#=GENOME_DIFF	1.0
#=CREATED	16:23:44 10 Oct 2025
#=PROGRAM	breseq 0.39.0 
#=COMMAND	breseq -j 8 -o /ld1/breseq_work/20250912_VH01894_36_AAGTVTVM5_run15_rmdup_trimmng-adaptors-polyG/ME8788_S22_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/ME8788_S22_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/ME8788_S22_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/ME8788_S22_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/ME8788_S22_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=CONVERTED-BASES	463484689
#=CONVERTED-READS	1569783
#=INPUT-BASES	463590100
#=INPUT-READS	1570142
#=MAPPED-BASES	443998854
#=MAPPED-READS	1504813
DEL	1	144,150	NC_000913	257908	776
SNP	2	16	NC_000913	366254	A
MOB	3	151,152	NC_000913	371758	IS30	1	2
SNP	4	87	NC_000913	803662	A
DEL	5	145,163	NC_000913	1299499	1199
SNP	6	102	NC_000913	1905761	A
DEL	7	146,165	NC_000913	1978503	776
DEL	8	111,112	NC_000913	2173363	2
INS	9	129	NC_000913	3560455	G
INS	10	138,139	NC_000913	4296381	GC
RA	11	.	NC_000913	12152	0	G	T	bias_e_value=149.6	bias_p_value=3.22299e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=144.6	fisher_strand_p_value=2.30539e-06	frequency=3.235e-01	ks_quality_p_value=1	major_base=G	major_cov=28/41	major_frequency=6.765e-01	minor_base=T	minor_cov=0/33	new_cov=0/33	polymorphism_frequency=3.235e-01	polymorphism_score=13.7	prediction=polymorphism	ref_cov=28/41	total_cov=28/74
RA	12	.	NC_000913	58065	0	C	A	bias_e_value=0.00625578	bias_p_value=1.34775e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=115.4	fisher_strand_p_value=5.47226e-11	frequency=3.804e-01	ks_quality_p_value=1	major_base=C	major_cov=21/36	major_frequency=6.196e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=3.804e-01	polymorphism_score=36.1	prediction=polymorphism	ref_cov=21/36	total_cov=56/36
RA	13	.	NC_000913	85651	0	G	T	bias_e_value=0.977726	bias_p_value=2.10642e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=192.6	fisher_strand_p_value=1.08943e-08	frequency=2.946e-01	ks_quality_p_value=1	major_base=G	major_cov=41/38	major_frequency=7.054e-01	minor_base=T	minor_cov=0/33	new_cov=0/33	polymorphism_frequency=2.946e-01	polymorphism_score=11.4	prediction=polymorphism	ref_cov=41/38	total_cov=41/71
RA	14	.	NC_000913	141849	0	C	A	bias_e_value=4.8206e-06	bias_p_value=1.03855e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=275.3	fisher_strand_p_value=3.23932e-14	frequency=2.847e-01	ks_quality_p_value=1	major_base=C	major_cov=38/65	major_frequency=7.153e-01	minor_base=A	minor_cov=41/0	new_cov=41/0	polymorphism_frequency=2.847e-01	polymorphism_score=11.6	prediction=polymorphism	ref_cov=38/65	total_cov=79/65
RA	15	.	NC_000913	232882	0	G	T	bias_e_value=1205.24	bias_p_value=0.000259657	consensus_reject=FREQUENCY_CUTOFF	consensus_score=140.5	fisher_strand_p_value=2.21603e-05	frequency=2.826e-01	ks_quality_p_value=1	major_base=G	major_cov=28/38	major_frequency=7.174e-01	minor_base=T	minor_cov=0/26	new_cov=0/26	polymorphism_frequency=2.826e-01	polymorphism_score=10.8	prediction=polymorphism	ref_cov=28/38	total_cov=28/64
RA	16	.	NC_000913	366254	0	C	A	consensus_score=234.8	frequency=1	major_base=A	major_cov=35/32	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=35/32	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=35/32
RA	17	.	NC_000913	581115	0	C	A	bias_e_value=1254650	bias_p_value=0.270302	consensus_reject=FREQUENCY_CUTOFF	consensus_score=129.3	fisher_strand_p_value=0.0753986	frequency=3.152e-01	ks_quality_p_value=1	major_base=C	major_cov=37/26	major_frequency=6.848e-01	minor_base=A	minor_cov=11/18	new_cov=11/18	polymorphism_frequency=3.152e-01	polymorphism_score=70.4	prediction=polymorphism	ref_cov=37/26	total_cov=48/44
RA	18	.	NC_000913	581121	0	A	C	bias_e_value=305768	bias_p_value=0.0658749	consensus_reject=FREQUENCY_CUTOFF	consensus_score=92.5	fisher_strand_p_value=0.0126412	frequency=3.011e-01	ks_quality_p_value=0.963623	major_base=A	major_cov=40/25	major_frequency=6.989e-01	minor_base=C	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=3.011e-01	polymorphism_score=89.9	prediction=polymorphism	ref_cov=40/25	total_cov=49/44
RA	19	.	NC_000913	581127	0	G	A	bias_e_value=155608	bias_p_value=0.0335243	consensus_reject=FREQUENCY_CUTOFF	consensus_score=97.6	fisher_strand_p_value=0.00544224	frequency=3.146e-01	ks_quality_p_value=0.989738	major_base=G	major_cov=40/21	major_frequency=6.854e-01	minor_base=A	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=3.146e-01	polymorphism_score=89.8	prediction=polymorphism	ref_cov=40/21	total_cov=49/40
RA	20	.	NC_000913	581130	0	G	A	bias_e_value=96412.8	bias_p_value=0.0207712	consensus_reject=FREQUENCY_CUTOFF	consensus_score=80.9	fisher_strand_p_value=0.00530315	frequency=3.256e-01	ks_quality_p_value=0.57688	major_base=G	major_cov=38/20	major_frequency=6.744e-01	minor_base=A	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=3.256e-01	polymorphism_score=90.0	prediction=polymorphism	ref_cov=38/20	total_cov=47/41
RA	21	.	NC_000913	581139	0	C	A	bias_e_value=180126	bias_p_value=0.0388065	consensus_reject=FREQUENCY_CUTOFF	consensus_score=110.0	fisher_strand_p_value=0.0114044	frequency=3.111e-01	ks_quality_p_value=0.562525	major_base=C	major_cov=39/23	major_frequency=6.889e-01	minor_base=A	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=3.111e-01	polymorphism_score=71.8	prediction=polymorphism	ref_cov=39/23	total_cov=48/43
RA	22	.	NC_000913	581141	0	G	A	bias_e_value=219787	bias_p_value=0.047351	consensus_reject=FREQUENCY_CUTOFF	consensus_score=96.0	fisher_strand_p_value=0.0114044	frequency=3.111e-01	ks_quality_p_value=0.714663	major_base=G	major_cov=39/23	major_frequency=6.889e-01	minor_base=A	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=3.111e-01	polymorphism_score=86.7	prediction=polymorphism	ref_cov=39/23	total_cov=48/43
RA	23	.	NC_000913	581145	0	C	T	bias_e_value=484812	bias_p_value=0.104448	consensus_reject=FREQUENCY_CUTOFF	consensus_score=112.7	fisher_strand_p_value=0.0216028	frequency=2.967e-01	ks_quality_p_value=1	major_base=C	major_cov=39/25	major_frequency=7.033e-01	minor_base=T	minor_cov=9/18	new_cov=9/18	polymorphism_frequency=2.967e-01	polymorphism_score=78.1	prediction=polymorphism	ref_cov=39/25	total_cov=48/43
RA	24	.	NC_000913	581154	0	A	G	bias_e_value=308510	bias_p_value=0.0664655	consensus_reject=FREQUENCY_CUTOFF	consensus_score=125.6	fisher_strand_p_value=0.0126412	frequency=3.011e-01	ks_quality_p_value=0.974236	major_base=A	major_cov=40/25	major_frequency=6.989e-01	minor_base=G	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=3.011e-01	polymorphism_score=81.9	prediction=polymorphism	ref_cov=40/25	total_cov=49/44
RA	25	.	NC_000913	581175	0	T	C	bias_e_value=75732.6	bias_p_value=0.0163159	consensus_reject=FREQUENCY_CUTOFF	consensus_score=134.3	fisher_strand_p_value=0.00298152	frequency=2.887e-01	ks_quality_p_value=0.773834	major_base=T	major_cov=46/23	major_frequency=7.113e-01	minor_base=C	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=2.887e-01	polymorphism_score=81.5	prediction=polymorphism	ref_cov=46/23	total_cov=55/42
RA	26	.	NC_000913	581178	0	T	G	bias_e_value=41046.2	bias_p_value=0.00884302	consensus_reject=FREQUENCY_CUTOFF	consensus_score=98.4	fisher_strand_p_value=0.00117848	frequency=2.979e-01	ks_quality_p_value=0.964538	major_base=T	major_cov=46/20	major_frequency=7.021e-01	minor_base=G	minor_cov=9/19	new_cov=9/19	polymorphism_frequency=2.979e-01	polymorphism_score=86.0	prediction=polymorphism	ref_cov=46/20	total_cov=55/39
RA	27	.	NC_000913	581196	0	C	G	bias_e_value=27131.8	bias_p_value=0.00584529	consensus_reject=FREQUENCY_CUTOFF	consensus_score=117.7	fisher_strand_p_value=0.000715048	frequency=3.085e-01	ks_quality_p_value=0.990552	major_base=C	major_cov=45/20	major_frequency=6.915e-01	minor_base=G	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.085e-01	polymorphism_score=96.2	prediction=polymorphism	ref_cov=45/20	total_cov=54/40
RA	28	.	NC_000913	581199	0	A	C	bias_e_value=23070.9	bias_p_value=0.00497042	consensus_reject=FREQUENCY_CUTOFF	consensus_score=84.1	fisher_strand_p_value=0.000715048	frequency=3.085e-01	ks_quality_p_value=0.823904	major_base=A	major_cov=45/20	major_frequency=6.915e-01	minor_base=C	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.085e-01	polymorphism_score=91.7	prediction=polymorphism	ref_cov=45/20	total_cov=54/40
RA	29	.	NC_000913	581202	0	T	A	bias_e_value=46336.8	bias_p_value=0.00998282	consensus_reject=FREQUENCY_CUTOFF	consensus_score=126.0	fisher_strand_p_value=0.00139944	frequency=3.053e-01	ks_quality_p_value=0.933657	major_base=T	major_cov=45/21	major_frequency=6.947e-01	minor_base=A	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.053e-01	polymorphism_score=116.5	prediction=polymorphism	ref_cov=45/21	total_cov=54/41
RA	30	.	NC_000913	581206	0	A	G	bias_e_value=30387	bias_p_value=0.00654658	consensus_reject=FREQUENCY_CUTOFF	consensus_score=116.8	fisher_strand_p_value=0.00139944	frequency=3.053e-01	ks_quality_p_value=0.575855	major_base=A	major_cov=45/21	major_frequency=6.947e-01	minor_base=G	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.053e-01	polymorphism_score=85.6	prediction=polymorphism	ref_cov=45/21	total_cov=54/41
RA	31	.	NC_000913	581208	0	T	A	bias_e_value=52411.2	bias_p_value=0.0112915	consensus_reject=FREQUENCY_CUTOFF	consensus_score=133.1	fisher_strand_p_value=0.00156116	frequency=3.021e-01	ks_quality_p_value=0.964573	major_base=T	major_cov=45/22	major_frequency=6.979e-01	minor_base=A	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.021e-01	polymorphism_score=115.6	prediction=polymorphism	ref_cov=45/22	total_cov=54/42
RA	32	.	NC_000913	581214	0	T	C	bias_e_value=32712.1	bias_p_value=0.00704752	consensus_reject=FREQUENCY_CUTOFF	consensus_score=120.5	fisher_strand_p_value=0.00156116	frequency=3.021e-01	ks_quality_p_value=0.561516	major_base=T	major_cov=45/22	major_frequency=6.979e-01	minor_base=C	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.021e-01	polymorphism_score=86.5	prediction=polymorphism	ref_cov=45/22	total_cov=54/42
