#=GENOME_DIFF	1.0
#=CREATED	13:57:23 22 Dec 2025
#=PROGRAM	breseq 0.39.0 
#=COMMAND	breseq -j 8 -o /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_run15_rmdup_trimmng-adaptors-polyG_16samples-rerun/ME9042_S32_R1R2_RMDUP_BOTH-RM1andRM2-DUP.cutadapt -r /ld1/E.coli_BL21_DE3_ref/ncbi_dataset/data/GCF_000022665.1/genomic.gbff /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME9042_S32_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/ME9042_S32_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=REFSEQ	/ld1/E.coli_BL21_DE3_ref/ncbi_dataset/data/GCF_000022665.1/genomic.gbff
#=READSEQ	/ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME9042_S32_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/ME9042_S32_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=CONVERTED-BASES	492858555
#=CONVERTED-READS	1670324
#=INPUT-BASES	492965806
#=INPUT-READS	1670692
#=MAPPED-BASES	477041226
#=MAPPED-READS	1617759
RA	1	.	NC_012971	12150	0	G	T	bias_e_value=1.47627	bias_p_value=3.23817e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=178.1	fisher_strand_p_value=1.71502e-08	frequency=3.190e-01	ks_quality_p_value=1	major_base=G	major_cov=38/41	major_frequency=6.810e-01	minor_base=T	minor_cov=0/37	new_cov=0/37	polymorphism_frequency=3.190e-01	polymorphism_score=16.7	prediction=polymorphism	ref_cov=38/41	total_cov=38/78
RA	2	.	NC_012971	46591	0	G	T	bias_e_value=22.3229	bias_p_value=4.8965e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=241.5	fisher_strand_p_value=3.0604e-07	frequency=2.171e-01	ks_quality_p_value=1	major_base=G	major_cov=48/53	major_frequency=7.829e-01	minor_base=T	minor_cov=0/28	new_cov=0/28	polymorphism_frequency=2.171e-01	polymorphism_score=10.0	prediction=polymorphism	ref_cov=48/53	total_cov=48/81
RA	3	.	NC_012971	88456	0	G	T	bias_e_value=144.98	bias_p_value=3.18011e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=176.2	fisher_strand_p_value=2.27237e-06	frequency=3.120e-01	ks_quality_p_value=1	major_base=G	major_cov=31/55	major_frequency=6.880e-01	minor_base=T	minor_cov=0/39	new_cov=0/39	polymorphism_frequency=3.120e-01	polymorphism_score=10.6	prediction=polymorphism	ref_cov=31/55	total_cov=31/94
RA	4	.	NC_012971	144653	0	C	A	bias_e_value=0.00111418	bias_p_value=2.44394e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=299.8	fisher_strand_p_value=9.25531e-12	frequency=2.449e-01	ks_quality_p_value=1	major_base=C	major_cov=46/65	major_frequency=7.551e-01	minor_base=A	minor_cov=36/0	new_cov=36/0	polymorphism_frequency=2.449e-01	polymorphism_score=10.7	prediction=polymorphism	ref_cov=46/65	total_cov=82/65
RA	5	.	NC_012971	284777	0	G	T	bias_e_value=1.10944e-05	bias_p_value=2.43354e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=314.0	fisher_strand_p_value=7.80442e-14	frequency=2.571e-01	ks_quality_p_value=1	major_base=G	major_cov=69/35	major_frequency=7.429e-01	minor_base=T	minor_cov=0/36	new_cov=0/36	polymorphism_frequency=2.571e-01	polymorphism_score=12.5	prediction=polymorphism	ref_cov=69/35	total_cov=69/71
RA	6	.	NC_012971	576592	0	C	A	bias_e_value=119.072	bias_p_value=2.61183e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=161.5	fisher_strand_p_value=1.83846e-06	frequency=2.637e-01	ks_quality_p_value=1	major_base=C	major_cov=28/39	major_frequency=7.363e-01	minor_base=A	minor_cov=23/1	new_cov=23/1	polymorphism_frequency=2.637e-01	polymorphism_score=13.4	prediction=polymorphism	ref_cov=28/39	total_cov=51/41
RA	7	.	NC_012971	731872	0	G	T	bias_e_value=14.6235	bias_p_value=3.20765e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=212.6	fisher_strand_p_value=1.9499e-07	frequency=2.385e-01	ks_quality_p_value=1	major_base=G	major_cov=49/34	major_frequency=7.615e-01	minor_base=T	minor_cov=1/25	new_cov=1/25	polymorphism_frequency=2.385e-01	polymorphism_score=17.7	prediction=polymorphism	ref_cov=49/34	total_cov=50/59
RA	8	.	NC_012971	831947	0	G	A	bias_e_value=1.09417e-05	bias_p_value=2.40005e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=208.5	fisher_strand_p_value=7.69349e-14	frequency=2.891e-01	ks_quality_p_value=1	major_base=G	major_cov=61/30	major_frequency=7.109e-01	minor_base=A	minor_cov=0/37	new_cov=0/37	polymorphism_frequency=2.891e-01	polymorphism_score=43.6	prediction=polymorphism	ref_cov=61/30	total_cov=61/67
RA	9	.	NC_012971	957544	0	G	T	bias_e_value=17.5615	bias_p_value=3.85209e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=143.3	fisher_strand_p_value=2.36974e-07	frequency=3.426e-01	ks_quality_p_value=1	major_base=G	major_cov=30/41	major_frequency=6.574e-01	minor_base=T	minor_cov=0/37	new_cov=0/37	polymorphism_frequency=3.426e-01	polymorphism_score=19.2	prediction=polymorphism	ref_cov=30/41	total_cov=30/78
RA	10	.	NC_012971	1006183	0	G	T	bias_e_value=120.416	bias_p_value=2.64131e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=172.7	fisher_strand_p_value=1.8608e-06	frequency=3.223e-01	ks_quality_p_value=1	major_base=G	major_cov=42/40	major_frequency=6.777e-01	minor_base=T	minor_cov=3/36	new_cov=3/36	polymorphism_frequency=3.223e-01	polymorphism_score=16.9	prediction=polymorphism	ref_cov=42/40	total_cov=45/76
RA	11	.	NC_012971	1020577	0	C	A	bias_e_value=0.0717224	bias_p_value=1.57322e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=249.0	fisher_strand_p_value=7.13111e-10	frequency=2.937e-01	ks_quality_p_value=1	major_base=C	major_cov=53/48	major_frequency=7.063e-01	minor_base=A	minor_cov=42/0	new_cov=42/0	polymorphism_frequency=2.937e-01	polymorphism_score=11.3	prediction=polymorphism	ref_cov=53/48	total_cov=95/48
