#=GENOME_DIFF	1.0
#=CREATED	14:20:04 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/ME9655_S39_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/ME9655_S39_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/ME9655_S39_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/ME9655_S39_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/ME9655_S39_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=CONVERTED-BASES	449035887
#=CONVERTED-READS	1519455
#=INPUT-BASES	449128887
#=INPUT-READS	1519772
#=MAPPED-BASES	436944701
#=MAPPED-READS	1479502
DEL	1	43,53	NC_012971	769173	6979
RA	2	.	NC_012971	62261	0	C	A	bias_e_value=0.00118782	bias_p_value=2.60546e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=135.5	fisher_strand_p_value=9.89189e-12	frequency=3.796e-01	ks_quality_p_value=1	major_base=C	major_cov=27/40	major_frequency=6.204e-01	minor_base=A	minor_cov=41/0	new_cov=41/0	polymorphism_frequency=3.796e-01	polymorphism_score=30.9	prediction=polymorphism	ref_cov=27/40	total_cov=68/40
RA	3	.	NC_012971	244640	0	C	A	bias_e_value=0.00299309	bias_p_value=6.5653e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=179.1	fisher_strand_p_value=2.58701e-11	frequency=3.208e-01	ks_quality_p_value=1	major_base=C	major_cov=27/45	major_frequency=6.792e-01	minor_base=A	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=3.208e-01	polymorphism_score=10.6	prediction=polymorphism	ref_cov=27/45	total_cov=61/45
RA	4	.	NC_012971	403189	0	G	T	bias_e_value=0.0458926	bias_p_value=1.00665e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=173.4	fisher_strand_p_value=4.46826e-10	frequency=2.889e-01	ks_quality_p_value=1	major_base=G	major_cov=43/21	major_frequency=7.111e-01	minor_base=T	minor_cov=0/26	new_cov=0/26	polymorphism_frequency=2.889e-01	polymorphism_score=10.9	prediction=polymorphism	ref_cov=43/21	total_cov=43/47
RA	5	.	NC_012971	622651	0	C	A	bias_e_value=6.06538e-05	bias_p_value=1.33043e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=248.8	fisher_strand_p_value=4.52147e-13	frequency=2.627e-01	ks_quality_p_value=1	major_base=C	major_cov=26/61	major_frequency=7.373e-01	minor_base=A	minor_cov=31/0	new_cov=31/0	polymorphism_frequency=2.627e-01	polymorphism_score=10.7	prediction=polymorphism	ref_cov=26/61	total_cov=57/61
RA	6	.	NC_012971	760575	0	G	A	bias_e_value=0.00712616	bias_p_value=1.56311e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=166.1	fisher_strand_p_value=6.38678e-11	frequency=2.500e-01	ks_quality_p_value=1	major_base=G	major_cov=48/12	major_frequency=7.500e-01	minor_base=A	minor_cov=0/20	new_cov=0/20	polymorphism_frequency=2.500e-01	polymorphism_score=22.1	prediction=polymorphism	ref_cov=48/12	total_cov=48/32
RA	7	.	NC_012971	831947	0	G	A	bias_e_value=0.01215	bias_p_value=2.66508e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=254.2	fisher_strand_p_value=1.11427e-10	frequency=2.231e-01	ks_quality_p_value=1	major_base=G	major_cov=63/38	major_frequency=7.769e-01	minor_base=A	minor_cov=0/29	new_cov=0/29	polymorphism_frequency=2.231e-01	polymorphism_score=29.6	prediction=polymorphism	ref_cov=63/38	total_cov=63/67
RA	8	.	NC_012971	846248	0	G	T	bias_e_value=4457.58	bias_p_value=0.000977765	consensus_reject=FREQUENCY_CUTOFF	consensus_score=48.9	fisher_strand_p_value=9.53142e-05	frequency=4.286e-01	ks_quality_p_value=1	major_base=G	major_cov=14/18	major_frequency=5.714e-01	minor_base=T	minor_cov=0/24	new_cov=0/24	polymorphism_frequency=4.286e-01	polymorphism_score=12.1	prediction=polymorphism	ref_cov=14/18	total_cov=14/42
RA	9	.	NC_012971	1006183	0	G	T	bias_e_value=615.849	bias_p_value=0.000135086	consensus_reject=FREQUENCY_CUTOFF	consensus_score=155.4	fisher_strand_p_value=1.0868e-05	frequency=2.947e-01	ks_quality_p_value=1	major_base=G	major_cov=33/34	major_frequency=7.053e-01	minor_base=T	minor_cov=1/27	new_cov=1/27	polymorphism_frequency=2.947e-01	polymorphism_score=13.7	prediction=polymorphism	ref_cov=33/34	total_cov=34/61
RA	10	.	NC_012971	1321336	0	A	C	bias_e_value=0.372127	bias_p_value=8.16255e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=326.1	fisher_strand_p_value=4.01436e-09	frequency=2.000e-01	ks_quality_p_value=1	major_base=A	major_cov=69/67	major_frequency=8.000e-01	minor_base=C	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=2.000e-01	polymorphism_score=23.7	prediction=polymorphism	ref_cov=69/67	total_cov=103/67
RA	11	.	NC_012971	1337830	0	C	A	bias_e_value=4.58658	bias_p_value=1.00606e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=114.1	fisher_strand_p_value=5.68973e-08	frequency=3.750e-01	ks_quality_p_value=1	major_base=C	major_cov=27/28	major_frequency=6.250e-01	minor_base=A	minor_cov=33/0	new_cov=33/0	polymorphism_frequency=3.750e-01	polymorphism_score=19.8	prediction=polymorphism	ref_cov=27/28	total_cov=60/28
RA	12	.	NC_012971	1456833	0	T	C	bias_e_value=1.62357	bias_p_value=3.56129e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=148.1	fisher_strand_p_value=1.89624e-08	frequency=2.874e-01	ks_quality_p_value=1	major_base=T	major_cov=38/24	major_frequency=7.126e-01	minor_base=C	minor_cov=0/25	new_cov=0/25	polymorphism_frequency=2.874e-01	polymorphism_score=26.6	prediction=polymorphism	ref_cov=38/24	total_cov=38/49
