#=GENOME_DIFF	1.0
#=CREATED	04:45:16 11 Oct 2025
#=PROGRAM	breseq 0.39.0 
#=COMMAND	breseq -j 8 -o /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_run15_rmdup_trimmng-adaptors-polyG/ME9900_S48_R1R2_RMDUP -r /ld1/E.coli_MG1655_ref/MG1655/ncbi_dataset/data/GCF_000005845.2/genomic.gbff /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME9900_S48_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/ME9900_S48_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=REFSEQ	/ld1/E.coli_MG1655_ref/MG1655/ncbi_dataset/data/GCF_000005845.2/genomic.gbff
#=READSEQ	/ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_QC/RUN15_RMDUP/results/p05_trimmed_fastq_by_cutadapt_-m30/ME9900_S48_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/ME9900_S48_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=CONVERTED-BASES	439290126
#=CONVERTED-READS	1492529
#=INPUT-BASES	439379511
#=INPUT-READS	1492834
#=MAPPED-BASES	425145994
#=MAPPED-READS	1445345
DEL	1	55,61	NC_000913	257908	776
MOB	2	78,82	NC_000913	1995620	IS5	-1	4
DEL	3	31,32	NC_000913	2173363	2
DEL	4	87	NC_000913	2535178	24
INS	5	46	NC_000913	3560455	G
INS	6	52,53	NC_000913	4296381	GC
SUB	7	58,96	NC_000913	4583270	3543	TGTAGGCTGGAGCTGCTTCGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCGAACTGCAGGTCGACGGATCCCCGGAAT
RA	8	.	NC_000913	58065	0	C	A	bias_e_value=0.0393859	bias_p_value=8.48533e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=152.6	fisher_strand_p_value=3.73677e-10	frequency=3.265e-01	ks_quality_p_value=1	major_base=C	major_cov=26/40	major_frequency=6.735e-01	minor_base=A	minor_cov=32/0	new_cov=32/0	polymorphism_frequency=3.265e-01	polymorphism_score=20.2	prediction=polymorphism	ref_cov=26/40	total_cov=58/40
RA	9	.	NC_000913	141849	0	C	A	bias_e_value=0.00247667	bias_p_value=5.33576e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=196.3	fisher_strand_p_value=2.08479e-11	frequency=3.036e-01	ks_quality_p_value=1	major_base=C	major_cov=29/49	major_frequency=6.964e-01	minor_base=A	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=3.036e-01	polymorphism_score=25.0	prediction=polymorphism	ref_cov=29/49	total_cov=63/49
RA	10	.	NC_000913	564850	0	G	T	bias_e_value=0.648191	bias_p_value=1.39647e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=186.8	fisher_strand_p_value=7.0642e-09	frequency=2.660e-01	ks_quality_p_value=1	major_base=G	major_cov=43/26	major_frequency=7.340e-01	minor_base=T	minor_cov=0/25	new_cov=0/25	polymorphism_frequency=2.660e-01	polymorphism_score=13.5	prediction=polymorphism	ref_cov=43/26	total_cov=43/51
RA	11	.	NC_000913	710830	0	G	T	bias_e_value=0.164569	bias_p_value=3.54548e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=238.3	fisher_strand_p_value=1.67165e-09	frequency=2.261e-01	ks_quality_p_value=1	major_base=G	major_cov=55/34	major_frequency=7.739e-01	minor_base=T	minor_cov=0/26	new_cov=0/26	polymorphism_frequency=2.261e-01	polymorphism_score=12.1	prediction=polymorphism	ref_cov=55/34	total_cov=55/60
RA	12	.	NC_000913	847955	0	G	A	bias_e_value=3.06434e-06	bias_p_value=6.60183e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=242.4	fisher_strand_p_value=2.02956e-14	frequency=2.590e-01	ks_quality_p_value=1	major_base=G	major_cov=70/33	major_frequency=7.410e-01	minor_base=A	minor_cov=0/36	new_cov=0/36	polymorphism_frequency=2.590e-01	polymorphism_score=37.3	prediction=polymorphism	ref_cov=70/33	total_cov=70/69
RA	13	.	NC_000913	1015488	0	C	A	bias_e_value=0.00890441	bias_p_value=1.91837e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=252.6	fisher_strand_p_value=7.90734e-11	frequency=2.615e-01	ks_quality_p_value=1	major_base=C	major_cov=40/56	major_frequency=7.385e-01	minor_base=A	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=2.615e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=40/56	total_cov=74/56
RA	14	.	NC_000913	1286831	0	T	A	bias_e_value=4049720	bias_p_value=0.872473	consensus_reject=FREQUENCY_CUTOFF	consensus_score=118.0	fisher_strand_p_value=0.58674	frequency=2.576e-01	ks_quality_p_value=0.919601	major_base=T	major_cov=22/27	major_frequency=7.424e-01	minor_base=A	minor_cov=9/8	new_cov=9/8	polymorphism_frequency=2.576e-01	polymorphism_score=52.7	prediction=polymorphism	ref_cov=22/27	total_cov=38/35
RA	15	.	NC_000913	1286870	0	C	A	bias_e_value=2778460	bias_p_value=0.598593	consensus_reject=FREQUENCY_CUTOFF	consensus_score=125.9	fisher_strand_p_value=0.25599	frequency=2.222e-01	ks_quality_p_value=0.982301	major_base=C	major_cov=24/32	major_frequency=7.778e-01	minor_base=A	minor_cov=10/6	new_cov=10/6	polymorphism_frequency=2.222e-01	polymorphism_score=13.5	prediction=polymorphism	ref_cov=24/32	total_cov=34/38
RA	16	.	NC_000913	1286874	0	G	A	bias_e_value=3489030	bias_p_value=0.751678	consensus_reject=FREQUENCY_CUTOFF	consensus_score=132.9	fisher_strand_p_value=0.384265	frequency=2.083e-01	ks_quality_p_value=0.999708	major_base=G	major_cov=25/32	major_frequency=7.917e-01	minor_base=A	minor_cov=9/6	new_cov=9/6	polymorphism_frequency=2.083e-01	polymorphism_score=23.0	prediction=polymorphism	ref_cov=25/32	total_cov=34/38
RA	17	.	NC_000913	1351463	0	C	A	bias_e_value=2038.86	bias_p_value=0.000439253	consensus_reject=FREQUENCY_CUTOFF	consensus_score=133.4	fisher_strand_p_value=3.94265e-05	frequency=2.716e-01	ks_quality_p_value=1	major_base=C	major_cov=33/26	major_frequency=7.284e-01	minor_base=A	minor_cov=22/0	new_cov=22/0	polymorphism_frequency=2.716e-01	polymorphism_score=10.3	prediction=polymorphism	ref_cov=33/26	total_cov=55/26
RA	18	.	NC_000913	1466201	0	T	C	bias_e_value=266522	bias_p_value=0.0574197	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.8	fisher_strand_p_value=0.010298	frequency=2.267e-01	ks_quality_p_value=1	major_base=T	major_cov=19/39	major_frequency=7.733e-01	minor_base=C	minor_cov=12/5	new_cov=12/5	polymorphism_frequency=2.267e-01	polymorphism_score=30.1	prediction=polymorphism	ref_cov=19/39	total_cov=31/44
RA	19	.	NC_000913	1466210	0	G	A	bias_e_value=464691	bias_p_value=0.100113	consensus_reject=FREQUENCY_CUTOFF	consensus_score=156.5	fisher_strand_p_value=0.0204802	frequency=2.133e-01	ks_quality_p_value=1	major_base=G	major_cov=20/39	major_frequency=7.867e-01	minor_base=A	minor_cov=11/5	new_cov=11/5	polymorphism_frequency=2.133e-01	polymorphism_score=32.6	prediction=polymorphism	ref_cov=20/39	total_cov=31/44
RA	20	.	NC_000913	1466393	0	C	T	bias_e_value=21231.2	bias_p_value=0.00457405	consensus_reject=FREQUENCY_CUTOFF	consensus_score=127.7	fisher_strand_p_value=0.000536164	frequency=2.188e-01	ks_quality_p_value=1	major_base=C	major_cov=30/20	major_frequency=7.812e-01	minor_base=T	minor_cov=1/13	new_cov=1/13	polymorphism_frequency=2.188e-01	polymorphism_score=14.6	prediction=polymorphism	ref_cov=30/20	total_cov=32/33
RA	21	.	NC_000913	1466432	0	A	G	bias_e_value=3552780	bias_p_value=0.765412	consensus_reject=FREQUENCY_CUTOFF	consensus_score=131.6	fisher_strand_p_value=0.398797	frequency=2.462e-01	ks_quality_p_value=1	major_base=A	major_cov=24/25	major_frequency=7.538e-01	minor_base=G	minor_cov=10/6	new_cov=10/6	polymorphism_frequency=2.462e-01	polymorphism_score=18.7	prediction=polymorphism	ref_cov=24/25	total_cov=34/31
