count_offset=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=294	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=119
JC	184	.	NC_000913	2068941	1	NC_000913	2317459	-1	0	alignment_overlap=1	coverage_minus=58	coverage_plus=52	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=298	key=NC_000913__2068941__1__NC_000913__2317460__-1__1____300__300__1__0	max_left=297	max_left_minus=297	max_left_plus=295	max_min_left=148	max_min_left_minus=148	max_min_left_plus=128	max_min_right=149	max_min_right_minus=149	max_min_right_plus=141	max_pos_hash_score=596	max_right=297	max_right_minus=297	max_right_plus=293	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=0.95	new_junction_read_count=114	polymorphism_frequency=1.000e+00	pos_hash_score=77	prediction=consensus	read_count_offset=5	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=1	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=293	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=110
JC	185	.	NC_000913	2288919	1	NC_000913	3189075	1	0	alignment_overlap=0	coverage_minus=73	coverage_plus=76	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__2288919__1__NC_000913__3189075__1__0____300__300__1__0	max_left=295	max_left_minus=295	max_left_plus=295	max_min_left=148	max_min_left_minus=132	max_min_left_plus=148	max_min_right=150	max_min_right_minus=149	max_min_right_plus=150	max_pos_hash_score=598	max_right=298	max_right_minus=298	max_right_plus=298	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.27	new_junction_read_count=153	polymorphism_frequency=9.869e-01	pos_hash_score=98	prediction=consensus	read_count_offset=4	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=0	side_2_possible_overlap_registers=295	side_2_read_count=2	side_2_redundant=0	total_non_overlap_reads=149
JC	186	.	NC_000913	2317455	1	NC_000913	2997691	-1	0	alignment_overlap=0	coverage_minus=76	coverage_plus=56	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__2317455__1__NC_000913__2997691__-1__0____300__300__0__1	max_left=299	max_left_minus=299	max_left_plus=295	max_min_left=149	max_min_left_minus=149	max_min_left_plus=137	max_min_right=147	max_min_right_minus=141	max_min_right_plus=147	max_pos_hash_score=598	max_right=297	max_right_minus=297	max_right_plus=297	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.11	new_junction_read_count=133	polymorphism_frequency=1.000e+00	pos_hash_score=84	prediction=consensus	read_count_offset=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=294	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=132
JC	187	.	NC_000913	2357652	-1	NC_000913	2357836	1	0	alignment_overlap=34	coverage_minus=3	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.308e-02	junction_possible_overlap_registers=265	key=NC_000913__2357652__-1__NC_000913__2357802__1__34____300__300__0__0	max_left=157	max_left_minus=157	max_left_plus=82	max_min_left=98	max_min_left_minus=98	max_min_left_plus=82	max_min_right=105	max_min_right_minus=105	max_min_right_plus=0	max_pos_hash_score=530	max_right=185	max_right_minus=185	max_right_plus=184	neg_log10_pos_hash_p_value=10.2	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.308e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.18	side_1_overlap=34	side_1_possible_overlap_registers=299	side_1_read_count=142	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.01	side_2_overlap=0	side_2_possible_overlap_registers=265	side_2_read_count=108	side_2_redundant=0	total_non_overlap_reads=4