RA	13	.	NC_012971	1456835	0	G	A	bias_e_value=68.1355	bias_p_value=1.49454e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=158.6	fisher_strand_p_value=1.00941e-06	frequency=2.326e-01	ks_quality_p_value=1	major_base=G	major_cov=38/28	major_frequency=7.674e-01	minor_base=A	minor_cov=0/20	new_cov=0/20	polymorphism_frequency=2.326e-01	polymorphism_score=15.5	prediction=polymorphism	ref_cov=38/28	total_cov=38/48
RA	14	.	NC_012971	1581200	0	G	T	bias_e_value=8.10752	bias_p_value=1.77837e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=143.0	fisher_strand_p_value=1.04135e-07	frequency=3.263e-01	ks_quality_p_value=1	major_base=G	major_cov=32/32	major_frequency=6.737e-01	minor_base=T	minor_cov=0/31	new_cov=0/31	polymorphism_frequency=3.263e-01	polymorphism_score=12.5	prediction=polymorphism	ref_cov=32/32	total_cov=32/63
RA	15	.	NC_012971	1654126	0	C	A	bias_e_value=316473	bias_p_value=0.0694179	consensus_reject=FREQUENCY_CUTOFF	consensus_score=146.3	fisher_strand_p_value=0.0129911	frequency=2.000e-01	ks_quality_p_value=1	major_base=C	major_cov=38/18	major_frequency=8.000e-01	minor_base=A	minor_cov=4/10	new_cov=4/10	polymorphism_frequency=2.000e-01	polymorphism_score=13.9	prediction=polymorphism	ref_cov=38/18	total_cov=42/28
RA	16	.	NC_012971	1654154	0	T	C	bias_e_value=2730400	bias_p_value=0.59891	consensus_reject=FREQUENCY_CUTOFF	consensus_score=181.3	fisher_strand_p_value=0.25169	frequency=2.105e-01	ks_quality_p_value=1	major_base=T	major_cov=38/22	major_frequency=7.895e-01	minor_base=C	minor_cov=7/9	new_cov=7/9	polymorphism_frequency=2.105e-01	polymorphism_score=21.4	prediction=polymorphism	ref_cov=38/22	total_cov=45/31
RA	17	.	NC_012971	2016684	0	G	T	bias_e_value=22.0202	bias_p_value=4.83011e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=111.7	fisher_strand_p_value=3.01616e-07	frequency=3.056e-01	ks_quality_p_value=1	major_base=G	major_cov=30/20	major_frequency=6.944e-01	minor_base=T	minor_cov=0/22	new_cov=0/22	polymorphism_frequency=3.056e-01	polymorphism_score=16.2	prediction=polymorphism	ref_cov=30/20	total_cov=30/42
RA	18	.	NC_012971	2051825	0	A	C	bias_e_value=3904550	bias_p_value=0.856457	consensus_reject=FREQUENCY_CUTOFF	consensus_score=263.1	fisher_strand_p_value=0.514561	frequency=2.063e-01	ks_quality_p_value=1	major_base=A	major_cov=46/54	major_frequency=7.937e-01	minor_base=C	minor_cov=14/12	new_cov=14/12	polymorphism_frequency=2.063e-01	polymorphism_score=59.6	prediction=polymorphism	ref_cov=46/54	total_cov=60/66
RA	19	.	NC_012971	2051885	0	T	G	bias_e_value=1475180	bias_p_value=0.323579	consensus_reject=FREQUENCY_CUTOFF	consensus_score=198.1	fisher_strand_p_value=0.0971174	frequency=2.110e-01	ks_quality_p_value=1	major_base=T	major_cov=34/52	major_frequency=7.890e-01	minor_base=G	minor_cov=14/9	new_cov=14/9	polymorphism_frequency=2.110e-01	polymorphism_score=49.6	prediction=polymorphism	ref_cov=34/52	total_cov=48/62
RA	20	.	NC_012971	2051887	0	T	C	bias_e_value=3287500	bias_p_value=0.72111	consensus_reject=FREQUENCY_CUTOFF	consensus_score=243.4	fisher_strand_p_value=0.353514	frequency=2.162e-01	ks_quality_p_value=1	major_base=T	major_cov=36/51	major_frequency=7.838e-01	minor_base=C	minor_cov=13/11	new_cov=13/11	polymorphism_frequency=2.162e-01	polymorphism_score=43.1	prediction=polymorphism	ref_cov=36/51	total_cov=49/62
RA	21	.	NC_012971	2052245	0	T	A	bias_e_value=4471910	bias_p_value=0.980908	consensus_reject=FREQUENCY_CUTOFF	consensus_score=191.0	fisher_strand_p_value=0.811067	frequency=2.447e-01	ks_quality_p_value=1	major_base=T	major_cov=40/31	major_frequency=7.553e-01	minor_base=A	minor_cov=12/11	new_cov=12/11	polymorphism_frequency=2.447e-01	polymorphism_score=71.6	prediction=polymorphism	ref_cov=40/31	total_cov=61/47
RA	22	.	NC_012971	2052318	0	T	G	bias_e_value=4558950	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=183.3	fisher_strand_p_value=1	frequency=2.277e-01	ks_quality_p_value=1	major_base=T	major_cov=36/42	major_frequency=7.723e-01	minor_base=G	minor_cov=10/13	new_cov=10/13	polymorphism_frequency=2.277e-01	polymorphism_score=34.7	prediction=polymorphism	ref_cov=36/42	total_cov=47/55
RA	23	.	NC_012971	2052319	0	C	T	bias_e_value=4480820	bias_p_value=0.982862	consensus_reject=FREQUENCY_CUTOFF	consensus_score=169.0	fisher_strand_p_value=0.82067	frequency=2.427e-01	ks_quality_p_value=1	major_base=C	major_cov=37/41	major_frequency=7.573e-01	minor_base=T	minor_cov=11/14	new_cov=11/14	polymorphism_frequency=2.427e-01	polymorphism_score=45.7	prediction=polymorphism	ref_cov=37/41	total_cov=48/55
RA	24	.	NC_012971	2052320	0	C	A	bias_e_value=3260490	bias_p_value=0.715184	consensus_reject=FREQUENCY_CUTOFF	consensus_score=201.1	fisher_strand_p_value=0.34786	frequency=2.255e-01	ks_quality_p_value=1	major_base=C	major_cov=35/44	major_frequency=7.745e-01	minor_base=A	minor_cov=13/10	new_cov=13/10	polymorphism_frequency=2.255e-01	polymorphism_score=30.1	prediction=polymorphism	ref_cov=35/44	total_cov=48/55
RA	25	.	NC_012971	2134898	0	G	T	bias_e_value=7.78278e-08	bias_p_value=1.70714e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=266.2	fisher_strand_p_value=4.70378e-16	frequency=2.880e-01	ks_quality_p_value=1	major_base=G	major_cov=66/23	major_frequency=7.120e-01	minor_base=T	minor_cov=0/36	new_cov=0/36	polymorphism_frequency=2.880e-01	polymorphism_score=18.0	prediction=polymorphism	ref_cov=66/23	total_cov=66/59
