#=GENOME_DIFF	1.0
#=CREATED	21:31:41 08 Jan 2025
#=PROGRAM	breseq 0.38.1 
#=COMMAND	breseq -j 16 -r /scratch/hb-JMvDijl/GerbrenSpoelstra/genomes/ATCC25586/GCA_003019295.1/Fusobacterium_nucleatum_subsp_nucleatum_ATCC25586.gbk /scratch/hb-JMvDijl/GerbrenSpoelstra/fastq/F.n_ATCC_Unknown_CL297-ZX01-010003_2.fq.gz /scratch/hb-JMvDijl/GerbrenSpoelstra/fastq/F.n_ATCC_Unknown_CL297-ZX01-010003_2.fq.gz -o /tmp/F.n_ATCC
#=REFSEQ	/scratch/hb-JMvDijl/GerbrenSpoelstra/genomes/ATCC25586/GCA_003019295.1/Fusobacterium_nucleatum_subsp_nucleatum_ATCC25586.gbk
#=READSEQ	/scratch/hb-JMvDijl/GerbrenSpoelstra/fastq/F.n_ATCC_Unknown_CL297-ZX01-010003_2.fq.gz
#=CONVERTED-BASES	528447000
#=CONVERTED-READS	3522980
#=INPUT-BASES	531293850
#=INPUT-READS	3541959
#=MAPPED-BASES	508191265
#=MAPPED-READS	3391253
SNP	1	19	CP028101	516032	A
SNP	2	23	CP028101	761062	G
SNP	3	29	CP028101	875381	G
RA	4	.	CP028101	81639	0	C	T	bias_e_value=7.55327e-14	bias_p_value=3.46464e-20	consensus_reject=FREQUENCY_CUTOFF	consensus_score=374.8	fisher_strand_p_value=6.96895e-22	frequency=2.982e-01	ks_quality_p_value=1	major_base=C	major_cov=62/98	major_frequency=7.018e-01	minor_base=T	minor_cov=68/0	new_cov=68/0	polymorphism_frequency=2.982e-01	polymorphism_score=27.3	prediction=polymorphism	ref_cov=62/98	total_cov=137/98
RA	5	.	CP028101	128387	0	G	A	bias_e_value=1.79407e-26	bias_p_value=8.2293e-33	consensus_reject=FREQUENCY_CUTOFF	consensus_score=490.1	fisher_strand_p_value=1.03839e-34	frequency=2.773e-01	ks_quality_p_value=1	major_base=G	major_cov=145/40	major_frequency=7.227e-01	minor_base=A	minor_cov=0/71	new_cov=0/71	polymorphism_frequency=2.773e-01	polymorphism_score=48.2	prediction=polymorphism	ref_cov=145/40	total_cov=145/115
RA	6	.	CP028101	158532	0	C	T	bias_e_value=1.57945e-06	bias_p_value=7.24487e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=461.8	fisher_strand_p_value=2.23383e-14	frequency=2.027e-01	ks_quality_p_value=1	major_base=C	major_cov=77/100	major_frequency=7.973e-01	minor_base=T	minor_cov=45/0	new_cov=45/0	polymorphism_frequency=2.027e-01	polymorphism_score=12.2	prediction=polymorphism	ref_cov=77/100	total_cov=124/100
RA	7	.	CP028101	158536	0	A	G	bias_e_value=1.50886e-14	bias_p_value=6.92104e-21	consensus_reject=FREQUENCY_CUTOFF	consensus_score=314.1	fisher_strand_p_value=1.34759e-22	frequency=3.165e-01	ks_quality_p_value=1	major_base=A	major_cov=50/99	major_frequency=6.835e-01	minor_base=G	minor_cov=68/1	new_cov=68/1	polymorphism_frequency=3.165e-01	polymorphism_score=80.7	prediction=polymorphism	ref_cov=50/99	total_cov=118/100
RA	8	.	CP028101	158537	0	C	G	bias_e_value=1.56195e-13	bias_p_value=7.16457e-20	consensus_reject=FREQUENCY_CUTOFF	consensus_score=378.2	fisher_strand_p_value=1.46294e-21	frequency=2.609e-01	ks_quality_p_value=1	major_base=C	major_cov=36/100	major_frequency=7.391e-01	minor_base=G	minor_cov=48/0	new_cov=48/0	polymorphism_frequency=2.609e-01	polymorphism_score=65.8	prediction=polymorphism	ref_cov=36/100	total_cov=115/100
RA	9	.	CP028101	158538	0	C	G	bias_e_value=7.46554e-15	bias_p_value=3.4244e-21	consensus_reject=FREQUENCY_CUTOFF	consensus_score=390.6	fisher_strand_p_value=6.57576e-23	frequency=2.821e-01	ks_quality_p_value=1	major_base=C	major_cov=40/100	major_frequency=7.179e-01	minor_base=G	minor_cov=55/0	new_cov=55/0	polymorphism_frequency=2.821e-01	polymorphism_score=83.8	prediction=polymorphism	ref_cov=40/100	total_cov=115/100
RA	10	.	CP028101	262600	0	C	T	bias_e_value=2.48422e-10	bias_p_value=1.1395e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=478.6	fisher_strand_p_value=2.75009e-18	frequency=2.174e-01	ks_quality_p_value=1	major_base=C	major_cov=81/117	major_frequency=7.826e-01	minor_base=T	minor_cov=55/0	new_cov=55/0	polymorphism_frequency=2.174e-01	polymorphism_score=13.5	prediction=polymorphism	ref_cov=81/117	total_cov=154/117