JC	188	.	NC_000913	2558698	-1	NC_000913	2565489	1	0	alignment_overlap=8	coverage_minus=33	coverage_plus=56	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=291	key=NC_000913__2558698__-1__NC_000913__2565481__1__8____300__300__0__0	max_left=290	max_left_minus=269	max_left_plus=290	max_min_left=141	max_min_left_minus=140	max_min_left_plus=141	max_min_right=146	max_min_right_minus=109	max_min_right_plus=146	max_pos_hash_score=582	max_right=291	max_right_minus=288	max_right_plus=291	neg_log10_pos_hash_p_value=0.6	new_junction_coverage=0.79	new_junction_read_count=92	polymorphism_frequency=1.000e+00	pos_hash_score=62	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=299	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=291	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=89
JC	189	.	NC_000913	2653419	-1	NC_000913	2653746	1	0	alignment_overlap=25	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=6.878e-02	junction_possible_overlap_registers=274	key=NC_000913__2653419__-1__NC_000913__2653721__1__25____300__300__0__0	max_left=150	max_left_minus=121	max_left_plus=150	max_min_left=121	max_min_left_minus=121	max_min_left_plus=50	max_min_right=108	max_min_right_minus=0	max_min_right_plus=108	max_pos_hash_score=548	max_right=268	max_right_minus=268	max_right_plus=246	neg_log10_pos_hash_p_value=9.2	new_junction_coverage=0.06	new_junction_read_count=7	polymorphism_frequency=6.878e-02	pos_hash_score=6	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.84	side_1_overlap=25	side_1_possible_overlap_registers=299	side_1_read_count=101	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.88	side_2_overlap=0	side_2_possible_overlap_registers=274	side_2_read_count=97	side_2_redundant=0	total_non_overlap_reads=7
JC	190	.	NC_000913	2700291	-1	NC_000913	2700540	1	0	alignment_overlap=19	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=2.983e-02	junction_possible_overlap_registers=280	key=NC_000913__2700291__-1__NC_000913__2700521__1__19____300__300__0__0	max_left=191	max_left_minus=191	max_left_plus=173	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=115	max_min_right_minus=102	max_min_right_plus=115	max_pos_hash_score=560	max_right=115	max_right_minus=102	max_right_plus=115	neg_log10_pos_hash_p_value=10.5	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=2.983e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.15	side_1_overlap=19	side_1_possible_overlap_registers=299	side_1_read_count=138	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.16	side_2_overlap=0	side_2_possible_overlap_registers=280	side_2_read_count=131	side_2_redundant=0	total_non_overlap_reads=4
JC	191	.	NC_000913	3130146	1	NC_000913	3189078	-1	0	alignment_overlap=0	coverage_minus=219	coverage_plus=108	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__3130146__1__NC_000913__3189078__-1__0____300__300__1__0	max_left=296	max_left_minus=294	max_left_plus=296	max_min_left=149	max_min_left_minus=146	max_min_left_plus=149	max_min_right=149	max_min_right_minus=149	max_min_right_plus=149	max_pos_hash_score=598	max_right=298	max_right_minus=298	max_right_plus=298	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=2.76	new_junction_read_count=332	polymorphism_frequency=9.939e-01	pos_hash_score=150	prediction=consensus	read_count_offset=4	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.02	side_2_overlap=0	side_2_possible_overlap_registers=295	side_2_read_count=2	side_2_redundant=0	total_non_overlap_reads=327
JC	192	.	NC_000913	3270072	1	NC_000913	4137788	1	-25	alignment_overlap=-25	coverage_minus=3	coverage_plus=0	flanking_left=300	flanking_right=300	frequency=3.510e-02	junction_possible_overlap_registers=274	key=NC_000913__3270072__1__NC_000913__4137788__1__-25__CAGATTGTTGAGTGCGCTTTATTCA__300__300__0__0	max_left=260	max_left_minus=260	max_left_plus=0	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=76	max_min_right_minus=76	max_min_right_plus=0	max_pos_hash_score=548	max_right=76	max_right_minus=76	max_right_plus=0	neg_log10_pos_hash_p_value=11.1	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.510e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.52	side_1_overlap=0	side_1_possible_overlap_registers=299	side_1_read_count=63	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.97	side_2_overlap=0	side_2_possible_overlap_registers=299	side_2_read_count=117	side_2_redundant=0	total_non_overlap_reads=3	unique_read_sequence=CAGATTGTTGAGTGCGCTTTATTCA
