#=GENOME_DIFF	1.0
#=CREATED	17:00:50 10 Oct 2025
#=PROGRAM	breseq 0.39.0 
#=COMMAND	breseq -j 8 -o /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_run15_rmdup_trimmng-adaptors-polyG/ME8913_S25_R1R2_RMDUP -r /ld1/E.coli_MG1655_ref/MG1655/ncbi_dataset/data/GCF_000005845.2/genomic.gbff /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME8913_S25_R1_RMDUP_RM-R2-DUP.cutadapt.fastq.gz /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME8913_S25_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=REFSEQ	/ld1/E.coli_MG1655_ref/MG1655/ncbi_dataset/data/GCF_000005845.2/genomic.gbff
#=READSEQ	/ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME8913_S25_R1_RMDUP_RM-R2-DUP.cutadapt.fastq.gz
#=READSEQ	/ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME8913_S25_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=CONVERTED-BASES	466783599
#=CONVERTED-READS	1578951
#=INPUT-BASES	466898108
#=INPUT-READS	1579342
#=MAPPED-BASES	451400765
#=MAPPED-READS	1527848
DEL	1	53,60	NC_000913	257908	776
SNP	2	15	NC_000913	803662	A
DEL	3	54,75	NC_000913	1299499	1199
SNP	4	30	NC_000913	1905761	A
DEL	5	55,76	NC_000913	1978503	776
DEL	6	32,33	NC_000913	2173363	2
INS	7	41	NC_000913	3560455	G
INS	8	49,50	NC_000913	4296381	GC
RA	9	.	NC_000913	58065	0	C	A	bias_e_value=0.00770068	bias_p_value=1.65904e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=153.5	fisher_strand_p_value=6.79597e-11	frequency=3.558e-01	ks_quality_p_value=1	major_base=C	major_cov=27/40	major_frequency=6.442e-01	minor_base=A	minor_cov=37/0	new_cov=37/0	polymorphism_frequency=3.558e-01	polymorphism_score=19.1	prediction=polymorphism	ref_cov=27/40	total_cov=64/40
RA	10	.	NC_000913	85651	0	G	T	bias_e_value=16.0202	bias_p_value=3.45141e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=175.0	fisher_strand_p_value=2.10808e-07	frequency=3.282e-01	ks_quality_p_value=1	major_base=G	major_cov=33/55	major_frequency=6.718e-01	minor_base=T	minor_cov=0/43	new_cov=0/43	polymorphism_frequency=3.282e-01	polymorphism_score=16.2	prediction=polymorphism	ref_cov=33/55	total_cov=33/98
RA	11	.	NC_000913	141849	0	C	A	bias_e_value=0.000324883	bias_p_value=6.9993e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=220.5	fisher_strand_p_value=2.52644e-12	frequency=2.941e-01	ks_quality_p_value=1	major_base=C	major_cov=30/54	major_frequency=7.059e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=2.941e-01	polymorphism_score=27.3	prediction=polymorphism	ref_cov=30/54	total_cov=65/54
RA	12	.	NC_000913	190843	0	C	A	bias_e_value=466.943	bias_p_value=0.000100598	consensus_reject=FREQUENCY_CUTOFF	consensus_score=109.4	fisher_strand_p_value=7.89014e-06	frequency=4.000e-01	ks_quality_p_value=1	major_base=C	major_cov=30/27	major_frequency=6.000e-01	minor_base=A	minor_cov=36/2	new_cov=36/2	polymorphism_frequency=4.000e-01	polymorphism_score=10.2	prediction=polymorphism	ref_cov=30/27	total_cov=66/29
RA	13	.	NC_000913	332975	0	C	A	bias_e_value=0.0306388	bias_p_value=6.60084e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=165.4	fisher_strand_p_value=2.87364e-10	frequency=3.208e-01	ks_quality_p_value=1	major_base=C	major_cov=30/42	major_frequency=6.792e-01	minor_base=A	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=3.208e-01	polymorphism_score=11.4	prediction=polymorphism	ref_cov=30/42	total_cov=64/42
RA	14	.	NC_000913	442471	0	C	A	bias_e_value=11.8379	bias_p_value=2.55035e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=121.6	fisher_strand_p_value=1.52768e-07	frequency=4.062e-01	ks_quality_p_value=1	major_base=C	major_cov=32/25	major_frequency=5.938e-01	minor_base=A	minor_cov=39/0	new_cov=39/0	polymorphism_frequency=4.062e-01	polymorphism_score=10.6	prediction=polymorphism	ref_cov=32/25	total_cov=71/26
RA	15	.	NC_000913	803662	0	C	A	consensus_score=569.7	frequency=1	major_base=A	major_cov=61/93	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=61/93	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=61/93
RA	16	.	NC_000913	847955	0	G	A	bias_e_value=1.60964e-06	bias_p_value=3.46782e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=182.7	fisher_strand_p_value=1.04476e-14	frequency=3.008e-01	ks_quality_p_value=1	major_base=G	major_cov=60/26	major_frequency=6.992e-01	minor_base=A	minor_cov=0/37	new_cov=0/37	polymorphism_frequency=3.008e-01	polymorphism_score=53.4	prediction=polymorphism	ref_cov=60/26	total_cov=60/63
RA	17	.	NC_000913	1015488	0	C	A	bias_e_value=0.580288	bias_p_value=1.25018e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=253.6	fisher_strand_p_value=6.2871e-09	frequency=2.482e-01	ks_quality_p_value=1	major_base=C	major_cov=54/52	major_frequency=7.518e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=2.482e-01	polymorphism_score=12.9	prediction=polymorphism	ref_cov=54/52	total_cov=89/52
RA	18	.	NC_000913	1097118	0	C	A	bias_e_value=3641280	bias_p_value=0.784479	consensus_reject=FREQUENCY_CUTOFF	consensus_score=75.3	fisher_strand_p_value=0.470733	frequency=2.400e-01	ks_quality_p_value=0.89254	major_base=C	major_cov=10/28	major_frequency=7.600e-01	minor_base=A	minor_cov=5/7	new_cov=5/7	polymorphism_frequency=2.400e-01	polymorphism_score=25.0	prediction=polymorphism	ref_cov=10/28	total_cov=15/35
RA	19	.	NC_000913	1217528	0	C	T	bias_e_value=4024370	bias_p_value=0.867012	consensus_reject=FREQUENCY_CUTOFF	consensus_score=154.0	fisher_strand_p_value=0.53083	frequency=2.963e-01	ks_quality_p_value=1	major_base=C	major_cov=39/37	major_frequency=7.037e-01	minor_base=T	minor_cov=14/18	new_cov=14/18	polymorphism_frequency=2.963e-01	polymorphism_score=95.9	prediction=polymorphism	ref_cov=39/37	total_cov=53/55
RA	20	.	NC_000913	1334966	0	A	C	bias_e_value=0.134369	bias_p_value=2.89486e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=314.1	fisher_strand_p_value=1.35134e-09	frequency=2.086e-01	ks_quality_p_value=1	major_base=A	major_cov=63/66	major_frequency=7.914e-01	minor_base=C	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=2.086e-01	polymorphism_score=16.6	prediction=polymorphism	ref_cov=63/66	total_cov=97/66
RA	21	.	NC_000913	1335034	0	G	T	bias_e_value=6.38127e-09	bias_p_value=1.37479e-15	consensus_reject=FREQUENCY_CUTOFF	consensus_score=351.4	fisher_strand_p_value=3.53588e-17	frequency=2.593e-01	ks_quality_p_value=1	major_base=G	major_cov=83/37	major_frequency=7.407e-01	minor_base=T	minor_cov=0/42	new_cov=0/42	polymorphism_frequency=2.593e-01	polymorphism_score=10.3	prediction=polymorphism	ref_cov=83/37	total_cov=83/79
RA	22	.	NC_000913	1351463	0	C	A	bias_e_value=120.072	bias_p_value=2.58684e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=112.5	fisher_strand_p_value=1.81955e-06	frequency=3.718e-01	ks_quality_p_value=1	major_base=C	major_cov=26/23	major_frequency=6.282e-01	minor_base=A	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=3.718e-01	polymorphism_score=10.5	prediction=polymorphism	ref_cov=26/23	total_cov=55/23
RA	23	.	NC_000913	1427992	0	G	T	bias_e_value=0.00285241	bias_p_value=6.14526e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=197.7	fisher_strand_p_value=2.41495e-11	frequency=3.361e-01	ks_quality_p_value=1	major_base=G	major_cov=45/36	major_frequency=6.639e-01	minor_base=T	minor_cov=0/41	new_cov=0/41	polymorphism_frequency=3.361e-01	polymorphism_score=10.0	prediction=polymorphism	ref_cov=45/36	total_cov=45/77