RA	11	.	CP028101	274795	0	T	C	bias_e_value=5.54135e-19	bias_p_value=2.54179e-25	consensus_reject=FREQUENCY_CUTOFF	consensus_score=554.5	fisher_strand_p_value=4.11592e-27	frequency=2.096e-01	ks_quality_p_value=1	major_base=T	major_cov=35/146	major_frequency=7.904e-01	minor_base=C	minor_cov=48/0	new_cov=48/0	polymorphism_frequency=2.096e-01	polymorphism_score=47.3	prediction=polymorphism	ref_cov=35/146	total_cov=84/146
RA	12	.	CP028101	276378	0	A	C	bias_e_value=3.09674e-14	bias_p_value=1.42046e-20	consensus_reject=FREQUENCY_CUTOFF	consensus_score=495.8	fisher_strand_p_value=2.80583e-22	frequency=2.642e-01	ks_quality_p_value=1	major_base=A	major_cov=49/107	major_frequency=7.358e-01	minor_base=C	minor_cov=56/0	new_cov=56/0	polymorphism_frequency=2.642e-01	polymorphism_score=46.2	prediction=polymorphism	ref_cov=49/107	total_cov=109/107
RA	13	.	CP028101	276396	0	G	T	bias_e_value=1.02206e-10	bias_p_value=4.68814e-17	consensus_reject=FREQUENCY_CUTOFF	consensus_score=572.9	fisher_strand_p_value=1.10714e-18	frequency=2.160e-01	ks_quality_p_value=1	major_base=G	major_cov=55/112	major_frequency=7.840e-01	minor_base=T	minor_cov=46/0	new_cov=46/0	polymorphism_frequency=2.160e-01	polymorphism_score=33.9	prediction=polymorphism	ref_cov=55/112	total_cov=103/112
RA	14	.	CP028101	345348	0	A	G	bias_e_value=3.28075e-27	bias_p_value=1.50486e-33	consensus_reject=FREQUENCY_CUTOFF	consensus_score=366.0	fisher_strand_p_value=1.85853e-35	frequency=3.312e-01	ks_quality_p_value=1	major_base=A	major_cov=69/137	major_frequency=6.688e-01	minor_base=G	minor_cov=102/0	new_cov=102/0	polymorphism_frequency=3.312e-01	polymorphism_score=139.6	prediction=polymorphism	ref_cov=69/137	total_cov=171/137
RA	15	.	CP028101	345350	0	C	G	bias_e_value=1.16057e-37	bias_p_value=5.32347e-44	consensus_reject=FREQUENCY_CUTOFF	consensus_score=429.6	fisher_strand_p_value=5.0556e-46	frequency=3.430e-01	ks_quality_p_value=1	major_base=C	major_cov=20/139	major_frequency=6.570e-01	minor_base=G	minor_cov=83/0	new_cov=83/0	polymorphism_frequency=3.430e-01	polymorphism_score=140.7	prediction=polymorphism	ref_cov=20/139	total_cov=171/139
RA	16	.	CP028101	480264	0	G	A	bias_e_value=8.46354e-08	bias_p_value=3.88218e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=570.4	fisher_strand_p_value=1.09518e-15	frequency=2.063e-01	ks_quality_p_value=1	major_base=G	major_cov=117/137	major_frequency=7.937e-01	minor_base=A	minor_cov=0/66	new_cov=0/66	polymorphism_frequency=2.063e-01	polymorphism_score=12.2	prediction=polymorphism	ref_cov=117/137	total_cov=117/221
RA	17	.	CP028101	480265	0	T	C	bias_e_value=2.34198e-08	bias_p_value=1.07425e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=571.2	fisher_strand_p_value=2.92161e-16	frequency=2.130e-01	ks_quality_p_value=1	major_base=T	major_cov=118/148	major_frequency=7.870e-01	minor_base=C	minor_cov=0/72	new_cov=0/72	polymorphism_frequency=2.130e-01	polymorphism_score=60.1	prediction=polymorphism	ref_cov=118/148	total_cov=118/220
RA	18	.	CP028101	502592	0	G	A	bias_e_value=4.3441e-11	bias_p_value=1.99262e-17	consensus_reject=FREQUENCY_CUTOFF	consensus_score=545.9	fisher_strand_p_value=4.61031e-19	frequency=2.068e-01	ks_quality_p_value=1	major_base=G	major_cov=128/83	major_frequency=7.932e-01	minor_base=A	minor_cov=0/55	new_cov=0/55	polymorphism_frequency=2.068e-01	polymorphism_score=14.4	prediction=polymorphism	ref_cov=128/83	total_cov=128/140
RA	19	.	CP028101	516032	0	G	A	consensus_score=1155.6	frequency=1	major_base=A	major_cov=155/149	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=155/149	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=155/149
RA	20	.	CP028101	618209	0	C	G	bias_e_value=2128230	bias_p_value=0.976205	consensus_reject=FREQUENCY_CUTOFF	consensus_score=196.9	fisher_strand_p_value=1	frequency=7.045e-01	ks_quality_p_value=0.789933	major_base=G	major_cov=92/94	major_frequency=7.045e-01	minor_base=C	minor_cov=39/39	new_cov=92/94	polymorphism_frequency=7.045e-01	polymorphism_score=inf	prediction=polymorphism	ref_cov=39/39	total_cov=132/133