RA	12	.	NC_012971	1321336	0	A	C	bias_e_value=0.206997	bias_p_value=4.54046e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=265.6	fisher_strand_p_value=2.16731e-09	frequency=2.418e-01	ks_quality_p_value=1	major_base=A	major_cov=60/56	major_frequency=7.582e-01	minor_base=C	minor_cov=37/0	new_cov=37/0	polymorphism_frequency=2.418e-01	polymorphism_score=16.5	prediction=polymorphism	ref_cov=60/56	total_cov=97/56
RA	13	.	NC_012971	1334448	0	C	T	bias_e_value=1.75546	bias_p_value=3.85058e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=208.3	fisher_strand_p_value=2.05932e-08	frequency=2.062e-01	ks_quality_p_value=1	major_base=C	major_cov=26/51	major_frequency=7.938e-01	minor_base=T	minor_cov=20/0	new_cov=20/0	polymorphism_frequency=2.062e-01	polymorphism_score=10.2	prediction=polymorphism	ref_cov=26/51	total_cov=53/51
RA	14	.	NC_012971	1456833	0	T	C	bias_e_value=0.259857	bias_p_value=5.69993e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=178.1	fisher_strand_p_value=2.75214e-09	frequency=2.474e-01	ks_quality_p_value=1	major_base=T	major_cov=48/25	major_frequency=7.526e-01	minor_base=C	minor_cov=0/24	new_cov=0/24	polymorphism_frequency=2.474e-01	polymorphism_score=18.5	prediction=polymorphism	ref_cov=48/25	total_cov=48/49
RA	15	.	NC_012971	1456835	0	G	A	bias_e_value=4.5976	bias_p_value=1.00848e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=183.5	fisher_strand_p_value=5.70423e-08	frequency=2.188e-01	ks_quality_p_value=1	major_base=G	major_cov=48/27	major_frequency=7.812e-01	minor_base=A	minor_cov=0/21	new_cov=0/21	polymorphism_frequency=2.188e-01	polymorphism_score=11.8	prediction=polymorphism	ref_cov=48/27	total_cov=48/48
RA	16	.	NC_012971	1535454	0	C	A	bias_e_value=0.00112747	bias_p_value=2.47309e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=289.4	fisher_strand_p_value=9.37006e-12	frequency=2.676e-01	ks_quality_p_value=1	major_base=C	major_cov=44/60	major_frequency=7.324e-01	minor_base=A	minor_cov=38/0	new_cov=38/0	polymorphism_frequency=2.676e-01	polymorphism_score=14.0	prediction=polymorphism	ref_cov=44/60	total_cov=82/60
RA	17	.	NC_012971	1581200	0	G	T	bias_e_value=1.14605	bias_p_value=2.51385e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=171.1	fisher_strand_p_value=1.31282e-08	frequency=2.644e-01	ks_quality_p_value=1	major_base=G	major_cov=41/23	major_frequency=7.356e-01	minor_base=T	minor_cov=0/23	new_cov=0/23	polymorphism_frequency=2.644e-01	polymorphism_score=14.6	prediction=polymorphism	ref_cov=41/23	total_cov=41/46
RA	18	.	NC_012971	1756922	0	G	T	bias_e_value=1.73431e-06	bias_p_value=3.80417e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=262.2	fisher_strand_p_value=1.1494e-14	frequency=2.977e-01	ks_quality_p_value=1	major_base=G	major_cov=62/30	major_frequency=7.023e-01	minor_base=T	minor_cov=0/39	new_cov=0/39	polymorphism_frequency=2.977e-01	polymorphism_score=17.5	prediction=polymorphism	ref_cov=62/30	total_cov=62/69
RA	19	.	NC_012971	1859990	0	A	C	bias_e_value=0.0363644	bias_p_value=7.97649e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=133.8	fisher_strand_p_value=3.50271e-10	frequency=3.524e-01	ks_quality_p_value=1	major_base=A	major_cov=30/38	major_frequency=6.476e-01	minor_base=C	minor_cov=37/0	new_cov=37/0	polymorphism_frequency=3.524e-01	polymorphism_score=22.1	prediction=polymorphism	ref_cov=30/38	total_cov=68/38
RA	20	.	NC_012971	2002158	0	C	A	bias_e_value=2064.76	bias_p_value=0.000452902	consensus_reject=FREQUENCY_CUTOFF	consensus_score=152.8	fisher_strand_p_value=4.07746e-05	frequency=2.674e-01	ks_quality_p_value=1	major_base=C	major_cov=27/36	major_frequency=7.326e-01	minor_base=A	minor_cov=0/23	new_cov=0/23	polymorphism_frequency=2.674e-01	polymorphism_score=40.2	prediction=polymorphism	ref_cov=27/36	total_cov=27/59
RA	21	.	NC_012971	2016684	0	G	T	bias_e_value=0.12362	bias_p_value=2.71159e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=206.8	fisher_strand_p_value=1.26175e-09	frequency=2.421e-01	ks_quality_p_value=1	major_base=G	major_cov=49/23	major_frequency=7.579e-01	minor_base=T	minor_cov=0/23	new_cov=0/23	polymorphism_frequency=2.421e-01	polymorphism_score=13.6	prediction=polymorphism	ref_cov=49/23	total_cov=49/46
RA	22	.	NC_012971	2051872	0	A	G	bias_e_value=3766180	bias_p_value=0.826106	consensus_reject=FREQUENCY_CUTOFF	consensus_score=251.5	fisher_strand_p_value=0.471653	frequency=2.095e-01	ks_quality_p_value=1	major_base=A	major_cov=39/44	major_frequency=7.905e-01	minor_base=G	minor_cov=8/14	new_cov=8/14	polymorphism_frequency=2.095e-01	polymorphism_score=39.1	prediction=polymorphism	ref_cov=39/44	total_cov=47/58
RA	23	.	NC_012971	2051887	0	T	C	bias_e_value=3313240	bias_p_value=0.726755	consensus_reject=FREQUENCY_CUTOFF	consensus_score=187.4	fisher_strand_p_value=0.358984	frequency=2.653e-01	ks_quality_p_value=1	major_base=T	major_cov=30/42	major_frequency=7.347e-01	minor_base=C	minor_cov=14/12	new_cov=14/12	polymorphism_frequency=2.653e-01	polymorphism_score=51.2	prediction=polymorphism	ref_cov=30/42	total_cov=44/54
RA	24	.	NC_012971	2052283	0	C	T	bias_e_value=4558950	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=198.0	fisher_strand_p_value=1	frequency=2.000e-01	ks_quality_p_value=1	major_base=C	major_cov=29/39	major_frequency=8.000e-01	minor_base=T	minor_cov=7/10	new_cov=7/10	polymorphism_frequency=2.000e-01	polymorphism_score=29.9	prediction=polymorphism	ref_cov=29/39	total_cov=45/54