RA	24	.	NC_000913	1466432	0	A	G	bias_e_value=2612750	bias_p_value=0.562893	consensus_reject=FREQUENCY_CUTOFF	consensus_score=140.4	fisher_strand_p_value=0.229399	frequency=2.059e-01	ks_quality_p_value=0.987474	major_base=A	major_cov=31/23	major_frequency=7.941e-01	minor_base=G	minor_cov=5/9	new_cov=5/9	polymorphism_frequency=2.059e-01	polymorphism_score=24.0	prediction=polymorphism	ref_cov=31/23	total_cov=36/32
RA	25	.	NC_000913	1502770	0	T	C	bias_e_value=0.174152	bias_p_value=3.75194e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=176.1	fisher_strand_p_value=1.77396e-09	frequency=2.604e-01	ks_quality_p_value=1	major_base=T	major_cov=46/25	major_frequency=7.396e-01	minor_base=C	minor_cov=0/25	new_cov=0/25	polymorphism_frequency=2.604e-01	polymorphism_score=18.6	prediction=polymorphism	ref_cov=46/25	total_cov=46/50
RA	26	.	NC_000913	1502772	0	G	A	bias_e_value=0.174152	bias_p_value=3.75194e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=174.0	fisher_strand_p_value=1.77396e-09	frequency=2.604e-01	ks_quality_p_value=1	major_base=G	major_cov=46/25	major_frequency=7.396e-01	minor_base=A	minor_cov=0/25	new_cov=0/25	polymorphism_frequency=2.604e-01	polymorphism_score=17.5	prediction=polymorphism	ref_cov=46/25	total_cov=46/51
RA	27	.	NC_000913	1579973	0	C	A	bias_e_value=0.00488719	bias_p_value=1.0529e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=310.3	fisher_strand_p_value=4.23089e-11	frequency=2.564e-01	ks_quality_p_value=1	major_base=C	major_cov=55/61	major_frequency=7.436e-01	minor_base=A	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=2.564e-01	polymorphism_score=15.8	prediction=polymorphism	ref_cov=55/61	total_cov=95/61
RA	28	.	NC_000913	1812509	0	G	T	bias_e_value=4.27364e-05	bias_p_value=9.20715e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=281.4	fisher_strand_p_value=3.08905e-13	frequency=2.721e-01	ks_quality_p_value=1	major_base=G	major_cov=68/31	major_frequency=7.279e-01	minor_base=T	minor_cov=1/36	new_cov=1/36	polymorphism_frequency=2.721e-01	polymorphism_score=20.6	prediction=polymorphism	ref_cov=68/31	total_cov=69/67
RA	29	.	NC_000913	1820763	0	G	T	bias_e_value=1.52002	bias_p_value=3.27474e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=112.2	fisher_strand_p_value=1.73548e-08	frequency=3.678e-01	ks_quality_p_value=1	major_base=G	major_cov=30/25	major_frequency=6.322e-01	minor_base=T	minor_cov=0/32	new_cov=0/32	polymorphism_frequency=3.678e-01	polymorphism_score=20.2	prediction=polymorphism	ref_cov=30/25	total_cov=30/57
RA	30	.	NC_000913	1905761	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=297.4	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=37/41	major_frequency=9.873e-01	minor_base=G	minor_cov=0/1	new_cov=37/41	polymorphism_frequency=9.873e-01	polymorphism_score=-5.9	prediction=consensus	ref_cov=0/1	total_cov=37/42
RA	31	.	NC_000913	2117652	0	G	T	bias_e_value=0.00878874	bias_p_value=1.89345e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.6	fisher_strand_p_value=7.80023e-11	frequency=3.103e-01	ks_quality_p_value=1	major_base=G	major_cov=42/18	major_frequency=6.897e-01	minor_base=T	minor_cov=0/27	new_cov=0/27	polymorphism_frequency=3.103e-01	polymorphism_score=11.5	prediction=polymorphism	ref_cov=42/18	total_cov=42/45
RA	32	.	NC_000913	2173363	0	C	.	consensus_score=399.7	frequency=1	major_base=.	major_cov=44/39	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=44/39	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=44/39
RA	33	.	NC_000913	2173364	0	C	.	consensus_score=399.7	frequency=1	major_base=.	major_cov=44/39	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=44/39	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=44/39
RA	34	.	NC_000913	2288418	0	G	T	bias_e_value=1.8922e-06	bias_p_value=4.07657e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=206.9	fisher_strand_p_value=1.23437e-14	frequency=3.582e-01	ks_quality_p_value=1	major_base=G	major_cov=53/33	major_frequency=6.418e-01	minor_base=T	minor_cov=0/48	new_cov=0/48	polymorphism_frequency=3.582e-01	polymorphism_score=29.1	prediction=polymorphism	ref_cov=53/33	total_cov=53/81
RA	35	.	NC_000913	2913085	0	G	T	bias_e_value=0.000997192	bias_p_value=2.14836e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=168.2	fisher_strand_p_value=8.09485e-12	frequency=3.585e-01	ks_quality_p_value=1	major_base=G	major_cov=42/26	major_frequency=6.415e-01	minor_base=T	minor_cov=0/38	new_cov=0/38	polymorphism_frequency=3.585e-01	polymorphism_score=14.4	prediction=polymorphism	ref_cov=42/26	total_cov=42/64
RA	36	.	NC_000913	3032307	0	C	T	bias_e_value=5.71858e-07	bias_p_value=1.23201e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=236.8	fisher_strand_p_value=3.59618e-15	frequency=2.458e-01	ks_quality_p_value=1	major_base=C	major_cov=19/70	major_frequency=7.542e-01	minor_base=T	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=2.458e-01	polymorphism_score=27.2	prediction=polymorphism	ref_cov=19/70	total_cov=49/70
RA	37	.	NC_000913	3054886	0	G	T	bias_e_value=0.21349	bias_p_value=4.59945e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=190.7	fisher_strand_p_value=2.19689e-09	frequency=2.800e-01	ks_quality_p_value=1	major_base=G	major_cov=23/49	major_frequency=7.200e-01	minor_base=T	minor_cov=27/1	new_cov=27/1	polymorphism_frequency=2.800e-01	polymorphism_score=22.8	prediction=polymorphism	ref_cov=23/49	total_cov=50/50
RA	38	.	NC_000913	3226224	0	G	T	bias_e_value=0.0220901	bias_p_value=4.75911e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=277.3	fisher_strand_p_value=2.04147e-10	frequency=2.240e-01	ks_quality_p_value=1	major_base=G	major_cov=61/36	major_frequency=7.760e-01	minor_base=T	minor_cov=0/28	new_cov=0/28	polymorphism_frequency=2.240e-01	polymorphism_score=10.3	prediction=polymorphism	ref_cov=61/36	total_cov=61/64
RA	39	.	NC_000913	3281067	0	C	A	bias_e_value=705.241	bias_p_value=0.000151938	consensus_reject=FREQUENCY_CUTOFF	consensus_score=141.1	fisher_strand_p_value=1.23509e-05	frequency=2.561e-01	ks_quality_p_value=1	major_base=C	major_cov=31/30	major_frequency=7.439e-01	minor_base=A	minor_cov=21/0	new_cov=21/0	polymorphism_frequency=2.561e-01	polymorphism_score=11.4	prediction=polymorphism	ref_cov=31/30	total_cov=52/30
RA	40	.	NC_000913	3431396	0	C	A	bias_e_value=0.448441	bias_p_value=9.66124e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=231.7	fisher_strand_p_value=4.79322e-09	frequency=2.756e-01	ks_quality_p_value=1	major_base=C	major_cov=46/46	major_frequency=7.244e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=2.756e-01	polymorphism_score=14.5	prediction=polymorphism	ref_cov=46/46	total_cov=81/46
RA	41	.	NC_000913	3560455	1	.	G	bias_e_value=4641650	bias_p_value=0.999999	consensus_score=452.5	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.998851	major_base=G	major_cov=54/63	major_frequency=9.832e-01	minor_base=.	minor_cov=1/1	new_cov=54/63	polymorphism_frequency=9.832e-01	polymorphism_score=-1.2	prediction=consensus	ref_cov=1/1	total_cov=55/64
RA	42	.	NC_000913	3741871	0	G	T	bias_e_value=0.00929306	bias_p_value=2.0021e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=191.7	fisher_strand_p_value=8.26765e-11	frequency=2.913e-01	ks_quality_p_value=1	major_base=G	major_cov=47/26	major_frequency=7.087e-01	minor_base=T	minor_cov=0/30	new_cov=0/30	polymorphism_frequency=2.913e-01	polymorphism_score=18.3	prediction=polymorphism	ref_cov=47/26	total_cov=47/56