RA	21	.	CP028101	628912	0	G	C	bias_e_value=1.80935e-18	bias_p_value=8.29938e-25	consensus_reject=FREQUENCY_CUTOFF	consensus_score=586.2	fisher_strand_p_value=1.37062e-26	frequency=2.154e-01	ks_quality_p_value=1	major_base=G	major_cov=147/46	major_frequency=7.846e-01	minor_base=C	minor_cov=0/53	new_cov=0/53	polymorphism_frequency=2.154e-01	polymorphism_score=83.3	prediction=polymorphism	ref_cov=147/46	total_cov=147/122
RA	22	.	CP028101	688652	0	G	C	bias_e_value=5.2946e-29	bias_p_value=2.4286e-35	consensus_reject=FREQUENCY_CUTOFF	consensus_score=476.1	fisher_strand_p_value=2.85223e-37	frequency=3.278e-01	ks_quality_p_value=1	major_base=G	major_cov=129/33	major_frequency=6.722e-01	minor_base=C	minor_cov=0/79	new_cov=0/79	polymorphism_frequency=3.278e-01	polymorphism_score=127.8	prediction=polymorphism	ref_cov=129/33	total_cov=129/126
RA	23	.	CP028101	761062	0	A	G	consensus_score=104.8	frequency=1	major_base=G	major_cov=17/18	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/18	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/18
RA	24	.	CP028101	845501	0	C	T	bias_e_value=5.49544e-14	bias_p_value=2.52073e-20	consensus_reject=FREQUENCY_CUTOFF	consensus_score=329.1	fisher_strand_p_value=5.03742e-22	frequency=2.842e-01	ks_quality_p_value=1	major_base=C	major_cov=40/96	major_frequency=7.158e-01	minor_base=T	minor_cov=54/0	new_cov=54/0	polymorphism_frequency=2.842e-01	polymorphism_score=45.2	prediction=polymorphism	ref_cov=40/96	total_cov=94/96
RA	25	.	CP028101	845508	0	C	T	bias_e_value=1.3625e-13	bias_p_value=6.2497e-20	consensus_reject=FREQUENCY_CUTOFF	consensus_score=303.2	fisher_strand_p_value=1.27251e-21	frequency=2.917e-01	ks_quality_p_value=1	major_base=C	major_cov=38/98	major_frequency=7.083e-01	minor_base=T	minor_cov=55/1	new_cov=55/1	polymorphism_frequency=2.917e-01	polymorphism_score=62.7	prediction=polymorphism	ref_cov=38/98	total_cov=93/99
RA	26	.	CP028101	849254	0	A	C	bias_e_value=4.31711e-13	bias_p_value=1.98023e-19	consensus_reject=FREQUENCY_CUTOFF	consensus_score=487.1	fisher_strand_p_value=4.13102e-21	frequency=2.376e-01	ks_quality_p_value=1	major_base=A	major_cov=33/105	major_frequency=7.624e-01	minor_base=C	minor_cov=43/0	new_cov=43/0	polymorphism_frequency=2.376e-01	polymorphism_score=24.1	prediction=polymorphism	ref_cov=33/105	total_cov=77/105
RA	27	.	CP028101	849257	0	A	C	bias_e_value=1.39669e-13	bias_p_value=6.40656e-20	consensus_reject=FREQUENCY_CUTOFF	consensus_score=461.7	fisher_strand_p_value=1.30512e-21	frequency=2.444e-01	ks_quality_p_value=1	major_base=A	major_cov=32/104	major_frequency=7.556e-01	minor_base=C	minor_cov=44/0	new_cov=44/0	polymorphism_frequency=2.444e-01	polymorphism_score=39.7	prediction=polymorphism	ref_cov=32/104	total_cov=80/105
RA	28	.	CP028101	849278	0	A	C	bias_e_value=1.56453e-10	bias_p_value=7.17642e-17	consensus_reject=FREQUENCY_CUTOFF	consensus_score=546.1	fisher_strand_p_value=1.7124e-18	frequency=2.162e-01	ks_quality_p_value=1	major_base=A	major_cov=40/105	major_frequency=7.838e-01	minor_base=C	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=2.162e-01	polymorphism_score=18.1	prediction=polymorphism	ref_cov=40/105	total_cov=80/105
RA	29	.	CP028101	875381	0	A	G	bias_e_value=110379	bias_p_value=0.0506304	consensus_score=25.6	fisher_strand_p_value=0.0677583	frequency=1	ks_quality_p_value=0.130435	major_base=G	major_cov=13/7	major_frequency=8.696e-01	minor_base=A	minor_cov=0/3	new_cov=13/7	polymorphism_frequency=8.696e-01	polymorphism_score=2.8	prediction=consensus	ref_cov=0/3	total_cov=13/10
RA	30	.	CP028101	915752	0	C	G	bias_e_value=4.71331e-12	bias_p_value=2.16197e-18	consensus_reject=FREQUENCY_CUTOFF	consensus_score=356.8	fisher_strand_p_value=4.7523e-20	frequency=2.500e-01	ks_quality_p_value=1	major_base=C	major_cov=27/93	major_frequency=7.500e-01	minor_base=G	minor_cov=40/0	new_cov=40/0	polymorphism_frequency=2.500e-01	polymorphism_score=50.9	prediction=polymorphism	ref_cov=27/93	total_cov=89/93