RA	33	.	NC_000913	581220	0	C	T	bias_e_value=10868.3	bias_p_value=0.00234146	consensus_reject=FREQUENCY_CUTOFF	consensus_score=102.4	fisher_strand_p_value=0.00182358	frequency=2.990e-01	ks_quality_p_value=0.13828	major_base=C	major_cov=45/23	major_frequency=7.010e-01	minor_base=T	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=2.990e-01	polymorphism_score=93.0	prediction=polymorphism	ref_cov=45/23	total_cov=54/43
RA	34	.	NC_000913	581223	0	C	T	bias_e_value=36803.2	bias_p_value=0.0079289	consensus_reject=FREQUENCY_CUTOFF	consensus_score=108.5	fisher_strand_p_value=0.00139944	frequency=3.053e-01	ks_quality_p_value=0.71676	major_base=C	major_cov=45/21	major_frequency=6.947e-01	minor_base=T	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.053e-01	polymorphism_score=93.3	prediction=polymorphism	ref_cov=45/21	total_cov=54/41
RA	35	.	NC_000913	581226	0	G	A	bias_e_value=33129.6	bias_p_value=0.00713747	consensus_reject=FREQUENCY_CUTOFF	consensus_score=106.0	fisher_strand_p_value=0.00139944	frequency=3.053e-01	ks_quality_p_value=0.635547	major_base=G	major_cov=45/21	major_frequency=6.947e-01	minor_base=A	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.053e-01	polymorphism_score=92.7	prediction=polymorphism	ref_cov=45/21	total_cov=54/41
RA	36	.	NC_000913	581227	0	A	G	bias_e_value=51614.7	bias_p_value=0.0111199	consensus_reject=FREQUENCY_CUTOFF	consensus_score=140.9	fisher_strand_p_value=0.00149255	frequency=2.990e-01	ks_quality_p_value=0.991245	major_base=A	major_cov=46/22	major_frequency=7.010e-01	minor_base=G	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=2.990e-01	polymorphism_score=83.3	prediction=polymorphism	ref_cov=46/22	total_cov=55/42
RA	37	.	NC_000913	581229	0	C	T	bias_e_value=56262.5	bias_p_value=0.0121212	consensus_reject=FREQUENCY_CUTOFF	consensus_score=99.9	fisher_strand_p_value=0.00163436	frequency=3.261e-01	ks_quality_p_value=1	major_base=C	major_cov=41/21	major_frequency=6.739e-01	minor_base=T	minor_cov=9/21	new_cov=9/21	polymorphism_frequency=3.261e-01	polymorphism_score=94.5	prediction=polymorphism	ref_cov=41/21	total_cov=50/42
RA	38	.	NC_000913	581232	0	C	T	bias_e_value=38325.4	bias_p_value=0.00825684	consensus_reject=FREQUENCY_CUTOFF	consensus_score=88.0	fisher_strand_p_value=0.00353375	frequency=3.187e-01	ks_quality_p_value=0.297338	major_base=C	major_cov=40/22	major_frequency=6.813e-01	minor_base=T	minor_cov=9/20	new_cov=9/20	polymorphism_frequency=3.187e-01	polymorphism_score=92.2	prediction=polymorphism	ref_cov=40/22	total_cov=50/42
RA	39	.	NC_000913	581241	0	G	T	bias_e_value=300438	bias_p_value=0.0647266	consensus_reject=FREQUENCY_CUTOFF	consensus_score=123.0	fisher_strand_p_value=0.0124261	frequency=3.524e-01	ks_quality_p_value=0.959391	major_base=G	major_cov=46/22	major_frequency=6.476e-01	minor_base=T	minor_cov=15/22	new_cov=15/22	polymorphism_frequency=3.524e-01	polymorphism_score=99.6	prediction=polymorphism	ref_cov=46/22	total_cov=61/44
RA	40	.	NC_000913	581250	0	T	C	bias_e_value=352985	bias_p_value=0.0760474	consensus_reject=FREQUENCY_CUTOFF	consensus_score=74.2	fisher_strand_p_value=0.0147182	frequency=3.883e-01	ks_quality_p_value=0.987747	major_base=T	major_cov=40/23	major_frequency=6.117e-01	minor_base=C	minor_cov=15/25	new_cov=15/25	polymorphism_frequency=3.883e-01	polymorphism_score=123.5	prediction=polymorphism	ref_cov=40/23	total_cov=55/48
RA	41	.	NC_000913	581253	0	T	C	bias_e_value=356522	bias_p_value=0.0768093	consensus_reject=FREQUENCY_CUTOFF	consensus_score=90.5	fisher_strand_p_value=0.0147182	frequency=3.883e-01	ks_quality_p_value=1	major_base=T	major_cov=40/23	major_frequency=6.117e-01	minor_base=C	minor_cov=15/25	new_cov=15/25	polymorphism_frequency=3.883e-01	polymorphism_score=108.3	prediction=polymorphism	ref_cov=40/23	total_cov=55/48
RA	42	.	NC_000913	581259	0	A	G	bias_e_value=1323290	bias_p_value=0.28509	consensus_reject=FREQUENCY_CUTOFF	consensus_score=80.7	fisher_strand_p_value=0.0863002	frequency=3.913e-01	ks_quality_p_value=0.940946	major_base=A	major_cov=43/27	major_frequency=6.087e-01	minor_base=G	minor_cov=20/25	new_cov=20/25	polymorphism_frequency=3.913e-01	polymorphism_score=137.4	prediction=polymorphism	ref_cov=43/27	total_cov=63/52
RA	43	.	NC_000913	581275	0	G	A	bias_e_value=1174640	bias_p_value=0.253065	consensus_reject=FREQUENCY_CUTOFF	consensus_score=48.6	fisher_strand_p_value=0.0971175	frequency=4.050e-01	ks_quality_p_value=0.708875	major_base=G	major_cov=41/31	major_frequency=5.950e-01	minor_base=A	minor_cov=20/29	new_cov=20/29	polymorphism_frequency=4.050e-01	polymorphism_score=166.0	prediction=polymorphism	ref_cov=41/31	total_cov=61/60
RA	44	.	NC_000913	581286	0	G	C	bias_e_value=1480820	bias_p_value=0.319028	consensus_reject=FREQUENCY_CUTOFF	consensus_score=75.8	fisher_strand_p_value=0.0951741	frequency=4.118e-01	ks_quality_p_value=1	major_base=G	major_cov=40/30	major_frequency=5.882e-01	minor_base=C	minor_cov=20/29	new_cov=20/29	polymorphism_frequency=4.118e-01	polymorphism_score=157.5	prediction=polymorphism	ref_cov=40/30	total_cov=60/61
RA	45	.	NC_000913	581289	0	A	G	bias_e_value=1920180	bias_p_value=0.413684	consensus_reject=FREQUENCY_CUTOFF	consensus_score=103.4	fisher_strand_p_value=0.139202	frequency=4.050e-01	ks_quality_p_value=1	major_base=A	major_cov=40/32	major_frequency=5.950e-01	minor_base=G	minor_cov=20/29	new_cov=20/29	polymorphism_frequency=4.050e-01	polymorphism_score=129.8	prediction=polymorphism	ref_cov=40/32	total_cov=60/61
RA	46	.	NC_000913	581290	0	C	A	bias_e_value=1920180	bias_p_value=0.413684	consensus_reject=FREQUENCY_CUTOFF	consensus_score=95.1	fisher_strand_p_value=0.139202	frequency=4.050e-01	ks_quality_p_value=1	major_base=C	major_cov=40/32	major_frequency=5.950e-01	minor_base=A	minor_cov=20/29	new_cov=20/29	polymorphism_frequency=4.050e-01	polymorphism_score=137.2	prediction=polymorphism	ref_cov=40/32	total_cov=60/61
RA	47	.	NC_000913	581291	0	G	A	bias_e_value=1920180	bias_p_value=0.413684	consensus_reject=FREQUENCY_CUTOFF	consensus_score=69.4	fisher_strand_p_value=0.139202	frequency=4.050e-01	ks_quality_p_value=1	major_base=G	major_cov=40/32	major_frequency=5.950e-01	minor_base=A	minor_cov=20/29	new_cov=20/29	polymorphism_frequency=4.050e-01	polymorphism_score=137.2	prediction=polymorphism	ref_cov=40/32	total_cov=60/61
RA	48	.	NC_000913	581295	0	T	C	bias_e_value=1959370	bias_p_value=0.422127	consensus_reject=FREQUENCY_CUTOFF	consensus_score=82.0	fisher_strand_p_value=0.14352	frequency=4.016e-01	ks_quality_p_value=0.999982	major_base=T	major_cov=40/33	major_frequency=5.984e-01	minor_base=C	minor_cov=20/29	new_cov=20/29	polymorphism_frequency=4.016e-01	polymorphism_score=148.7	prediction=polymorphism	ref_cov=40/33	total_cov=60/62
RA	49	.	NC_000913	581301	0	C	T	bias_e_value=1903080	bias_p_value=0.41	consensus_reject=FREQUENCY_CUTOFF	consensus_score=62.7	fisher_strand_p_value=0.14352	frequency=4.016e-01	ks_quality_p_value=0.956939	major_base=C	major_cov=40/33	major_frequency=5.984e-01	minor_base=T	minor_cov=20/29	new_cov=20/29	polymorphism_frequency=4.016e-01	polymorphism_score=159.7	prediction=polymorphism	ref_cov=40/33	total_cov=60/62
RA	50	.	NC_000913	581322	0	C	T	bias_e_value=488763	bias_p_value=0.105299	consensus_reject=SCORE_CUTOFF,FREQUENCY_CUTOFF	consensus_score=6.5	fisher_strand_p_value=0.0600951	frequency=4.526e-01	ks_quality_p_value=0.363176	major_base=C	major_cov=44/31	major_frequency=5.474e-01	minor_base=T	minor_cov=26/36	new_cov=26/36	polymorphism_frequency=4.526e-01	polymorphism_score=211.3	prediction=polymorphism	ref_cov=44/31	total_cov=71/67
RA	51	.	NC_000913	581335	0	C	A	bias_e_value=865530	bias_p_value=0.18647	consensus_reject=FREQUENCY_CUTOFF	consensus_score=79.2	fisher_strand_p_value=0.0456209	frequency=4.521e-01	ks_quality_p_value=1	major_base=C	major_cov=47/33	major_frequency=5.479e-01	minor_base=A	minor_cov=27/39	new_cov=27/39	polymorphism_frequency=4.521e-01	polymorphism_score=180.9	prediction=polymorphism	ref_cov=47/33	total_cov=74/72
RA	52	.	NC_000913	581337	0	G	A	bias_e_value=456038	bias_p_value=0.0982491	consensus_reject=FREQUENCY_CUTOFF	consensus_score=14.4	fisher_strand_p_value=0.0200022	frequency=4.621e-01	ks_quality_p_value=1	major_base=G	major_cov=47/31	major_frequency=5.379e-01	minor_base=A	minor_cov=27/40	new_cov=27/40	polymorphism_frequency=4.621e-01	polymorphism_score=226.0	prediction=polymorphism	ref_cov=47/31	total_cov=74/71
RA	53	.	NC_000913	581380	0	C	G	bias_e_value=3020500	bias_p_value=0.650738	consensus_reject=FREQUENCY_CUTOFF	consensus_score=102.5	fisher_strand_p_value=0.29142	frequency=4.135e-01	ks_quality_p_value=1	major_base=C	major_cov=39/39	major_frequency=5.865e-01	minor_base=G	minor_cov=22/33	new_cov=22/33	polymorphism_frequency=4.135e-01	polymorphism_score=178.2	prediction=polymorphism	ref_cov=39/39	total_cov=61/74
RA	54	.	NC_000913	581381	0	A	G	bias_e_value=3030250	bias_p_value=0.652838	consensus_reject=FREQUENCY_CUTOFF	consensus_score=96.5	fisher_strand_p_value=0.29352	frequency=4.148e-01	ks_quality_p_value=0.998661	major_base=A	major_cov=39/40	major_frequency=5.852e-01	minor_base=G	minor_cov=22/34	new_cov=22/34	polymorphism_frequency=4.148e-01	polymorphism_score=175.7	prediction=polymorphism	ref_cov=39/40	total_cov=61/74
RA	55	.	NC_000913	581388	0	G	A	bias_e_value=4558090	bias_p_value=0.981997	consensus_reject=FREQUENCY_CUTOFF	consensus_score=134.8	fisher_strand_p_value=0.843355	frequency=3.304e-01	ks_quality_p_value=0.967976	major_base=G	major_cov=39/38	major_frequency=6.696e-01	minor_base=A	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.304e-01	polymorphism_score=119.3	prediction=polymorphism	ref_cov=39/38	total_cov=57/59
RA	56	.	NC_000913	581392	0	T	C	bias_e_value=4639250	bias_p_value=0.999482	consensus_reject=FREQUENCY_CUTOFF	consensus_score=157.5	fisher_strand_p_value=1	frequency=3.304e-01	ks_quality_p_value=0.967976	major_base=T	major_cov=38/39	major_frequency=6.696e-01	minor_base=C	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.304e-01	polymorphism_score=113.5	prediction=polymorphism	ref_cov=38/39	total_cov=56/59