RA	22	.	NC_000913	1466438	0	T	G	bias_e_value=4641650	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=118.7	fisher_strand_p_value=1	frequency=2.000e-01	ks_quality_p_value=1	major_base=T	major_cov=27/25	major_frequency=8.000e-01	minor_base=G	minor_cov=7/6	new_cov=7/6	polymorphism_frequency=2.000e-01	polymorphism_score=17.8	prediction=polymorphism	ref_cov=27/25	total_cov=35/31
RA	23	.	NC_000913	1502770	0	T	C	bias_e_value=0.0103957	bias_p_value=2.23965e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=164.7	fisher_strand_p_value=9.29351e-11	frequency=2.900e-01	ks_quality_p_value=1	major_base=T	major_cov=47/24	major_frequency=7.100e-01	minor_base=C	minor_cov=0/29	new_cov=0/29	polymorphism_frequency=2.900e-01	polymorphism_score=33.8	prediction=polymorphism	ref_cov=47/24	total_cov=47/53
RA	24	.	NC_000913	1502772	0	G	A	bias_e_value=0.000907874	bias_p_value=1.95593e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=151.2	fisher_strand_p_value=7.34282e-12	frequency=3.131e-01	ks_quality_p_value=1	major_base=G	major_cov=47/21	major_frequency=6.869e-01	minor_base=A	minor_cov=0/31	new_cov=0/31	polymorphism_frequency=3.131e-01	polymorphism_score=26.7	prediction=polymorphism	ref_cov=47/21	total_cov=47/53
RA	25	.	NC_000913	1708930	0	C	A	bias_e_value=613958	bias_p_value=0.132271	consensus_reject=FREQUENCY_CUTOFF	consensus_score=189.4	fisher_strand_p_value=0.0291691	frequency=2.048e-01	ks_quality_p_value=1	major_base=C	major_cov=40/26	major_frequency=7.952e-01	minor_base=A	minor_cov=5/12	new_cov=5/12	polymorphism_frequency=2.048e-01	polymorphism_score=24.6	prediction=polymorphism	ref_cov=40/26	total_cov=45/38
RA	26	.	NC_000913	1812509	0	G	T	bias_e_value=0.00302377	bias_p_value=6.51442e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=211.0	fisher_strand_p_value=2.56614e-11	frequency=2.920e-01	ks_quality_p_value=1	major_base=G	major_cov=50/30	major_frequency=7.080e-01	minor_base=T	minor_cov=0/33	new_cov=0/33	polymorphism_frequency=2.920e-01	polymorphism_score=12.0	prediction=polymorphism	ref_cov=50/30	total_cov=51/63
RA	27	.	NC_000913	1902613	0	C	A	bias_e_value=9.95658	bias_p_value=2.14505e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=200.7	fisher_strand_p_value=1.27089e-07	frequency=2.553e-01	ks_quality_p_value=1	major_base=C	major_cov=25/45	major_frequency=7.447e-01	minor_base=A	minor_cov=23/1	new_cov=23/1	polymorphism_frequency=2.553e-01	polymorphism_score=10.3	prediction=polymorphism	ref_cov=25/45	total_cov=48/46
RA	28	.	NC_000913	1955561	0	C	A	bias_e_value=27.2941	bias_p_value=5.88025e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=119.7	fisher_strand_p_value=3.72069e-07	frequency=3.200e-01	ks_quality_p_value=1	major_base=C	major_cov=22/29	major_frequency=6.800e-01	minor_base=A	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=3.200e-01	polymorphism_score=12.2	prediction=polymorphism	ref_cov=22/29	total_cov=46/29
RA	29	.	NC_000913	2047219	0	C	A	bias_e_value=1.7417e-05	bias_p_value=3.75233e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=233.1	fisher_strand_p_value=1.22091e-13	frequency=3.125e-01	ks_quality_p_value=1	major_base=C	major_cov=32/56	major_frequency=6.875e-01	minor_base=A	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=3.125e-01	polymorphism_score=20.1	prediction=polymorphism	ref_cov=32/56	total_cov=72/56
RA	30	.	NC_000913	2144907	0	G	T	bias_e_value=0.00170012	bias_p_value=3.66275e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=269.2	fisher_strand_p_value=1.40955e-11	frequency=2.422e-01	ks_quality_p_value=1	major_base=G	major_cov=62/35	major_frequency=7.578e-01	minor_base=T	minor_cov=0/31	new_cov=0/31	polymorphism_frequency=2.422e-01	polymorphism_score=12.5	prediction=polymorphism	ref_cov=62/35	total_cov=62/66
RA	31	.	NC_000913	2173363	0	C	.	bias_e_value=3598360	bias_p_value=0.775233	consensus_score=392.1	fisher_strand_p_value=0.409639	frequency=1	ks_quality_p_value=1	major_base=.	major_cov=33/49	major_frequency=9.880e-01	minor_base=C	minor_cov=1/0	new_cov=33/49	polymorphism_frequency=9.880e-01	polymorphism_score=-4.1	prediction=consensus	ref_cov=1/0	total_cov=34/49
RA	32	.	NC_000913	2173364	0	C	.	bias_e_value=3557920	bias_p_value=0.766519	consensus_score=393.0	fisher_strand_p_value=0.409639	frequency=1	ks_quality_p_value=0.976479	major_base=.	major_cov=33/49	major_frequency=9.880e-01	minor_base=C	minor_cov=1/0	new_cov=33/49	polymorphism_frequency=9.880e-01	polymorphism_score=-2.4	prediction=consensus	ref_cov=1/0	total_cov=34/49
RA	33	.	NC_000913	2427716	0	C	A	bias_e_value=23.2227	bias_p_value=5.0031e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=188.6	fisher_strand_p_value=3.13152e-07	frequency=2.500e-01	ks_quality_p_value=1	major_base=C	major_cov=32/40	major_frequency=7.500e-01	minor_base=A	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=2.500e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=32/40	total_cov=56/40
RA	34	.	NC_000913	2767443	0	C	A	bias_e_value=5.58798e-09	bias_p_value=1.20388e-15	consensus_reject=FREQUENCY_CUTOFF	consensus_score=209.9	fisher_strand_p_value=3.0855e-17	frequency=3.125e-01	ks_quality_p_value=1	major_base=C	major_cov=9/57	major_frequency=6.875e-01	minor_base=A	minor_cov=30/0	new_cov=30/0	polymorphism_frequency=3.125e-01	polymorphism_score=12.1	prediction=polymorphism	ref_cov=9/57	total_cov=40/57
RA	35	.	NC_000913	2767444	0	C	A	bias_e_value=5.85151e-06	bias_p_value=1.26065e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=217.3	fisher_strand_p_value=3.95675e-14	frequency=2.708e-01	ks_quality_p_value=1	major_base=C	major_cov=13/57	major_frequency=7.292e-01	minor_base=A	minor_cov=26/0	new_cov=26/0	polymorphism_frequency=2.708e-01	polymorphism_score=11.0	prediction=polymorphism	ref_cov=13/57	total_cov=40/57
RA	36	.	NC_000913	2767445	0	C	A	bias_e_value=1.17163e-09	bias_p_value=2.52417e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=201.1	fisher_strand_p_value=6.21415e-18	frequency=3.263e-01	ks_quality_p_value=1	major_base=C	major_cov=8/56	major_frequency=6.737e-01	minor_base=A	minor_cov=31/0	new_cov=31/0	polymorphism_frequency=3.263e-01	polymorphism_score=16.0	prediction=polymorphism	ref_cov=8/56	total_cov=40/57
RA	37	.	NC_000913	2767447	0	C	A	bias_e_value=3.47003e-05	bias_p_value=7.47585e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=248.7	fisher_strand_p_value=2.49019e-13	frequency=2.524e-01	ks_quality_p_value=1	major_base=C	major_cov=17/60	major_frequency=7.476e-01	minor_base=A	minor_cov=26/0	new_cov=26/0	polymorphism_frequency=2.524e-01	polymorphism_score=10.4	prediction=polymorphism	ref_cov=17/60	total_cov=44/60
RA	38	.	NC_000913	2767449	0	C	A	bias_e_value=0.00440177	bias_p_value=9.4832e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=243.7	fisher_strand_p_value=3.79404e-11	frequency=2.500e-01	ks_quality_p_value=1	major_base=C	major_cov=19/59	major_frequency=7.500e-01	minor_base=A	minor_cov=25/1	new_cov=25/1	polymorphism_frequency=2.500e-01	polymorphism_score=13.6	prediction=polymorphism	ref_cov=19/59	total_cov=44/60
RA	39	.	NC_000913	2821955	0	C	A	bias_e_value=923.439	bias_p_value=0.000198946	consensus_reject=FREQUENCY_CUTOFF	consensus_score=232.9	fisher_strand_p_value=1.65677e-05	frequency=2.105e-01	ks_quality_p_value=1	major_base=C	major_cov=52/38	major_frequency=7.895e-01	minor_base=A	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=2.105e-01	polymorphism_score=11.9	prediction=polymorphism	ref_cov=52/38	total_cov=76/38