RA	43	.	NC_000913	3768435	0	C	A	bias_e_value=3.08904e-07	bias_p_value=6.65505e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=357.3	fisher_strand_p_value=1.90727e-15	frequency=2.349e-01	ks_quality_p_value=1	major_base=C	major_cov=33/81	major_frequency=7.651e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=2.349e-01	polymorphism_score=11.5	prediction=polymorphism	ref_cov=33/81	total_cov=68/81
RA	44	.	NC_000913	3843750	0	C	A	bias_e_value=58.2331	bias_p_value=1.25458e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=279.5	fisher_strand_p_value=8.36732e-07	frequency=2.230e-01	ks_quality_p_value=1	major_base=C	major_cov=69/46	major_frequency=7.770e-01	minor_base=A	minor_cov=33/0	new_cov=33/0	polymorphism_frequency=2.230e-01	polymorphism_score=12.2	prediction=polymorphism	ref_cov=69/46	total_cov=102/47
RA	45	.	NC_000913	3896780	0	C	A	bias_e_value=0.00025092	bias_p_value=5.40583e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=314.7	fisher_strand_p_value=1.93257e-12	frequency=2.214e-01	ks_quality_p_value=1	major_base=C	major_cov=37/72	major_frequency=7.786e-01	minor_base=A	minor_cov=31/0	new_cov=31/0	polymorphism_frequency=2.214e-01	polymorphism_score=13.6	prediction=polymorphism	ref_cov=37/72	total_cov=68/72
RA	46	.	NC_000913	3911533	0	C	A	bias_e_value=0.0129366	bias_p_value=2.78708e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=175.3	fisher_strand_p_value=1.16756e-10	frequency=3.657e-01	ks_quality_p_value=1	major_base=C	major_cov=44/41	major_frequency=6.343e-01	minor_base=A	minor_cov=49/0	new_cov=49/0	polymorphism_frequency=3.657e-01	polymorphism_score=24.1	prediction=polymorphism	ref_cov=44/41	total_cov=93/41
RA	47	.	NC_000913	4296190	0	A	G	bias_e_value=3468610	bias_p_value=0.74728	consensus_reject=FREQUENCY_CUTOFF	consensus_score=57.3	fisher_strand_p_value=0.413363	frequency=2.121e-01	ks_quality_p_value=0.918284	major_base=A	major_cov=13/13	major_frequency=7.879e-01	minor_base=G	minor_cov=5/2	new_cov=5/2	polymorphism_frequency=2.121e-01	polymorphism_score=14.6	prediction=polymorphism	ref_cov=13/13	total_cov=18/16
RA	48	.	NC_000913	4296191	0	A	C	bias_e_value=3748710	bias_p_value=0.807624	consensus_reject=FREQUENCY_CUTOFF	consensus_score=38.6	fisher_strand_p_value=0.447871	frequency=2.647e-01	ks_quality_p_value=1	major_base=A	major_cov=12/13	major_frequency=7.353e-01	minor_base=C	minor_cov=6/3	new_cov=6/3	polymorphism_frequency=2.647e-01	polymorphism_score=17.0	prediction=polymorphism	ref_cov=12/13	total_cov=18/16
RA	49	.	NC_000913	4296380	1	.	C	bias_e_value=3909950	bias_p_value=0.842362	consensus_score=294.1	fisher_strand_p_value=0.494263	frequency=1	ks_quality_p_value=0.999419	major_base=C	major_cov=41/41	major_frequency=9.762e-01	minor_base=.	minor_cov=2/0	new_cov=41/41	polymorphism_frequency=9.762e-01	polymorphism_score=-0.8	prediction=consensus	ref_cov=2/0	total_cov=43/41
RA	50	.	NC_000913	4296380	2	.	G	bias_e_value=3907130	bias_p_value=0.841754	consensus_score=291.5	fisher_strand_p_value=0.494263	frequency=1	ks_quality_p_value=0.99768	major_base=G	major_cov=41/41	major_frequency=9.762e-01	minor_base=.	minor_cov=2/0	new_cov=41/41	polymorphism_frequency=9.762e-01	polymorphism_score=1.0	prediction=consensus	ref_cov=2/0	total_cov=43/41
RA	51	.	NC_000913	4360965	0	C	A	bias_e_value=5.14616e-11	bias_p_value=1.10869e-17	consensus_reject=FREQUENCY_CUTOFF	consensus_score=306.0	fisher_strand_p_value=2.53005e-19	frequency=2.925e-01	ks_quality_p_value=1	major_base=C	major_cov=26/78	major_frequency=7.075e-01	minor_base=A	minor_cov=43/0	new_cov=43/0	polymorphism_frequency=2.925e-01	polymorphism_score=22.8	prediction=polymorphism	ref_cov=26/78	total_cov=69/78
RA	52	.	NC_000913	4540411	0	C	A	bias_e_value=1.26199e-05	bias_p_value=2.71883e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=332.0	fisher_strand_p_value=8.75152e-14	frequency=2.644e-01	ks_quality_p_value=1	major_base=C	major_cov=56/72	major_frequency=7.356e-01	minor_base=A	minor_cov=46/0	new_cov=46/0	polymorphism_frequency=2.644e-01	polymorphism_score=11.5	prediction=polymorphism	ref_cov=56/72	total_cov=102/72
MC	53	.	NC_000913	257908	258683	767	0	left_inside_cov=0	left_outside_cov=119	right_inside_cov=0	right_outside_cov=119
MC	54	.	NC_000913	1299499	1300697	1198	0	left_inside_cov=0	left_outside_cov=154	right_inside_cov=0	right_outside_cov=156
MC	55	.	NC_000913	1978503	1979278	767	0	left_inside_cov=0	left_outside_cov=114	right_inside_cov=6	right_outside_cov=120
MC	56	.	NC_000913	3423891	3424482	343	244	left_inside_cov=32	left_outside_cov=34	right_inside_cov=32	right_outside_cov=34
JC	57	.	NC_000913	1	1	NC_000913	4641652	-1	0	alignment_overlap=0	coverage_minus=76	coverage_plus=58	flanking_left=300	flanking_right=300	frequency=1	ignore=CIRCULAR_CHROMOSOME	junction_possible_overlap_registers=294	key=NC_000913__1__1__NC_000913__4641652__-1__0____300__300__0__0	max_left=296	max_left_minus=296	max_left_plus=281	max_min_left=149	max_min_left_minus=149	max_min_left_plus=147	max_min_right=147	max_min_right_minus=147	max_min_right_plus=134	max_pos_hash_score=590	max_right=297	max_right_minus=297	max_right_plus=296	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.39	new_junction_read_count=135	polymorphism_frequency=1.000e+00	pos_hash_score=77	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=294	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=294	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=134
JC	58	.	NC_000913	45574	-1	NC_000913	45934	1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=6.152e-02	junction_possible_overlap_registers=283	key=NC_000913__45574__-1__NC_000913__45923__1__11____300__300__0__0	max_left=215	max_left_minus=215	max_left_plus=215	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=95	max_min_right_minus=74	max_min_right_plus=95	max_pos_hash_score=568	max_right=95	max_right_minus=74	max_right_plus=95	neg_log10_pos_hash_p_value=9.2	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=6.152e-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=0.81	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=79	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.49	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=46	side_2_redundant=0	total_non_overlap_reads=4
JC	59	.	NC_000913	126288	-1	NC_000913	126829	1	0	alignment_overlap=18	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.910e-02	junction_possible_overlap_registers=276	key=NC_000913__126288__-1__NC_000913__126811__1__18____300__300__0__0	max_left=110	max_left_minus=110	max_left_plus=110	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=25	max_min_right_minus=25	max_min_right_plus=25	max_pos_hash_score=554	max_right=25	max_right_minus=25	max_right_plus=25	neg_log10_pos_hash_p_value=8.5	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.910e-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=18	side_1_possible_overlap_registers=294	side_1_read_count=83	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.84	side_2_overlap=0	side_2_possible_overlap_registers=276	side_2_read_count=77	side_2_redundant=0	total_non_overlap_reads=4