RA	57	.	NC_000913	581394	0	T	C	bias_e_value=4641650	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=173.4	fisher_strand_p_value=1	frequency=3.304e-01	ks_quality_p_value=1	major_base=T	major_cov=38/39	major_frequency=6.696e-01	minor_base=C	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.304e-01	polymorphism_score=104.3	prediction=polymorphism	ref_cov=38/39	total_cov=56/59
RA	58	.	NC_000913	581397	0	T	C	bias_e_value=4641650	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.7	fisher_strand_p_value=1	frequency=3.276e-01	ks_quality_p_value=1	major_base=T	major_cov=38/40	major_frequency=6.724e-01	minor_base=C	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.276e-01	polymorphism_score=108.7	prediction=polymorphism	ref_cov=38/40	total_cov=56/60
RA	59	.	NC_000913	581398	0	C	G	bias_e_value=3716700	bias_p_value=0.800728	consensus_reject=FREQUENCY_CUTOFF	consensus_score=155.0	fisher_strand_p_value=1	frequency=3.276e-01	ks_quality_p_value=0.439387	major_base=C	major_cov=37/41	major_frequency=6.724e-01	minor_base=G	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.276e-01	polymorphism_score=126.9	prediction=polymorphism	ref_cov=37/41	total_cov=56/61
RA	60	.	NC_000913	581404	0	C	G	bias_e_value=3310350	bias_p_value=0.713184	consensus_reject=FREQUENCY_CUTOFF	consensus_score=145.6	fisher_strand_p_value=1	frequency=3.333e-01	ks_quality_p_value=0.34597	major_base=C	major_cov=36/40	major_frequency=6.667e-01	minor_base=G	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.333e-01	polymorphism_score=127.9	prediction=polymorphism	ref_cov=36/40	total_cov=54/61
RA	61	.	NC_000913	581407	0	G	T	bias_e_value=4641480	bias_p_value=0.999963	consensus_reject=FREQUENCY_CUTOFF	consensus_score=161.7	fisher_strand_p_value=1	frequency=3.304e-01	ks_quality_p_value=0.991454	major_base=G	major_cov=36/41	major_frequency=6.696e-01	minor_base=T	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.304e-01	polymorphism_score=106.3	prediction=polymorphism	ref_cov=36/41	total_cov=54/61
RA	62	.	NC_000913	581410	0	T	A	bias_e_value=4560980	bias_p_value=0.982621	consensus_reject=FREQUENCY_CUTOFF	consensus_score=193.0	fisher_strand_p_value=1	frequency=3.248e-01	ks_quality_p_value=0.819451	major_base=T	major_cov=36/43	major_frequency=6.752e-01	minor_base=A	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.248e-01	polymorphism_score=156.4	prediction=polymorphism	ref_cov=36/43	total_cov=54/63
RA	63	.	NC_000913	581412	0	G	T	bias_e_value=4561720	bias_p_value=0.98278	consensus_reject=FREQUENCY_CUTOFF	consensus_score=169.1	fisher_strand_p_value=0.843461	frequency=3.248e-01	ks_quality_p_value=0.972484	major_base=G	major_cov=35/44	major_frequency=6.752e-01	minor_base=T	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.248e-01	polymorphism_score=103.8	prediction=polymorphism	ref_cov=35/44	total_cov=53/64
RA	64	.	NC_000913	581413	0	C	T	bias_e_value=4010880	bias_p_value=0.864105	consensus_reject=FREQUENCY_CUTOFF	consensus_score=140.8	fisher_strand_p_value=1	frequency=3.130e-01	ks_quality_p_value=0.526272	major_base=C	major_cov=35/44	major_frequency=6.870e-01	minor_base=T	minor_cov=16/20	new_cov=16/20	polymorphism_frequency=3.130e-01	polymorphism_score=117.1	prediction=polymorphism	ref_cov=35/44	total_cov=51/64
RA	65	.	NC_000913	581416	0	A	G	bias_e_value=4398970	bias_p_value=0.947716	consensus_reject=FREQUENCY_CUTOFF	consensus_score=172.5	fisher_strand_p_value=0.694575	frequency=3.248e-01	ks_quality_p_value=1	major_base=A	major_cov=34/45	major_frequency=6.752e-01	minor_base=G	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.248e-01	polymorphism_score=107.8	prediction=polymorphism	ref_cov=34/45	total_cov=53/65
RA	66	.	NC_000913	581421	0	T	A	bias_e_value=4586730	bias_p_value=0.988167	consensus_reject=FREQUENCY_CUTOFF	consensus_score=213.2	fisher_strand_p_value=1	frequency=3.140e-01	ks_quality_p_value=0.850158	major_base=T	major_cov=38/45	major_frequency=6.860e-01	minor_base=A	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.140e-01	polymorphism_score=154.0	prediction=polymorphism	ref_cov=38/45	total_cov=56/65
RA	67	.	NC_000913	581423	0	A	C	bias_e_value=4639480	bias_p_value=0.999532	consensus_reject=FREQUENCY_CUTOFF	consensus_score=138.4	fisher_strand_p_value=1	frequency=3.167e-01	ks_quality_p_value=0.969578	major_base=A	major_cov=38/44	major_frequency=6.833e-01	minor_base=C	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.167e-01	polymorphism_score=117.5	prediction=polymorphism	ref_cov=38/44	total_cov=56/64
RA	68	.	NC_000913	581425	0	G	A	bias_e_value=4634730	bias_p_value=0.998508	consensus_reject=FREQUENCY_CUTOFF	consensus_score=156.1	fisher_strand_p_value=1	frequency=3.167e-01	ks_quality_p_value=0.945872	major_base=G	major_cov=38/44	major_frequency=6.833e-01	minor_base=A	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.167e-01	polymorphism_score=118.8	prediction=polymorphism	ref_cov=38/44	total_cov=56/64
RA	69	.	NC_000913	581428	0	G	T	bias_e_value=3846570	bias_p_value=0.828707	consensus_reject=FREQUENCY_CUTOFF	consensus_score=163.1	fisher_strand_p_value=0.701614	frequency=3.277e-01	ks_quality_p_value=0.677198	major_base=G	major_cov=40/40	major_frequency=6.723e-01	minor_base=T	minor_cov=18/21	new_cov=18/21	polymorphism_frequency=3.277e-01	polymorphism_score=107.8	prediction=polymorphism	ref_cov=40/40	total_cov=58/61
RA	70	.	NC_000913	581434	0	A	G	bias_e_value=4581640	bias_p_value=0.987071	consensus_reject=FREQUENCY_CUTOFF	consensus_score=186.5	fisher_strand_p_value=1	frequency=3.115e-01	ks_quality_p_value=0.843565	major_base=A	major_cov=41/43	major_frequency=6.885e-01	minor_base=G	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.115e-01	polymorphism_score=112.8	prediction=polymorphism	ref_cov=41/43	total_cov=59/63
RA	71	.	NC_000913	581437	0	G	A	bias_e_value=4577480	bias_p_value=0.986176	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.2	fisher_strand_p_value=0.844522	frequency=3.058e-01	ks_quality_p_value=0.992746	major_base=G	major_cov=41/43	major_frequency=6.942e-01	minor_base=A	minor_cov=17/20	new_cov=17/20	polymorphism_frequency=3.058e-01	polymorphism_score=116.6	prediction=polymorphism	ref_cov=41/43	total_cov=59/63
RA	72	.	NC_000913	581440	0	C	G	bias_e_value=4639640	bias_p_value=0.999567	consensus_reject=FREQUENCY_CUTOFF	consensus_score=193.3	fisher_strand_p_value=1	frequency=3.083e-01	ks_quality_p_value=0.970718	major_base=C	major_cov=40/43	major_frequency=6.917e-01	minor_base=G	minor_cov=18/19	new_cov=18/19	polymorphism_frequency=3.083e-01	polymorphism_score=120.6	prediction=polymorphism	ref_cov=40/43	total_cov=59/63
RA	73	.	NC_000913	581443	0	C	G	bias_e_value=2339700	bias_p_value=0.504066	consensus_reject=FREQUENCY_CUTOFF	consensus_score=171.7	fisher_strand_p_value=1	frequency=3.167e-01	ks_quality_p_value=0.189114	major_base=C	major_cov=39/43	major_frequency=6.833e-01	minor_base=G	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.167e-01	polymorphism_score=128.0	prediction=polymorphism	ref_cov=39/43	total_cov=59/63
RA	74	.	NC_000913	581455	0	G	A	bias_e_value=4072990	bias_p_value=0.877488	consensus_reject=FREQUENCY_CUTOFF	consensus_score=139.0	fisher_strand_p_value=1	frequency=3.193e-01	ks_quality_p_value=0.547796	major_base=G	major_cov=38/43	major_frequency=6.807e-01	minor_base=A	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.193e-01	polymorphism_score=120.3	prediction=polymorphism	ref_cov=38/43	total_cov=56/63
RA	75	.	NC_000913	581458	0	T	C	bias_e_value=4582070	bias_p_value=0.987164	consensus_reject=FREQUENCY_CUTOFF	consensus_score=171.3	fisher_strand_p_value=1	frequency=3.167e-01	ks_quality_p_value=0.844113	major_base=T	major_cov=38/44	major_frequency=6.833e-01	minor_base=C	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.167e-01	polymorphism_score=113.1	prediction=polymorphism	ref_cov=38/44	total_cov=56/64
RA	76	.	NC_000913	581460	0	C	A	bias_e_value=4559680	bias_p_value=0.982339	consensus_reject=FREQUENCY_CUTOFF	consensus_score=199.5	fisher_strand_p_value=0.846786	frequency=3.115e-01	ks_quality_p_value=0.966056	major_base=C	major_cov=38/46	major_frequency=6.885e-01	minor_base=A	minor_cov=18/20	new_cov=18/20	polymorphism_frequency=3.115e-01	polymorphism_score=96.2	prediction=polymorphism	ref_cov=38/46	total_cov=56/66
RA	77	.	NC_000913	581476	0	G	C	bias_e_value=4580770	bias_p_value=0.986884	consensus_reject=FREQUENCY_CUTOFF	consensus_score=174.5	fisher_strand_p_value=1	frequency=3.077e-01	ks_quality_p_value=0.842472	major_base=G	major_cov=37/44	major_frequency=6.923e-01	minor_base=C	minor_cov=17/19	new_cov=17/19	polymorphism_frequency=3.077e-01	polymorphism_score=111.8	prediction=polymorphism	ref_cov=37/44	total_cov=55/66
RA	78	.	NC_000913	581482	0	A	G	bias_e_value=4556610	bias_p_value=0.981678	consensus_reject=FREQUENCY_CUTOFF	consensus_score=181.9	fisher_strand_p_value=0.840467	frequency=3.103e-01	ks_quality_p_value=0.969442	major_base=A	major_cov=35/45	major_frequency=6.897e-01	minor_base=G	minor_cov=17/19	new_cov=17/19	polymorphism_frequency=3.103e-01	polymorphism_score=100.6	prediction=polymorphism	ref_cov=35/45	total_cov=52/64
RA	79	.	NC_000913	581485	0	C	G	bias_e_value=3728210	bias_p_value=0.803209	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.9	fisher_strand_p_value=0.691295	frequency=3.162e-01	ks_quality_p_value=0.639982	major_base=C	major_cov=35/45	major_frequency=6.838e-01	minor_base=G	minor_cov=18/19	new_cov=18/19	polymorphism_frequency=3.162e-01	polymorphism_score=122.6	prediction=polymorphism	ref_cov=35/45	total_cov=53/64
RA	80	.	NC_000913	581488	0	A	C	bias_e_value=4389040	bias_p_value=0.945577	consensus_reject=FREQUENCY_CUTOFF	consensus_score=152.3	fisher_strand_p_value=0.694722	frequency=3.136e-01	ks_quality_p_value=0.991435	major_base=A	major_cov=36/45	major_frequency=6.864e-01	minor_base=C	minor_cov=18/19	new_cov=18/19	polymorphism_frequency=3.136e-01	polymorphism_score=107.4	prediction=polymorphism	ref_cov=36/45	total_cov=54/64
RA	81	.	NC_000913	581512	0	A	G	bias_e_value=4383790	bias_p_value=0.944447	consensus_reject=FREQUENCY_CUTOFF	consensus_score=213.6	fisher_strand_p_value=0.837206	frequency=2.712e-01	ks_quality_p_value=0.819102	major_base=A	major_cov=43/43	major_frequency=7.288e-01	minor_base=G	minor_cov=15/17	new_cov=15/17	polymorphism_frequency=2.712e-01	polymorphism_score=90.5	prediction=polymorphism	ref_cov=43/43	total_cov=58/60