RA	40	.	NC_000913	2856087	0	G	T	bias_e_value=137.979	bias_p_value=2.97262e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=129.3	fisher_strand_p_value=2.11314e-06	frequency=3.093e-01	ks_quality_p_value=1	major_base=G	major_cov=29/38	major_frequency=6.907e-01	minor_base=T	minor_cov=0/30	new_cov=0/30	polymorphism_frequency=3.093e-01	polymorphism_score=15.5	prediction=polymorphism	ref_cov=29/38	total_cov=29/68
RA	41	.	NC_000913	3054886	0	G	T	bias_e_value=0.348517	bias_p_value=7.50847e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=210.3	fisher_strand_p_value=3.6768e-09	frequency=2.330e-01	ks_quality_p_value=1	major_base=G	major_cov=28/51	major_frequency=7.670e-01	minor_base=T	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=2.330e-01	polymorphism_score=14.0	prediction=polymorphism	ref_cov=28/51	total_cov=52/51
RA	42	.	NC_000913	3054894	0	G	T	bias_e_value=88.3316	bias_p_value=1.90302e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=152.0	fisher_strand_p_value=1.3082e-06	frequency=2.308e-01	ks_quality_p_value=1	major_base=G	major_cov=21/49	major_frequency=7.692e-01	minor_base=T	minor_cov=19/2	new_cov=19/2	polymorphism_frequency=2.308e-01	polymorphism_score=10.4	prediction=polymorphism	ref_cov=21/49	total_cov=40/51
RA	43	.	NC_000913	3191376	0	G	T	bias_e_value=1.08391	bias_p_value=2.33519e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=267.1	fisher_strand_p_value=1.21458e-08	frequency=2.537e-01	ks_quality_p_value=1	major_base=G	major_cov=49/51	major_frequency=7.463e-01	minor_base=T	minor_cov=0/34	new_cov=0/34	polymorphism_frequency=2.537e-01	polymorphism_score=11.6	prediction=polymorphism	ref_cov=49/51	total_cov=49/85
RA	44	.	NC_000913	3469569	0	G	A	bias_e_value=19.9361	bias_p_value=4.29504e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=211.4	fisher_strand_p_value=2.66123e-07	frequency=2.056e-01	ks_quality_p_value=1	major_base=G	major_cov=48/37	major_frequency=7.944e-01	minor_base=A	minor_cov=0/22	new_cov=0/22	polymorphism_frequency=2.056e-01	polymorphism_score=15.6	prediction=polymorphism	ref_cov=48/37	total_cov=48/60
RA	45	.	NC_000913	3469862	0	C	A	bias_e_value=228.378	bias_p_value=4.9202e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=186.8	fisher_strand_p_value=3.63811e-06	frequency=2.655e-01	ks_quality_p_value=1	major_base=C	major_cov=49/34	major_frequency=7.345e-01	minor_base=A	minor_cov=30/0	new_cov=30/0	polymorphism_frequency=2.655e-01	polymorphism_score=12.5	prediction=polymorphism	ref_cov=49/34	total_cov=79/34
RA	46	.	NC_000913	3560455	1	.	G	bias_e_value=3912790	bias_p_value=0.842974	consensus_score=366.2	fisher_strand_p_value=0.494845	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=49/47	major_frequency=9.897e-01	minor_base=A	minor_cov=0/1	new_cov=49/47	polymorphism_frequency=9.897e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=50/48
RA	47	.	NC_000913	3741871	0	G	T	bias_e_value=0.000579902	bias_p_value=1.24934e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=211.2	fisher_strand_p_value=4.60963e-12	frequency=2.816e-01	ks_quality_p_value=1	major_base=G	major_cov=52/22	major_frequency=7.184e-01	minor_base=T	minor_cov=0/29	new_cov=0/29	polymorphism_frequency=2.816e-01	polymorphism_score=14.8	prediction=polymorphism	ref_cov=52/22	total_cov=52/51
RA	48	.	NC_000913	3791179	0	G	T	bias_e_value=0.0529128	bias_p_value=1.13996e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=201.4	fisher_strand_p_value=5.08938e-10	frequency=3.043e-01	ks_quality_p_value=1	major_base=G	major_cov=45/35	major_frequency=6.957e-01	minor_base=T	minor_cov=0/35	new_cov=0/35	polymorphism_frequency=3.043e-01	polymorphism_score=11.7	prediction=polymorphism	ref_cov=45/35	total_cov=46/70
RA	49	.	NC_000913	3911533	0	C	A	bias_e_value=8.66321e-06	bias_p_value=1.86641e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=214.8	fisher_strand_p_value=5.93347e-14	frequency=3.456e-01	ks_quality_p_value=1	major_base=C	major_cov=36/53	major_frequency=6.544e-01	minor_base=A	minor_cov=47/0	new_cov=47/0	polymorphism_frequency=3.456e-01	polymorphism_score=20.2	prediction=polymorphism	ref_cov=36/53	total_cov=83/53
RA	50	.	NC_000913	4296191	0	A	C	bias_e_value=1680440	bias_p_value=0.362035	consensus_reject=FREQUENCY_CUTOFF	consensus_score=23.7	fisher_strand_p_value=0.11422	frequency=3.448e-01	ks_quality_p_value=1	major_base=A	major_cov=5/14	major_frequency=6.552e-01	minor_base=C	minor_cov=6/4	new_cov=6/4	polymorphism_frequency=3.448e-01	polymorphism_score=14.2	prediction=polymorphism	ref_cov=5/14	total_cov=11/18
RA	51	.	NC_000913	4296268	0	T	C	bias_e_value=4641650	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=26.9	fisher_strand_p_value=1	frequency=2.609e-01	ks_quality_p_value=1	major_base=T	major_cov=8/9	major_frequency=7.391e-01	minor_base=C	minor_cov=3/3	new_cov=3/3	polymorphism_frequency=2.609e-01	polymorphism_score=10.8	prediction=polymorphism	ref_cov=8/9	total_cov=12/12
RA	52	.	NC_000913	4296380	1	.	C	bias_e_value=2870380	bias_p_value=0.618396	consensus_score=183.0	fisher_strand_p_value=0.266667	frequency=1	ks_quality_p_value=0.997904	major_base=C	major_cov=30/22	major_frequency=9.455e-01	minor_base=.	minor_cov=3/0	new_cov=30/22	polymorphism_frequency=9.455e-01	polymorphism_score=4.5	prediction=consensus	ref_cov=3/0	total_cov=33/22
RA	53	.	NC_000913	4296380	2	.	G	bias_e_value=2870380	bias_p_value=0.618396	consensus_score=184.8	fisher_strand_p_value=0.266667	frequency=1	ks_quality_p_value=0.997904	major_base=G	major_cov=30/22	major_frequency=9.455e-01	minor_base=.	minor_cov=3/0	new_cov=30/22	polymorphism_frequency=9.455e-01	polymorphism_score=2.7	prediction=consensus	ref_cov=3/0	total_cov=33/22
RA	54	.	NC_000913	4360965	0	C	A	bias_e_value=1.87215e-09	bias_p_value=4.03337e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=296.1	fisher_strand_p_value=1.00485e-17	frequency=2.925e-01	ks_quality_p_value=1	major_base=C	major_cov=30/74	major_frequency=7.075e-01	minor_base=A	minor_cov=43/0	new_cov=43/0	polymorphism_frequency=2.925e-01	polymorphism_score=17.1	prediction=polymorphism	ref_cov=30/74	total_cov=73/74
MC	55	.	NC_000913	257908	258683	766	0	left_inside_cov=0	left_outside_cov=119	right_inside_cov=1	right_outside_cov=121
MC	56	.	NC_000913	1978503	1979392	766	0	left_inside_cov=1	left_outside_cov=116	right_inside_cov=0	right_outside_cov=119
MC	57	.	NC_000913	4047917	4049788	0	0	left_inside_cov=28	left_outside_cov=30	right_inside_cov=29	right_outside_cov=31
MC	58	.	NC_000913	4583270	4586812	0	0	left_inside_cov=0	left_outside_cov=81	right_inside_cov=0	right_outside_cov=84
JC	59	.	NC_000913	1	1	NC_000913	4641652	-1	0	alignment_overlap=0	coverage_minus=73	coverage_plus=53	flanking_left=300	flanking_right=300	frequency=1	ignore=CIRCULAR_CHROMOSOME	junction_possible_overlap_registers=293	key=NC_000913__1__1__NC_000913__4641652__-1__0____300__300__0__0	max_left=294	max_left_minus=294	max_left_plus=230	max_min_left=149	max_min_left_minus=149	max_min_left_plus=148	max_min_right=145	max_min_right_minus=145	max_min_right_plus=144	max_pos_hash_score=586	max_right=289	max_right_minus=268	max_right_plus=289	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.42	new_junction_read_count=130	polymorphism_frequency=1.000e+00	pos_hash_score=76	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=293	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=293	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=126