RA	31	.	CP028101	958957	0	T	G	bias_e_value=4.43222e-11	bias_p_value=2.03303e-17	consensus_reject=FREQUENCY_CUTOFF	consensus_score=530.1	fisher_strand_p_value=4.70606e-19	frequency=2.271e-01	ks_quality_p_value=1	major_base=T	major_cov=108/52	major_frequency=7.729e-01	minor_base=G	minor_cov=0/47	new_cov=0/47	polymorphism_frequency=2.271e-01	polymorphism_score=14.3	prediction=polymorphism	ref_cov=108/52	total_cov=109/102
RA	32	.	CP028101	967944	0	A	C	bias_e_value=4.73787e-09	bias_p_value=2.17323e-15	consensus_reject=FREQUENCY_CUTOFF	consensus_score=562.6	fisher_strand_p_value=5.65786e-17	frequency=2.150e-01	ks_quality_p_value=1	major_base=A	major_cov=61/107	major_frequency=7.850e-01	minor_base=C	minor_cov=46/0	new_cov=46/0	polymorphism_frequency=2.150e-01	polymorphism_score=22.6	prediction=polymorphism	ref_cov=61/107	total_cov=108/107
RA	33	.	CP028101	967957	0	A	C	bias_e_value=7.0731e-07	bias_p_value=3.24439e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=515.1	fisher_strand_p_value=9.75432e-15	frequency=2.174e-01	ks_quality_p_value=1	major_base=A	major_cov=60/102	major_frequency=7.826e-01	minor_base=C	minor_cov=44/1	new_cov=44/1	polymorphism_frequency=2.174e-01	polymorphism_score=27.7	prediction=polymorphism	ref_cov=60/102	total_cov=104/104
RA	34	.	CP028101	1119638	0	G	A	bias_e_value=1.20043e-11	bias_p_value=5.50633e-18	consensus_reject=FREQUENCY_CUTOFF	consensus_score=349.6	fisher_strand_p_value=1.23635e-19	frequency=2.986e-01	ks_quality_p_value=1	major_base=G	major_cov=89/59	major_frequency=7.014e-01	minor_base=A	minor_cov=0/63	new_cov=0/63	polymorphism_frequency=2.986e-01	polymorphism_score=34.2	prediction=polymorphism	ref_cov=89/59	total_cov=89/123
RA	35	.	CP028101	1153298	0	A	G	bias_e_value=1.95994e-16	bias_p_value=8.99015e-23	consensus_reject=FREQUENCY_CUTOFF	consensus_score=423.9	fisher_strand_p_value=1.61158e-24	frequency=2.553e-01	ks_quality_p_value=1	major_base=A	major_cov=48/127	major_frequency=7.447e-01	minor_base=G	minor_cov=59/1	new_cov=59/1	polymorphism_frequency=2.553e-01	polymorphism_score=73.0	prediction=polymorphism	ref_cov=48/127	total_cov=107/128
RA	36	.	CP028101	1153299	0	A	G	bias_e_value=3.7781e-36	bias_p_value=1.73299e-42	consensus_reject=FREQUENCY_CUTOFF	consensus_score=245.0	fisher_strand_p_value=1.70266e-44	frequency=3.915e-01	ks_quality_p_value=1	major_base=A	major_cov=17/126	major_frequency=6.085e-01	minor_base=G	minor_cov=90/2	new_cov=90/2	polymorphism_frequency=3.915e-01	polymorphism_score=184.9	prediction=polymorphism	ref_cov=17/126	total_cov=107/128
RA	37	.	CP028101	1374796	0	T	C	bias_e_value=5.244e-10	bias_p_value=2.40539e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=259.7	fisher_strand_p_value=5.91454e-18	frequency=3.179e-01	ks_quality_p_value=1	major_base=T	major_cov=77/56	major_frequency=6.821e-01	minor_base=C	minor_cov=0/62	new_cov=0/62	polymorphism_frequency=3.179e-01	polymorphism_score=72.5	prediction=polymorphism	ref_cov=77/56	total_cov=77/118
RA	38	.	CP028101	1393372	0	A	G	bias_e_value=1.05349e-05	bias_p_value=4.83231e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=274.8	fisher_strand_p_value=1.58579e-13	frequency=2.626e-01	ks_quality_p_value=1	major_base=A	major_cov=60/72	major_frequency=7.374e-01	minor_base=G	minor_cov=47/0	new_cov=47/0	polymorphism_frequency=2.626e-01	polymorphism_score=49.6	prediction=polymorphism	ref_cov=60/72	total_cov=107/72
RA	39	.	CP028101	1515247	0	T	G	bias_e_value=2.97497e-18	bias_p_value=1.3646e-24	consensus_reject=FREQUENCY_CUTOFF	consensus_score=329.1	fisher_strand_p_value=2.27258e-26	frequency=3.444e-01	ks_quality_p_value=1	major_base=T	major_cov=90/28	major_frequency=6.556e-01	minor_base=G	minor_cov=0/62	new_cov=0/62	polymorphism_frequency=3.444e-01	polymorphism_score=76.7	prediction=polymorphism	ref_cov=90/28	total_cov=91/90