RA	26	.	NC_012971	2183267	0	G	T	bias_e_value=0.000661389	bias_p_value=1.45075e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=288.4	fisher_strand_p_value=5.38358e-12	frequency=2.550e-01	ks_quality_p_value=1	major_base=G	major_cov=64/47	major_frequency=7.450e-01	minor_base=T	minor_cov=0/38	new_cov=0/38	polymorphism_frequency=2.550e-01	polymorphism_score=20.5	prediction=polymorphism	ref_cov=64/47	total_cov=64/85
RA	27	.	NC_012971	2198186	0	C	T	bias_e_value=4185840	bias_p_value=0.918158	consensus_reject=FREQUENCY_CUTOFF	consensus_score=69.9	fisher_strand_p_value=0.717192	frequency=2.174e-01	ks_quality_p_value=0.869694	major_base=C	major_cov=15/21	major_frequency=7.826e-01	minor_base=T	minor_cov=3/7	new_cov=3/7	polymorphism_frequency=2.174e-01	polymorphism_score=19.4	prediction=polymorphism	ref_cov=15/21	total_cov=19/28
RA	28	.	NC_012971	2217074	0	C	A	bias_e_value=4.25893	bias_p_value=9.3419e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=153.3	fisher_strand_p_value=5.25991e-08	frequency=2.759e-01	ks_quality_p_value=1	major_base=C	major_cov=25/38	major_frequency=7.241e-01	minor_base=A	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=2.759e-01	polymorphism_score=10.2	prediction=polymorphism	ref_cov=25/38	total_cov=49/38
RA	29	.	NC_012971	2314969	0	C	A	bias_e_value=1.92927	bias_p_value=4.23182e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=166.9	fisher_strand_p_value=2.27535e-08	frequency=2.747e-01	ks_quality_p_value=1	major_base=C	major_cov=26/40	major_frequency=7.253e-01	minor_base=A	minor_cov=25/0	new_cov=25/0	polymorphism_frequency=2.747e-01	polymorphism_score=11.6	prediction=polymorphism	ref_cov=26/40	total_cov=51/40
RA	30	.	NC_012971	2589438	0	G	T	bias_e_value=3.71464e-05	bias_p_value=8.14802e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=210.9	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=16.1	prediction=polymorphism	ref_cov=54/27	total_cov=54/63
RA	31	.	NC_012971	2727510	0	G	T	bias_e_value=0.014933	bias_p_value=3.27553e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=141.9	fisher_strand_p_value=1.38194e-10	frequency=3.200e-01	ks_quality_p_value=1	major_base=G	major_cov=38/13	major_frequency=6.800e-01	minor_base=T	minor_cov=0/24	new_cov=0/24	polymorphism_frequency=3.200e-01	polymorphism_score=12.3	prediction=polymorphism	ref_cov=38/13	total_cov=38/37
RA	32	.	NC_012971	3057477	0	G	T	bias_e_value=0.0088016	bias_p_value=1.93062e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=323.7	fisher_strand_p_value=7.96e-11	frequency=2.288e-01	ks_quality_p_value=1	major_base=G	major_cov=66/52	major_frequency=7.712e-01	minor_base=T	minor_cov=0/35	new_cov=0/35	polymorphism_frequency=2.288e-01	polymorphism_score=10.6	prediction=polymorphism	ref_cov=66/52	total_cov=66/87
RA	33	.	NC_012971	3147260	0	C	A	bias_e_value=357085	bias_p_value=0.078326	consensus_reject=FREQUENCY_CUTOFF	consensus_score=122.3	fisher_strand_p_value=0.0150787	frequency=2.603e-01	ks_quality_p_value=1	major_base=C	major_cov=35/19	major_frequency=7.397e-01	minor_base=A	minor_cov=18/1	new_cov=18/1	polymorphism_frequency=2.603e-01	polymorphism_score=12.7	prediction=polymorphism	ref_cov=35/19	total_cov=53/20
RA	34	.	NC_012971	3485921	0	G	A	bias_e_value=0.104207	bias_p_value=2.28576e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=281.2	fisher_strand_p_value=1.05481e-09	frequency=2.071e-01	ks_quality_p_value=1	major_base=G	major_cov=64/47	major_frequency=7.929e-01	minor_base=A	minor_cov=0/29	new_cov=0/29	polymorphism_frequency=2.071e-01	polymorphism_score=14.7	prediction=polymorphism	ref_cov=64/47	total_cov=64/81
RA	35	.	NC_012971	3561696	0	A	G	bias_e_value=670437	bias_p_value=0.14706	consensus_reject=FREQUENCY_CUTOFF	consensus_score=118.3	fisher_strand_p_value=0.0334371	frequency=2.817e-01	ks_quality_p_value=1	major_base=A	major_cov=35/16	major_frequency=7.183e-01	minor_base=G	minor_cov=8/12	new_cov=8/12	polymorphism_frequency=2.817e-01	polymorphism_score=36.9	prediction=polymorphism	ref_cov=35/16	total_cov=43/28
RA	36	.	NC_012971	3706612	0	G	T	bias_e_value=0.0674523	bias_p_value=1.47956e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=251.3	fisher_strand_p_value=6.68706e-10	frequency=2.703e-01	ks_quality_p_value=1	major_base=G	major_cov=53/55	major_frequency=7.297e-01	minor_base=T	minor_cov=0/40	new_cov=0/40	polymorphism_frequency=2.703e-01	polymorphism_score=13.5	prediction=polymorphism	ref_cov=53/55	total_cov=53/95
RA	37	.	NC_012971	3764190	0	G	A	bias_e_value=0.00396181	bias_p_value=8.69017e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=285.7	fisher_strand_p_value=3.46416e-11	frequency=2.086e-01	ks_quality_p_value=1	major_base=G	major_cov=70/40	major_frequency=7.914e-01	minor_base=A	minor_cov=0/29	new_cov=0/29	polymorphism_frequency=2.086e-01	polymorphism_score=22.9	prediction=polymorphism	ref_cov=70/40	total_cov=70/70
RA	38	.	NC_012971	3800334	0	C	A	bias_e_value=1.30189e-07	bias_p_value=2.85567e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=314.5	fisher_strand_p_value=7.98479e-16	frequency=2.798e-01	ks_quality_p_value=1	major_base=C	major_cov=46/75	major_frequency=7.202e-01	minor_base=A	minor_cov=47/0	new_cov=47/0	polymorphism_frequency=2.798e-01	polymorphism_score=12.4	prediction=polymorphism	ref_cov=46/75	total_cov=93/75