JC	60	.	NC_000913	129668	-1	NC_000913	129861	1	0	alignment_overlap=9	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.648e-02	junction_possible_overlap_registers=284	key=NC_000913__129668__-1__NC_000913__129852__1__9____300__300__0__0	max_left=282	max_left_minus=206	max_left_plus=282	max_min_left=128	max_min_left_minus=0	max_min_left_plus=128	max_min_right=85	max_min_right_minus=85	max_min_right_plus=6	max_pos_hash_score=568	max_right=161	max_right_minus=85	max_right_plus=161	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.648e-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=0.89	side_1_overlap=9	side_1_possible_overlap_registers=293	side_1_read_count=82	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.89	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=79	side_2_redundant=0	total_non_overlap_reads=3
JC	61	.	NC_000913	257907	-1	NC_000913	258684	1	0	alignment_overlap=8	coverage_minus=52	coverage_plus=65	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=285	key=NC_000913__257907__-1__NC_000913__258676__1__8____300__300__0__0	max_left=288	max_left_minus=288	max_left_plus=282	max_min_left=143	max_min_left_minus=135	max_min_left_plus=143	max_min_right=145	max_min_right_minus=143	max_min_right_plus=145	max_pos_hash_score=570	max_right=283	max_right_minus=283	max_right_plus=267	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.33	new_junction_read_count=119	polymorphism_frequency=1.000e+00	pos_hash_score=74	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=293	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=285	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=117
JC	62	.	NC_000913	696441	-1	NC_000913	696768	1	0	alignment_overlap=12	coverage_minus=1	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=4.975e-02	junction_possible_overlap_registers=281	key=NC_000913__696441__-1__NC_000913__696756__1__12____300__300__0__0	max_left=156	max_left_minus=71	max_left_plus=156	max_min_left=71	max_min_left_minus=71	max_min_left_plus=69	max_min_right=107	max_min_right_minus=0	max_min_right_plus=107	max_pos_hash_score=562	max_right=155	max_right_minus=155	max_right_plus=155	neg_log10_pos_hash_p_value=7.9	new_junction_coverage=0.05	new_junction_read_count=4	polymorphism_frequency=4.975e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.85	side_1_overlap=12	side_1_possible_overlap_registers=293	side_1_read_count=78	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.89	side_2_overlap=0	side_2_possible_overlap_registers=281	side_2_read_count=78	side_2_redundant=0	total_non_overlap_reads=4
JC	63	.	NC_000913	781222	-1	NC_000913	781653	1	0	alignment_overlap=76	coverage_minus=5	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=1.443e-01	junction_possible_overlap_registers=217	key=NC_000913__781222__-1__NC_000913__781577__1__76____300__300__0__0	max_left=200	max_left_minus=200	max_left_plus=138	max_min_left=50	max_min_left_minus=50	max_min_left_plus=17	max_min_right=60	max_min_right_minus=58	max_min_right_plus=60	max_pos_hash_score=434	max_right=91	max_right_minus=58	max_right_plus=91	neg_log10_pos_hash_p_value=5.6	new_junction_coverage=0.12	new_junction_read_count=8	polymorphism_frequency=1.443e-01	pos_hash_score=6	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.76	side_1_overlap=76	side_1_possible_overlap_registers=293	side_1_read_count=70	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=217	side_2_read_count=43	side_2_redundant=0	total_non_overlap_reads=7
JC	64	.	NC_000913	781222	-1	NC_000913	781809	1	0	alignment_overlap=18	coverage_minus=5	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=8.605e-02	junction_possible_overlap_registers=275	key=NC_000913__781222__-1__NC_000913__781791__1__18____300__300__0__0	max_left=258	max_left_minus=258	max_left_plus=67	max_min_left=67	max_min_left_minus=67	max_min_left_plus=67	max_min_right=42	max_min_right_minus=42	max_min_right_plus=0	max_pos_hash_score=550	max_right=95	max_right_minus=95	max_right_plus=95	neg_log10_pos_hash_p_value=6.8	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=8.605e-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=0.76	side_1_overlap=18	side_1_possible_overlap_registers=293	side_1_read_count=70	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=275	side_2_read_count=83	side_2_redundant=0	total_non_overlap_reads=6
JC	65	.	NC_000913	781282	-1	NC_000913	781771	1	0	alignment_overlap=8	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=6.169e-02	junction_possible_overlap_registers=285	key=NC_000913__781282__-1__NC_000913__781763__1__8____300__300__0__0	max_left=41	max_left_minus=41	max_left_plus=41	max_min_left=41	max_min_left_minus=41	max_min_left_plus=41	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=570	max_right=136	max_right_minus=136	max_right_plus=136	neg_log10_pos_hash_p_value=8.0	new_junction_coverage=0.06	new_junction_read_count=5	polymorphism_frequency=6.169e-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=0.76	side_1_overlap=8	side_1_possible_overlap_registers=293	side_1_read_count=70	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.94	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=84	side_2_redundant=0	total_non_overlap_reads=5
JC	66	.	NC_000913	781369	1	NC_000913	2521006	-1	-2	alignment_overlap=-2	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=8.144e-02	junction_possible_overlap_registers=291	key=NC_000913__781369__1__NC_000913__2521006__-1__-2__GG__300__300__0__0	max_left=169	max_left_minus=169	max_left_plus=169	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=58	max_pos_hash_score=582	max_right=58	max_right_minus=58	max_right_plus=58	neg_log10_pos_hash_p_value=7.6	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=8.144e-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=0.61	side_1_overlap=0	side_1_possible_overlap_registers=293	side_1_read_count=56	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.12	side_2_overlap=0	side_2_possible_overlap_registers=293	side_2_read_count=103	side_2_redundant=0	total_non_overlap_reads=5	unique_read_sequence=GG
JC	67	.	NC_000913	781369	1	NC_000913	2521127	-1	-1	alignment_overlap=-1	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=7.296e-02	junction_possible_overlap_registers=292	key=NC_000913__781369__1__NC_000913__2521127__-1__-1__G__300__300__0__0	max_left=169	max_left_minus=169	max_left_plus=169	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=59	max_min_right_minus=59	max_min_right_plus=59	max_pos_hash_score=584	max_right=59	max_right_minus=59	max_right_plus=59	neg_log10_pos_hash_p_value=7.6	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=7.296e-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=0.61	side_1_overlap=0	side_1_possible_overlap_registers=293	side_1_read_count=56	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.06	side_2_overlap=0	side_2_possible_overlap_registers=293	side_2_read_count=97	side_2_redundant=0	total_non_overlap_reads=5	unique_read_sequence=G