RA	25	.	NC_012971	2052319	0	C	T	bias_e_value=4120790	bias_p_value=0.90389	consensus_reject=FREQUENCY_CUTOFF	consensus_score=163.4	fisher_strand_p_value=0.594942	frequency=2.073e-01	ks_quality_p_value=1	major_base=C	major_cov=28/37	major_frequency=7.927e-01	minor_base=T	minor_cov=6/11	new_cov=6/11	polymorphism_frequency=2.073e-01	polymorphism_score=33.4	prediction=polymorphism	ref_cov=28/37	total_cov=34/48
RA	26	.	NC_012971	2058334	0	C	T	bias_e_value=262.984	bias_p_value=5.76851e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=169.4	fisher_strand_p_value=4.32027e-06	frequency=2.386e-01	ks_quality_p_value=1	major_base=C	major_cov=32/35	major_frequency=7.614e-01	minor_base=T	minor_cov=21/0	new_cov=21/0	polymorphism_frequency=2.386e-01	polymorphism_score=18.6	prediction=polymorphism	ref_cov=32/35	total_cov=54/35
RA	27	.	NC_012971	2134898	0	G	T	bias_e_value=1.74573e-05	bias_p_value=3.82923e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=268.9	fisher_strand_p_value=1.24678e-13	frequency=2.480e-01	ks_quality_p_value=1	major_base=G	major_cov=67/27	major_frequency=7.520e-01	minor_base=T	minor_cov=0/31	new_cov=0/31	polymorphism_frequency=2.480e-01	polymorphism_score=12.9	prediction=polymorphism	ref_cov=67/27	total_cov=67/58
RA	28	.	NC_012971	2183267	0	G	T	bias_e_value=3.63874e-07	bias_p_value=7.98153e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=323.6	fisher_strand_p_value=2.29976e-15	frequency=2.517e-01	ks_quality_p_value=1	major_base=G	major_cov=77/36	major_frequency=7.483e-01	minor_base=T	minor_cov=0/38	new_cov=0/38	polymorphism_frequency=2.517e-01	polymorphism_score=16.7	prediction=polymorphism	ref_cov=77/36	total_cov=77/74
RA	29	.	NC_012971	2217074	0	C	A	bias_e_value=1.38166e-05	bias_p_value=3.03065e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=259.6	fisher_strand_p_value=9.79059e-14	frequency=2.847e-01	ks_quality_p_value=1	major_base=C	major_cov=35/63	major_frequency=7.153e-01	minor_base=A	minor_cov=39/0	new_cov=39/0	polymorphism_frequency=2.847e-01	polymorphism_score=15.4	prediction=polymorphism	ref_cov=35/63	total_cov=74/63
RA	30	.	NC_012971	2355153	0	A	C	bias_e_value=0.000175823	bias_p_value=3.85666e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=217.5	fisher_strand_p_value=1.36171e-12	frequency=2.472e-01	ks_quality_p_value=1	major_base=A	major_cov=12/55	major_frequency=7.528e-01	minor_base=C	minor_cov=22/0	new_cov=22/0	polymorphism_frequency=2.472e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=12/55	total_cov=34/55
RA	31	.	NC_012971	2540079	0	C	A	bias_e_value=0.741633	bias_p_value=1.62676e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=246.1	fisher_strand_p_value=8.29667e-09	frequency=2.143e-01	ks_quality_p_value=1	major_base=C	major_cov=34/54	major_frequency=7.857e-01	minor_base=A	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=2.143e-01	polymorphism_score=10.9	prediction=polymorphism	ref_cov=34/54	total_cov=58/54
RA	32	.	NC_012971	2589438	0	G	T	bias_e_value=3.71464e-05	bias_p_value=8.14802e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=217.7	fisher_strand_p_value=2.72216e-13	frequency=3.077e-01	ks_quality_p_value=1	major_base=G	major_cov=54/27	major_frequency=6.923e-01	minor_base=T	minor_cov=0/36	new_cov=0/36	polymorphism_frequency=3.077e-01	polymorphism_score=12.2	prediction=polymorphism	ref_cov=54/27	total_cov=54/63
RA	33	.	NC_012971	2727510	0	G	T	bias_e_value=0.151635	bias_p_value=3.3261e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=179.7	fisher_strand_p_value=1.56327e-09	frequency=2.826e-01	ks_quality_p_value=1	major_base=G	major_cov=43/23	major_frequency=7.174e-01	minor_base=T	minor_cov=0/26	new_cov=0/26	polymorphism_frequency=2.826e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=43/23	total_cov=43/49
RA	34	.	NC_012971	2885744	0	G	T	bias_e_value=6.54721e-05	bias_p_value=1.43612e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=216.8	fisher_strand_p_value=4.89382e-13	frequency=2.869e-01	ks_quality_p_value=1	major_base=G	major_cov=29/58	major_frequency=7.131e-01	minor_base=T	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=2.869e-01	polymorphism_score=28.4	prediction=polymorphism	ref_cov=29/58	total_cov=64/58
RA	35	.	NC_012971	2885752	0	G	T	bias_e_value=0.00357647	bias_p_value=7.84493e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=198.1	fisher_strand_p_value=3.11399e-11	frequency=2.685e-01	ks_quality_p_value=1	major_base=G	major_cov=22/57	major_frequency=7.315e-01	minor_base=T	minor_cov=28/1	new_cov=28/1	polymorphism_frequency=2.685e-01	polymorphism_score=18.6	prediction=polymorphism	ref_cov=22/57	total_cov=50/58
RA	36	.	NC_012971	2956910	0	C	A	bias_e_value=0.00202839	bias_p_value=4.44925e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=317.0	fisher_strand_p_value=1.72566e-11	frequency=2.342e-01	ks_quality_p_value=1	major_base=C	major_cov=53/68	major_frequency=7.658e-01	minor_base=A	minor_cov=37/0	new_cov=37/0	polymorphism_frequency=2.342e-01	polymorphism_score=11.7	prediction=polymorphism	ref_cov=53/68	total_cov=90/68
RA	37	.	NC_012971	2958510	0	C	T	bias_e_value=0.000682597	bias_p_value=1.49727e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=261.2	fisher_strand_p_value=5.56297e-12	frequency=2.483e-01	ks_quality_p_value=1	major_base=C	major_cov=44/65	major_frequency=7.517e-01	minor_base=T	minor_cov=36/0	new_cov=36/0	polymorphism_frequency=2.483e-01	polymorphism_score=25.1	prediction=polymorphism	ref_cov=44/65	total_cov=95/65