RA	39	.	NC_012971	4045014	0	A	C	bias_e_value=1760.74	bias_p_value=0.000386216	consensus_reject=FREQUENCY_CUTOFF	consensus_score=192.2	fisher_strand_p_value=3.42319e-05	frequency=2.174e-01	ks_quality_p_value=1	major_base=A	major_cov=38/34	major_frequency=7.826e-01	minor_base=C	minor_cov=20/0	new_cov=20/0	polymorphism_frequency=2.174e-01	polymorphism_score=11.7	prediction=polymorphism	ref_cov=38/34	total_cov=59/35
RA	40	.	NC_012971	4268051	0	C	A	bias_e_value=5.74991e-12	bias_p_value=1.26124e-18	consensus_reject=FREQUENCY_CUTOFF	consensus_score=332.7	fisher_strand_p_value=2.73919e-20	frequency=2.857e-01	ks_quality_p_value=1	major_base=C	major_cov=30/85	major_frequency=7.143e-01	minor_base=A	minor_cov=46/0	new_cov=46/0	polymorphism_frequency=2.857e-01	polymorphism_score=17.9	prediction=polymorphism	ref_cov=30/85	total_cov=76/85
RA	41	.	NC_012971	4283488	0	C	A	bias_e_value=1883.49	bias_p_value=0.000413141	consensus_reject=FREQUENCY_CUTOFF	consensus_score=195.3	fisher_strand_p_value=3.686e-05	frequency=2.791e-01	ks_quality_p_value=1	major_base=C	major_cov=54/39	major_frequency=7.209e-01	minor_base=A	minor_cov=34/2	new_cov=34/2	polymorphism_frequency=2.791e-01	polymorphism_score=14.4	prediction=polymorphism	ref_cov=54/39	total_cov=88/41
RA	42	.	NC_012971	4448933	0	C	A	bias_e_value=1.28918e-05	bias_p_value=2.82781e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=347.5	fisher_strand_p_value=9.1142e-14	frequency=2.556e-01	ks_quality_p_value=1	major_base=C	major_cov=59/75	major_frequency=7.444e-01	minor_base=A	minor_cov=46/0	new_cov=46/0	polymorphism_frequency=2.556e-01	polymorphism_score=12.5	prediction=polymorphism	ref_cov=59/75	total_cov=105/75
MC	43	.	NC_012971	769173	776151	0	0	left_inside_cov=0	left_outside_cov=96	right_inside_cov=1	right_outside_cov=96
JC	44	.	NC_012971	1	1	NC_012971	4558953	-1	0	alignment_overlap=0	coverage_minus=75	coverage_plus=62	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=293	max_min_left=149	max_min_left_minus=149	max_min_left_plus=148	max_min_right=148	max_min_right_minus=139	max_min_right_plus=148	max_pos_hash_score=590	max_right=296	max_right_minus=287	max_right_plus=296	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.46	new_junction_read_count=140	polymorphism_frequency=1.000e+00	pos_hash_score=66	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=137
JC	45	.	NC_012971	582976	-1	NC_012971	583310	1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=4.081e-02	junction_possible_overlap_registers=283	key=NC_012971__582976__-1__NC_012971__583299__1__11____300__300__0__0	max_left=284	max_left_minus=284	max_left_plus=204	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=62	max_min_right_minus=62	max_min_right_plus=62	max_pos_hash_score=568	max_right=62	max_right_minus=62	max_right_plus=62	neg_log10_pos_hash_p_value=9.1	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=4.081e-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=11	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=0.69	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=64	side_2_redundant=0	total_non_overlap_reads=3
JC	46	.	NC_012971	656311	-1	NC_012971	656425	1	0	alignment_overlap=3	coverage_minus=3	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=4.348e-02	junction_possible_overlap_registers=291	key=NC_012971__656311__-1__NC_012971__656422__1__3____300__300__0__0	max_left=208	max_left_minus=208	max_left_plus=116	max_min_left=130	max_min_left_minus=130	max_min_left_plus=116	max_min_right=88	max_min_right_minus=88	max_min_right_plus=0	max_pos_hash_score=584	max_right=276	max_right_minus=276	max_right_plus=181	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.348e-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=1.02	side_1_overlap=3	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=0.83	side_2_overlap=0	side_2_possible_overlap_registers=291	side_2_read_count=79	side_2_redundant=0	total_non_overlap_reads=4
JC	47	.	NC_012971	656340	-1	NC_012971	656667	1	0	alignment_overlap=10	coverage_minus=3	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=8.917e-02	junction_possible_overlap_registers=284	key=NC_012971__656340__-1__NC_012971__656657__1__10____300__300__0__0	max_left=195	max_left_minus=195	max_left_plus=141	max_min_left=141	max_min_left_minus=81	max_min_left_plus=141	max_min_right=95	max_min_right_minus=95	max_min_right_plus=0	max_pos_hash_score=570	max_right=219	max_right_minus=95	max_right_plus=219	neg_log10_pos_hash_p_value=7.5	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=8.917e-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=0.92	side_1_overlap=10	side_1_possible_overlap_registers=294	side_1_read_count=88	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.63	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=58	side_2_redundant=0	total_non_overlap_reads=6