JC	193	.	NC_000913	3621836	-1	NC_000913	3622017	1	0	alignment_overlap=12	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=6.098e-01	junction_possible_overlap_registers=287	key=NC_000913__3621848__-1__NC_000913__3622017__1__12____300__300__1__0	max_left=157	max_left_minus=157	max_left_plus=53	max_min_left=120	max_min_left_minus=120	max_min_left_plus=53	max_min_right=131	max_min_right_minus=131	max_min_right_plus=0	max_pos_hash_score=574	max_right=235	max_right_minus=168	max_right_plus=235	neg_log10_pos_hash_p_value=11.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=6.098e-01	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	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=12	side_2_possible_overlap_registers=299	side_2_read_count=2	side_2_redundant=0	total_non_overlap_reads=3
JC	194	.	NC_000913	3648146	-1	NC_000913	3648378	1	0	alignment_overlap=58	coverage_minus=7	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.169e-01	junction_possible_overlap_registers=241	key=NC_000913__3648146__-1__NC_000913__3648320__1__58____300__300__0__0	max_left=233	max_left_minus=233	max_left_plus=196	max_min_left=114	max_min_left_minus=114	max_min_left_plus=113	max_min_right=67	max_min_right_minus=67	max_min_right_plus=46	max_pos_hash_score=482	max_right=220	max_right_minus=205	max_right_plus=220	neg_log10_pos_hash_p_value=5.6	new_junction_coverage=0.14	new_junction_read_count=14	polymorphism_frequency=1.169e-01	pos_hash_score=13	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.09	side_1_overlap=58	side_1_possible_overlap_registers=299	side_1_read_count=131	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.09	side_2_overlap=0	side_2_possible_overlap_registers=241	side_2_read_count=106	side_2_redundant=0	total_non_overlap_reads=14
JC	195	.	NC_000913	3720633	1	NC_000913	3762460	1	0	alignment_overlap=0	coverage_minus=45	coverage_plus=70	flanking_left=300	flanking_right=300	frequency=NA	junction_possible_overlap_registers=299	key=NC_000913__3720633__1__NC_000913__3762460__1__0____300__300__0__1	max_left=298	max_left_minus=297	max_left_plus=298	max_min_left=147	max_min_left_minus=147	max_min_left_plus=145	max_min_right=150	max_min_right_minus=141	max_min_right_plus=150	max_pos_hash_score=598	max_right=299	max_right_minus=295	max_right_plus=299	neg_log10_pos_hash_p_value=0.6	new_junction_coverage=0.96	new_junction_read_count=116	polymorphism_frequency=NA	pos_hash_score=64	prediction=unknown	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=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=115
JC	196	.	NC_000913	3722075	-1	NC_000913	3762462	-1	0	alignment_overlap=0	coverage_minus=44	coverage_plus=57	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=299	key=NC_000913__3722075__-1__NC_000913__3762462__-1__0____300__300__0__0	max_left=298	max_left_minus=298	max_left_plus=296	max_min_left=143	max_min_left_minus=143	max_min_left_plus=141	max_min_right=138	max_min_right_minus=138	max_min_right_plus=137	max_pos_hash_score=598	max_right=295	max_right_minus=295	max_right_plus=295	neg_log10_pos_hash_p_value=0.7	new_junction_coverage=0.86	new_junction_read_count=104	polymorphism_frequency=1.000e+00	pos_hash_score=61	prediction=consensus	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=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=299	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=101