JC	60	.	NC_000913	257907	-1	NC_000913	258684	1	0	alignment_overlap=8	coverage_minus=51	coverage_plus=67	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=286	key=NC_000913__257907__-1__NC_000913__258676__1__8____300__300__0__0	max_left=289	max_left_minus=289	max_left_plus=287	max_min_left=137	max_min_left_minus=92	max_min_left_plus=137	max_min_right=144	max_min_right_minus=122	max_min_right_plus=144	max_pos_hash_score=574	max_right=289	max_right_minus=287	max_right_plus=289	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.26	new_junction_read_count=119	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=8	side_1_possible_overlap_registers=294	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=286	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=118
JC	61	.	NC_000913	374939	-1	NC_000913	375344	1	0	alignment_overlap=17	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.587e-02	junction_possible_overlap_registers=277	key=NC_000913__374939__-1__NC_000913__375327__1__17____300__300__0__0	max_left=215	max_left_minus=215	max_left_plus=152	max_min_left=89	max_min_left_minus=0	max_min_left_plus=89	max_min_right=131	max_min_right_minus=109	max_min_right_plus=131	max_pos_hash_score=556	max_right=194	max_right_minus=109	max_right_plus=194	neg_log10_pos_hash_p_value=8.5	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=5.587e-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=0.68	side_1_overlap=17	side_1_possible_overlap_registers=294	side_1_read_count=66	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.80	side_2_overlap=0	side_2_possible_overlap_registers=277	side_2_read_count=73	side_2_redundant=0	total_non_overlap_reads=4
JC	62	.	NC_000913	696455	-1	NC_000913	696690	1	0	alignment_overlap=12	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=2.935e-02	junction_possible_overlap_registers=282	key=NC_000913__696455__-1__NC_000913__696678__1__12____300__300__0__0	max_left=95	max_left_minus=95	max_left_plus=95	max_min_left=95	max_min_left_minus=95	max_min_left_plus=95	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=566	max_right=161	max_right_minus=161	max_right_plus=161	neg_log10_pos_hash_p_value=9.2	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.935e-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=1.15	side_1_overlap=12	side_1_possible_overlap_registers=294	side_1_read_count=112	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=282	side_2_read_count=91	side_2_redundant=0	total_non_overlap_reads=3
JC	63	.	NC_000913	696506	-1	NC_000913	696619	1	0	alignment_overlap=77	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.038e-02	junction_possible_overlap_registers=217	key=NC_000913__696506__-1__NC_000913__696542__1__77____300__300__0__0	max_left=153	max_left_minus=81	max_left_plus=153	max_min_left=101	max_min_left_minus=0	max_min_left_plus=101	max_min_right=68	max_min_right_minus=15	max_min_right_plus=68	max_pos_hash_score=436	max_right=122	max_right_minus=15	max_right_plus=122	neg_log10_pos_hash_p_value=7.8	new_junction_coverage=0.04	new_junction_read_count=3	polymorphism_frequency=4.038e-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=1.00	side_1_overlap=77	side_1_possible_overlap_registers=294	side_1_read_count=97	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=217	side_2_read_count=71	side_2_redundant=0	total_non_overlap_reads=3
JC	64	.	NC_000913	696506	-1	NC_000913	697057	1	-45	alignment_overlap=-45	coverage_minus=6	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=1.072e-01	junction_possible_overlap_registers=249	key=NC_000913__696506__-1__NC_000913__697057__1__-45__AAATTGGTTTTGAATTTGCCGAACATATTCGATACATTCAGAATT__300__300__0__0	max_left=230	max_left_minus=62	max_left_plus=230	max_min_left=62	max_min_left_minus=62	max_min_left_plus=62	max_min_right=77	max_min_right_minus=0	max_min_right_plus=77	max_pos_hash_score=500	max_right=133	max_right_minus=133	max_right_plus=133	neg_log10_pos_hash_p_value=6.0	new_junction_coverage=0.11	new_junction_read_count=9	polymorphism_frequency=1.072e-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=1.00	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=97	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.82	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=80	side_2_redundant=0	total_non_overlap_reads=9	unique_read_sequence=AAATTGGTTTTGAATTTGCCGAACATATTCGATACATTCAGAATT
JC	65	.	NC_000913	696741	-1	NC_000913	697135	1	0	alignment_overlap=78	coverage_minus=9	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=2.023e-01	junction_possible_overlap_registers=216	key=NC_000913__696741__-1__NC_000913__697057__1__78____300__300__0__0	max_left=149	max_left_minus=149	max_left_plus=149	max_min_left=18	max_min_left_minus=0	max_min_left_plus=18	max_min_right=62	max_min_right_minus=62	max_min_right_plus=62	max_pos_hash_score=434	max_right=136	max_right_minus=62	max_right_plus=136	neg_log10_pos_hash_p_value=4.2	new_junction_coverage=0.20	new_junction_read_count=14	polymorphism_frequency=2.023e-01	pos_hash_score=11	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.72	side_1_overlap=78	side_1_possible_overlap_registers=294	side_1_read_count=70	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.82	side_2_overlap=0	side_2_possible_overlap_registers=216	side_2_read_count=59	side_2_redundant=0	total_non_overlap_reads=14
JC	66	.	NC_000913	732239	-1	NC_000913	3622029	1	0	alignment_overlap=12	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=1.697e-01	junction_possible_overlap_registers=282	key=NC_000913__732239__-1__NC_000913__3622017__1__12____300__300__0__0	max_left=206	max_left_minus=206	max_left_plus=120	max_min_left=41	max_min_left_minus=0	max_min_left_plus=41	max_min_right=131	max_min_right_minus=131	max_min_right_plus=94	max_pos_hash_score=566	max_right=247	max_right_minus=131	max_right_plus=247	neg_log10_pos_hash_p_value=8.0	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=1.697e-01	pos_hash_score=5	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.52	side_1_overlap=12	side_1_possible_overlap_registers=294	side_1_read_count=51	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=282	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=5
JC	67	.	NC_000913	732239	-1	NC_000913	3765020	1	0	alignment_overlap=12	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=1.615e-01	junction_possible_overlap_registers=282	key=NC_000913__732239__-1__NC_000913__3765008__1__12____300__300__0__0	max_left=206	max_left_minus=206	max_left_plus=120	max_min_left=41	max_min_left_minus=0	max_min_left_plus=41	max_min_right=131	max_min_right_minus=131	max_min_right_plus=94	max_pos_hash_score=566	max_right=247	max_right_minus=131	max_right_plus=247	neg_log10_pos_hash_p_value=8.0	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=1.615e-01	pos_hash_score=5	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.52	side_1_overlap=12	side_1_possible_overlap_registers=294	side_1_read_count=51	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.03	side_2_overlap=0	side_2_possible_overlap_registers=282	side_2_read_count=3	side_2_redundant=0	total_non_overlap_reads=5
JC	68	.	NC_000913	781222	-1	NC_000913	781445	1	0	alignment_overlap=76	coverage_minus=9	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.931e-01	junction_possible_overlap_registers=218	key=NC_000913__781222__-1__NC_000913__781369__1__76____300__300__0__0	max_left=180	max_left_minus=180	max_left_plus=131	max_min_left=108	max_min_left_minus=89	max_min_left_plus=108	max_min_right=105	max_min_right_minus=105	max_min_right_plus=93	max_pos_hash_score=438	max_right=116	max_right_minus=105	max_right_plus=116	neg_log10_pos_hash_p_value=4.0	new_junction_coverage=0.21	new_junction_read_count=15	polymorphism_frequency=1.931e-01	pos_hash_score=12	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.82	side_1_overlap=76	side_1_possible_overlap_registers=294	side_1_read_count=80	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.91	side_2_overlap=0	side_2_possible_overlap_registers=218	side_2_read_count=66	side_2_redundant=0	total_non_overlap_reads=14