JC	48	.	NC_012971	739215	1	NC_012971	739503	-1	0	alignment_overlap=76	coverage_minus=0	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=8.234e-02	junction_possible_overlap_registers=218	key=NC_012971__739215__1__NC_012971__739579__-1__76____300__300__0__0	max_left=3	max_left_minus=0	max_left_plus=3	max_min_left=3	max_min_left_minus=0	max_min_left_plus=3	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=438	max_right=193	max_right_minus=0	max_right_plus=193	neg_log10_pos_hash_p_value=7.1	new_junction_coverage=0.07	new_junction_read_count=5	polymorphism_frequency=8.234e-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=76	side_1_possible_overlap_registers=294	side_1_read_count=95	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.58	side_2_overlap=0	side_2_possible_overlap_registers=218	side_2_read_count=41	side_2_redundant=0	total_non_overlap_reads=5
JC	49	.	NC_012971	739290	-1	NC_012971	739580	1	0	alignment_overlap=76	coverage_minus=5	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=1.843e-01	junction_possible_overlap_registers=218	key=NC_012971__739290__-1__NC_012971__739504__1__76____300__300__0__0	max_left=212	max_left_minus=197	max_left_plus=212	max_min_left=103	max_min_left_minus=0	max_min_left_plus=103	max_min_right=86	max_min_right_minus=86	max_min_right_plus=69	max_pos_hash_score=438	max_right=121	max_right_minus=86	max_right_plus=121	neg_log10_pos_hash_p_value=4.9	new_junction_coverage=0.17	new_junction_read_count=12	polymorphism_frequency=1.843e-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=0.92	side_1_overlap=76	side_1_possible_overlap_registers=294	side_1_read_count=88	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.58	side_2_overlap=0	side_2_possible_overlap_registers=218	side_2_read_count=41	side_2_redundant=0	total_non_overlap_reads=11
JC	50	.	NC_012971	739579	-1	NC_012971	740008	1	0	alignment_overlap=76	coverage_minus=12	coverage_plus=8	flanking_left=300	flanking_right=300	frequency=2.886e-01	junction_possible_overlap_registers=218	key=NC_012971__739579__-1__NC_012971__739932__1__76____300__300__0__0	max_left=193	max_left_minus=193	max_left_plus=121	max_min_left=88	max_min_left_minus=88	max_min_left_plus=88	max_min_right=71	max_min_right_minus=71	max_min_right_plus=71	max_pos_hash_score=438	max_right=107	max_right_minus=107	max_right_plus=107	neg_log10_pos_hash_p_value=3.4	new_junction_coverage=0.29	new_junction_read_count=21	polymorphism_frequency=2.886e-01	pos_hash_score=14	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.58	side_1_overlap=76	side_1_possible_overlap_registers=294	side_1_read_count=56	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.87	side_2_overlap=0	side_2_possible_overlap_registers=218	side_2_read_count=62	side_2_redundant=0	total_non_overlap_reads=20
JC	51	.	NC_012971	739785	-1	NC_012971	740008	1	0	alignment_overlap=76	coverage_minus=8	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.909e-01	junction_possible_overlap_registers=218	key=NC_012971__739785__-1__NC_012971__739932__1__76____300__300__0__0	max_left=212	max_left_minus=175	max_left_plus=212	max_min_left=96	max_min_left_minus=96	max_min_left_plus=68	max_min_right=90	max_min_right_minus=71	max_min_right_plus=90	max_pos_hash_score=438	max_right=154	max_right_minus=125	max_right_plus=154	neg_log10_pos_hash_p_value=3.7	new_junction_coverage=0.18	new_junction_read_count=13	polymorphism_frequency=1.909e-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=0.68	side_1_overlap=76	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=0.87	side_2_overlap=0	side_2_possible_overlap_registers=218	side_2_read_count=62	side_2_redundant=0	total_non_overlap_reads=13
JC	52	.	NC_012971	740009	-1	NC_012971	740218	1	0	alignment_overlap=78	coverage_minus=4	coverage_plus=8	flanking_left=300	flanking_right=300	frequency=1.430e-01	junction_possible_overlap_registers=216	key=NC_012971__740009__-1__NC_012971__740140__1__78____300__300__0__0	max_left=113	max_left_minus=113	max_left_plus=71	max_min_left=90	max_min_left_minus=90	max_min_left_plus=71	max_min_right=107	max_min_right_minus=107	max_min_right_plus=0	max_pos_hash_score=434	max_right=190	max_right_minus=155	max_right_plus=190	neg_log10_pos_hash_p_value=4.5	new_junction_coverage=0.17	new_junction_read_count=12	polymorphism_frequency=1.430e-01	pos_hash_score=10	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=78	side_1_possible_overlap_registers=294	side_1_read_count=95	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.05	side_2_overlap=0	side_2_possible_overlap_registers=216	side_2_read_count=74	side_2_redundant=0	total_non_overlap_reads=12
JC	53	.	NC_012971	769172	-1	NC_012971	776152	1	0	alignment_overlap=3	coverage_minus=40	coverage_plus=53	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=291	key=NC_012971__769172__-1__NC_012971__776149__1__3____300__300__0__0	max_left=293	max_left_minus=293	max_left_plus=281	max_min_left=147	max_min_left_minus=110	max_min_left_plus=147	max_min_right=146	max_min_right_minus=126	max_min_right_plus=146	max_pos_hash_score=584	max_right=290	max_right_minus=280	max_right_plus=290	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.00	new_junction_read_count=95	polymorphism_frequency=1.000e+00	pos_hash_score=64	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=3	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=291	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=93