JC	197	.	NC_000913	3764827	-1	NC_000913	3765008	1	0	alignment_overlap=12	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.846e-01	junction_possible_overlap_registers=287	key=NC_000913__3764839__-1__NC_000913__3765008__1__12____300__300__1__0	max_left=157	max_left_minus=157	max_left_plus=53	max_min_left=120	max_min_left_minus=120	max_min_left_plus=53	max_min_right=131	max_min_right_minus=131	max_min_right_plus=0	max_pos_hash_score=574	max_right=235	max_right_minus=168	max_right_plus=235	neg_log10_pos_hash_p_value=11.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.846e-01	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	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=12	side_2_possible_overlap_registers=299	side_2_read_count=5	side_2_redundant=0	total_non_overlap_reads=3
JC	198	.	NC_000913	4392437	-1	NC_000913	4392661	1	0	alignment_overlap=78	coverage_minus=4	coverage_plus=0	flanking_left=300	flanking_right=300	frequency=4.510e-02	junction_possible_overlap_registers=221	key=NC_000913__4392437__-1__NC_000913__4392583__1__78____300__300__0__0	max_left=133	max_left_minus=133	max_left_plus=0	max_min_left=67	max_min_left_minus=67	max_min_left_plus=0	max_min_right=80	max_min_right_minus=80	max_min_right_plus=0	max_pos_hash_score=442	max_right=169	max_right_minus=169	max_right_plus=0	neg_log10_pos_hash_p_value=9.0	new_junction_coverage=0.05	new_junction_read_count=4	polymorphism_frequency=4.510e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.85	side_1_overlap=78	side_1_possible_overlap_registers=299	side_1_read_count=102	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.06	side_2_overlap=0	side_2_possible_overlap_registers=221	side_2_read_count=94	side_2_redundant=0	total_non_overlap_reads=4
JC	199	.	NC_000913	4542682	1	NC_000913	4542996	1	0	alignment_overlap=9	coverage_minus=38	coverage_plus=51	flanking_left=300	flanking_right=300	frequency=4.600e-01	junction_possible_overlap_registers=290	key=NC_000913__4542682__1__NC_000913__4542987__1__9____300__300__0__0	max_left=287	max_left_minus=287	max_left_plus=280	max_min_left=141	max_min_left_minus=141	max_min_left_plus=128	max_min_right=143	max_min_right_minus=143	max_min_right_plus=133	max_pos_hash_score=580	max_right=288	max_right_minus=288	max_right_plus=280	neg_log10_pos_hash_p_value=0.6	new_junction_coverage=0.77	new_junction_read_count=90	polymorphism_frequency=4.600e-01	pos_hash_score=61	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.02	side_1_overlap=9	side_1_possible_overlap_registers=299	side_1_read_count=123	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=290	side_2_read_count=92	side_2_redundant=0	total_non_overlap_reads=89
JC	200	.	NC_000913	4542690	-1	NC_000913	4542986	-1	0	alignment_overlap=9	coverage_minus=47	coverage_plus=28	flanking_left=300	flanking_right=300	frequency=4.139e-01	junction_possible_overlap_registers=290	key=NC_000913__4542690__-1__NC_000913__4542995__-1__9____300__300__0__0	max_left=280	max_left_minus=280	max_left_plus=275	max_min_left=145	max_min_left_minus=145	max_min_left_plus=143	max_min_right=143	max_min_right_minus=140	max_min_right_plus=143	max_pos_hash_score=580	max_right=288	max_right_minus=288	max_right_plus=282	neg_log10_pos_hash_p_value=0.9	new_junction_coverage=0.66	new_junction_read_count=77	polymorphism_frequency=4.139e-01	pos_hash_score=55	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.08	side_1_overlap=9	side_1_possible_overlap_registers=299	side_1_read_count=130	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=290	side_2_read_count=92	side_2_redundant=0	total_non_overlap_reads=75