JC	69	.	NC_000913	781446	-1	NC_000913	781655	1	0	alignment_overlap=78	coverage_minus=1	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=6.280e-02	junction_possible_overlap_registers=216	key=NC_000913__781446__-1__NC_000913__781577__1__78____300__300__0__0	max_left=71	max_left_minus=71	max_left_plus=71	max_min_left=71	max_min_left_minus=71	max_min_left_plus=71	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=434	max_right=110	max_right_minus=110	max_right_plus=110	neg_log10_pos_hash_p_value=7.1	new_junction_coverage=0.06	new_junction_read_count=4	polymorphism_frequency=6.280e-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=0.91	side_1_overlap=78	side_1_possible_overlap_registers=294	side_1_read_count=89	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.75	side_2_overlap=0	side_2_possible_overlap_registers=216	side_2_read_count=54	side_2_redundant=0	total_non_overlap_reads=4
JC	70	.	NC_000913	1038037	-1	NC_000913	1038512	1	0	alignment_overlap=11	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=6.585e-02	junction_possible_overlap_registers=283	key=NC_000913__1038037__-1__NC_000913__1038501__1__11____300__300__0__0	max_left=66	max_left_minus=66	max_left_plus=66	max_min_left=66	max_min_left_minus=66	max_min_left_plus=66	max_min_right=45	max_min_right_minus=45	max_min_right_plus=0	max_pos_hash_score=568	max_right=76	max_right_minus=76	max_right_plus=76	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.06	new_junction_read_count=6	polymorphism_frequency=6.585e-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=1.04	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=101	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.78	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=73	side_2_redundant=0	total_non_overlap_reads=5
JC	71	.	NC_000913	1207790	1	NC_000913	1209619	1	0	alignment_overlap=16	coverage_minus=30	coverage_plus=30	flanking_left=300	flanking_right=300	frequency=5.847e-01	junction_possible_overlap_registers=278	key=NC_000913__1207790__1__NC_000913__1209603__1__16____300__300__0__0	max_left=281	max_left_minus=271	max_left_plus=281	max_min_left=139	max_min_left_minus=136	max_min_left_plus=139	max_min_right=140	max_min_right_minus=134	max_min_right_plus=140	max_pos_hash_score=558	max_right=280	max_right_minus=254	max_right_plus=280	neg_log10_pos_hash_p_value=0.7	new_junction_coverage=0.65	new_junction_read_count=60	polymorphism_frequency=5.847e-01	pos_hash_score=45	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.52	side_1_overlap=16	side_1_possible_overlap_registers=294	side_1_read_count=51	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.40	side_2_overlap=0	side_2_possible_overlap_registers=278	side_2_read_count=37	side_2_redundant=0	total_non_overlap_reads=60
JC	72	.	NC_000913	1207805	-1	NC_000913	1209602	-1	0	alignment_overlap=16	coverage_minus=29	coverage_plus=16	flanking_left=300	flanking_right=300	frequency=5.221e-01	junction_possible_overlap_registers=278	key=NC_000913__1207805__-1__NC_000913__1209618__-1__16____300__300__0__0	max_left=282	max_left_minus=282	max_left_plus=255	max_min_left=141	max_min_left_minus=141	max_min_left_plus=94	max_min_right=125	max_min_right_minus=125	max_min_right_plus=123	max_pos_hash_score=558	max_right=267	max_right_minus=262	max_right_plus=267	neg_log10_pos_hash_p_value=1.4	new_junction_coverage=0.49	new_junction_read_count=45	polymorphism_frequency=5.221e-01	pos_hash_score=35	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.49	side_1_overlap=16	side_1_possible_overlap_registers=294	side_1_read_count=48	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.40	side_2_overlap=0	side_2_possible_overlap_registers=278	side_2_read_count=37	side_2_redundant=0	total_non_overlap_reads=45
JC	73	.	NC_000913	1286906	-1	NC_000913	1287557	1	0	alignment_overlap=20	coverage_minus=2	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=8.642e-02	junction_possible_overlap_registers=274	key=NC_000913__1286906__-1__NC_000913__1287537__1__20____300__300__0__0	max_left=258	max_left_minus=258	max_left_plus=243	max_min_left=16	max_min_left_minus=0	max_min_left_plus=16	max_min_right=50	max_min_right_minus=50	max_min_right_plus=49	max_pos_hash_score=550	max_right=239	max_right_minus=50	max_right_plus=239	neg_log10_pos_hash_p_value=7.9	new_junction_coverage=0.06	new_junction_read_count=5	polymorphism_frequency=8.642e-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=0.65	side_1_overlap=20	side_1_possible_overlap_registers=294	side_1_read_count=63	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.52	side_2_overlap=0	side_2_possible_overlap_registers=274	side_2_read_count=47	side_2_redundant=0	total_non_overlap_reads=5
JC	74	.	NC_000913	1287084	-1	NC_000913	1287557	1	0	alignment_overlap=20	coverage_minus=2	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.061e-01	junction_possible_overlap_registers=274	key=NC_000913__1287084__-1__NC_000913__1287537__1__20____300__300__0__0	max_left=211	max_left_minus=163	max_left_plus=211	max_min_left=21	max_min_left_minus=21	max_min_left_plus=21	max_min_right=128	max_min_right_minus=117	max_min_right_plus=128	max_pos_hash_score=550	max_right=258	max_right_minus=258	max_right_plus=145	neg_log10_pos_hash_p_value=7.4	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=1.061e-01	pos_hash_score=6	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.60	side_1_overlap=20	side_1_possible_overlap_registers=294	side_1_read_count=58	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.52	side_2_overlap=0	side_2_possible_overlap_registers=274	side_2_read_count=47	side_2_redundant=0	total_non_overlap_reads=6
JC	75	.	NC_000913	1299498	-1	NC_000913	1300698	1	0	alignment_overlap=4	coverage_minus=74	coverage_plus=77	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=290	key=NC_000913__1299498__-1__NC_000913__1300694__1__4____300__300__0__0	max_left=287	max_left_minus=287	max_left_plus=286	max_min_left=146	max_min_left_minus=133	max_min_left_plus=146	max_min_right=143	max_min_right_minus=143	max_min_right_plus=142	max_pos_hash_score=582	max_right=291	max_right_minus=291	max_right_plus=286	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.60	new_junction_read_count=154	polymorphism_frequency=1.000e+00	pos_hash_score=94	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=294	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=290	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=151
JC	76	.	NC_000913	1978502	-1	NC_000913	1979279	1	0	alignment_overlap=8	coverage_minus=55	coverage_plus=55	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=286	key=NC_000913__1978502__-1__NC_000913__1979271__1__8____300__300__0__0	max_left=286	max_left_minus=262	max_left_plus=286	max_min_left=144	max_min_left_minus=133	max_min_left_plus=144	max_min_right=130	max_min_right_minus=112	max_min_right_plus=130	max_pos_hash_score=574	max_right=291	max_right_minus=291	max_right_plus=286	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.19	new_junction_read_count=113	polymorphism_frequency=1.000e+00	pos_hash_score=70	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=294	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=286	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=110