JC	68	.	NC_000913	1053263	-1	NC_000913	1053282	1	0	alignment_overlap=2	coverage_minus=1	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=5.016e-02	junction_possible_overlap_registers=291	key=NC_000913__1053263__-1__NC_000913__1053280__1__2____300__300__0__0	max_left=291	max_left_minus=291	max_left_plus=225	max_min_left=87	max_min_left_minus=0	max_min_left_plus=87	max_min_right=138	max_min_right_minus=7	max_min_right_plus=138	max_pos_hash_score=582	max_right=210	max_right_minus=7	max_right_plus=210	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=5.016e-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=0.84	side_1_overlap=2	side_1_possible_overlap_registers=293	side_1_read_count=77	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=291	side_2_read_count=75	side_2_redundant=0	total_non_overlap_reads=4
JC	69	.	NC_000913	1166125	-1	NC_000913	1166621	1	0	alignment_overlap=15	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=8.224e-02	junction_possible_overlap_registers=278	key=NC_000913__1166125__-1__NC_000913__1166606__1__15____300__300__0__0	max_left=151	max_left_minus=151	max_left_plus=109	max_min_left=34	max_min_left_minus=34	max_min_left_plus=8	max_min_right=74	max_min_right_minus=74	max_min_right_plus=74	max_pos_hash_score=556	max_right=187	max_right_minus=94	max_right_plus=187	neg_log10_pos_hash_p_value=6.4	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=8.224e-02	pos_hash_score=7	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.01	side_1_overlap=15	side_1_possible_overlap_registers=293	side_1_read_count=93	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.78	side_2_overlap=0	side_2_possible_overlap_registers=278	side_2_read_count=68	side_2_redundant=0	total_non_overlap_reads=7
JC	70	.	NC_000913	1207790	1	NC_000913	1209619	1	0	alignment_overlap=16	coverage_minus=32	coverage_plus=30	flanking_left=300	flanking_right=300	frequency=6.685e-01	junction_possible_overlap_registers=277	key=NC_000913__1207790__1__NC_000913__1209603__1__16____300__300__0__0	max_left=279	max_left_minus=279	max_left_plus=236	max_min_left=139	max_min_left_minus=133	max_min_left_plus=139	max_min_right=135	max_min_right_minus=135	max_min_right_plus=135	max_pos_hash_score=554	max_right=282	max_right_minus=250	max_right_plus=282	neg_log10_pos_hash_p_value=0.7	new_junction_coverage=0.75	new_junction_read_count=65	polymorphism_frequency=6.685e-01	pos_hash_score=43	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.30	side_1_overlap=16	side_1_possible_overlap_registers=293	side_1_read_count=28	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.44	side_2_overlap=0	side_2_possible_overlap_registers=277	side_2_read_count=38	side_2_redundant=0	total_non_overlap_reads=62
JC	71	.	NC_000913	1207798	-1	NC_000913	1209608	-1	-1	alignment_overlap=-1	coverage_minus=0	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=9.668e-02	junction_possible_overlap_registers=292	key=NC_000913__1207798__-1__NC_000913__1209608__-1__-1__T__300__300__0__0	max_left=251	max_left_minus=0	max_left_plus=251	max_min_left=130	max_min_left_minus=0	max_min_left_plus=130	max_min_right=140	max_min_right_minus=0	max_min_right_plus=140	max_pos_hash_score=584	max_right=241	max_right_minus=0	max_right_plus=241	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=9.668e-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=0.30	side_1_overlap=0	side_1_possible_overlap_registers=293	side_1_read_count=28	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.51	side_2_overlap=0	side_2_possible_overlap_registers=293	side_2_read_count=47	side_2_redundant=0	total_non_overlap_reads=4	unique_read_sequence=T
JC	72	.	NC_000913	1207798	1	NC_000913	1209612	1	-1	alignment_overlap=-1	coverage_minus=3	coverage_plus=0	flanking_left=300	flanking_right=300	frequency=7.619e-02	junction_possible_overlap_registers=292	key=NC_000913__1207798__1__NC_000913__1209612__1__-1__A__300__300__0__0	max_left=260	max_left_minus=260	max_left_plus=0	max_min_left=85	max_min_left_minus=85	max_min_left_plus=0	max_min_right=131	max_min_right_minus=131	max_min_right_plus=0	max_pos_hash_score=584	max_right=208	max_right_minus=208	max_right_plus=0	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=7.619e-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=0.29	side_1_overlap=0	side_1_possible_overlap_registers=293	side_1_read_count=27	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.50	side_2_overlap=0	side_2_possible_overlap_registers=293	side_2_read_count=46	side_2_redundant=0	total_non_overlap_reads=3	unique_read_sequence=A
JC	73	.	NC_000913	1207805	-1	NC_000913	1209602	-1	0	alignment_overlap=16	coverage_minus=24	coverage_plus=20	flanking_left=300	flanking_right=300	frequency=5.701e-01	junction_possible_overlap_registers=277	key=NC_000913__1207805__-1__NC_000913__1209618__-1__16____300__300__0__0	max_left=275	max_left_minus=275	max_left_plus=272	max_min_left=141	max_min_left_minus=141	max_min_left_plus=121	max_min_right=121	max_min_right_minus=121	max_min_right_plus=117	max_pos_hash_score=554	max_right=274	max_right_minus=262	max_right_plus=274	neg_log10_pos_hash_p_value=1.5	new_junction_coverage=0.51	new_junction_read_count=44	polymorphism_frequency=5.701e-01	pos_hash_score=31	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.33	side_1_overlap=16	side_1_possible_overlap_registers=293	side_1_read_count=30	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.44	side_2_overlap=0	side_2_possible_overlap_registers=277	side_2_read_count=38	side_2_redundant=0	total_non_overlap_reads=44
JC	74	.	NC_000913	1252386	-1	NC_000913	1252402	1	0	alignment_overlap=8	coverage_minus=3	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=4.631e-02	junction_possible_overlap_registers=285	key=NC_000913__1252386__-1__NC_000913__1252394__1__8____300__300__0__0	max_left=193	max_left_minus=193	max_left_plus=186	max_min_left=1	max_min_left_minus=1	max_min_left_plus=0	max_min_right=133	max_min_right_minus=133	max_min_right_plus=105	max_pos_hash_score=570	max_right=291	max_right_minus=291	max_right_plus=105	neg_log10_pos_hash_p_value=8.0	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.631e-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=8	side_1_possible_overlap_registers=293	side_1_read_count=83	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.94	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=84	side_2_redundant=0	total_non_overlap_reads=4
JC	75	.	NC_000913	1286906	-1	NC_000913	1287557	1	0	alignment_overlap=20	coverage_minus=2	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.276e-01	junction_possible_overlap_registers=273	key=NC_000913__1286906__-1__NC_000913__1287537__1__20____300__300__0__0	max_left=275	max_left_minus=180	max_left_plus=275	max_min_left=129	max_min_left_minus=0	max_min_left_plus=129	max_min_right=34	max_min_right_minus=34	max_min_right_plus=34	max_pos_hash_score=546	max_right=276	max_right_minus=34	max_right_plus=276	neg_log10_pos_hash_p_value=6.3	new_junction_coverage=0.09	new_junction_read_count=8	polymorphism_frequency=1.276e-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=0.73	side_1_overlap=20	side_1_possible_overlap_registers=293	side_1_read_count=67	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.55	side_2_overlap=0	side_2_possible_overlap_registers=273	side_2_read_count=47	side_2_redundant=0	total_non_overlap_reads=7