RA	40	.	CP028101	1530400	1	.	C	bias_e_value=1870310	bias_p_value=0.8579	consensus_reject=FREQUENCY_CUTOFF	consensus_score=90.8	fisher_strand_p_value=1	frequency=3.175e-01	ks_quality_p_value=0.516741	major_base=.	major_cov=1/42	major_frequency=6.825e-01	minor_base=C	minor_cov=0/20	new_cov=0/20	polymorphism_frequency=3.175e-01	polymorphism_score=112.9	prediction=polymorphism	ref_cov=1/42	total_cov=1/62
RA	41	.	CP028101	1675289	0	C	T	bias_e_value=1.6619e-07	bias_p_value=7.62306e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=441.7	fisher_strand_p_value=2.19348e-15	frequency=2.064e-01	ks_quality_p_value=1	major_base=C	major_cov=70/103	major_frequency=7.936e-01	minor_base=T	minor_cov=45/0	new_cov=45/0	polymorphism_frequency=2.064e-01	polymorphism_score=16.9	prediction=polymorphism	ref_cov=70/103	total_cov=115/103
RA	42	.	CP028101	1727846	0	G	A	bias_e_value=1.70354e-06	bias_p_value=7.81406e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=388.6	fisher_strand_p_value=2.41514e-14	frequency=2.120e-01	ks_quality_p_value=1	major_base=G	major_cov=91/54	major_frequency=7.880e-01	minor_base=A	minor_cov=0/39	new_cov=0/39	polymorphism_frequency=2.120e-01	polymorphism_score=11.9	prediction=polymorphism	ref_cov=91/54	total_cov=91/95
RA	43	.	CP028101	1847131	0	C	T	bias_e_value=2.16821e-08	bias_p_value=9.94545e-15	consensus_reject=FREQUENCY_CUTOFF	consensus_score=320.7	fisher_strand_p_value=2.69901e-16	frequency=3.136e-01	ks_quality_p_value=1	major_base=C	major_cov=86/76	major_frequency=6.864e-01	minor_base=T	minor_cov=74/0	new_cov=74/0	polymorphism_frequency=3.136e-01	polymorphism_score=38.6	prediction=polymorphism	ref_cov=86/76	total_cov=169/76
RA	44	.	CP028101	1860126	0	G	C	bias_e_value=7.50735e-17	bias_p_value=3.44358e-23	consensus_reject=FREQUENCY_CUTOFF	consensus_score=346.1	fisher_strand_p_value=6.06672e-25	frequency=3.486e-01	ks_quality_p_value=1	major_base=G	major_cov=85/29	major_frequency=6.514e-01	minor_base=C	minor_cov=0/61	new_cov=0/61	polymorphism_frequency=3.486e-01	polymorphism_score=96.8	prediction=polymorphism	ref_cov=85/29	total_cov=85/100
RA	45	.	CP028101	1872607	0	A	G	bias_e_value=7.35283e-13	bias_p_value=3.3727e-19	consensus_reject=FREQUENCY_CUTOFF	consensus_score=384.2	fisher_strand_p_value=7.11663e-21	frequency=2.687e-01	ks_quality_p_value=1	major_base=A	major_cov=62/104	major_frequency=7.313e-01	minor_base=G	minor_cov=61/0	new_cov=61/0	polymorphism_frequency=2.687e-01	polymorphism_score=75.3	prediction=polymorphism	ref_cov=62/104	total_cov=123/104
RA	46	.	CP028101	1889727	0	C	G	bias_e_value=8.737e-19	bias_p_value=4.00761e-25	consensus_reject=FREQUENCY_CUTOFF	consensus_score=250.5	fisher_strand_p_value=6.53855e-27	frequency=4.183e-01	ks_quality_p_value=1	major_base=C	major_cov=18/71	major_frequency=5.817e-01	minor_base=G	minor_cov=64/0	new_cov=64/0	polymorphism_frequency=4.183e-01	polymorphism_score=109.7	prediction=polymorphism	ref_cov=18/71	total_cov=109/71
RA	47	.	CP028101	1951385	0	A	G	bias_e_value=3.24203e-11	bias_p_value=1.4871e-17	consensus_reject=FREQUENCY_CUTOFF	consensus_score=297.1	fisher_strand_p_value=3.41702e-19	frequency=2.892e-01	ks_quality_p_value=1	major_base=A	major_cov=56/89	major_frequency=7.108e-01	minor_base=G	minor_cov=59/0	new_cov=59/0	polymorphism_frequency=2.892e-01	polymorphism_score=91.8	prediction=polymorphism	ref_cov=56/89	total_cov=115/89
RA	48	.	CP028101	1951387	0	C	T	bias_e_value=4.38567e-16	bias_p_value=2.01168e-22	consensus_reject=FREQUENCY_CUTOFF	consensus_score=298.1	fisher_strand_p_value=3.65996e-24	frequency=3.469e-01	ks_quality_p_value=1	major_base=C	major_cov=41/87	major_frequency=6.531e-01	minor_base=T	minor_cov=68/0	new_cov=68/0	polymorphism_frequency=3.469e-01	polymorphism_score=40.2	prediction=polymorphism	ref_cov=41/87	total_cov=114/87
RA	49	.	CP028101	2013568	0	C	T	bias_e_value=3.82204e-06	bias_p_value=1.75315e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=295.6	fisher_strand_p_value=5.56198e-14	frequency=2.342e-01	ks_quality_p_value=1	major_base=C	major_cov=42/79	major_frequency=7.658e-01	minor_base=T	minor_cov=37/0	new_cov=37/0	polymorphism_frequency=2.342e-01	polymorphism_score=10.8	prediction=polymorphism	ref_cov=42/79	total_cov=116/79