JC	77	.	NC_000913	2036340	-1	NC_000913	2036754	1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.885e-02	junction_possible_overlap_registers=283	key=NC_000913__2036340__-1__NC_000913__2036743__1__11____300__300__0__0	max_left=59	max_left_minus=59	max_left_plus=59	max_min_left=59	max_min_left_minus=59	max_min_left_plus=59	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=568	max_right=173	max_right_minus=116	max_right_plus=173	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.885e-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=1.12	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=109	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=283	side_2_read_count=93	side_2_redundant=0	total_non_overlap_reads=4
JC	78	.	NC_000913	2357690	-1	NC_000913	2357874	1	0	alignment_overlap=25	coverage_minus=4	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=9.490e-02	junction_possible_overlap_registers=269	key=NC_000913__2357690__-1__NC_000913__2357849__1__25____300__300__0__0	max_left=240	max_left_minus=240	max_left_plus=130	max_min_left=130	max_min_left_minus=0	max_min_left_plus=130	max_min_right=136	max_min_right_minus=136	max_min_right_plus=54	max_pos_hash_score=540	max_right=250	max_right_minus=136	max_right_plus=250	neg_log10_pos_hash_p_value=6.8	new_junction_coverage=0.10	new_junction_read_count=9	polymorphism_frequency=9.490e-02	pos_hash_score=7	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.01	side_1_overlap=25	side_1_possible_overlap_registers=294	side_1_read_count=98	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.92	side_2_overlap=0	side_2_possible_overlap_registers=269	side_2_read_count=82	side_2_redundant=0	total_non_overlap_reads=9
JC	79	.	NC_000913	2357713	-1	NC_000913	2357910	1	-1	alignment_overlap=-1	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.056e-02	junction_possible_overlap_registers=293	key=NC_000913__2357713__-1__NC_000913__2357910__1__-1__C__300__300__0__0	max_left=175	max_left_minus=175	max_left_plus=119	max_min_left=119	max_min_left_minus=0	max_min_left_plus=119	max_min_right=124	max_min_right_minus=124	max_min_right_plus=0	max_pos_hash_score=588	max_right=178	max_right_minus=124	max_right_plus=178	neg_log10_pos_hash_p_value=9.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.056e-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=1.05	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=102	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.91	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=89	side_2_redundant=0	total_non_overlap_reads=3	unique_read_sequence=C
JC	80	.	NC_000913	2357742	-1	NC_000913	2357938	1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=5.512e-02	junction_possible_overlap_registers=283	key=NC_000913__2357742__-1__NC_000913__2357927__1__11____300__300__0__0	max_left=248	max_left_minus=248	max_left_plus=206	max_min_left=49	max_min_left_minus=0	max_min_left_plus=49	max_min_right=82	max_min_right_minus=46	max_min_right_plus=82	max_pos_hash_score=568	max_right=82	max_right_minus=46	max_right_plus=82	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=5.512e-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=0.99	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=96	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.84	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=79	side_2_redundant=0	total_non_overlap_reads=5
JC	81	.	NC_000913	2518116	-1	NC_000913	2518232	1	0	alignment_overlap=81	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=9.146e-02	junction_possible_overlap_registers=213	key=NC_000913__2518116__-1__NC_000913__2518151__1__81____300__300__0__0	max_left=202	max_left_minus=199	max_left_plus=202	max_min_left=69	max_min_left_minus=69	max_min_left_plus=69	max_min_right=84	max_min_right_minus=19	max_min_right_plus=84	max_pos_hash_score=428	max_right=160	max_right_minus=160	max_right_plus=150	neg_log10_pos_hash_p_value=5.6	new_junction_coverage=0.10	new_junction_read_count=7	polymorphism_frequency=9.146e-02	pos_hash_score=7	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.08	side_1_overlap=81	side_1_possible_overlap_registers=294	side_1_read_count=105	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.89	side_2_overlap=0	side_2_possible_overlap_registers=213	side_2_read_count=63	side_2_redundant=0	total_non_overlap_reads=7
JC	82	.	NC_000913	2568222	-1	NC_000913	2568323	1	0	alignment_overlap=22	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.092e-02	junction_possible_overlap_registers=272	key=NC_000913__2568222__-1__NC_000913__2568301__1__22____300__300__0__0	max_left=144	max_left_minus=139	max_left_plus=144	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=133	max_min_right_minus=62	max_min_right_plus=133	max_pos_hash_score=546	max_right=133	max_right_minus=62	max_right_plus=133	neg_log10_pos_hash_p_value=9.0	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=4.092e-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=0.74	side_1_overlap=22	side_1_possible_overlap_registers=294	side_1_read_count=72	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.82	side_2_overlap=0	side_2_possible_overlap_registers=272	side_2_read_count=74	side_2_redundant=0	total_non_overlap_reads=3
JC	83	.	NC_000913	2653419	-1	NC_000913	2653746	1	0	alignment_overlap=25	coverage_minus=8	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.310e-01	junction_possible_overlap_registers=269	key=NC_000913__2653419__-1__NC_000913__2653721__1__25____300__300__0__0	max_left=217	max_left_minus=217	max_left_plus=217	max_min_left=124	max_min_left_minus=124	max_min_left_plus=5	max_min_right=106	max_min_right_minus=106	max_min_right_plus=106	max_pos_hash_score=540	max_right=190	max_right_minus=190	max_right_plus=190	neg_log10_pos_hash_p_value=5.0	new_junction_coverage=0.15	new_junction_read_count=13	polymorphism_frequency=1.310e-01	pos_hash_score=12	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.91	side_1_overlap=25	side_1_possible_overlap_registers=294	side_1_read_count=89	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.02	side_2_overlap=0	side_2_possible_overlap_registers=269	side_2_read_count=91	side_2_redundant=0	total_non_overlap_reads=12
JC	84	.	NC_000913	3269938	-1	NC_000913	3270266	1	0	alignment_overlap=22	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=5.915e-02	junction_possible_overlap_registers=272	key=NC_000913__3269938__-1__NC_000913__3270244__1__22____300__300__0__0	max_left=152	max_left_minus=152	max_left_plus=124	max_min_left=120	max_min_left_minus=100	max_min_left_plus=120	max_min_right=38	max_min_right_minus=33	max_min_right_plus=38	max_pos_hash_score=546	max_right=203	max_right_minus=152	max_right_plus=203	neg_log10_pos_hash_p_value=6.9	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=5.915e-02	pos_hash_score=7	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.14	side_1_overlap=22	side_1_possible_overlap_registers=294	side_1_read_count=111	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.33	side_2_overlap=0	side_2_possible_overlap_registers=272	side_2_read_count=120	side_2_redundant=0	total_non_overlap_reads=7