RA	38	.	NC_012971	3329170	0	G	A	bias_e_value=8.62432	bias_p_value=1.89173e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=240.9	fisher_strand_p_value=1.112e-07	frequency=2.016e-01	ks_quality_p_value=1	major_base=G	major_cov=53/46	major_frequency=7.984e-01	minor_base=A	minor_cov=0/25	new_cov=0/25	polymorphism_frequency=2.016e-01	polymorphism_score=19.7	prediction=polymorphism	ref_cov=53/46	total_cov=53/71
RA	39	.	NC_012971	3561696	0	A	G	bias_e_value=4458920	bias_p_value=0.978058	consensus_reject=FREQUENCY_CUTOFF	consensus_score=169.7	fisher_strand_p_value=0.797964	frequency=2.222e-01	ks_quality_p_value=1	major_base=A	major_cov=28/42	major_frequency=7.778e-01	minor_base=G	minor_cov=9/11	new_cov=9/11	polymorphism_frequency=2.222e-01	polymorphism_score=45.6	prediction=polymorphism	ref_cov=28/42	total_cov=37/53
RA	40	.	NC_012971	3631564	0	C	A	bias_e_value=5.28969e-08	bias_p_value=1.16029e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=353.4	fisher_strand_p_value=3.1624e-16	frequency=2.560e-01	ks_quality_p_value=1	major_base=C	major_cov=43/82	major_frequency=7.440e-01	minor_base=A	minor_cov=43/0	new_cov=43/0	polymorphism_frequency=2.560e-01	polymorphism_score=16.3	prediction=polymorphism	ref_cov=43/82	total_cov=86/82
RA	41	.	NC_012971	3706612	0	G	T	bias_e_value=0.0282547	bias_p_value=6.19763e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=362.2	fisher_strand_p_value=2.69039e-10	frequency=2.368e-01	ks_quality_p_value=1	major_base=G	major_cov=66/79	major_frequency=7.632e-01	minor_base=T	minor_cov=0/45	new_cov=0/45	polymorphism_frequency=2.368e-01	polymorphism_score=11.5	prediction=polymorphism	ref_cov=66/79	total_cov=66/124
RA	42	.	NC_012971	3764190	0	G	A	bias_e_value=0.00527048	bias_p_value=1.15607e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=271.0	fisher_strand_p_value=4.66373e-11	frequency=2.077e-01	ks_quality_p_value=1	major_base=G	major_cov=68/35	major_frequency=7.923e-01	minor_base=A	minor_cov=0/27	new_cov=0/27	polymorphism_frequency=2.077e-01	polymorphism_score=19.4	prediction=polymorphism	ref_cov=68/35	total_cov=68/66
RA	43	.	NC_012971	3800334	0	C	A	bias_e_value=2.14471e-05	bias_p_value=4.7044e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=227.7	fisher_strand_p_value=1.54241e-13	frequency=3.464e-01	ks_quality_p_value=1	major_base=C	major_cov=42/58	major_frequency=6.536e-01	minor_base=A	minor_cov=52/1	new_cov=52/1	polymorphism_frequency=3.464e-01	polymorphism_score=28.0	prediction=polymorphism	ref_cov=42/58	total_cov=94/59
RA	44	.	NC_012971	4268051	0	C	A	bias_e_value=5.9458e-06	bias_p_value=1.3042e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=343.0	fisher_strand_p_value=4.09796e-14	frequency=2.215e-01	ks_quality_p_value=1	major_base=C	major_cov=36/80	major_frequency=7.785e-01	minor_base=A	minor_cov=33/0	new_cov=33/0	polymorphism_frequency=2.215e-01	polymorphism_score=14.9	prediction=polymorphism	ref_cov=36/80	total_cov=69/80
RA	45	.	NC_012971	4341185	0	C	A	bias_e_value=1.01288e-10	bias_p_value=2.22173e-17	consensus_reject=FREQUENCY_CUTOFF	consensus_score=452.3	fisher_strand_p_value=5.1537e-19	frequency=2.400e-01	ks_quality_p_value=1	major_base=C	major_cov=50/102	major_frequency=7.600e-01	minor_base=A	minor_cov=48/0	new_cov=48/0	polymorphism_frequency=2.400e-01	polymorphism_score=15.4	prediction=polymorphism	ref_cov=50/102	total_cov=98/102
JC	46	.	NC_012971	1	1	NC_012971	4558953	-1	0	alignment_overlap=0	coverage_minus=87	coverage_plus=71	flanking_left=300	flanking_right=300	frequency=1	ignore=CIRCULAR_CHROMOSOME	junction_possible_overlap_registers=294	key=NC_012971__1__1__NC_012971__4558953__-1__0____300__300__0__0	max_left=297	max_left_minus=297	max_left_plus=289	max_min_left=149	max_min_left_minus=149	max_min_left_plus=140	max_min_right=148	max_min_right_minus=147	max_min_right_plus=148	max_pos_hash_score=588	max_right=286	max_right_minus=284	max_right_plus=286	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.53	new_junction_read_count=160	polymorphism_frequency=1.000e+00	pos_hash_score=81	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=158
JC	47	.	NC_012971	132475	-1	NC_012971	132572	1	0	alignment_overlap=11	coverage_minus=7	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=7.549e-02	junction_possible_overlap_registers=283	key=NC_012971__132475__-1__NC_012971__132561__1__11____300__300__0__0	max_left=268	max_left_minus=268	max_left_plus=113	max_min_left=113	max_min_left_minus=102	max_min_left_plus=113	max_min_right=100	max_min_right_minus=100	max_min_right_plus=0	max_pos_hash_score=566	max_right=248	max_right_minus=248	max_right_plus=207	neg_log10_pos_hash_p_value=6.7	new_junction_coverage=0.09	new_junction_read_count=9	polymorphism_frequency=7.549e-02	pos_hash_score=9	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.17	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=122	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=283	side_2_read_count=103	side_2_redundant=0	total_non_overlap_reads=9