JC	54	.	NC_012971	1099967	1	NC_012971	1426589	1	0	alignment_overlap=0	coverage_minus=4	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.429e-01	junction_possible_overlap_registers=294	key=NC_012971__1099967__1__NC_012971__1426589__1__0____300__300__0__1	max_left=274	max_left_minus=254	max_left_plus=274	max_min_left=110	max_min_left_minus=110	max_min_left_plus=0	max_min_right=135	max_min_right_minus=91	max_min_right_plus=135	max_pos_hash_score=590	max_right=190	max_right_minus=190	max_right_plus=135	neg_log10_pos_hash_p_value=6.8	new_junction_coverage=0.08	new_junction_read_count=8	polymorphism_frequency=1.429e-01	pos_hash_score=8	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.50	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=48	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=8
JC	55	.	NC_012971	1099967	1	NC_012971	2827816	1	0	alignment_overlap=1	coverage_minus=4	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=7.698e-02	junction_possible_overlap_registers=293	key=NC_012971__1099967__1__NC_012971__2827815__1__1____300__300__0__0	max_left=273	max_left_minus=253	max_left_plus=273	max_min_left=109	max_min_left_minus=109	max_min_left_plus=0	max_min_right=135	max_min_right_minus=91	max_min_right_plus=135	max_pos_hash_score=588	max_right=190	max_right_minus=190	max_right_plus=135	neg_log10_pos_hash_p_value=6.8	new_junction_coverage=0.08	new_junction_read_count=8	polymorphism_frequency=7.698e-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=0.50	side_1_overlap=1	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=1.50	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	56	.	NC_012971	1099967	1	NC_012971	4432707	1	0	alignment_overlap=0	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.000e-02	junction_possible_overlap_registers=294	key=NC_012971__1099967__1__NC_012971__4432707__1__0____300__300__0__0	max_left=274	max_left_minus=254	max_left_plus=274	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=55	max_min_right_minus=55	max_min_right_plus=44	max_pos_hash_score=590	max_right=55	max_right_minus=55	max_right_plus=44	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.000e-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=0.52	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=50	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.48	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=142	side_2_redundant=0	total_non_overlap_reads=4
JC	57	.	NC_012971	1168700	-1	NC_012971	1169196	1	0	alignment_overlap=15	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.080e-02	junction_possible_overlap_registers=279	key=NC_012971__1168700__-1__NC_012971__1169181__1__15____300__300__0__0	max_left=75	max_left_minus=75	max_left_plus=75	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=58	max_min_right_minus=58	max_min_right_plus=27	max_pos_hash_score=560	max_right=58	max_right_minus=58	max_right_plus=27	neg_log10_pos_hash_p_value=9.0	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=5.080e-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=15	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=1.00	side_2_overlap=0	side_2_possible_overlap_registers=279	side_2_read_count=91	side_2_redundant=0	total_non_overlap_reads=5
JC	58	.	NC_012971	1275121	-1	NC_012971	1275416	1	0	alignment_overlap=87	coverage_minus=4	coverage_plus=8	flanking_left=300	flanking_right=300	frequency=2.553e-01	junction_possible_overlap_registers=207	key=NC_012971__1275121__-1__NC_012971__1275329__1__87____300__300__0__0	max_left=201	max_left_minus=201	max_left_plus=175	max_min_left=73	max_min_left_minus=59	max_min_left_plus=73	max_min_right=86	max_min_right_minus=54	max_min_right_plus=86	max_pos_hash_score=416	max_right=209	max_right_minus=135	max_right_plus=209	neg_log10_pos_hash_p_value=4.0	new_junction_coverage=0.18	new_junction_read_count=12	polymorphism_frequency=2.553e-01	pos_hash_score=11	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.56	side_1_overlap=87	side_1_possible_overlap_registers=294	side_1_read_count=54	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.47	side_2_overlap=0	side_2_possible_overlap_registers=207	side_2_read_count=32	side_2_redundant=0	total_non_overlap_reads=12
JC	59	.	NC_012971	1344734	-1	NC_012971	1344858	1	0	alignment_overlap=10	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.896e-02	junction_possible_overlap_registers=284	key=NC_012971__1344734__-1__NC_012971__1344848__1__10____300__300__0__0	max_left=197	max_left_minus=197	max_left_plus=67	max_min_left=67	max_min_left_minus=33	max_min_left_plus=67	max_min_right=93	max_min_right_minus=93	max_min_right_plus=0	max_pos_hash_score=570	max_right=255	max_right_minus=255	max_right_plus=223	neg_log10_pos_hash_p_value=8.5	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=5.896e-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=0.73	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=0.99	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=92	side_2_redundant=0	total_non_overlap_reads=5