RA	82	.	NC_000913	581513	0	C	T	bias_e_value=4641550	bias_p_value=0.999978	consensus_reject=FREQUENCY_CUTOFF	consensus_score=187.7	fisher_strand_p_value=1	frequency=2.821e-01	ks_quality_p_value=0.993307	major_base=C	major_cov=42/42	major_frequency=7.179e-01	minor_base=T	minor_cov=16/17	new_cov=16/17	polymorphism_frequency=2.821e-01	polymorphism_score=99.2	prediction=polymorphism	ref_cov=42/42	total_cov=58/59
RA	83	.	NC_000913	581518	0	C	G	bias_e_value=4555530	bias_p_value=0.981445	consensus_reject=FREQUENCY_CUTOFF	consensus_score=198.5	fisher_strand_p_value=1	frequency=2.845e-01	ks_quality_p_value=0.813652	major_base=C	major_cov=41/42	major_frequency=7.155e-01	minor_base=G	minor_cov=16/17	new_cov=16/17	polymorphism_frequency=2.845e-01	polymorphism_score=109.0	prediction=polymorphism	ref_cov=41/42	total_cov=57/60
RA	84	.	NC_000913	581524	0	G	A	bias_e_value=3993830	bias_p_value=0.860433	consensus_reject=FREQUENCY_CUTOFF	consensus_score=203.2	fisher_strand_p_value=0.520599	frequency=2.589e-01	ks_quality_p_value=1	major_base=G	major_cov=41/42	major_frequency=7.411e-01	minor_base=A	minor_cov=12/17	new_cov=12/17	polymorphism_frequency=2.589e-01	polymorphism_score=77.2	prediction=polymorphism	ref_cov=41/42	total_cov=53/59
RA	85	.	NC_000913	581527	0	G	C	bias_e_value=3444050	bias_p_value=0.741987	consensus_reject=FREQUENCY_CUTOFF	consensus_score=224.5	fisher_strand_p_value=0.520599	frequency=2.589e-01	ks_quality_p_value=0.718712	major_base=G	major_cov=41/42	major_frequency=7.411e-01	minor_base=C	minor_cov=12/17	new_cov=12/17	polymorphism_frequency=2.589e-01	polymorphism_score=95.6	prediction=polymorphism	ref_cov=41/42	total_cov=53/59
RA	86	.	NC_000913	581530	0	C	G	bias_e_value=4466630	bias_p_value=0.962293	consensus_reject=FREQUENCY_CUTOFF	consensus_score=195.2	fisher_strand_p_value=0.82716	frequency=2.736e-01	ks_quality_p_value=0.892528	major_base=C	major_cov=35/42	major_frequency=7.264e-01	minor_base=G	minor_cov=12/17	new_cov=12/17	polymorphism_frequency=2.736e-01	polymorphism_score=90.2	prediction=polymorphism	ref_cov=35/42	total_cov=48/59
RA	87	.	NC_000913	803662	0	C	A	bias_e_value=4641650	bias_p_value=1	consensus_score=568.7	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=68/87	major_frequency=9.936e-01	minor_base=G	minor_cov=0/1	new_cov=68/87	polymorphism_frequency=9.936e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=68/88
RA	88	.	NC_000913	834674	0	C	A	bias_e_value=0.00461837	bias_p_value=9.94984e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=286.5	fisher_strand_p_value=3.98871e-11	frequency=2.326e-01	ks_quality_p_value=1	major_base=C	major_cov=31/68	major_frequency=7.674e-01	minor_base=A	minor_cov=29/1	new_cov=29/1	polymorphism_frequency=2.326e-01	polymorphism_score=17.8	prediction=polymorphism	ref_cov=31/68	total_cov=60/69
RA	89	.	NC_000913	847955	0	G	A	bias_e_value=0.62885	bias_p_value=1.3548e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=109.4	fisher_strand_p_value=6.84237e-09	frequency=3.143e-01	ks_quality_p_value=1	major_base=G	major_cov=39/33	major_frequency=6.857e-01	minor_base=A	minor_cov=0/33	new_cov=0/33	polymorphism_frequency=3.143e-01	polymorphism_score=53.0	prediction=polymorphism	ref_cov=39/33	total_cov=40/66
RA	90	.	NC_000913	964392	0	G	T	bias_e_value=1178.81	bias_p_value=0.000253964	consensus_reject=FREQUENCY_CUTOFF	consensus_score=217.9	fisher_strand_p_value=2.16297e-05	frequency=2.115e-01	ks_quality_p_value=1	major_base=G	major_cov=43/39	major_frequency=7.885e-01	minor_base=T	minor_cov=1/21	new_cov=1/21	polymorphism_frequency=2.115e-01	polymorphism_score=11.4	prediction=polymorphism	ref_cov=43/39	total_cov=44/60
RA	91	.	NC_000913	1001094	0	G	T	bias_e_value=0.0138109	bias_p_value=2.97542e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=179.6	fisher_strand_p_value=1.25004e-10	frequency=3.148e-01	ks_quality_p_value=1	major_base=G	major_cov=44/30	major_frequency=6.852e-01	minor_base=T	minor_cov=0/34	new_cov=0/34	polymorphism_frequency=3.148e-01	polymorphism_score=12.3	prediction=polymorphism	ref_cov=44/30	total_cov=44/64
RA	92	.	NC_000913	1097118	0	C	A	bias_e_value=2414820	bias_p_value=0.520251	consensus_reject=FREQUENCY_CUTOFF	consensus_score=33.8	fisher_strand_p_value=0.261911	frequency=3.023e-01	ks_quality_p_value=0.759742	major_base=C	major_cov=6/24	major_frequency=6.977e-01	minor_base=A	minor_cov=5/8	new_cov=5/8	polymorphism_frequency=3.023e-01	polymorphism_score=36.6	prediction=polymorphism	ref_cov=6/24	total_cov=11/32
RA	93	.	NC_000913	1097158	0	C	T	bias_e_value=2463250	bias_p_value=0.530685	consensus_reject=FREQUENCY_CUTOFF	consensus_score=31.1	fisher_strand_p_value=0.205513	frequency=2.581e-01	ks_quality_p_value=1	major_base=C	major_cov=7/16	major_frequency=7.419e-01	minor_base=T	minor_cov=5/3	new_cov=5/3	polymorphism_frequency=2.581e-01	polymorphism_score=16.5	prediction=polymorphism	ref_cov=7/16	total_cov=12/19
RA	94	.	NC_000913	1286870	0	C	A	bias_e_value=1853430	bias_p_value=0.399304	consensus_reject=FREQUENCY_CUTOFF	consensus_score=144.8	fisher_strand_p_value=0.132005	frequency=2.090e-01	ks_quality_p_value=1	major_base=C	major_cov=24/29	major_frequency=7.910e-01	minor_base=A	minor_cov=10/4	new_cov=10/4	polymorphism_frequency=2.090e-01	polymorphism_score=12.7	prediction=polymorphism	ref_cov=24/29	total_cov=34/36
RA	95	.	NC_000913	1334966	0	A	C	bias_e_value=0.00516646	bias_p_value=1.11306e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=295.2	fisher_strand_p_value=4.48308e-11	frequency=2.349e-01	ks_quality_p_value=1	major_base=A	major_cov=60/67	major_frequency=7.651e-01	minor_base=C	minor_cov=39/0	new_cov=39/0	polymorphism_frequency=2.349e-01	polymorphism_score=14.5	prediction=polymorphism	ref_cov=60/67	total_cov=99/67
RA	96	.	NC_000913	1351463	0	C	A	bias_e_value=4921.7	bias_p_value=0.00106033	consensus_reject=FREQUENCY_CUTOFF	consensus_score=108.3	fisher_strand_p_value=0.000104277	frequency=3.368e-01	ks_quality_p_value=1	major_base=C	major_cov=43/20	major_frequency=6.632e-01	minor_base=A	minor_cov=32/0	new_cov=32/0	polymorphism_frequency=3.368e-01	polymorphism_score=14.2	prediction=polymorphism	ref_cov=43/20	total_cov=75/20
RA	97	.	NC_000913	1405739	0	C	A	bias_e_value=0.174992	bias_p_value=3.77003e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=216.9	fisher_strand_p_value=1.78294e-09	frequency=2.602e-01	ks_quality_p_value=1	major_base=C	major_cov=41/50	major_frequency=7.398e-01	minor_base=A	minor_cov=32/0	new_cov=32/0	polymorphism_frequency=2.602e-01	polymorphism_score=19.7	prediction=polymorphism	ref_cov=41/50	total_cov=73/50
RA	98	.	NC_000913	1427992	0	G	T	bias_e_value=0.616812	bias_p_value=1.32886e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=130.3	fisher_strand_p_value=6.70449e-09	frequency=3.725e-01	ks_quality_p_value=1	major_base=G	major_cov=32/32	major_frequency=6.275e-01	minor_base=T	minor_cov=0/38	new_cov=0/38	polymorphism_frequency=3.725e-01	polymorphism_score=14.0	prediction=polymorphism	ref_cov=32/32	total_cov=32/70
RA	99	.	NC_000913	1466432	0	A	G	bias_e_value=4490490	bias_p_value=0.967434	consensus_reject=FREQUENCY_CUTOFF	consensus_score=121.3	fisher_strand_p_value=0.755892	frequency=2.063e-01	ks_quality_p_value=1	major_base=A	major_cov=24/26	major_frequency=7.937e-01	minor_base=G	minor_cov=5/8	new_cov=5/8	polymorphism_frequency=2.063e-01	polymorphism_score=15.3	prediction=polymorphism	ref_cov=24/26	total_cov=29/34
RA	100	.	NC_000913	1708718	0	G	A	bias_e_value=2765300	bias_p_value=0.595758	consensus_reject=FREQUENCY_CUTOFF	consensus_score=122.9	fisher_strand_p_value=0.249412	frequency=2.424e-01	ks_quality_p_value=1	major_base=G	major_cov=21/29	major_frequency=7.576e-01	minor_base=A	minor_cov=10/6	new_cov=10/6	polymorphism_frequency=2.424e-01	polymorphism_score=23.0	prediction=polymorphism	ref_cov=21/29	total_cov=32/35
RA	101	.	NC_000913	1877796	0	G	T	bias_e_value=0.0814449	bias_p_value=1.75465e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=186.9	fisher_strand_p_value=7.99494e-10	frequency=3.056e-01	ks_quality_p_value=1	major_base=G	major_cov=43/32	major_frequency=6.944e-01	minor_base=T	minor_cov=0/33	new_cov=0/33	polymorphism_frequency=3.056e-01	polymorphism_score=11.9	prediction=polymorphism	ref_cov=43/32	total_cov=43/65
RA	102	.	NC_000913	1905761	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=277.9	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=35/45	major_frequency=9.877e-01	minor_base=C	minor_cov=0/1	new_cov=35/45	polymorphism_frequency=9.877e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=35/46
RA	103	.	NC_000913	1951320	0	G	A	bias_e_value=3761910	bias_p_value=0.810469	consensus_reject=FREQUENCY_CUTOFF	consensus_score=178.2	fisher_strand_p_value=0.451431	frequency=2.333e-01	ks_quality_p_value=1	major_base=G	major_cov=28/41	major_frequency=7.667e-01	minor_base=A	minor_cov=11/10	new_cov=11/10	polymorphism_frequency=2.333e-01	polymorphism_score=56.7	prediction=polymorphism	ref_cov=28/41	total_cov=39/51
RA	104	.	NC_000913	1951332	0	T	C	bias_e_value=3706670	bias_p_value=0.798566	consensus_reject=FREQUENCY_CUTOFF	consensus_score=211.0	fisher_strand_p_value=0.469466	frequency=2.211e-01	ks_quality_p_value=0.93035	major_base=T	major_cov=32/42	major_frequency=7.789e-01	minor_base=C	minor_cov=11/10	new_cov=11/10	polymorphism_frequency=2.211e-01	polymorphism_score=55.9	prediction=polymorphism	ref_cov=32/42	total_cov=43/52
RA	105	.	NC_000913	1951335	0	C	T	bias_e_value=3826840	bias_p_value=0.824457	consensus_reject=FREQUENCY_CUTOFF	consensus_score=201.5	fisher_strand_p_value=0.469466	frequency=2.211e-01	ks_quality_p_value=1	major_base=C	major_cov=32/42	major_frequency=7.789e-01	minor_base=T	minor_cov=11/10	new_cov=11/10	polymorphism_frequency=2.211e-01	polymorphism_score=53.2	prediction=polymorphism	ref_cov=32/42	total_cov=43/52
RA	106	.	NC_000913	1951338	0	C	T	bias_e_value=4256690	bias_p_value=0.917063	consensus_reject=FREQUENCY_CUTOFF	consensus_score=205.4	fisher_strand_p_value=0.621427	frequency=2.188e-01	ks_quality_p_value=1	major_base=C	major_cov=33/42	major_frequency=7.812e-01	minor_base=T	minor_cov=11/10	new_cov=11/10	polymorphism_frequency=2.188e-01	polymorphism_score=57.5	prediction=polymorphism	ref_cov=33/42	total_cov=44/52