JC	50	.	CP028101	1	1	CP028101	2180101	-1	0	alignment_overlap=0	coverage_minus=99	coverage_plus=104	flanking_left=150	flanking_right=150	frequency=1	ignore=CIRCULAR_CHROMOSOME	junction_possible_overlap_registers=149	key=CP028101__1__1__CP028101__2180101__-1__0____150__150__0__0	max_left=147	max_left_minus=146	max_left_plus=147	max_min_left=74	max_min_left_minus=74	max_min_left_plus=74	max_min_right=75	max_min_right_minus=75	max_min_right_plus=74	max_pos_hash_score=298	max_right=149	max_right_minus=147	max_right_plus=149	neg_log10_pos_hash_p_value=0.7	new_junction_coverage=0.90	new_junction_read_count=207	polymorphism_frequency=1.000e+00	pos_hash_score=99	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=149	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=149	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=203
JC	51	.	CP028101	14211	1	CP028101	272963	1	0	alignment_overlap=1	coverage_minus=1	coverage_plus=3	flanking_left=150	flanking_right=150	frequency=1.611e-02	junction_possible_overlap_registers=148	key=CP028101__14210__1__CP028101__272963__1__1____150__150__1__0	max_left=110	max_left_minus=11	max_left_plus=110	max_min_left=65	max_min_left_minus=11	max_min_left_plus=65	max_min_right=39	max_min_right_minus=0	max_min_right_plus=39	max_pos_hash_score=296	max_right=138	max_right_minus=138	max_right_plus=126	neg_log10_pos_hash_p_value=16.2	new_junction_coverage=0.02	new_junction_read_count=4	polymorphism_frequency=1.611e-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=1.06	side_2_overlap=1	side_2_possible_overlap_registers=149	side_2_read_count=246	side_2_redundant=0	total_non_overlap_reads=4
JC	52	.	CP028101	131134	-1	CP028101	131139	-1	0	alignment_overlap=13	coverage_minus=0	coverage_plus=4	flanking_left=150	flanking_right=150	frequency=1.793e-02	junction_possible_overlap_registers=136	key=CP028101__131134__-1__CP028101__131152__-1__13____150__150__0__0	max_left=100	max_left_minus=0	max_left_plus=100	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=67	max_min_right_minus=0	max_min_right_plus=67	max_pos_hash_score=272	max_right=67	max_right_minus=0	max_right_plus=67	neg_log10_pos_hash_p_value=16.3	new_junction_coverage=0.02	new_junction_read_count=4	polymorphism_frequency=1.793e-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=13	side_1_possible_overlap_registers=149	side_1_read_count=238	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.05	side_2_overlap=0	side_2_possible_overlap_registers=136	side_2_read_count=221	side_2_redundant=0	total_non_overlap_reads=4
JC	53	.	CP028101	336796	-1	CP028101	534770	-1	-4	alignment_overlap=-4	coverage_minus=184	coverage_plus=82	flanking_left=150	flanking_right=150	frequency=1	junction_possible_overlap_registers=145	key=CP028101__336796__-1__CP028101__534770__-1__-4__TTTT__150__150__1__0	max_left=141	max_left_minus=141	max_left_plus=136	max_min_left=72	max_min_left_minus=71	max_min_left_plus=72	max_min_right=73	max_min_right_minus=73	max_min_right_plus=73	max_pos_hash_score=290	max_right=144	max_right_minus=144	max_right_plus=142	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.24	new_junction_read_count=279	polymorphism_frequency=1.000e+00	pos_hash_score=119	prediction=consensus	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=149	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=266	unique_read_sequence=TTTT