JC	201	.	NC_000913	4606166	-1	NC_000913	4606403	1	0	alignment_overlap=89	coverage_minus=4	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=6.117e-02	junction_possible_overlap_registers=210	key=NC_000913__4606166__-1__NC_000913__4606314__1__89____300__300__0__0	max_left=190	max_left_minus=190	max_left_plus=37	max_min_left=93	max_min_left_minus=93	max_min_left_plus=37	max_min_right=2	max_min_right_minus=2	max_min_right_plus=0	max_pos_hash_score=420	max_right=174	max_right_minus=141	max_right_plus=174	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.06	new_junction_read_count=5	polymorphism_frequency=6.117e-02	pos_hash_score=5	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.96	side_1_overlap=89	side_1_possible_overlap_registers=299	side_1_read_count=116	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.85	side_2_overlap=0	side_2_possible_overlap_registers=210	side_2_read_count=72	side_2_redundant=0	total_non_overlap_reads=5
UN	202	.	NC_000913	15664	16449
UN	203	.	NC_000913	20073	20277
UN	204	.	NC_000913	224019	224509
UN	205	.	NC_000913	225164	225310
UN	206	.	NC_000913	225317	225317
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UN	208	.	NC_000913	253488	258675
UN	209	.	NC_000913	270812	270812
UN	210	.	NC_000913	270817	271007
UN	211	.	NC_000913	274249	274867
UN	212	.	NC_000913	279424	279657
UN	213	.	NC_000913	290919	291128
UN	214	.	NC_000913	315516	315516
UN	215	.	NC_000913	315519	316208
UN	216	.	NC_000913	381532	382322
UN	217	.	NC_000913	382332	382332
UN	218	.	NC_000913	391984	392688
UN	219	.	NC_000913	526146	526451
UN	220	.	NC_000913	567046	567786
UN	221	.	NC_000913	567788	567788
UN	222	.	NC_000913	567790	567790
UN	223	.	NC_000913	567795	567795
UN	224	.	NC_000913	574871	575499
UN	225	.	NC_000913	575502	575502
UN	226	.	NC_000913	608265	608265
UN	227	.	NC_000913	608267	609069
UN	228	.	NC_000913	688131	688765
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UN	230	.	NC_000913	1095235	1095235
UN	231	.	NC_000913	1095245	1095245
UN	232	.	NC_000913	1196374	1211413
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UN	236	.	NC_000913	1468171	1468968
UN	237	.	NC_000913	1469553	1469553
UN	238	.	NC_000913	1469557	1469557
UN	239	.	NC_000913	1469563	1470226
UN	240	.	NC_000913	1528552	1528917
UN	241	.	NC_000913	1651133	1651133
UN	242	.	NC_000913	1651135	1651272
UN	243	.	NC_000913	1978495	1979270
UN	244	.	NC_000913	2067008	2067035
UN	245	.	NC_000913	2067037	2067037
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UN	248	.	NC_000913	2102029	2102657
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UN	265	.	NC_000913	3130423	3131052
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UN	267	.	NC_000913	3365846	3366464
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UN	270	.	NC_000913	3427206	3428298
UN	271	.	NC_000913	3583710	3583914
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UN	276	.	NC_000913	3652315	3652945
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UN	279	.	NC_000913	3764337	3764337
UN	280	.	NC_000913	3764341	3764342
UN	281	.	NC_000913	3764344	3765048
UN	282	.	NC_000913	3942320	3943131
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UN	285	.	NC_000913	4035446	4035446
UN	286	.	NC_000913	4035448	4035448
UN	287	.	NC_000913	4035450	4035453
UN	288	.	NC_000913	4035455	4035461
UN	289	.	NC_000913	4035999	4036830
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UN	291	.	NC_000913	4039015	4039110
UN	292	.	NC_000913	4039113	4039115
UN	293	.	NC_000913	4039664	4039666
UN	294	.	NC_000913	4039669	4039669
UN	295	.	NC_000913	4039671	4040322
UN	296	.	NC_000913	4166585	4166604
UN	297	.	NC_000913	4166925	4167944
UN	298	.	NC_000913	4167948	4167948
UN	299	.	NC_000913	4168846	4171375
UN	300	.	NC_000913	4171378	4171378
UN	301	.	NC_000913	4208386	4209460
UN	302	.	NC_000913	4210290	4210292
UN	303	.	NC_000913	4210294	4210296
UN	304	.	NC_000913	4210299	4212840
UN	305	.	NC_000913	4498476	4499242
UN	306	.	NC_000913	4507752	4508408