JC	76	.	NC_000913	1287084	-1	NC_000913	1287557	1	0	alignment_overlap=20	coverage_minus=1	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.207e-01	junction_possible_overlap_registers=273	key=NC_000913__1287084__-1__NC_000913__1287537__1__20____300__300__0__0	max_left=163	max_left_minus=163	max_left_plus=129	max_min_left=129	max_min_left_minus=0	max_min_left_plus=129	max_min_right=117	max_min_right_minus=117	max_min_right_plus=0	max_pos_hash_score=546	max_right=276	max_right_minus=117	max_right_plus=276	neg_log10_pos_hash_p_value=7.8	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=1.207e-01	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.64	side_1_overlap=20	side_1_possible_overlap_registers=293	side_1_read_count=59	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.55	side_2_overlap=0	side_2_possible_overlap_registers=273	side_2_read_count=47	side_2_redundant=0	total_non_overlap_reads=5
JC	77	.	NC_000913	1299498	-1	NC_000913	1300698	1	0	alignment_overlap=4	coverage_minus=77	coverage_plus=59	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=289	key=NC_000913__1299498__-1__NC_000913__1300694__1__4____300__300__0__0	max_left=285	max_left_minus=285	max_left_plus=264	max_min_left=139	max_min_left_minus=139	max_min_left_plus=139	max_min_right=144	max_min_right_minus=144	max_min_right_plus=142	max_pos_hash_score=578	max_right=295	max_right_minus=281	max_right_plus=295	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.56	new_junction_read_count=141	polymorphism_frequency=1.000e+00	pos_hash_score=80	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=293	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=289	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=136
JC	78	.	NC_000913	1397238	-1	NC_000913	1995623	-1	0	alignment_overlap=0	coverage_minus=63	coverage_plus=52	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=293	key=NC_000913__1397238__-1__NC_000913__1995623__-1__0____300__300__1__0	max_left=294	max_left_minus=283	max_left_plus=294	max_min_left=139	max_min_left_minus=139	max_min_left_plus=129	max_min_right=143	max_min_right_minus=136	max_min_right_plus=143	max_pos_hash_score=586	max_right=298	max_right_minus=298	max_right_plus=291	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.29	new_junction_read_count=118	polymorphism_frequency=1.000e+00	pos_hash_score=67	prediction=consensus	read_count_offset=4	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=0	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=289	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=115
JC	79	.	NC_000913	1918928	-1	NC_000913	1919349	1	0	alignment_overlap=13	coverage_minus=2	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=7.816e-02	junction_possible_overlap_registers=280	key=NC_000913__1918928__-1__NC_000913__1919336__1__13____300__300__0__0	max_left=139	max_left_minus=139	max_left_plus=135	max_min_left=15	max_min_left_minus=0	max_min_left_plus=15	max_min_right=36	max_min_right_minus=36	max_min_right_plus=36	max_pos_hash_score=560	max_right=77	max_right_minus=36	max_right_plus=77	neg_log10_pos_hash_p_value=7.4	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=7.816e-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=0.85	side_1_overlap=13	side_1_possible_overlap_registers=293	side_1_read_count=78	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.76	side_2_overlap=0	side_2_possible_overlap_registers=280	side_2_read_count=67	side_2_redundant=0	total_non_overlap_reads=5
JC	80	.	NC_000913	1978502	-1	NC_000913	2070273	-1	-117	alignment_overlap=-117	coverage_minus=33	coverage_plus=37	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=176	key=NC_000913__1978502__-1__NC_000913__2070273__-1__-117__TATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATA__300__300__0__1	max_left=180	max_left_minus=180	max_left_plus=178	max_min_left=81	max_min_left_minus=81	max_min_left_plus=77	max_min_right=82	max_min_right_minus=82	max_min_right_plus=76	max_pos_hash_score=352	max_right=182	max_right_minus=182	max_right_plus=175	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.27	new_junction_read_count=70	polymorphism_frequency=9.915e-01	pos_hash_score=39	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=0	side_1_possible_overlap_registers=293	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=70	unique_read_sequence=TATAAGTCATACTTTTGTTTTGGGTGTATTTCAATCTGTTAAAAAGTTTTTCGCTACGCTAGCAAGCAAAAATGAAACAGGAATAATCGAAATGGGATGTTGCGCACAGTCAAAATA
JC	81	.	NC_000913	1979393	1	NC_000913	2068941	1	0	alignment_overlap=1	coverage_minus=42	coverage_plus=74	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=292	key=NC_000913__1979392__1__NC_000913__2068941__1__1____300__300__0__1	max_left=298	max_left_minus=293	max_left_plus=298	max_min_left=140	max_min_left_minus=132	max_min_left_plus=140	max_min_right=148	max_min_right_minus=144	max_min_right_plus=148	max_pos_hash_score=584	max_right=293	max_right_minus=293	max_right_plus=283	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.30	new_junction_read_count=119	polymorphism_frequency=1.000e+00	pos_hash_score=69	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=292	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=1	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=116
JC	82	.	NC_000913	1995620	1	NC_000913	2290113	-1	0	alignment_overlap=0	coverage_minus=48	coverage_plus=66	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=293	key=NC_000913__1995620__1__NC_000913__2290113__-1__0____300__300__0__1	max_left=296	max_left_minus=294	max_left_plus=296	max_min_left=143	max_min_left_minus=143	max_min_left_plus=94	max_min_right=146	max_min_right_minus=139	max_min_right_plus=146	max_pos_hash_score=586	max_right=293	max_right_minus=293	max_right_plus=282	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.25	new_junction_read_count=115	polymorphism_frequency=1.000e+00	pos_hash_score=72	prediction=consensus	read_count_offset=4	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=289	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=114
JC	83	.	NC_000913	1995623	-1	NC_000913	2066159	1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=0	flanking_left=300	flanking_right=300	frequency=7.500e-01	junction_possible_overlap_registers=293	key=NC_000913__1995623__-1__NC_000913__2066159__1__0____300__300__0__0	max_left=131	max_left_minus=131	max_left_plus=0	max_min_left=131	max_min_left_minus=131	max_min_left_plus=0	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=586	max_right=291	max_right_minus=291	max_right_plus=0	neg_log10_pos_hash_p_value=8.8	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=7.500e-01	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.01	side_1_overlap=0	side_1_possible_overlap_registers=293	side_1_read_count=1	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=0	total_non_overlap_reads=3
JC	84	.	NC_000913	2357730	-1	NC_000913	2357926	1	0	alignment_overlap=40	coverage_minus=4	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.503e-02	junction_possible_overlap_registers=253	key=NC_000913__2357730__-1__NC_000913__2357886__1__40____300__300__0__0	max_left=165	max_left_minus=164	max_left_plus=165	max_min_left=64	max_min_left_minus=64	max_min_left_plus=6	max_min_right=94	max_min_right_minus=94	max_min_right_plus=94	max_pos_hash_score=506	max_right=254	max_right_minus=249	max_right_plus=254	neg_log10_pos_hash_p_value=6.4	new_junction_coverage=0.08	new_junction_read_count=6	polymorphism_frequency=5.503e-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=1.35	side_1_overlap=40	side_1_possible_overlap_registers=293	side_1_read_count=124	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=253	side_2_read_count=99	side_2_redundant=0	total_non_overlap_reads=6