JC	48	.	NC_012971	493489	-1	NC_012971	493937	1	0	alignment_overlap=14	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=280	key=NC_012971__493503__-1__NC_012971__493937__1__14____300__300__1__0	max_left=99	max_left_minus=99	max_left_plus=99	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=80	max_min_right_minus=80	max_min_right_plus=80	max_pos_hash_score=560	max_right=80	max_right_minus=80	max_right_plus=80	neg_log10_pos_hash_p_value=9.7	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=1.000e+00	pos_hash_score=3	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=14	side_2_possible_overlap_registers=294	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=3
JC	49	.	NC_012971	614353	-1	NC_012971	614786	1	0	alignment_overlap=10	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=2.881e-02	junction_possible_overlap_registers=284	key=NC_012971__614353__-1__NC_012971__614776__1__10____300__300__0__0	max_left=69	max_left_minus=69	max_left_plus=69	max_min_left=69	max_min_left_minus=69	max_min_left_plus=69	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=568	max_right=190	max_right_minus=190	max_right_plus=190	neg_log10_pos_hash_p_value=9.8	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.881e-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=1.04	side_1_overlap=10	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=0.96	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=97	side_2_redundant=0	total_non_overlap_reads=3
JC	50	.	NC_012971	656315	-1	NC_012971	656751	1	0	alignment_overlap=12	coverage_minus=5	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.277e-01	junction_possible_overlap_registers=282	key=NC_012971__656315__-1__NC_012971__656739__1__12____300__300__0__0	max_left=163	max_left_minus=163	max_left_plus=159	max_min_left=84	max_min_left_minus=84	max_min_left_plus=84	max_min_right=124	max_min_right_minus=124	max_min_right_plus=124	max_pos_hash_score=564	max_right=242	max_right_minus=124	max_right_plus=242	neg_log10_pos_hash_p_value=6.0	new_junction_coverage=0.12	new_junction_read_count=12	polymorphism_frequency=1.277e-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=0.94	side_1_overlap=12	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=0.70	side_2_overlap=0	side_2_possible_overlap_registers=282	side_2_read_count=70	side_2_redundant=0	total_non_overlap_reads=12
JC	51	.	NC_012971	656380	-1	NC_012971	656930	1	-45	alignment_overlap=-45	coverage_minus=5	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=7.530e-02	junction_possible_overlap_registers=249	key=NC_012971__656380__-1__NC_012971__656930__1__-45__AAATTGGTTTTGAATTTGCCGAACATATTCGACACATTCAGAATT__300__300__0__0	max_left=181	max_left_minus=181	max_left_plus=56	max_min_left=71	max_min_left_minus=71	max_min_left_plus=56	max_min_right=74	max_min_right_minus=74	max_min_right_plus=0	max_pos_hash_score=498	max_right=199	max_right_minus=184	max_right_plus=199	neg_log10_pos_hash_p_value=7.3	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=7.530e-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=0.93	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=0.74	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=77	side_2_redundant=0	total_non_overlap_reads=6	unique_read_sequence=AAATTGGTTTTGAATTTGCCGAACATATTCGACACATTCAGAATT
JC	52	.	NC_012971	656615	-1	NC_012971	657008	1	0	alignment_overlap=78	coverage_minus=9	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=2.087e-01	junction_possible_overlap_registers=216	key=NC_012971__656615__-1__NC_012971__656930__1__78____300__300__0__0	max_left=151	max_left_minus=149	max_left_plus=151	max_min_left=101	max_min_left_minus=21	max_min_left_plus=101	max_min_right=106	max_min_right_minus=106	max_min_right_plus=24	max_pos_hash_score=432	max_right=121	max_right_minus=111	max_right_plus=121	neg_log10_pos_hash_p_value=4.0	new_junction_coverage=0.19	new_junction_read_count=15	polymorphism_frequency=2.087e-01	pos_hash_score=13	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.80	side_1_overlap=78	side_1_possible_overlap_registers=294	side_1_read_count=84	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.68	side_2_overlap=0	side_2_possible_overlap_registers=216	side_2_read_count=52	side_2_redundant=0	total_non_overlap_reads=15
JC	53	.	NC_012971	739290	-1	NC_012971	739580	1	0	alignment_overlap=76	coverage_minus=2	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.214e-01	junction_possible_overlap_registers=218	key=NC_012971__739290__-1__NC_012971__739504__1__76____300__300__0__0	max_left=223	max_left_minus=151	max_left_plus=223	max_min_left=24	max_min_left_minus=0	max_min_left_plus=24	max_min_right=97	max_min_right_minus=72	max_min_right_plus=97	max_pos_hash_score=436	max_right=97	max_right_minus=72	max_right_plus=97	neg_log10_pos_hash_p_value=5.7	new_junction_coverage=0.13	new_junction_read_count=10	polymorphism_frequency=1.214e-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=1.08	side_1_overlap=76	side_1_possible_overlap_registers=294	side_1_read_count=113	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=218	side_2_read_count=61	side_2_redundant=0	total_non_overlap_reads=9
JC	54	.	NC_012971	739290	-1	NC_012971	739786	1	0	alignment_overlap=76	coverage_minus=3	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=8.548e-02	junction_possible_overlap_registers=218	key=NC_012971__739290__-1__NC_012971__739710__1__76____300__300__0__0	max_left=165	max_left_minus=165	max_left_plus=105	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=71	max_min_right_minus=71	max_min_right_plus=71	max_pos_hash_score=436	max_right=71	max_right_minus=71	max_right_plus=71	neg_log10_pos_hash_p_value=6.5	new_junction_coverage=0.09	new_junction_read_count=7	polymorphism_frequency=8.548e-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=1.08	side_1_overlap=76	side_1_possible_overlap_registers=294	side_1_read_count=113	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=218	side_2_read_count=66	side_2_redundant=0	total_non_overlap_reads=6