RA	107	.	NC_000913	1951386	0	C	T	bias_e_value=4546410	bias_p_value=0.979481	consensus_reject=FREQUENCY_CUTOFF	consensus_score=187.9	fisher_strand_p_value=0.804995	frequency=2.198e-01	ks_quality_p_value=0.999242	major_base=C	major_cov=33/38	major_frequency=7.802e-01	minor_base=T	minor_cov=10/10	new_cov=10/10	polymorphism_frequency=2.198e-01	polymorphism_score=52.6	prediction=polymorphism	ref_cov=33/38	total_cov=45/48
RA	108	.	NC_000913	1951387	0	A	C	bias_e_value=4640320	bias_p_value=0.999713	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.1	fisher_strand_p_value=1	frequency=2.174e-01	ks_quality_p_value=0.976135	major_base=A	major_cov=35/37	major_frequency=7.826e-01	minor_base=C	minor_cov=10/10	new_cov=10/10	polymorphism_frequency=2.174e-01	polymorphism_score=54.6	prediction=polymorphism	ref_cov=35/37	total_cov=45/47
RA	109	.	NC_000913	1951412	0	A	G	bias_e_value=4075810	bias_p_value=0.878095	consensus_reject=FREQUENCY_CUTOFF	consensus_score=216.3	fisher_strand_p_value=0.807757	frequency=2.143e-01	ks_quality_p_value=0.679418	major_base=A	major_cov=37/40	major_frequency=7.857e-01	minor_base=G	minor_cov=11/10	new_cov=11/10	polymorphism_frequency=2.143e-01	polymorphism_score=56.3	prediction=polymorphism	ref_cov=37/40	total_cov=48/50
RA	110	.	NC_000913	2073613	0	G	T	bias_e_value=0.740068	bias_p_value=1.59441e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=171.6	fisher_strand_p_value=8.12288e-09	frequency=2.857e-01	ks_quality_p_value=1	major_base=G	major_cov=40/25	major_frequency=7.143e-01	minor_base=T	minor_cov=0/26	new_cov=0/26	polymorphism_frequency=2.857e-01	polymorphism_score=10.9	prediction=polymorphism	ref_cov=40/25	total_cov=40/51
RA	111	.	NC_000913	2173363	0	C	.	consensus_score=535.8	frequency=1	major_base=.	major_cov=54/54	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=54/54	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=54/54
RA	112	.	NC_000913	2173364	0	C	.	consensus_score=535.8	frequency=1	major_base=.	major_cov=54/54	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=54/54	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=54/54
RA	113	.	NC_000913	2185849	0	G	T	bias_e_value=0.000207284	bias_p_value=4.46574e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=269.5	fisher_strand_p_value=1.58527e-12	frequency=2.348e-01	ks_quality_p_value=1	major_base=G	major_cov=64/24	major_frequency=7.652e-01	minor_base=T	minor_cov=0/27	new_cov=0/27	polymorphism_frequency=2.348e-01	polymorphism_score=10.6	prediction=polymorphism	ref_cov=64/24	total_cov=64/52
RA	114	.	NC_000913	2472817	0	C	A	bias_e_value=2.75092	bias_p_value=5.92661e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=165.2	fisher_strand_p_value=3.24881e-08	frequency=2.887e-01	ks_quality_p_value=1	major_base=C	major_cov=31/38	major_frequency=7.113e-01	minor_base=A	minor_cov=28/0	new_cov=28/0	polymorphism_frequency=2.887e-01	polymorphism_score=14.9	prediction=polymorphism	ref_cov=31/38	total_cov=59/38
RA	115	.	NC_000913	2477265	0	A	C	bias_e_value=4.43809e-08	bias_p_value=9.56144e-15	consensus_reject=FREQUENCY_CUTOFF	consensus_score=158.5	fisher_strand_p_value=2.59195e-16	frequency=3.095e-01	ks_quality_p_value=1	major_base=A	major_cov=6/52	major_frequency=6.905e-01	minor_base=C	minor_cov=26/0	new_cov=26/0	polymorphism_frequency=3.095e-01	polymorphism_score=19.9	prediction=polymorphism	ref_cov=6/52	total_cov=32/52
RA	116	.	NC_000913	2559939	0	C	A	bias_e_value=263.829	bias_p_value=5.68395e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=167.3	fisher_strand_p_value=4.25186e-06	frequency=2.653e-01	ks_quality_p_value=1	major_base=C	major_cov=39/33	major_frequency=7.347e-01	minor_base=A	minor_cov=26/0	new_cov=26/0	polymorphism_frequency=2.653e-01	polymorphism_score=10.2	prediction=polymorphism	ref_cov=39/33	total_cov=65/33
RA	117	.	NC_000913	2767443	0	C	A	bias_e_value=3.27568e-07	bias_p_value=7.05715e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=177.9	fisher_strand_p_value=2.02601e-15	frequency=3.125e-01	ks_quality_p_value=1	major_base=C	major_cov=6/49	major_frequency=6.875e-01	minor_base=A	minor_cov=25/0	new_cov=25/0	polymorphism_frequency=3.125e-01	polymorphism_score=11.6	prediction=polymorphism	ref_cov=6/49	total_cov=31/49
RA	118	.	NC_000913	2767445	0	C	A	bias_e_value=3.27568e-07	bias_p_value=7.05715e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=174.0	fisher_strand_p_value=2.02601e-15	frequency=3.125e-01	ks_quality_p_value=1	major_base=C	major_cov=6/49	major_frequency=6.875e-01	minor_base=A	minor_cov=25/0	new_cov=25/0	polymorphism_frequency=3.125e-01	polymorphism_score=12.1	prediction=polymorphism	ref_cov=6/49	total_cov=31/49
RA	119	.	NC_000913	2767447	0	C	A	bias_e_value=1.93777e-09	bias_p_value=4.17475e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=189.8	fisher_strand_p_value=1.04099e-17	frequency=3.294e-01	ks_quality_p_value=1	major_base=C	major_cov=5/52	major_frequency=6.706e-01	minor_base=A	minor_cov=28/0	new_cov=28/0	polymorphism_frequency=3.294e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=5/52	total_cov=33/52
RA	120	.	NC_000913	2767449	0	C	A	bias_e_value=6.35889e-06	bias_p_value=1.36996e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=196.7	fisher_strand_p_value=4.31146e-14	frequency=2.824e-01	ks_quality_p_value=1	major_base=C	major_cov=9/52	major_frequency=7.176e-01	minor_base=A	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=2.824e-01	polymorphism_score=11.0	prediction=polymorphism	ref_cov=9/52	total_cov=33/52
RA	121	.	NC_000913	2856087	0	G	T	bias_e_value=128.509	bias_p_value=2.7686e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=226.0	fisher_strand_p_value=1.95745e-06	frequency=2.069e-01	ks_quality_p_value=1	major_base=G	major_cov=45/47	major_frequency=7.931e-01	minor_base=T	minor_cov=0/24	new_cov=0/24	polymorphism_frequency=2.069e-01	polymorphism_score=11.6	prediction=polymorphism	ref_cov=45/47	total_cov=46/71
RA	122	.	NC_000913	2990480	0	C	A	bias_e_value=0.000109314	bias_p_value=2.35508e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=204.2	fisher_strand_p_value=8.16787e-13	frequency=3.551e-01	ks_quality_p_value=1	major_base=C	major_cov=40/49	major_frequency=6.449e-01	minor_base=A	minor_cov=49/0	new_cov=49/0	polymorphism_frequency=3.551e-01	polymorphism_score=33.0	prediction=polymorphism	ref_cov=40/49	total_cov=89/49
RA	123	.	NC_000913	3032307	0	C	T	bias_e_value=0.359374	bias_p_value=7.74238e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=203.9	fisher_strand_p_value=3.79734e-09	frequency=2.088e-01	ks_quality_p_value=1	major_base=C	major_cov=20/52	major_frequency=7.912e-01	minor_base=T	minor_cov=19/0	new_cov=19/0	polymorphism_frequency=2.088e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=20/52	total_cov=41/52
RA	124	.	NC_000913	3054886	0	G	T	bias_e_value=53.1805	bias_p_value=1.14572e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=163.8	fisher_strand_p_value=7.59211e-07	frequency=2.469e-01	ks_quality_p_value=1	major_base=G	major_cov=25/36	major_frequency=7.531e-01	minor_base=T	minor_cov=20/0	new_cov=20/0	polymorphism_frequency=2.469e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=25/36	total_cov=45/36
RA	125	.	NC_000913	3054894	0	G	T	bias_e_value=83.6088	bias_p_value=1.80127e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=130.7	fisher_strand_p_value=1.23325e-06	frequency=2.400e-01	ks_quality_p_value=1	major_base=G	major_cov=22/35	major_frequency=7.600e-01	minor_base=T	minor_cov=18/0	new_cov=18/0	polymorphism_frequency=2.400e-01	polymorphism_score=11.2	prediction=polymorphism	ref_cov=22/35	total_cov=40/35
RA	126	.	NC_000913	3157420	0	C	A	bias_e_value=0.0040206	bias_p_value=8.66199e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=267.3	fisher_strand_p_value=3.45246e-11	frequency=2.018e-01	ks_quality_p_value=1	major_base=C	major_cov=22/65	major_frequency=7.982e-01	minor_base=A	minor_cov=22/0	new_cov=22/0	polymorphism_frequency=2.018e-01	polymorphism_score=11.3	prediction=polymorphism	ref_cov=22/65	total_cov=44/65
RA	127	.	NC_000913	3168264	0	G	T	bias_e_value=178.123	bias_p_value=3.8375e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=196.7	fisher_strand_p_value=2.78237e-06	frequency=2.455e-01	ks_quality_p_value=1	major_base=G	major_cov=37/46	major_frequency=7.545e-01	minor_base=T	minor_cov=0/27	new_cov=0/27	polymorphism_frequency=2.455e-01	polymorphism_score=13.5	prediction=polymorphism	ref_cov=37/46	total_cov=37/73
RA	128	.	NC_000913	3433680	0	C	A	bias_e_value=0.00325093	bias_p_value=7.00381e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=181.1	fisher_strand_p_value=2.76714e-11	frequency=3.419e-01	ks_quality_p_value=1	major_base=C	major_cov=33/44	major_frequency=6.581e-01	minor_base=A	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=3.419e-01	polymorphism_score=15.8	prediction=polymorphism	ref_cov=33/44	total_cov=73/44
RA	129	.	NC_000913	3560455	1	.	G	bias_e_value=3873940	bias_p_value=0.834604	consensus_score=334.6	fisher_strand_p_value=0.483146	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=46/42	major_frequency=9.888e-01	minor_base=A	minor_cov=0/1	new_cov=46/42	polymorphism_frequency=9.888e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=46/44
RA	130	.	NC_000913	3741871	0	G	T	bias_e_value=3.23988	bias_p_value=6.98001e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=171.4	fisher_strand_p_value=3.86292e-08	frequency=2.889e-01	ks_quality_p_value=1	major_base=G	major_cov=37/27	major_frequency=7.111e-01	minor_base=T	minor_cov=0/26	new_cov=0/26	polymorphism_frequency=2.889e-01	polymorphism_score=10.7	prediction=polymorphism	ref_cov=37/27	total_cov=37/53
RA	131	.	NC_000913	3843750	0	C	A	bias_e_value=0.0219513	bias_p_value=4.7292e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=368.7	fisher_strand_p_value=2.02807e-10	frequency=2.143e-01	ks_quality_p_value=1	major_base=C	major_cov=71/72	major_frequency=7.857e-01	minor_base=A	minor_cov=39/0	new_cov=39/0	polymorphism_frequency=2.143e-01	polymorphism_score=14.6	prediction=polymorphism	ref_cov=71/72	total_cov=110/72