JC	54	.	CP028101	493674	-1	CP028101	493722	1	-54	alignment_overlap=-54	coverage_minus=67	coverage_plus=56	flanking_left=150	flanking_right=150	frequency=NA	junction_possible_overlap_registers=95	key=CP028101__493674__-1__CP028101__493722__1__-54__GTTCAAGGAACAACAGCCACTCCAGAAGCAAGTGAAAATAAATAGGGGGTCGAG__150__150__1__1	max_left=95	max_left_minus=95	max_left_plus=91	max_min_left=46	max_min_left_minus=46	max_min_left_plus=46	max_min_right=46	max_min_right_minus=45	max_min_right_plus=46	max_pos_hash_score=190	max_right=95	max_right_minus=95	max_right_plus=89	neg_log10_pos_hash_p_value=0.7	new_junction_coverage=0.90	new_junction_read_count=133	polymorphism_frequency=NA	pos_hash_score=61	prediction=unknown	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=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=123	unique_read_sequence=GTTCAAGGAACAACAGCCACTCCAGAAGCAAGTGAAAATAAATAGGGGGTCGAG
JC	55	.	CP028101	593405	1	CP028101	593422	1	0	alignment_overlap=8	coverage_minus=3	coverage_plus=0	flanking_left=150	flanking_right=150	frequency=9.747e-03	junction_possible_overlap_registers=141	key=CP028101__593405__1__CP028101__593414__1__8____150__150__0__0	max_left=95	max_left_minus=95	max_left_plus=0	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=65	max_min_right_minus=65	max_min_right_plus=0	max_pos_hash_score=282	max_right=65	max_right_minus=65	max_right_plus=0	neg_log10_pos_hash_p_value=16.5	new_junction_coverage=0.01	new_junction_read_count=3	polymorphism_frequency=9.747e-03	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.41	side_1_overlap=8	side_1_possible_overlap_registers=149	side_1_read_count=325	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.38	side_2_overlap=0	side_2_possible_overlap_registers=141	side_2_read_count=302	side_2_redundant=0	total_non_overlap_reads=3
JC	56	.	CP028101	696834	-1	CP028101	696838	-1	0	alignment_overlap=9	coverage_minus=0	coverage_plus=4	flanking_left=150	flanking_right=150	frequency=NA	junction_possible_overlap_registers=140	key=CP028101__696834__-1__CP028101__696847__-1__9____150__150__1__1	max_left=124	max_left_minus=0	max_left_plus=124	max_min_left=54	max_min_left_minus=0	max_min_left_plus=54	max_min_right=45	max_min_right_minus=0	max_min_right_plus=45	max_pos_hash_score=280	max_right=87	max_right_minus=0	max_right_plus=87	neg_log10_pos_hash_p_value=15.7	new_junction_coverage=0.02	new_junction_read_count=4	polymorphism_frequency=NA	pos_hash_score=4	prediction=unknown	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=9	side_1_read_count=NA	side_1_redundant=1	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	57	.	CP028101	718084	1	CP028101	718110	1	0	alignment_overlap=11	coverage_minus=3	coverage_plus=0	flanking_left=150	flanking_right=150	frequency=1.605e-02	junction_possible_overlap_registers=138	key=CP028101__718084__1__CP028101__718099__1__11____150__150__0__0	max_left=138	max_left_minus=138	max_left_plus=0	max_min_left=69	max_min_left_minus=69	max_min_left_plus=0	max_min_right=1	max_min_right_minus=1	max_min_right_plus=0	max_pos_hash_score=276	max_right=104	max_right_minus=104	max_right_plus=0	neg_log10_pos_hash_p_value=16.4	new_junction_coverage=0.01	new_junction_read_count=3	polymorphism_frequency=1.605e-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=11	side_1_possible_overlap_registers=149	side_1_read_count=207	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=138	side_2_read_count=176	side_2_redundant=0	total_non_overlap_reads=3
JC	58	.	CP028101	900717	-1	CP028101	900717	1	-10	alignment_overlap=-10	coverage_minus=100	coverage_plus=65	flanking_left=150	flanking_right=150	frequency=NA	junction_possible_overlap_registers=139	key=CP028101__900717__-1__CP028101__900717__1__-10__CCACTTTATC__150__150__1__1	max_left=135	max_left_minus=135	max_left_plus=134	max_min_left=69	max_min_left_minus=67	max_min_left_plus=69	max_min_right=66	max_min_right_minus=66	max_min_right_plus=64	max_pos_hash_score=278	max_right=139	max_right_minus=139	max_right_plus=138	neg_log10_pos_hash_p_value=0.7	new_junction_coverage=0.79	new_junction_read_count=170	polymorphism_frequency=NA	pos_hash_score=91	prediction=unknown	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=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=165	unique_read_sequence=CCACTTTATC