JC	55	.	NC_012971	739579	-1	NC_012971	740008	1	0	alignment_overlap=76	coverage_minus=4	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=1.658e-01	junction_possible_overlap_registers=218	key=NC_012971__739579__-1__NC_012971__739932__1__76____300__300__0__0	max_left=174	max_left_minus=174	max_left_plus=171	max_min_left=49	max_min_left_minus=49	max_min_left_plus=49	max_min_right=50	max_min_right_minus=30	max_min_right_plus=50	max_pos_hash_score=436	max_right=154	max_right_minus=154	max_right_plus=154	neg_log10_pos_hash_p_value=5.3	new_junction_coverage=0.15	new_junction_read_count=12	polymorphism_frequency=1.658e-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=0.82	side_1_overlap=76	side_1_possible_overlap_registers=294	side_1_read_count=86	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.73	side_2_overlap=0	side_2_possible_overlap_registers=218	side_2_read_count=57	side_2_redundant=0	total_non_overlap_reads=10
JC	56	.	NC_012971	739785	-1	NC_012971	740008	1	0	alignment_overlap=76	coverage_minus=6	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.850e-01	junction_possible_overlap_registers=218	key=NC_012971__739785__-1__NC_012971__739932__1__76____300__300__0__0	max_left=133	max_left_minus=133	max_left_plus=133	max_min_left=84	max_min_left_minus=84	max_min_left_plus=30	max_min_right=52	max_min_right_minus=52	max_min_right_plus=52	max_pos_hash_score=436	max_right=194	max_right_minus=140	max_right_plus=194	neg_log10_pos_hash_p_value=5.3	new_junction_coverage=0.17	new_junction_read_count=13	polymorphism_frequency=1.850e-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=76	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=0.72	side_2_overlap=0	side_2_possible_overlap_registers=218	side_2_read_count=56	side_2_redundant=0	total_non_overlap_reads=13
JC	57	.	NC_012971	739932	1	NC_012971	2397543	-1	-2	alignment_overlap=-2	coverage_minus=6	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.236e-01	junction_possible_overlap_registers=292	key=NC_012971__739932__1__NC_012971__2397543__-1__-2__GG__300__300__0__0	max_left=230	max_left_minus=230	max_left_plus=230	max_min_left=72	max_min_left_minus=72	max_min_left_plus=48	max_min_right=67	max_min_right_minus=63	max_min_right_plus=67	max_pos_hash_score=584	max_right=271	max_right_minus=271	max_right_plus=237	neg_log10_pos_hash_p_value=6.2	new_junction_coverage=0.11	new_junction_read_count=11	polymorphism_frequency=1.236e-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=0.75	side_1_overlap=0	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=0.74	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=78	side_2_redundant=0	total_non_overlap_reads=11	unique_read_sequence=GG
JC	58	.	NC_012971	739932	1	NC_012971	2397664	-1	-1	alignment_overlap=-1	coverage_minus=5	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=9.553e-02	junction_possible_overlap_registers=293	key=NC_012971__739932__1__NC_012971__2397664__-1__-1__G__300__300__0__0	max_left=230	max_left_minus=230	max_left_plus=230	max_min_left=25	max_min_left_minus=25	max_min_left_plus=0	max_min_right=68	max_min_right_minus=64	max_min_right_plus=68	max_pos_hash_score=586	max_right=272	max_right_minus=272	max_right_plus=68	neg_log10_pos_hash_p_value=7.3	new_junction_coverage=0.08	new_junction_read_count=8	polymorphism_frequency=9.553e-02	pos_hash_score=8	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.75	side_1_overlap=0	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=0.70	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=73	side_2_redundant=0	total_non_overlap_reads=8	unique_read_sequence=G
JC	59	.	NC_012971	1099967	1	NC_012971	1426589	1	0	alignment_overlap=0	coverage_minus=5	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=7.921e-02	junction_possible_overlap_registers=294	key=NC_012971__1099967__1__NC_012971__1426589__1__0____300__300__0__0	max_left=221	max_left_minus=221	max_left_plus=221	max_min_left=104	max_min_left_minus=0	max_min_left_plus=104	max_min_right=111	max_min_right_minus=111	max_min_right_plus=78	max_pos_hash_score=588	max_right=196	max_right_minus=111	max_right_plus=196	neg_log10_pos_hash_p_value=7.3	new_junction_coverage=0.08	new_junction_read_count=8	polymorphism_frequency=7.921e-02	pos_hash_score=8	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.65	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=68	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.13	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=118	side_2_redundant=0	total_non_overlap_reads=8
JC	60	.	NC_012971	1099967	1	NC_012971	2827816	1	0	alignment_overlap=1	coverage_minus=5	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=7.025e-02	junction_possible_overlap_registers=293	key=NC_012971__1099967__1__NC_012971__2827815__1__1____300__300__0__0	max_left=220	max_left_minus=220	max_left_plus=220	max_min_left=103	max_min_left_minus=0	max_min_left_plus=103	max_min_right=111	max_min_right_minus=111	max_min_right_plus=78	max_pos_hash_score=586	max_right=196	max_right_minus=111	max_right_plus=196	neg_log10_pos_hash_p_value=7.3	new_junction_coverage=0.08	new_junction_read_count=8	polymorphism_frequency=7.025e-02	pos_hash_score=8	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.65	side_1_overlap=1	side_1_possible_overlap_registers=294	side_1_read_count=68	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.38	side_2_overlap=0	side_2_possible_overlap_registers=293	side_2_read_count=144	side_2_redundant=0	total_non_overlap_reads=8