RA	132	.	NC_000913	3896780	0	C	A	bias_e_value=0.00260292	bias_p_value=5.60774e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=331.4	fisher_strand_p_value=2.19549e-11	frequency=2.252e-01	ks_quality_p_value=1	major_base=C	major_cov=42/75	major_frequency=7.748e-01	minor_base=A	minor_cov=33/1	new_cov=33/1	polymorphism_frequency=2.252e-01	polymorphism_score=14.4	prediction=polymorphism	ref_cov=42/75	total_cov=75/76
RA	133	.	NC_000913	3911533	0	C	A	bias_e_value=0.000267531	bias_p_value=5.7637e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=181.8	fisher_strand_p_value=2.06542e-12	frequency=3.600e-01	ks_quality_p_value=1	major_base=C	major_cov=34/46	major_frequency=6.400e-01	minor_base=A	minor_cov=45/0	new_cov=45/0	polymorphism_frequency=3.600e-01	polymorphism_score=19.7	prediction=polymorphism	ref_cov=34/46	total_cov=79/46
RA	134	.	NC_000913	3926595	0	C	A	bias_e_value=0.0233289	bias_p_value=5.02598e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=138.9	fisher_strand_p_value=2.16123e-10	frequency=3.289e-01	ks_quality_p_value=1	major_base=C	major_cov=14/37	major_frequency=6.711e-01	minor_base=A	minor_cov=25/0	new_cov=25/0	polymorphism_frequency=3.289e-01	polymorphism_score=10.3	prediction=polymorphism	ref_cov=14/37	total_cov=39/37
RA	135	.	NC_000913	4065656	0	G	T	bias_e_value=1.35329	bias_p_value=2.91552e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=188.3	fisher_strand_p_value=1.53513e-08	frequency=3.043e-01	ks_quality_p_value=1	major_base=G	major_cov=40/40	major_frequency=6.957e-01	minor_base=T	minor_cov=0/35	new_cov=0/35	polymorphism_frequency=3.043e-01	polymorphism_score=14.4	prediction=polymorphism	ref_cov=40/40	total_cov=40/75
RA	136	.	NC_000913	4261040	0	C	A	bias_e_value=0.0373553	bias_p_value=8.04785e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=304.3	fisher_strand_p_value=3.5355e-10	frequency=2.158e-01	ks_quality_p_value=1	major_base=C	major_cov=45/64	major_frequency=7.842e-01	minor_base=A	minor_cov=30/0	new_cov=30/0	polymorphism_frequency=2.158e-01	polymorphism_score=10.6	prediction=polymorphism	ref_cov=45/64	total_cov=75/64
RA	137	.	NC_000913	4296268	0	T	C	bias_e_value=3593700	bias_p_value=0.774228	consensus_reject=FREQUENCY_CUTOFF	consensus_score=49.6	fisher_strand_p_value=0.418357	frequency=2.500e-01	ks_quality_p_value=0.976472	major_base=T	major_cov=13/8	major_frequency=7.500e-01	minor_base=C	minor_cov=3/4	new_cov=3/4	polymorphism_frequency=2.500e-01	polymorphism_score=13.6	prediction=polymorphism	ref_cov=13/8	total_cov=16/13
RA	138	.	NC_000913	4296380	1	.	C	bias_e_value=4639350	bias_p_value=0.999504	consensus_score=188.7	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.968683	major_base=C	major_cov=32/23	major_frequency=9.821e-01	minor_base=T	minor_cov=1/0	new_cov=32/23	polymorphism_frequency=9.821e-01	polymorphism_score=-3.7	prediction=consensus	ref_cov=0/0	total_cov=33/23
RA	139	.	NC_000913	4296380	2	.	G	consensus_score=199.9	frequency=1	major_base=G	major_cov=33/23	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=33/23	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=33/23
RA	140	.	NC_000913	4325948	0	A	G	bias_e_value=2287940	bias_p_value=0.492915	consensus_reject=FREQUENCY_CUTOFF	consensus_score=55.3	fisher_strand_p_value=0.227787	frequency=2.353e-01	ks_quality_p_value=0.80114	major_base=A	major_cov=9/17	major_frequency=7.647e-01	minor_base=G	minor_cov=5/3	new_cov=5/3	polymorphism_frequency=2.353e-01	polymorphism_score=14.6	prediction=polymorphism	ref_cov=9/17	total_cov=14/20
RA	141	.	NC_000913	4360965	0	C	A	bias_e_value=5.9319e-08	bias_p_value=1.27797e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=258.3	fisher_strand_p_value=3.49261e-16	frequency=2.906e-01	ks_quality_p_value=1	major_base=C	major_cov=19/64	major_frequency=7.094e-01	minor_base=A	minor_cov=34/0	new_cov=34/0	polymorphism_frequency=2.906e-01	polymorphism_score=10.5	prediction=polymorphism	ref_cov=19/64	total_cov=53/64
RA	142	.	NC_000913	4427822	0	C	A	bias_e_value=7.90579e-05	bias_p_value=1.70323e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=222.4	fisher_strand_p_value=5.83917e-13	frequency=3.125e-01	ks_quality_p_value=1	major_base=C	major_cov=34/54	major_frequency=6.875e-01	minor_base=A	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=3.125e-01	polymorphism_score=12.9	prediction=polymorphism	ref_cov=34/54	total_cov=74/54
RA	143	.	NC_000913	4622176	0	C	A	bias_e_value=888.26	bias_p_value=0.000191367	consensus_reject=FREQUENCY_CUTOFF	consensus_score=173.5	fisher_strand_p_value=1.58806e-05	frequency=2.959e-01	ks_quality_p_value=1	major_base=C	major_cov=30/39	major_frequency=7.041e-01	minor_base=A	minor_cov=26/3	new_cov=26/3	polymorphism_frequency=2.959e-01	polymorphism_score=13.1	prediction=polymorphism	ref_cov=30/39	total_cov=56/43
MC	144	.	NC_000913	257908	258683	0	0	left_inside_cov=0	left_outside_cov=119	right_inside_cov=2	right_outside_cov=121
MC	145	.	NC_000913	1299499	1300697	1197	0	left_inside_cov=0	left_outside_cov=135	right_inside_cov=1	right_outside_cov=136
MC	146	.	NC_000913	1978503	1979278	0	0	left_inside_cov=0	left_outside_cov=133	right_inside_cov=8	right_outside_cov=142
MC	147	.	NC_000913	3423807	3424508	425	269	left_inside_cov=31	left_outside_cov=32	right_inside_cov=31	right_outside_cov=34
JC	148	.	NC_000913	1	1	NC_000913	4641652	-1	0	alignment_overlap=0	coverage_minus=57	coverage_plus=51	flanking_left=300	flanking_right=300	frequency=1	ignore=CIRCULAR_CHROMOSOME	junction_possible_overlap_registers=294	key=NC_000913__1__1__NC_000913__4641652__-1__0____300__300__0__0	max_left=293	max_left_minus=293	max_left_plus=246	max_min_left=149	max_min_left_minus=149	max_min_left_plus=148	max_min_right=147	max_min_right_minus=147	max_min_right_plus=146	max_pos_hash_score=588	max_right=295	max_right_minus=287	max_right_plus=295	neg_log10_pos_hash_p_value=0.3	new_junction_coverage=1.19	new_junction_read_count=114	polymorphism_frequency=1.000e+00	pos_hash_score=58	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=108
JC	149	.	NC_000913	126288	-1	NC_000913	126829	1	0	alignment_overlap=18	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.556e-02	junction_possible_overlap_registers=276	key=NC_000913__126288__-1__NC_000913__126811__1__18____300__300__0__0	max_left=75	max_left_minus=49	max_left_plus=75	max_min_left=75	max_min_left_minus=0	max_min_left_plus=75	max_min_right=21	max_min_right_minus=21	max_min_right_plus=21	max_pos_hash_score=552	max_right=112	max_right_minus=21	max_right_plus=112	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.556e-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=0.90	side_1_overlap=18	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=0.91	side_2_overlap=0	side_2_possible_overlap_registers=276	side_2_read_count=82	side_2_redundant=0	total_non_overlap_reads=3
JC	150	.	NC_000913	257907	-1	NC_000913	258684	1	0	alignment_overlap=8	coverage_minus=53	coverage_plus=64	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=286	key=NC_000913__257907__-1__NC_000913__258676__1__8____300__300__0__0	max_left=288	max_left_minus=288	max_left_plus=287	max_min_left=137	max_min_left_minus=89	max_min_left_plus=137	max_min_right=145	max_min_right_minus=145	max_min_right_plus=144	max_pos_hash_score=572	max_right=283	max_right_minus=283	max_right_plus=271	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.28	new_junction_read_count=119	polymorphism_frequency=1.000e+00	pos_hash_score=63	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=294	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=286	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=117
JC	151	.	NC_000913	270541	1	NC_000913	371759	-1	0	alignment_overlap=0	coverage_minus=59	coverage_plus=45	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=294	key=NC_000913__270541__1__NC_000913__371759__-1__0____300__300__1__0	max_left=294	max_left_minus=277	max_left_plus=294	max_min_left=149	max_min_left_minus=139	max_min_left_plus=149	max_min_right=145	max_min_right_minus=145	max_min_right_plus=130	max_pos_hash_score=588	max_right=298	max_right_minus=294	max_right_plus=298	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.10	new_junction_read_count=105	polymorphism_frequency=1.000e+00	pos_hash_score=65	prediction=consensus	read_count_offset=2	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=292	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=104
JC	152	.	NC_000913	371758	1	NC_000913	1470516	-1	0	alignment_overlap=0	coverage_minus=68	coverage_plus=61	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=294	key=NC_000913__371758__1__NC_000913__1470516__-1__0____300__300__0__1	max_left=299	max_left_minus=299	max_left_plus=292	max_min_left=145	max_min_left_minus=145	max_min_left_plus=126	max_min_right=149	max_min_right_minus=149	max_min_right_plus=135	max_pos_hash_score=588	max_right=299	max_right_minus=299	max_right_plus=286	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.35	new_junction_read_count=129	polymorphism_frequency=1.000e+00	pos_hash_score=77	prediction=consensus	read_count_offset=2	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=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=129
JC	153	.	NC_000913	628867	-1	NC_000913	629478	1	0	alignment_overlap=9	coverage_minus=1	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=4.860e-02	junction_possible_overlap_registers=285	key=NC_000913__628867__-1__NC_000913__629469__1__9____300__300__0__0	max_left=39	max_left_minus=39	max_left_plus=39	max_min_left=22	max_min_left_minus=0	max_min_left_plus=22	max_min_right=39	max_min_right_minus=39	max_min_right_plus=39	max_pos_hash_score=570	max_right=64	max_right_minus=39	max_right_plus=64	neg_log10_pos_hash_p_value=8.8	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.860e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.81	side_1_overlap=9	side_1_possible_overlap_registers=294	side_1_read_count=78	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=285	side_2_read_count=81	side_2_redundant=0	total_non_overlap_reads=4