JC	60	.	NC_012971	2519344	-1	NC_012971	2519671	1	0	alignment_overlap=25	coverage_minus=10	coverage_plus=10	flanking_left=300	flanking_right=300	frequency=1.614e-01	junction_possible_overlap_registers=269	key=NC_012971__2519344__-1__NC_012971__2519646__1__25____300__300__0__0	max_left=171	max_left_minus=171	max_left_plus=171	max_min_left=100	max_min_left_minus=100	max_min_left_plus=61	max_min_right=65	max_min_right_minus=65	max_min_right_plus=65	max_pos_hash_score=540	max_right=270	max_right_minus=212	max_right_plus=270	neg_log10_pos_hash_p_value=3.7	new_junction_coverage=0.23	new_junction_read_count=20	polymorphism_frequency=1.614e-01	pos_hash_score=17	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.11	side_1_overlap=25	side_1_possible_overlap_registers=294	side_1_read_count=107	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.25	side_2_overlap=0	side_2_possible_overlap_registers=269	side_2_read_count=110	side_2_redundant=0	total_non_overlap_reads=20
JC	61	.	NC_012971	2657908	-1	NC_012971	2658458	1	0	alignment_overlap=20	coverage_minus=1	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=9.711e-02	junction_possible_overlap_registers=274	key=NC_012971__2657908__-1__NC_012971__2658438__1__20____300__300__0__0	max_left=239	max_left_minus=23	max_left_plus=239	max_min_left=23	max_min_left_minus=23	max_min_left_plus=23	max_min_right=44	max_min_right_minus=0	max_min_right_plus=44	max_pos_hash_score=550	max_right=138	max_right_minus=138	max_right_plus=138	neg_log10_pos_hash_p_value=7.8	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=9.711e-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=0.74	side_1_overlap=20	side_1_possible_overlap_registers=294	side_1_read_count=71	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=274	side_2_read_count=64	side_2_redundant=0	total_non_overlap_reads=5
JC	62	.	NC_012971	2658241	-1	NC_012971	2658517	1	0	alignment_overlap=79	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.437e-01	junction_possible_overlap_registers=215	key=NC_012971__2658241__-1__NC_012971__2658438__1__79____300__300__0__0	max_left=111	max_left_minus=94	max_left_plus=111	max_min_left=94	max_min_left_minus=94	max_min_left_plus=94	max_min_right=97	max_min_right_minus=0	max_min_right_plus=97	max_pos_hash_score=432	max_right=165	max_right_minus=142	max_right_plus=165	neg_log10_pos_hash_p_value=5.5	new_junction_coverage=0.10	new_junction_read_count=7	polymorphism_frequency=1.437e-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=0.45	side_1_overlap=79	side_1_possible_overlap_registers=294	side_1_read_count=43	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=215	side_2_read_count=52	side_2_redundant=0	total_non_overlap_reads=7
JC	63	.	NC_012971	3192461	-1	NC_012971	3192811	1	0	alignment_overlap=10	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.717e-02	junction_possible_overlap_registers=284	key=NC_012971__3192461__-1__NC_012971__3192801__1__10____300__300__0__0	max_left=151	max_left_minus=151	max_left_plus=151	max_min_left=54	max_min_left_minus=54	max_min_left_plus=54	max_min_right=17	max_min_right_minus=17	max_min_right_plus=17	max_pos_hash_score=570	max_right=185	max_right_minus=185	max_right_plus=185	neg_log10_pos_hash_p_value=8.5	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.717e-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=1.16	side_1_overlap=10	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=1.08	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=100	side_2_redundant=0	total_non_overlap_reads=4
JC	64	.	NC_012971	3253254	-1	NC_012971	3253529	1	0	alignment_overlap=29	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=6.825e-02	junction_possible_overlap_registers=265	key=NC_012971__3253254__-1__NC_012971__3253500__1__29____300__300__0__0	max_left=210	max_left_minus=210	max_left_plus=132	max_min_left=132	max_min_left_minus=0	max_min_left_plus=132	max_min_right=127	max_min_right_minus=127	max_min_right_plus=0	max_pos_hash_score=532	max_right=146	max_right_minus=127	max_right_plus=146	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.06	new_junction_read_count=5	polymorphism_frequency=6.825e-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=0.90	side_1_overlap=29	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=0.68	side_2_overlap=0	side_2_possible_overlap_registers=265	side_2_read_count=59	side_2_redundant=0	total_non_overlap_reads=4
JC	65	.	NC_012971	3264671	-1	NC_012971	3265083	1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.031e-02	junction_possible_overlap_registers=285	key=NC_012971__3264671__-1__NC_012971__3265074__1__9____300__300__0__0	max_left=287	max_left_minus=287	max_left_plus=27	max_min_left=27	max_min_left_minus=27	max_min_left_plus=27	max_min_right=1	max_min_right_minus=1	max_min_right_plus=0	max_pos_hash_score=572	max_right=42	max_right_minus=42	max_right_plus=42	neg_log10_pos_hash_p_value=9.2	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.031e-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=9	side_1_possible_overlap_registers=294	side_1_read_count=100	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=285	side_2_read_count=95	side_2_redundant=0	total_non_overlap_reads=3