JC	61	.	NC_012971	1239917	-1	NC_012971	1240255	1	0	alignment_overlap=2	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.401e-02	junction_possible_overlap_registers=292	key=NC_012971__1239917__-1__NC_012971__1240253__1__2____300__300__0__0	max_left=227	max_left_minus=227	max_left_plus=227	max_min_left=55	max_min_left_minus=55	max_min_left_plus=55	max_min_right=44	max_min_right_minus=44	max_min_right_plus=44	max_pos_hash_score=584	max_right=115	max_right_minus=115	max_right_plus=115	neg_log10_pos_hash_p_value=9.3	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.401e-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=1.04	side_1_overlap=2	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=1.14	side_2_overlap=0	side_2_possible_overlap_registers=292	side_2_read_count=119	side_2_redundant=0	total_non_overlap_reads=4
JC	62	.	NC_012971	1275046	-1	NC_012971	1275342	1	0	alignment_overlap=4	coverage_minus=4	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=1.013e-01	junction_possible_overlap_registers=290	key=NC_012971__1275046__-1__NC_012971__1275338__1__4____300__300__0__0	max_left=266	max_left_minus=266	max_left_plus=101	max_min_left=101	max_min_left_minus=101	max_min_left_plus=101	max_min_right=12	max_min_right_minus=12	max_min_right_plus=0	max_pos_hash_score=580	max_right=272	max_right_minus=264	max_right_plus=272	neg_log10_pos_hash_p_value=7.7	new_junction_coverage=0.07	new_junction_read_count=7	polymorphism_frequency=1.013e-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=0.59	side_1_overlap=4	side_1_possible_overlap_registers=294	side_1_read_count=62	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.61	side_2_overlap=0	side_2_possible_overlap_registers=290	side_2_read_count=63	side_2_redundant=0	total_non_overlap_reads=7
JC	63	.	NC_012971	1461017	-1	NC_012971	1461440	1	0	alignment_overlap=12	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.508e-02	junction_possible_overlap_registers=282	key=NC_012971__1461017__-1__NC_012971__1461428__1__12____300__300__0__0	max_left=138	max_left_minus=72	max_left_plus=138	max_min_left=29	max_min_left_minus=29	max_min_left_plus=29	max_min_right=79	max_min_right_minus=20	max_min_right_plus=79	max_pos_hash_score=564	max_right=79	max_right_minus=79	max_right_plus=79	neg_log10_pos_hash_p_value=9.7	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.508e-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=0.83	side_1_overlap=12	side_1_possible_overlap_registers=294	side_1_read_count=87	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.86	side_2_overlap=0	side_2_possible_overlap_registers=282	side_2_read_count=86	side_2_redundant=0	total_non_overlap_reads=4
JC	64	.	NC_012971	2519344	-1	NC_012971	2519671	1	0	alignment_overlap=25	coverage_minus=9	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.502e-01	junction_possible_overlap_registers=269	key=NC_012971__2519344__-1__NC_012971__2519646__1__25____300__300__0__0	max_left=260	max_left_minus=260	max_left_plus=260	max_min_left=124	max_min_left_minus=100	max_min_left_plus=124	max_min_right=109	max_min_right_minus=109	max_min_right_plus=106	max_pos_hash_score=538	max_right=151	max_right_minus=109	max_right_plus=151	neg_log10_pos_hash_p_value=5.1	new_junction_coverage=0.18	new_junction_read_count=17	polymorphism_frequency=1.502e-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=0.96	side_1_overlap=25	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=1.04	side_2_overlap=0	side_2_possible_overlap_registers=269	side_2_read_count=100	side_2_redundant=0	total_non_overlap_reads=16
JC	65	.	NC_012971	2560250	-1	NC_012971	2560400	1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.839e-02	junction_possible_overlap_registers=285	key=NC_012971__2560250__-1__NC_012971__2560391__1__9____300__300__0__0	max_left=181	max_left_minus=181	max_left_plus=54	max_min_left=54	max_min_left_minus=0	max_min_left_plus=54	max_min_right=116	max_min_right_minus=116	max_min_right_plus=0	max_pos_hash_score=570	max_right=282	max_right_minus=116	max_right_plus=282	neg_log10_pos_hash_p_value=9.1	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=5.839e-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=0.62	side_1_overlap=9	side_1_possible_overlap_registers=294	side_1_read_count=65	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.65	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=66	side_2_redundant=0	total_non_overlap_reads=4
JC	66	.	NC_012971	2736508	-1	NC_012971	2736936	1	0	alignment_overlap=30	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.962e-02	junction_possible_overlap_registers=264	key=NC_012971__2736508__-1__NC_012971__2736906__1__30____300__300__0__0	max_left=39	max_left_minus=39	max_left_plus=39	max_min_left=39	max_min_left_minus=39	max_min_left_plus=39	max_min_right=2	max_min_right_minus=2	max_min_right_plus=0	max_pos_hash_score=528	max_right=43	max_right_minus=43	max_right_plus=43	neg_log10_pos_hash_p_value=9.3	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.962e-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=0.71	side_1_overlap=30	side_1_possible_overlap_registers=294	side_1_read_count=74	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=264	side_2_read_count=79	side_2_redundant=0	total_non_overlap_reads=3