JC	154	.	NC_000913	732239	-1	NC_000913	732420	1	0	alignment_overlap=12	coverage_minus=4	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=9.022e-02	junction_possible_overlap_registers=282	key=NC_000913__732239__-1__NC_000913__732408__1__12____300__300__0__0	max_left=275	max_left_minus=275	max_left_plus=65	max_min_left=122	max_min_left_minus=122	max_min_left_plus=65	max_min_right=13	max_min_right_minus=13	max_min_right_plus=0	max_pos_hash_score=564	max_right=269	max_right_minus=269	max_right_plus=223	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=9.022e-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=0.55	side_1_overlap=12	side_1_possible_overlap_registers=294	side_1_read_count=53	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.54	side_2_overlap=0	side_2_possible_overlap_registers=282	side_2_read_count=50	side_2_redundant=0	total_non_overlap_reads=5
JC	155	.	NC_000913	732408	1	NC_000913	3621836	-1	0	alignment_overlap=12	coverage_minus=1	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=7.698e-02	junction_possible_overlap_registers=282	key=NC_000913__732408__1__NC_000913__3621848__-1__12____300__300__0__1	max_left=269	max_left_minus=223	max_left_plus=269	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=122	max_min_right_minus=65	max_min_right_plus=122	max_pos_hash_score=564	max_right=122	max_right_minus=65	max_right_plus=122	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=7.698e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.52	side_1_overlap=12	side_1_possible_overlap_registers=294	side_1_read_count=50	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=4
JC	156	.	NC_000913	1207790	1	NC_000913	1209619	1	0	alignment_overlap=16	coverage_minus=26	coverage_plus=27	flanking_left=300	flanking_right=300	frequency=4.295e-01	junction_possible_overlap_registers=278	key=NC_000913__1207790__1__NC_000913__1209603__1__16____300__300__0__0	max_left=281	max_left_minus=281	max_left_plus=250	max_min_left=139	max_min_left_minus=136	max_min_left_plus=139	max_min_right=142	max_min_right_minus=126	max_min_right_plus=142	max_pos_hash_score=556	max_right=280	max_right_minus=250	max_right_plus=280	neg_log10_pos_hash_p_value=1.3	new_junction_coverage=0.59	new_junction_read_count=53	polymorphism_frequency=4.295e-01	pos_hash_score=35	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.80	side_1_overlap=16	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=0.75	side_2_overlap=0	side_2_possible_overlap_registers=278	side_2_read_count=68	side_2_redundant=0	total_non_overlap_reads=53
JC	157	.	NC_000913	1207800	1	NC_000913	1209610	1	-1	alignment_overlap=-1	coverage_minus=7	coverage_plus=0	flanking_left=300	flanking_right=300	frequency=9.846e-02	junction_possible_overlap_registers=293	key=NC_000913__1207800__1__NC_000913__1209610__1__-1__A__300__300__0__0	max_left=292	max_left_minus=292	max_left_plus=0	max_min_left=139	max_min_left_minus=139	max_min_left_plus=0	max_min_right=105	max_min_right_minus=105	max_min_right_plus=0	max_pos_hash_score=586	max_right=236	max_right_minus=236	max_right_plus=0	neg_log10_pos_hash_p_value=6.9	new_junction_coverage=0.08	new_junction_read_count=8	polymorphism_frequency=9.846e-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=0.81	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=78	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=294	side_2_read_count=69	side_2_redundant=0	total_non_overlap_reads=7	unique_read_sequence=A
JC	158	.	NC_000913	1207805	-1	NC_000913	1209602	-1	0	alignment_overlap=16	coverage_minus=16	coverage_plus=10	flanking_left=300	flanking_right=300	frequency=2.684e-01	junction_possible_overlap_registers=278	key=NC_000913__1207805__-1__NC_000913__1209618__-1__16____300__300__0__0	max_left=272	max_left_minus=174	max_left_plus=272	max_min_left=140	max_min_left_minus=140	max_min_left_plus=124	max_min_right=142	max_min_right_minus=142	max_min_right_plus=117	max_pos_hash_score=556	max_right=270	max_right_minus=270	max_right_plus=267	neg_log10_pos_hash_p_value=2.9	new_junction_coverage=0.29	new_junction_read_count=26	polymorphism_frequency=2.684e-01	pos_hash_score=21	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.81	side_1_overlap=16	side_1_possible_overlap_registers=294	side_1_read_count=78	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.75	side_2_overlap=0	side_2_possible_overlap_registers=278	side_2_read_count=68	side_2_redundant=0	total_non_overlap_reads=26
JC	159	.	NC_000913	1286728	-1	NC_000913	1287263	1	0	alignment_overlap=21	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.737e-02	junction_possible_overlap_registers=273	key=NC_000913__1286728__-1__NC_000913__1287242__1__21____300__300__0__0	max_left=92	max_left_minus=92	max_left_plus=92	max_min_left=62	max_min_left_minus=0	max_min_left_plus=62	max_min_right=34	max_min_right_minus=34	max_min_right_plus=34	max_pos_hash_score=546	max_right=70	max_right_minus=34	max_right_plus=70	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.737e-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=0.79	side_1_overlap=21	side_1_possible_overlap_registers=294	side_1_read_count=76	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=273	side_2_read_count=84	side_2_redundant=0	total_non_overlap_reads=3
JC	160	.	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=1.229e-01	junction_possible_overlap_registers=274	key=NC_000913__1286906__-1__NC_000913__1287537__1__20____300__300__0__0	max_left=270	max_left_minus=270	max_left_plus=241	max_min_left=2	max_min_left_minus=0	max_min_left_plus=2	max_min_right=49	max_min_right_minus=43	max_min_right_plus=49	max_pos_hash_score=548	max_right=153	max_right_minus=43	max_right_plus=153	neg_log10_pos_hash_p_value=7.0	new_junction_coverage=0.10	new_junction_read_count=9	polymorphism_frequency=1.229e-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=0.69	side_1_overlap=20	side_1_possible_overlap_registers=294	side_1_read_count=66	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.75	side_2_overlap=0	side_2_possible_overlap_registers=274	side_2_read_count=67	side_2_redundant=0	total_non_overlap_reads=7
JC	161	.	NC_000913	1287262	-1	NC_000913	1287382	1	0	alignment_overlap=21	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.268e-02	junction_possible_overlap_registers=273	key=NC_000913__1287262__-1__NC_000913__1287361__1__21____300__300__0__0	max_left=72	max_left_minus=72	max_left_plus=55	max_min_left=72	max_min_left_minus=72	max_min_left_plus=55	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=546	max_right=253	max_right_minus=100	max_right_plus=253	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=5.268e-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=0.90	side_1_overlap=21	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=0.72	side_2_overlap=0	side_2_possible_overlap_registers=273	side_2_read_count=64	side_2_redundant=0	total_non_overlap_reads=3
JC	162	.	NC_000913	1287329	-1	NC_000913	1287624	1	0	alignment_overlap=87	coverage_minus=4	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.858e-01	junction_possible_overlap_registers=207	key=NC_000913__1287329__-1__NC_000913__1287537__1__87____300__300__0__0	max_left=168	max_left_minus=168	max_left_plus=168	max_min_left=83	max_min_left_minus=73	max_min_left_plus=83	max_min_right=54	max_min_right_minus=54	max_min_right_plus=23	max_pos_hash_score=414	max_right=140	max_right_minus=86	max_right_plus=140	neg_log10_pos_hash_p_value=5.1	new_junction_coverage=0.16	new_junction_read_count=11	polymorphism_frequency=1.858e-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=0.76	side_1_overlap=87	side_1_possible_overlap_registers=294	side_1_read_count=73	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.67	side_2_overlap=0	side_2_possible_overlap_registers=207	side_2_read_count=45	side_2_redundant=0	total_non_overlap_reads=9
JC	163	.	NC_000913	1299498	-1	NC_000913	1300698	1	0	alignment_overlap=4	coverage_minus=78	coverage_plus=55	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=290	key=NC_000913__1299498__-1__NC_000913__1300694__1__4____300__300__0__0	max_left=294	max_left_minus=285	max_left_plus=294	max_min_left=144	max_min_left_minus=127	max_min_left_plus=144	max_min_right=142	max_min_right_minus=128	max_min_right_plus=142	max_pos_hash_score=580	max_right=289	max_right_minus=289	max_right_plus=268	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.43	new_junction_read_count=135	polymorphism_frequency=1.000e+00	pos_hash_score=71	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=4	side_1_possible_overlap_registers=294	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=290	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=133
JC	164	.	NC_000913	1944237	-1	NC_000913	1944335	1	0	alignment_overlap=17	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.800e-02	junction_possible_overlap_registers=277	key=NC_000913__1944237__-1__NC_000913__1944318__1__17____300__300__0__0	max_left=197	max_left_minus=81	max_left_plus=197	max_min_left=135	max_min_left_minus=81	max_min_left_plus=135	max_min_right=85	max_min_right_minus=0	max_min_right_plus=85	max_pos_hash_score=554	max_right=202	max_right_minus=202	max_right_plus=146	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=4.800e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.72	side_1_overlap=17	side_1_possible_overlap_registers=294	side_1_read_count=69	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.60	side_2_overlap=0	side_2_possible_overlap_registers=277	side_2_read_count=54	side_2_redundant=0	total_non_overlap_reads=3
JC	165	.	NC_000913	1978502	-1	NC_000913	1979279	1	0	alignment_overlap=8	coverage_minus=61	coverage_plus=71	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=286	key=NC_000913__1978502__-1__NC_000913__1979271__1__8____300__300__0__0	max_left=290	max_left_minus=290	max_left_plus=286	max_min_left=144	max_min_left_minus=144	max_min_left_plus=144	max_min_right=142	max_min_right_minus=135	max_min_right_plus=142	max_pos_hash_score=572	max_right=291	max_right_minus=291	max_right_plus=286	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.44	new_junction_read_count=134	polymorphism_frequency=1.000e+00	pos_hash_score=83	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=8	side_1_possible_overlap_registers=294	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.00	side_2_overlap=0	side_2_possible_overlap_registers=286	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=132