JC	85	.	NC_000913	2515616	-1	NC_000913	2536312	1	0	alignment_overlap=2	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.371e-02	junction_possible_overlap_registers=291	key=NC_000913__2515616__-1__NC_000913__2536310__1__2____300__300__1__0	max_left=295	max_left_minus=295	max_left_plus=140	max_min_left=140	max_min_left_minus=0	max_min_left_plus=140	max_min_right=2	max_min_right_minus=2	max_min_right_plus=0	max_pos_hash_score=582	max_right=175	max_right_minus=2	max_right_plus=175	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.371e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=2	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.94	side_2_overlap=0	side_2_possible_overlap_registers=291	side_2_read_count=86	side_2_redundant=0	total_non_overlap_reads=3
JC	86	.	NC_000913	2518116	-1	NC_000913	2518232	1	0	alignment_overlap=81	coverage_minus=3	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=6.984e-02	junction_possible_overlap_registers=212	key=NC_000913__2518116__-1__NC_000913__2518151__1__81____300__300__0__0	max_left=203	max_left_minus=203	max_left_plus=135	max_min_left=59	max_min_left_minus=59	max_min_left_plus=0	max_min_right=84	max_min_right_minus=82	max_min_right_plus=84	max_pos_hash_score=424	max_right=152	max_right_minus=152	max_right_plus=84	neg_log10_pos_hash_p_value=6.5	new_junction_coverage=0.06	new_junction_read_count=4	polymorphism_frequency=6.984e-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=0.81	side_1_overlap=81	side_1_possible_overlap_registers=293	side_1_read_count=74	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.80	side_2_overlap=0	side_2_possible_overlap_registers=212	side_2_read_count=53	side_2_redundant=0	total_non_overlap_reads=4
JC	87	.	NC_000913	2535177	-1	NC_000913	2535202	1	0	alignment_overlap=8	coverage_minus=54	coverage_plus=32	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=285	key=NC_000913__2535177__-1__NC_000913__2535194__1__8____300__300__0__0	max_left=283	max_left_minus=283	max_left_plus=276	max_min_left=144	max_min_left_minus=144	max_min_left_plus=135	max_min_right=142	max_min_right_minus=142	max_min_right_plus=127	max_pos_hash_score=570	max_right=284	max_right_minus=284	max_right_plus=273	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.01	new_junction_read_count=90	polymorphism_frequency=8.549e-01	pos_hash_score=57	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.17	side_1_overlap=8	side_1_possible_overlap_registers=293	side_1_read_count=16	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.17	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=15	side_2_redundant=0	total_non_overlap_reads=86
JC	88	.	NC_000913	2818197	1	NC_000913	2818471	-1	0	alignment_overlap=79	coverage_minus=6	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=1.651e-01	junction_possible_overlap_registers=214	key=NC_000913__2818197__1__NC_000913__2818550__-1__79____300__300__0__0	max_left=138	max_left_minus=138	max_left_plus=138	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=74	max_min_right_minus=74	max_min_right_plus=74	max_pos_hash_score=428	max_right=74	max_right_minus=74	max_right_plus=74	neg_log10_pos_hash_p_value=4.7	new_junction_coverage=0.15	new_junction_read_count=10	polymorphism_frequency=1.651e-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=0.60	side_1_overlap=79	side_1_possible_overlap_registers=293	side_1_read_count=55	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.91	side_2_overlap=0	side_2_possible_overlap_registers=214	side_2_read_count=61	side_2_redundant=0	total_non_overlap_reads=9
JC	89	.	NC_000913	3051553	-1	NC_000913	3051906	1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.454e-02	junction_possible_overlap_registers=284	key=NC_000913__3051553__-1__NC_000913__3051897__1__9____300__300__0__0	max_left=286	max_left_minus=286	max_left_plus=122	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=115	max_pos_hash_score=568	max_right=115	max_right_minus=115	max_right_plus=115	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.454e-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=0.82	side_1_overlap=9	side_1_possible_overlap_registers=293	side_1_read_count=75	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.07	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=95	side_2_redundant=0	total_non_overlap_reads=3
JC	90	.	NC_000913	3223287	-1	NC_000913	3223756	1	0	alignment_overlap=10	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.302e-02	junction_possible_overlap_registers=283	key=NC_000913__3223287__-1__NC_000913__3223746__1__10____300__300__0__0	max_left=135	max_left_minus=135	max_left_plus=135	max_min_left=71	max_min_left_minus=0	max_min_left_plus=71	max_min_right=70	max_min_right_minus=70	max_min_right_plus=70	max_pos_hash_score=566	max_right=96	max_right_minus=70	max_right_plus=96	neg_log10_pos_hash_p_value=8.0	new_junction_coverage=0.05	new_junction_read_count=4	polymorphism_frequency=4.302e-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=0.97	side_1_overlap=10	side_1_possible_overlap_registers=293	side_1_read_count=89	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=283	side_2_read_count=92	side_2_redundant=0	total_non_overlap_reads=4
JC	91	.	NC_000913	3468779	-1	NC_000913	3469104	1	0	alignment_overlap=17	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.422e-02	junction_possible_overlap_registers=276	key=NC_000913__3468779__-1__NC_000913__3469087__1__17____300__300__0__0	max_left=262	max_left_minus=97	max_left_plus=262	max_min_left=97	max_min_left_minus=97	max_min_left_plus=97	max_min_right=21	max_min_right_minus=0	max_min_right_plus=21	max_pos_hash_score=552	max_right=178	max_right_minus=178	max_right_plus=178	neg_log10_pos_hash_p_value=8.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.422e-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=0.87	side_1_overlap=17	side_1_possible_overlap_registers=293	side_1_read_count=80	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.09	side_2_overlap=0	side_2_possible_overlap_registers=276	side_2_read_count=94	side_2_redundant=0	total_non_overlap_reads=3
JC	92	.	NC_000913	3584195	-1	NC_000913	3992537	1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=4.878e-02	junction_possible_overlap_registers=293	key=NC_000913__3584195__-1__NC_000913__3992537__1__0____300__300__1__0	max_left=274	max_left_minus=274	max_left_plus=4	max_min_left=149	max_min_left_minus=149	max_min_left_plus=4	max_min_right=139	max_min_right_minus=139	max_min_right_plus=0	max_pos_hash_score=586	max_right=296	max_right_minus=151	max_right_plus=296	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.878e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	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=0.85	side_2_overlap=0	side_2_possible_overlap_registers=293	side_2_read_count=78	side_2_redundant=0	total_non_overlap_reads=4