JC	85	.	NC_000913	3469040	-1	NC_000913	3469344	1	0	alignment_overlap=20	coverage_minus=4	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.377e-02	junction_possible_overlap_registers=274	key=NC_000913__3469040__-1__NC_000913__3469324__1__20____300__300__0__0	max_left=222	max_left_minus=222	max_left_plus=149	max_min_left=111	max_min_left_minus=0	max_min_left_plus=111	max_min_right=106	max_min_right_minus=106	max_min_right_plus=84	max_pos_hash_score=550	max_right=169	max_right_minus=106	max_right_plus=169	neg_log10_pos_hash_p_value=7.4	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=5.377e-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=1.18	side_1_overlap=20	side_1_possible_overlap_registers=294	side_1_read_count=115	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.15	side_2_overlap=0	side_2_possible_overlap_registers=274	side_2_read_count=104	side_2_redundant=0	total_non_overlap_reads=6
JC	86	.	NC_000913	3470196	-1	NC_000913	3470386	1	0	alignment_overlap=13	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.821e-02	junction_possible_overlap_registers=281	key=NC_000913__3470196__-1__NC_000913__3470373__1__13____300__300__0__1	max_left=260	max_left_minus=260	max_left_plus=221	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=131	max_min_right_minus=27	max_min_right_plus=131	max_pos_hash_score=564	max_right=131	max_right_minus=27	max_right_plus=131	neg_log10_pos_hash_p_value=9.2	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.821e-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=0.81	side_1_overlap=13	side_1_possible_overlap_registers=294	side_1_read_count=79	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=3
JC	87	.	NC_000913	3621836	-1	NC_000913	3622017	1	0	alignment_overlap=12	coverage_minus=4	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=282	key=NC_000913__3621848__-1__NC_000913__3622017__1__12____300__300__1__0	max_left=274	max_left_minus=274	max_left_plus=120	max_min_left=41	max_min_left_minus=0	max_min_left_plus=41	max_min_right=131	max_min_right_minus=131	max_min_right_plus=94	max_pos_hash_score=566	max_right=247	max_right_minus=131	max_right_plus=247	neg_log10_pos_hash_p_value=7.5	new_junction_coverage=0.06	new_junction_read_count=6	polymorphism_frequency=1.000e+00	pos_hash_score=6	prediction=consensus	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=0.00	side_2_overlap=12	side_2_possible_overlap_registers=294	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=6
JC	88	.	NC_000913	3647886	-1	NC_000913	3648089	1	-3	alignment_overlap=-3	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=2.859e-02	junction_possible_overlap_registers=291	key=NC_000913__3647886__-1__NC_000913__3648089__1__-3__AGC__300__300__0__0	max_left=286	max_left_minus=286	max_left_plus=150	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=6	max_min_right_minus=6	max_min_right_plus=1	max_pos_hash_score=584	max_right=6	max_right_minus=6	max_right_plus=1	neg_log10_pos_hash_p_value=9.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.859e-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=1.02	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=99	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.10	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=107	side_2_redundant=0	total_non_overlap_reads=3	unique_read_sequence=AGC
JC	89	.	NC_000913	3647886	-1	NC_000913	3648317	1	0	alignment_overlap=25	coverage_minus=3	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=6.297e-02	junction_possible_overlap_registers=269	key=NC_000913__3647886__-1__NC_000913__3648292__1__25____300__300__0__0	max_left=261	max_left_minus=261	max_left_plus=125	max_min_left=30	max_min_left_minus=30	max_min_left_plus=30	max_min_right=9	max_min_right_minus=9	max_min_right_plus=4	max_pos_hash_score=540	max_right=271	max_right_minus=71	max_right_plus=271	neg_log10_pos_hash_p_value=7.3	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=6.297e-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=1.02	side_1_overlap=25	side_1_possible_overlap_registers=294	side_1_read_count=99	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=269	side_2_read_count=88	side_2_redundant=0	total_non_overlap_reads=6
JC	90	.	NC_000913	3764827	-1	NC_000913	3765008	1	0	alignment_overlap=12	coverage_minus=4	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=6.759e-01	junction_possible_overlap_registers=282	key=NC_000913__3764839__-1__NC_000913__3765008__1__12____300__300__1__0	max_left=274	max_left_minus=274	max_left_plus=120	max_min_left=41	max_min_left_minus=0	max_min_left_plus=41	max_min_right=131	max_min_right_minus=131	max_min_right_plus=94	max_pos_hash_score=566	max_right=247	max_right_minus=131	max_right_plus=247	neg_log10_pos_hash_p_value=7.5	new_junction_coverage=0.06	new_junction_read_count=6	polymorphism_frequency=6.759e-01	pos_hash_score=6	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=0.03	side_2_overlap=12	side_2_possible_overlap_registers=294	side_2_read_count=3	side_2_redundant=0	total_non_overlap_reads=6
JC	91	.	NC_000913	3849280	-1	NC_000913	3849600	1	0	alignment_overlap=10	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.174e-02	junction_possible_overlap_registers=284	key=NC_000913__3849280__-1__NC_000913__3849590__1__10____300__300__0__0	max_left=203	max_left_minus=203	max_left_plus=147	max_min_left=135	max_min_left_minus=0	max_min_left_plus=135	max_min_right=86	max_min_right_minus=86	max_min_right_plus=14	max_pos_hash_score=570	max_right=154	max_right_minus=86	max_right_plus=154	neg_log10_pos_hash_p_value=9.3	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=5.174e-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=0.72	side_1_overlap=10	side_1_possible_overlap_registers=294	side_1_read_count=70	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.84	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=79	side_2_redundant=0	total_non_overlap_reads=3
JC	92	.	NC_000913	4066508	-1	NC_000913	4066695	1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.528e-02	junction_possible_overlap_registers=283	key=NC_000913__4066508__-1__NC_000913__4066684__1__11____300__300__0__0	max_left=177	max_left_minus=177	max_left_plus=27	max_min_left=125	max_min_left_minus=125	max_min_left_plus=27	max_min_right=112	max_min_right_minus=112	max_min_right_plus=0	max_pos_hash_score=568	max_right=280	max_right_minus=164	max_right_plus=280	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.528e-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=0.91	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=89	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.89	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=83	side_2_redundant=0	total_non_overlap_reads=4
JC	93	.	NC_000913	4295870	-1	NC_000913	4296434	1	0	alignment_overlap=39	coverage_minus=3	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=6.744e-02	junction_possible_overlap_registers=255	key=NC_000913__4295870__-1__NC_000913__4296395__1__39____300__300__0__0	max_left=190	max_left_minus=190	max_left_plus=186	max_min_left=10	max_min_left_minus=0	max_min_left_plus=10	max_min_right=73	max_min_right_minus=73	max_min_right_plus=73	max_pos_hash_score=512	max_right=73	max_right_minus=73	max_right_plus=73	neg_log10_pos_hash_p_value=7.5	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=6.744e-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=0.93	side_1_overlap=39	side_1_possible_overlap_registers=294	side_1_read_count=91	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.03	side_2_overlap=0	side_2_possible_overlap_registers=255	side_2_read_count=87	side_2_redundant=0	total_non_overlap_reads=6