JC	166	.	NC_000913	2066553	1	NC_000913	3131426	1	0	alignment_overlap=8	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.452e-02	junction_possible_overlap_registers=286	key=NC_000913__2066553__1__NC_000913__3131418__1__8____300__300__0__0	max_left=62	max_left_minus=62	max_left_plus=62	max_min_left=25	max_min_left_minus=25	max_min_left_plus=25	max_min_right=36	max_min_right_minus=36	max_min_right_plus=36	max_pos_hash_score=572	max_right=36	max_right_minus=36	max_right_plus=36	neg_log10_pos_hash_p_value=8.2	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.452e-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=0.88	side_1_overlap=8	side_1_possible_overlap_registers=294	side_1_read_count=84	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.97	side_2_overlap=0	side_2_possible_overlap_registers=286	side_2_read_count=90	side_2_redundant=0	total_non_overlap_reads=4
JC	167	.	NC_000913	2357742	-1	NC_000913	2357938	1	0	alignment_overlap=11	coverage_minus=3	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=5.290e-02	junction_possible_overlap_registers=283	key=NC_000913__2357742__-1__NC_000913__2357927__1__11____300__300__0__0	max_left=255	max_left_minus=255	max_left_plus=206	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=123	max_min_right_minus=96	max_min_right_plus=123	max_pos_hash_score=566	max_right=123	max_right_minus=96	max_right_plus=123	neg_log10_pos_hash_p_value=7.1	new_junction_coverage=0.07	new_junction_read_count=6	polymorphism_frequency=5.290e-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=1.16	side_1_overlap=11	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=1.17	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=108	side_2_redundant=0	total_non_overlap_reads=6
JC	168	.	NC_000913	2653386	-1	NC_000913	2653714	1	-1	alignment_overlap=-1	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.067e-02	junction_possible_overlap_registers=293	key=NC_000913__2653386__-1__NC_000913__2653714__1__-1__C__300__300__0__0	max_left=121	max_left_minus=121	max_left_plus=74	max_min_left=121	max_min_left_minus=121	max_min_left_plus=74	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=586	max_right=245	max_right_minus=186	max_right_plus=245	neg_log10_pos_hash_p_value=7.8	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=5.067e-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=0.87	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=83	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.10	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=105	side_2_redundant=0	total_non_overlap_reads=5	unique_read_sequence=C
JC	169	.	NC_000913	2904285	-1	NC_000913	2904347	1	0	alignment_overlap=28	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=5.026e-02	junction_possible_overlap_registers=266	key=NC_000913__2904285__-1__NC_000913__2904319__1__28____300__300__0__0	max_left=60	max_left_minus=60	max_left_plus=60	max_min_left=60	max_min_left_minus=60	max_min_left_plus=60	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=532	max_right=240	max_right_minus=240	max_right_plus=208	neg_log10_pos_hash_p_value=8.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=5.026e-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=0.62	side_1_overlap=28	side_1_possible_overlap_registers=294	side_1_read_count=59	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=266	side_2_read_count=60	side_2_redundant=0	total_non_overlap_reads=3
JC	170	.	NC_000913	3095995	-1	NC_000913	3096266	1	0	alignment_overlap=11	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.047e-02	junction_possible_overlap_registers=283	key=NC_000913__3095995__-1__NC_000913__3096255__1__11____300__300__0__0	max_left=243	max_left_minus=243	max_left_plus=124	max_min_left=120	max_min_left_minus=0	max_min_left_plus=120	max_min_right=142	max_min_right_minus=142	max_min_right_plus=76	max_pos_hash_score=566	max_right=169	max_right_minus=142	max_right_plus=169	neg_log10_pos_hash_p_value=7.6	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=5.047e-02	pos_hash_score=5	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.08	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=103	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.97	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=89	side_2_redundant=0	total_non_overlap_reads=5
JC	171	.	NC_000913	3130938	-1	NC_000913	3131418	1	0	alignment_overlap=8	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.346e-02	junction_possible_overlap_registers=286	key=NC_000913__3130946__-1__NC_000913__3131418__1__8____300__300__1__0	max_left=289	max_left_minus=289	max_left_plus=62	max_min_left=25	max_min_left_minus=25	max_min_left_plus=25	max_min_right=36	max_min_right_minus=36	max_min_right_plus=36	max_pos_hash_score=572	max_right=36	max_right_minus=36	max_right_plus=36	neg_log10_pos_hash_p_value=7.7	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=5.346e-02	pos_hash_score=5	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=0.95	side_2_overlap=8	side_2_possible_overlap_registers=294	side_2_read_count=91	side_2_redundant=0	total_non_overlap_reads=5
JC	172	.	NC_000913	3323962	-1	NC_000913	3324312	1	0	alignment_overlap=10	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=2.719e-02	junction_possible_overlap_registers=284	key=NC_000913__3323962__-1__NC_000913__3324302__1__10____300__300__0__0	max_left=206	max_left_minus=206	max_left_plus=161	max_min_left=44	max_min_left_minus=0	max_min_left_plus=44	max_min_right=128	max_min_right_minus=84	max_min_right_plus=128	max_pos_hash_score=568	max_right=128	max_right_minus=84	max_right_plus=128	neg_log10_pos_hash_p_value=8.8	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.719e-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=1.03	side_1_overlap=10	side_1_possible_overlap_registers=294	side_1_read_count=99	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.29	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=119	side_2_redundant=0	total_non_overlap_reads=3
JC	173	.	NC_000913	3444364	-1	NC_000913	3444680	1	0	alignment_overlap=14	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=2.868e-02	junction_possible_overlap_registers=280	key=NC_000913__3444364__-1__NC_000913__3444666__1__14____300__300__0__0	max_left=92	max_left_minus=92	max_left_plus=82	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=80	max_min_right_minus=80	max_min_right_plus=80	max_pos_hash_score=560	max_right=80	max_right_minus=80	max_right_plus=80	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.868e-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=14	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=1.17	side_2_overlap=0	side_2_possible_overlap_registers=280	side_2_read_count=107	side_2_redundant=0	total_non_overlap_reads=3
JC	174	.	NC_000913	3648156	-1	NC_000913	3648388	1	0	alignment_overlap=5	coverage_minus=5	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=1.120e-01	junction_possible_overlap_registers=289	key=NC_000913__3648156__-1__NC_000913__3648383__1__5____300__300__0__0	max_left=246	max_left_minus=228	max_left_plus=246	max_min_left=133	max_min_left_minus=0	max_min_left_plus=133	max_min_right=140	max_min_right_minus=140	max_min_right_plus=92	max_pos_hash_score=578	max_right=162	max_right_minus=140	max_right_plus=162	neg_log10_pos_hash_p_value=6.0	new_junction_coverage=0.12	new_junction_read_count=11	polymorphism_frequency=1.120e-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=0.95	side_1_overlap=5	side_1_possible_overlap_registers=294	side_1_read_count=91	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.90	side_2_overlap=0	side_2_possible_overlap_registers=289	side_2_read_count=85	side_2_redundant=0	total_non_overlap_reads=10
JC	175	.	NC_000913	4542682	1	NC_000913	4542996	1	0	alignment_overlap=9	coverage_minus=4	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=6.834e-02	junction_possible_overlap_registers=285	key=NC_000913__4542682__1__NC_000913__4542987__1__9____300__300__0__0	max_left=249	max_left_minus=136	max_left_plus=249	max_min_left=141	max_min_left_minus=136	max_min_left_plus=141	max_min_right=73	max_min_right_minus=0	max_min_right_plus=73	max_pos_hash_score=570	max_right=242	max_right_minus=209	max_right_plus=242	neg_log10_pos_hash_p_value=5.6	new_junction_coverage=0.11	new_junction_read_count=10	polymorphism_frequency=6.834e-02	pos_hash_score=10	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.48	side_1_overlap=9	side_1_possible_overlap_registers=294	side_1_read_count=142	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.45	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=135	side_2_redundant=0	total_non_overlap_reads=10
JC	176	.	NC_000913	4542690	-1	NC_000913	4542986	-1	0	alignment_overlap=9	coverage_minus=7	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=8.708e-02	junction_possible_overlap_registers=285	key=NC_000913__4542690__-1__NC_000913__4542995__-1__9____300__300__0__0	max_left=282	max_left_minus=268	max_left_plus=282	max_min_left=133	max_min_left_minus=127	max_min_left_plus=133	max_min_right=140	max_min_right_minus=140	max_min_right_plus=114	max_pos_hash_score=570	max_right=280	max_right_minus=280	max_right_plus=158	neg_log10_pos_hash_p_value=5.9	new_junction_coverage=0.14	new_junction_read_count=13	polymorphism_frequency=8.708e-02	pos_hash_score=9	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.50	side_1_overlap=9	side_1_possible_overlap_registers=294	side_1_read_count=144	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.43	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=133	side_2_redundant=0	total_non_overlap_reads=12
UN	177	.	NC_000913	15650	16469
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