JC	66	.	NC_012971	3638677	-1	NC_012971	3638872	1	0	alignment_overlap=12	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.794e-02	junction_possible_overlap_registers=282	key=NC_012971__3638677__-1__NC_012971__3638860__1__12____300__300__0__0	max_left=118	max_left_minus=118	max_left_plus=76	max_min_left=118	max_min_left_minus=118	max_min_left_plus=76	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=566	max_right=212	max_right_minus=207	max_right_plus=212	neg_log10_pos_hash_p_value=9.1	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.794e-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=12	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=1.15	side_2_overlap=0	side_2_possible_overlap_registers=282	side_2_read_count=106	side_2_redundant=0	total_non_overlap_reads=4
JC	67	.	NC_012971	3643247	-1	NC_012971	3643269	1	0	alignment_overlap=4	coverage_minus=4	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=8.463e-02	junction_possible_overlap_registers=290	key=NC_012971__3643247__-1__NC_012971__3643265__1__4____300__300__0__0	max_left=255	max_left_minus=255	max_left_plus=226	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=126	max_min_right_minus=126	max_min_right_plus=82	max_pos_hash_score=582	max_right=126	max_right_minus=126	max_right_plus=82	neg_log10_pos_hash_p_value=7.6	new_junction_coverage=0.10	new_junction_read_count=9	polymorphism_frequency=8.463e-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=1.01	side_1_overlap=4	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=1.05	side_2_overlap=0	side_2_possible_overlap_registers=290	side_2_read_count=99	side_2_redundant=0	total_non_overlap_reads=6
JC	68	.	NC_012971	3847306	-1	NC_012971	3847538	1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=4.135e-02	junction_possible_overlap_registers=283	key=NC_012971__3847306__-1__NC_012971__3847527__1__11____300__300__0__0	max_left=172	max_left_minus=172	max_left_plus=167	max_min_left=72	max_min_left_minus=72	max_min_left_plus=0	max_min_right=120	max_min_right_minus=117	max_min_right_plus=120	max_pos_hash_score=568	max_right=216	max_right_minus=216	max_right_plus=120	neg_log10_pos_hash_p_value=9.1	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=4.135e-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=0.80	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=77	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=283	side_2_read_count=65	side_2_redundant=0	total_non_overlap_reads=3
JC	69	.	NC_012971	4507768	-1	NC_012971	4508182	1	0	alignment_overlap=11	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.040e-02	junction_possible_overlap_registers=283	key=NC_012971__4507768__-1__NC_012971__4508171__1__11____300__300__0__0	max_left=88	max_left_minus=88	max_left_plus=88	max_min_left=88	max_min_left_minus=88	max_min_left_plus=88	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=568	max_right=172	max_right_minus=172	max_right_plus=172	neg_log10_pos_hash_p_value=8.5	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.040e-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=1.10	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=106	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=283	side_2_read_count=88	side_2_redundant=0	total_non_overlap_reads=4
JC	70	.	NC_012971	4524541	-1	NC_012971	4524778	1	0	alignment_overlap=89	coverage_minus=2	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=1.209e-01	junction_possible_overlap_registers=205	key=NC_012971__4524541__-1__NC_012971__4524689__1__89____300__300__0__0	max_left=186	max_left_minus=160	max_left_plus=186	max_min_left=65	max_min_left_minus=0	max_min_left_plus=65	max_min_right=86	max_min_right_minus=51	max_min_right_plus=86	max_pos_hash_score=412	max_right=138	max_right_minus=51	max_right_plus=138	neg_log10_pos_hash_p_value=5.3	new_junction_coverage=0.12	new_junction_read_count=8	polymorphism_frequency=1.209e-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=0.92	side_1_overlap=89	side_1_possible_overlap_registers=294	side_1_read_count=88	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=205	side_2_read_count=55	side_2_redundant=0	total_non_overlap_reads=8
UN	71	.	NC_012971	15646	16463
UN	72	.	NC_012971	16465	16467
UN	73	.	NC_012971	23541	23774
UN	74	.	NC_012971	23777	23777
UN	75	.	NC_012971	227311	228253
UN	76	.	NC_012971	228256	228256
UN	77	.	NC_012971	228262	228262
UN	78	.	NC_012971	228850	228850
UN	79	.	NC_012971	228855	231571
UN	80	.	NC_012971	241547	241744
UN	81	.	NC_012971	263068	263069
UN	82	.	NC_012971	263073	263280
UN	83	.	NC_012971	336220	336838
UN	84	.	NC_012971	336841	336841
UN	85	.	NC_012971	336843	336844
UN	86	.	NC_012971	350518	350747
UN	87	.	NC_012971	373994	374223
UN	88	.	NC_012971	426749	426749
UN	89	.	NC_012971	426758	427543
UN	90	.	NC_012971	493180	493180
UN	91	.	NC_012971	493190	493193
UN	92	.	NC_012971	493197	493197
UN	93	.	NC_012971	493199	493199
UN	94	.	NC_012971	493201	493202
UN	95	.	NC_012971	493204	493205
UN	96	.	NC_012971	493207	493207
UN	97	.	NC_012971	493213	493214
UN	98	.	NC_012971	493216	493216
UN	99	.	NC_012971	493222	493222
UN	100	.	NC_012971	493224	495089
UN	101	.	NC_012971	543917	544159
UN	102	.	NC_012971	544164	544164
UN	103	.	NC_012971	566544	566544
UN	104	.	NC_012971	566561	567057
UN	105	.	NC_012971	567059	567060
UN	106	.	NC_012971	567617	567819
UN	107	.	NC_012971	568773	569570
UN	108	.	NC_012971	597153	597153
UN	109	.	NC_012971	597156	597381
UN	110	.	NC_012971	612042	612251
UN	111	.	NC_012971	642755	643641
UN	112	.	NC_012971	643643	643643
UN	113	.	NC_012971	643646	643646
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