JC	94	.	NC_000913	4542682	1	NC_000913	4542996	1	0	alignment_overlap=9	coverage_minus=4	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.879e-02	junction_possible_overlap_registers=285	key=NC_000913__4542682__1__NC_000913__4542987__1__9____300__300__0__0	max_left=237	max_left_minus=176	max_left_plus=237	max_min_left=141	max_min_left_minus=141	max_min_left_plus=0	max_min_right=114	max_min_right_minus=114	max_min_right_plus=54	max_pos_hash_score=572	max_right=278	max_right_minus=278	max_right_plus=54	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.06	new_junction_read_count=6	polymorphism_frequency=4.879e-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=1.37	side_1_overlap=9	side_1_possible_overlap_registers=294	side_1_read_count=133	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.11	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=105	side_2_redundant=0	total_non_overlap_reads=6
JC	95	.	NC_000913	4542690	-1	NC_000913	4542986	-1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=4.712e-02	junction_possible_overlap_registers=285	key=NC_000913__4542690__-1__NC_000913__4542995__-1__9____300__300__0__0	max_left=276	max_left_minus=134	max_left_plus=276	max_min_left=134	max_min_left_minus=134	max_min_left_plus=0	max_min_right=134	max_min_right_minus=0	max_min_right_plus=134	max_pos_hash_score=572	max_right=157	max_right_minus=157	max_right_plus=134	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.06	new_junction_read_count=6	polymorphism_frequency=4.712e-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=1.46	side_1_overlap=9	side_1_possible_overlap_registers=294	side_1_read_count=142	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.11	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=105	side_2_redundant=0	total_non_overlap_reads=6
JC	96	.	NC_000913	4606166	-1	NC_000913	4606403	1	0	alignment_overlap=89	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.181e-01	junction_possible_overlap_registers=205	key=NC_000913__4606166__-1__NC_000913__4606314__1__89____300__300__0__0	max_left=208	max_left_minus=144	max_left_plus=208	max_min_left=56	max_min_left_minus=56	max_min_left_plus=56	max_min_right=83	max_min_right_minus=14	max_min_right_plus=83	max_pos_hash_score=412	max_right=138	max_right_minus=138	max_right_plus=138	neg_log10_pos_hash_p_value=5.4	new_junction_coverage=0.12	new_junction_read_count=8	polymorphism_frequency=1.181e-01	pos_hash_score=7	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.83	side_1_overlap=89	side_1_possible_overlap_registers=294	side_1_read_count=81	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=205	side_2_read_count=63	side_2_redundant=0	total_non_overlap_reads=7
UN	97	.	NC_000913	15647	16464
UN	98	.	NC_000913	20076	20276
UN	99	.	NC_000913	224019	224492
UN	100	.	NC_000913	224508	224508
UN	101	.	NC_000913	225171	225331
UN	102	.	NC_000913	225334	225334
UN	103	.	NC_000913	227270	228414
UN	104	.	NC_000913	257908	258683
UN	105	.	NC_000913	270798	270798
UN	106	.	NC_000913	270808	271002
UN	107	.	NC_000913	271004	271006
UN	108	.	NC_000913	271020	271020
UN	109	.	NC_000913	274235	274869
UN	110	.	NC_000913	279427	279681
UN	111	.	NC_000913	290918	291129
UN	112	.	NC_000913	291131	291132
UN	113	.	NC_000913	291136	291136
UN	114	.	NC_000913	291139	291139
UN	115	.	NC_000913	315498	315498
UN	116	.	NC_000913	315504	315504
UN	117	.	NC_000913	315507	315507
UN	118	.	NC_000913	315509	316197
UN	119	.	NC_000913	381513	382315
UN	120	.	NC_000913	382318	382318
UN	121	.	NC_000913	382324	382324
UN	122	.	NC_000913	391987	391988
UN	123	.	NC_000913	391991	391991
UN	124	.	NC_000913	391993	391994
UN	125	.	NC_000913	391996	392700
UN	126	.	NC_000913	526103	526103
UN	127	.	NC_000913	526107	526107
UN	128	.	NC_000913	526115	526116
UN	129	.	NC_000913	526118	526448
UN	130	.	NC_000913	567034	567034
UN	131	.	NC_000913	567041	567756
UN	132	.	NC_000913	574871	575505
UN	133	.	NC_000913	608292	608292
UN	134	.	NC_000913	608295	609087
UN	135	.	NC_000913	688131	688765
UN	136	.	NC_000913	1094509	1095215
UN	137	.	NC_000913	1095219	1095219
UN	138	.	NC_000913	1299499	1300697
UN	139	.	NC_000913	1396324	1396975
UN	140	.	NC_000913	1468162	1468953
UN	141	.	NC_000913	1469546	1470228
UN	142	.	NC_000913	1528585	1528964
UN	143	.	NC_000913	1651117	1651270
UN	144	.	NC_000913	1978503	1979277
UN	145	.	NC_000913	2067003	2067003
UN	146	.	NC_000913	2067008	2067021
UN	147	.	NC_000913	2067024	2067024
UN	148	.	NC_000913	2067029	2067029
UN	149	.	NC_000913	2069196	2069985
UN	150	.	NC_000913	2069989	2069989
UN	151	.	NC_000913	2102021	2102663
UN	152	.	NC_000913	2170440	2171164
UN	153	.	NC_000913	2289199	2289827
UN	154	.	NC_000913	2514549	2515350
UN	155	.	NC_000913	2726308	2729017
UN	156	.	NC_000913	2729815	2730715
UN	157	.	NC_000913	2730717	2730720
UN	158	.	NC_000913	2730722	2730723
UN	159	.	NC_000913	2730726	2730729
UN	160	.	NC_000913	2730732	2730732
UN	161	.	NC_000913	2730736	2730738
UN	162	.	NC_000913	2996630	2997418
UN	163	.	NC_000913	3130426	3131062
UN	164	.	NC_000913	3186352	3186352
UN	165	.	NC_000913	3186362	3187156
UN	166	.	NC_000913	3365812	3366470
UN	167	.	NC_000913	3423935	3424378
UN	168	.	NC_000913	3424380	3424380
UN	169	.	NC_000913	3424386	3424386
UN	170	.	NC_000913	3424934	3426584
UN	171	.	NC_000913	3427148	3427148
UN	172	.	NC_000913	3427177	3427177
UN	173	.	NC_000913	3427180	3427180
UN	174	.	NC_000913	3427199	3427199
UN	175	.	NC_000913	3427208	3427208
UN	176	.	NC_000913	3427210	3428311
UN	177	.	NC_000913	3583689	3583910
UN	178	.	NC_000913	3619552	3619552
UN	179	.	NC_000913	3619557	3620814
UN	180	.	NC_000913	3621349	3622057
UN	181	.	NC_000913	3652298	3652950
UN	182	.	NC_000913	3762528	3762528
UN	183	.	NC_000913	3762530	3763849
UN	184	.	NC_000913	3763851	3763851
UN	185	.	NC_000913	3763855	3763855
UN	186	.	NC_000913	3764337	3764337
UN	187	.	NC_000913	3764339	3764339
UN	188	.	NC_000913	3764344	3765019
UN	189	.	NC_000913	3765025	3765025
UN	190	.	NC_000913	3765034	3765034
UN	191	.	NC_000913	3765042	3765042
UN	192	.	NC_000913	3765045	3765045
UN	193	.	NC_000913	3942295	3943136
UN	194	.	NC_000913	3944320	3944325
UN	195	.	NC_000913	3944328	3945295
UN	196	.	NC_000913	4035397	4035397
UN	197	.	NC_000913	4035400	4035409
UN	198	.	NC_000913	4035411	4035422
UN	199	.	NC_000913	4035424	4035427
UN	200	.	NC_000913	4035430	4035430
UN	201	.	NC_000913	4035432	4035432
UN	202	.	NC_000913	4035434	4035436
UN	203	.	NC_000913	4035439	4035439
UN	204	.	NC_000913	4035447	4035447
UN	205	.	NC_000913	4035454	4035461
UN	206	.	NC_000913	4036018	4036868
UN	207	.	NC_000913	4038102	4038402
UN	208	.	NC_000913	4038994	4038994
UN	209	.	NC_000913	4038997	4039105
UN	210	.	NC_000913	4039671	4040317
UN	211	.	NC_000913	4166551	4166552
UN	212	.	NC_000913	4166556	4166557
UN	213	.	NC_000913	4166559	4166609
UN	214	.	NC_000913	4166907	4167956
UN	215	.	NC_000913	4168807	4171369
UN	216	.	NC_000913	4171372	4171373
UN	217	.	NC_000913	4176834	4176837
UN	218	.	NC_000913	4208389	4209489
UN	219	.	NC_000913	4210270	4210272
UN	220	.	NC_000913	4210275	4210275
UN	221	.	NC_000913	4210280	4210282
UN	222	.	NC_000913	4210287	4212840
UN	223	.	NC_000913	4498470	4499228
UN	224	.	NC_000913	4507741	4507741
UN	225	.	NC_000913	4507743	4507744
UN	226	.	NC_000913	4507747	4508428