JC	93	.	NC_000913	3992343	-1	NC_000913	3992359	1	0	alignment_overlap=0	coverage_minus=11	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=2.061e-01	junction_possible_overlap_registers=293	key=NC_000913__3992343__-1__NC_000913__3992359__1__0____300__300__0__0	max_left=294	max_left_minus=294	max_left_plus=259	max_min_left=144	max_min_left_minus=144	max_min_left_plus=111	max_min_right=87	max_min_right_minus=19	max_min_right_plus=87	max_pos_hash_score=586	max_right=279	max_right_minus=279	max_right_plus=271	neg_log10_pos_hash_p_value=4.5	new_junction_coverage=0.19	new_junction_read_count=17	polymorphism_frequency=2.061e-01	pos_hash_score=14	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.74	side_1_overlap=0	side_1_possible_overlap_registers=293	side_1_read_count=68	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=293	side_2_read_count=63	side_2_redundant=0	total_non_overlap_reads=17
JC	94	.	NC_000913	4542682	1	NC_000913	4542996	1	0	alignment_overlap=9	coverage_minus=8	coverage_plus=13	flanking_left=300	flanking_right=300	frequency=1.790e-01	junction_possible_overlap_registers=284	key=NC_000913__4542682__1__NC_000913__4542987__1__9____300__300__0__0	max_left=287	max_left_minus=287	max_left_plus=260	max_min_left=129	max_min_left_minus=129	max_min_left_plus=114	max_min_right=114	max_min_right_minus=114	max_min_right_plus=71	max_pos_hash_score=568	max_right=288	max_right_minus=288	max_right_plus=263	neg_log10_pos_hash_p_value=4.1	new_junction_coverage=0.24	new_junction_read_count=21	polymorphism_frequency=1.790e-01	pos_hash_score=15	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.19	side_1_overlap=9	side_1_possible_overlap_registers=293	side_1_read_count=109	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.98	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=87	side_2_redundant=0	total_non_overlap_reads=21
JC	95	.	NC_000913	4542690	-1	NC_000913	4542986	-1	0	alignment_overlap=9	coverage_minus=13	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.678e-01	junction_possible_overlap_registers=284	key=NC_000913__4542690__-1__NC_000913__4542995__-1__9____300__300__0__0	max_left=276	max_left_minus=261	max_left_plus=276	max_min_left=139	max_min_left_minus=139	max_min_left_plus=139	max_min_right=130	max_min_right_minus=111	max_min_right_plus=130	max_pos_hash_score=568	max_right=285	max_right_minus=285	max_right_plus=285	neg_log10_pos_hash_p_value=3.6	new_junction_coverage=0.22	new_junction_read_count=20	polymorphism_frequency=1.678e-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=1.27	side_1_overlap=9	side_1_possible_overlap_registers=293	side_1_read_count=117	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=85	side_2_redundant=0	total_non_overlap_reads=20
JC	96	.	NC_000913	4583269	-1	NC_000913	4586813	1	-81	alignment_overlap=-81	coverage_minus=29	coverage_plus=33	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=212	key=NC_000913__4583269__-1__NC_000913__4586813__1__-81__TGTAGGCTGGAGCTGCTTCGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCGAACTGCAGGTCGACGGATCCCCGGAAT__300__300__0__0	max_left=213	max_left_minus=213	max_left_plus=196	max_min_left=95	max_min_left_minus=95	max_min_left_plus=82	max_min_right=104	max_min_right_minus=104	max_min_right_plus=102	max_pos_hash_score=424	max_right=215	max_right_minus=215	max_right_plus=212	neg_log10_pos_hash_p_value=0.6	new_junction_coverage=0.96	new_junction_read_count=64	polymorphism_frequency=1.000e+00	pos_hash_score=34	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=293	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=293	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=62	unique_read_sequence=TGTAGGCTGGAGCTGCTTCGAAGTTCCTATACTTTCTAGAGAATAGGAACTTCGAACTGCAGGTCGACGGATCCCCGGAAT
JC	97	.	NC_000913	4606166	-1	NC_000913	4606403	1	0	alignment_overlap=89	coverage_minus=2	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=6.936e-02	junction_possible_overlap_registers=204	key=NC_000913__4606166__-1__NC_000913__4606314__1__89____300__300__0__0	max_left=160	max_left_minus=160	max_left_plus=70	max_min_left=70	max_min_left_minus=0	max_min_left_plus=70	max_min_right=50	max_min_right_minus=14	max_min_right_plus=50	max_pos_hash_score=408	max_right=96	max_right_minus=14	max_right_plus=96	neg_log10_pos_hash_p_value=5.8	new_junction_coverage=0.08	new_junction_read_count=5	polymorphism_frequency=6.936e-02	pos_hash_score=5	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.93	side_1_overlap=89	side_1_possible_overlap_registers=293	side_1_read_count=85	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.17	side_2_overlap=0	side_2_possible_overlap_registers=204	side_2_read_count=75	side_2_redundant=0	total_non_overlap_reads=5
UN	98	.	NC_000913	15664	16469
UN	99	.	NC_000913	20081	20277
UN	100	.	NC_000913	224018	224509
UN	101	.	NC_000913	225164	225317
UN	102	.	NC_000913	227256	227258
UN	103	.	NC_000913	227260	227263
UN	104	.	NC_000913	227265	228403
UN	105	.	NC_000913	228409	228409
UN	106	.	NC_000913	257908	258683
UN	107	.	NC_000913	270795	270795
UN	108	.	NC_000913	270797	270798
UN	109	.	NC_000913	270800	270800
UN	110	.	NC_000913	270802	270802
UN	111	.	NC_000913	270808	271047
UN	112	.	NC_000913	274248	274865
UN	113	.	NC_000913	279432	279432
UN	114	.	NC_000913	279448	279670
UN	115	.	NC_000913	279680	279680
UN	116	.	NC_000913	290912	290912
UN	117	.	NC_000913	290917	291128
UN	118	.	NC_000913	315509	316201
UN	119	.	NC_000913	316212	316212
UN	120	.	NC_000913	381526	381526
UN	121	.	NC_000913	381533	382324
UN	122	.	NC_000913	382326	382326
UN	123	.	NC_000913	391985	391985
UN	124	.	NC_000913	391987	392696
UN	125	.	NC_000913	526103	526103
UN	126	.	NC_000913	526108	526108
UN	127	.	NC_000913	526112	526112
UN	128	.	NC_000913	526116	526116
UN	129	.	NC_000913	526118	526478
UN	130	.	NC_000913	526480	526480
UN	131	.	NC_000913	567034	567766
UN	132	.	NC_000913	567768	567770
UN	133	.	NC_000913	574869	575505
UN	134	.	NC_000913	608271	609084
UN	135	.	NC_000913	609087	609087
UN	136	.	NC_000913	688131	688765
UN	137	.	NC_000913	1094510	1094510
UN	138	.	NC_000913	1094521	1094521
UN	139	.	NC_000913	1094523	1094523
UN	140	.	NC_000913	1094527	1095222
UN	141	.	NC_000913	1299499	1300697
UN	142	.	NC_000913	1396322	1396958
UN	143	.	NC_000913	1468158	1468158
UN	144	.	NC_000913	1468175	1468967
UN	145	.	NC_000913	1469550	1470234
UN	146	.	NC_000913	1528551	1528551
UN	147	.	NC_000913	1528554	1528555
UN	148	.	NC_000913	1528557	1528558
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UN	150	.	NC_000913	1651118	1651293
UN	151	.	NC_000913	1978503	1979392
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UN	157	.	NC_000913	2170417	2170418
UN	158	.	NC_000913	2170424	2170424
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UN	169	.	NC_000913	2726336	2726336
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UN	212	.	NC_000913	3764323	3764324
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UN	214	.	NC_000913	3765045	3765045
UN	215	.	NC_000913	3942295	3943130
UN	216	.	NC_000913	3944342	3944342
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UN	218	.	NC_000913	3944348	3945289
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UN	233	.	NC_000913	4047989	4049753
UN	234	.	NC_000913	4166557	4166557
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UN	236	.	NC_000913	4166571	4166571
UN	237	.	NC_000913	4166573	4166575
UN	238	.	NC_000913	4166578	4166578
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UN	242	.	NC_000913	4167949	4167956
UN	243	.	NC_000913	4167960	4167960
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UN	253	.	NC_000913	4499245	4499245
UN	254	.	NC_000913	4507743	4508425
UN	255	.	NC_000913	4583270	4586812