JC	67	.	NC_012971	3136199	-1	NC_012971	3136433	1	0	alignment_overlap=26	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=2.201e-02	junction_possible_overlap_registers=268	key=NC_012971__3136199__-1__NC_012971__3136407__1__26____300__300__0__0	max_left=211	max_left_minus=211	max_left_plus=129	max_min_left=129	max_min_left_minus=0	max_min_left_plus=129	max_min_right=63	max_min_right_minus=63	max_min_right_plus=0	max_pos_hash_score=536	max_right=145	max_right_minus=63	max_right_plus=145	neg_log10_pos_hash_p_value=9.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.201e-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=1.56	side_1_overlap=26	side_1_possible_overlap_registers=294	side_1_read_count=163	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.24	side_2_overlap=0	side_2_possible_overlap_registers=268	side_2_read_count=118	side_2_redundant=0	total_non_overlap_reads=3
JC	68	.	NC_012971	3136294	1	NC_012971	4046335	1	-53	alignment_overlap=-53	coverage_minus=2	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=4.856e-02	junction_possible_overlap_registers=241	key=NC_012971__3136294__1__NC_012971__4046335__1__-53__GTACGTAATAAACCGTTCCGGCGGGTTTCAGATTGTTGAGTGCGCTTTATTCA__300__300__0__0	max_left=176	max_left_minus=154	max_left_plus=176	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=93	max_min_right_minus=93	max_min_right_plus=77	max_pos_hash_score=482	max_right=93	max_right_minus=93	max_right_plus=77	neg_log10_pos_hash_p_value=8.8	new_junction_coverage=0.06	new_junction_read_count=5	polymorphism_frequency=4.856e-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=1.33	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=139	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.95	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=100	side_2_redundant=0	total_non_overlap_reads=5	unique_read_sequence=GTACGTAATAAACCGTTCCGGCGGGTTTCAGATTGTTGAGTGCGCTTTATTCA
JC	69	.	NC_012971	3510532	-1	NC_012971	3510764	1	0	alignment_overlap=58	coverage_minus=6	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=1.078e-01	junction_possible_overlap_registers=236	key=NC_012971__3510532__-1__NC_012971__3510706__1__58____300__300__0__0	max_left=212	max_left_minus=212	max_left_plus=147	max_min_left=75	max_min_left_minus=27	max_min_left_plus=75	max_min_right=106	max_min_right_minus=106	max_min_right_plus=93	max_pos_hash_score=472	max_right=222	max_right_minus=215	max_right_plus=222	neg_log10_pos_hash_p_value=4.7	new_junction_coverage=0.15	new_junction_read_count=13	polymorphism_frequency=1.078e-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=1.16	side_1_overlap=58	side_1_possible_overlap_registers=294	side_1_read_count=121	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.40	side_2_overlap=0	side_2_possible_overlap_registers=236	side_2_read_count=118	side_2_redundant=0	total_non_overlap_reads=12
JC	70	.	NC_012971	3643247	-1	NC_012971	3643269	1	0	alignment_overlap=4	coverage_minus=5	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=6.100e-02	junction_possible_overlap_registers=290	key=NC_012971__3643247__-1__NC_012971__3643265__1__4____300__300__0__0	max_left=250	max_left_minus=250	max_left_plus=187	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=104	max_min_right_minus=104	max_min_right_plus=104	max_pos_hash_score=580	max_right=104	max_right_minus=104	max_right_plus=104	neg_log10_pos_hash_p_value=7.3	new_junction_coverage=0.09	new_junction_read_count=9	polymorphism_frequency=6.100e-02	pos_hash_score=8	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.34	side_1_overlap=4	side_1_possible_overlap_registers=294	side_1_read_count=140	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.35	side_2_overlap=0	side_2_possible_overlap_registers=290	side_2_read_count=139	side_2_redundant=0	total_non_overlap_reads=8
JC	71	.	NC_012971	3643499	1	NC_012971	3643502	-1	-17	alignment_overlap=-17	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=5.642e-02	junction_possible_overlap_registers=277	key=NC_012971__3643499__1__NC_012971__3643502__-1__-17__AATATTGGAAGTGTTAT__300__300__0__0	max_left=209	max_left_minus=182	max_left_plus=209	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=115	max_min_right_minus=115	max_min_right_plus=105	max_pos_hash_score=554	max_right=115	max_right_minus=115	max_right_plus=105	neg_log10_pos_hash_p_value=7.4	new_junction_coverage=0.08	new_junction_read_count=8	polymorphism_frequency=5.642e-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=1.36	side_1_overlap=0	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=1.36	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=142	side_2_redundant=0	total_non_overlap_reads=7	unique_read_sequence=AATATTGGAAGTGTTAT
UN	72	.	NC_012971	15642	16450
UN	73	.	NC_012971	23559	23559
UN	74	.	NC_012971	23562	23562
UN	75	.	NC_012971	23569	23571
UN	76	.	NC_012971	23573	23784
UN	77	.	NC_012971	23786	23786
UN	78	.	NC_012971	23788	23788
UN	79	.	NC_012971	23790	23791
UN	80	.	NC_012971	227292	228267
UN	81	.	NC_012971	228269	228269
UN	82	.	NC_012971	228271	228272
UN	83	.	NC_012971	228274	228274
UN	84	.	NC_012971	228824	228825
UN	85	.	NC_012971	228829	228829
UN	86	.	NC_012971	228836	228836
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