JC	59	.	CP028101	1727048	-1	CP028101	1727052	-1	0	alignment_overlap=8	coverage_minus=2	coverage_plus=2	flanking_left=150	flanking_right=150	frequency=1.860e-02	junction_possible_overlap_registers=141	key=CP028101__1727048__-1__CP028101__1727060__-1__8____150__150__0__0	max_left=71	max_left_minus=10	max_left_plus=71	max_min_left=60	max_min_left_minus=10	max_min_left_plus=60	max_min_right=71	max_min_right_minus=0	max_min_right_plus=71	max_pos_hash_score=282	max_right=132	max_right_minus=132	max_right_plus=82	neg_log10_pos_hash_p_value=16.5	new_junction_coverage=0.02	new_junction_read_count=4	polymorphism_frequency=1.860e-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=0.96	side_1_overlap=8	side_1_possible_overlap_registers=149	side_1_read_count=222	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=141	side_2_read_count=212	side_2_redundant=0	total_non_overlap_reads=4
JC	60	.	CP028101	1754063	1	CP028101	1754096	1	0	alignment_overlap=16	coverage_minus=4	coverage_plus=0	flanking_left=150	flanking_right=150	frequency=2.310e-02	junction_possible_overlap_registers=133	key=CP028101__1754063__1__CP028101__1754080__1__16____150__150__0__0	max_left=62	max_left_minus=62	max_left_plus=0	max_min_left=62	max_min_left_minus=62	max_min_left_plus=0	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=266	max_right=122	max_right_minus=122	max_right_plus=0	neg_log10_pos_hash_p_value=15.3	new_junction_coverage=0.02	new_junction_read_count=4	polymorphism_frequency=2.310e-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=0.83	side_1_overlap=16	side_1_possible_overlap_registers=149	side_1_read_count=192	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.81	side_2_overlap=0	side_2_possible_overlap_registers=133	side_2_read_count=167	side_2_redundant=0	total_non_overlap_reads=4
JC	61	.	CP028101	2136413	-1	CP028101	2136935	1	0	alignment_overlap=0	coverage_minus=10	coverage_plus=10	flanking_left=150	flanking_right=150	frequency=9.231e-02	junction_possible_overlap_registers=149	key=CP028101__2136413__-1__CP028101__2136935__1__0____150__150__0__0	max_left=133	max_left_minus=116	max_left_plus=133	max_min_left=69	max_min_left_minus=69	max_min_left_plus=66	max_min_right=67	max_min_right_minus=53	max_min_right_plus=67	max_pos_hash_score=298	max_right=148	max_right_minus=127	max_right_plus=148	neg_log10_pos_hash_p_value=11.0	new_junction_coverage=0.09	new_junction_read_count=21	polymorphism_frequency=9.231e-02	pos_hash_score=15	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=0	side_1_possible_overlap_registers=149	side_1_read_count=203	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=149	side_2_read_count=210	side_2_redundant=0	total_non_overlap_reads=20
UN	62	.	CP028101	14344	15752
UN	63	.	CP028101	69297	69360
UN	64	.	CP028101	172749	174030
UN	65	.	CP028101	298803	305043
UN	66	.	CP028101	305436	306822
UN	67	.	CP028101	306827	306827
UN	68	.	CP028101	332310	336818
UN	69	.	CP028101	491648	494016
UN	70	.	CP028101	505725	508090
UN	71	.	CP028101	514422	514596
UN	72	.	CP028101	534771	536196
UN	73	.	CP028101	536671	539534
UN	74	.	CP028101	610690	611386
UN	75	.	CP028101	613622	618004
UN	76	.	CP028101	693925	694304
UN	77	.	CP028101	696516	697793
UN	78	.	CP028101	759662	761048
UN	79	.	CP028101	761627	767867
UN	80	.	CP028101	770992	771126
UN	81	.	CP028101	771937	773212
UN	82	.	CP028101	873320	875369
UN	83	.	CP028101	880777	880956
UN	84	.	CP028101	900564	901210
UN	85	.	CP028101	901212	901213
UN	86	.	CP028101	1001062	1002511
UN	87	.	CP028101	1040891	1042394
UN	88	.	CP028101	1079616	1084278
UN	89	.	CP028101	1138298	1138984
UN	90	.	CP028101	1166433	1167713
UN	91	.	CP028101	1192429	1193868
UN	92	.	CP028101	1261844	1262495
UN	93	.	CP028101	1450119	1451292
UN	94	.	CP028101	1509092	1510068
UN	95	.	CP028101	1999481	2000697
UN	96	.	CP028101	2015620	2016753
UN	97	.	CP028101	2051379	2056050
UN	98	.	CP028101	2100219	2100915
UN	99	.	CP028101	2117780	2118935
UN	100	.	CP028101	2124021	2124397