#=GENOME_DIFF	1.0
#=CREATED	14:45:32 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/ME8562_S14_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/ME8562_S14_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/ME8562_S14_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/ME8562_S14_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/ME8562_S14_R2_RMDUP_RM-R1-DUP.cutadapt.fastq.gz
#=CONVERTED-BASES	518602756
#=CONVERTED-READS	1754668
#=INPUT-BASES	518708615
#=INPUT-READS	1755030
#=MAPPED-BASES	486679147
#=MAPPED-READS	1647514
SNP	1	101	NC_000913	246747	T
DEL	2	257,265	NC_000913	257908	776
SNP	3	102	NC_000913	284535	G
SNP	4	103	NC_000913	313543	A
SNP	5	105	NC_000913	339935	T
SNP	6	106	NC_000913	339941	T
SNP	7	107	NC_000913	339958	A
SUB	8	113,114	NC_000913	480295	2	AA
SNP	9	115	NC_000913	556023	T
SNP	10	117	NC_000913	657424	A
SNP	11	118	NC_000913	690948	A
SNP	12	119	NC_000913	700038	A
SUB	13	121,122	NC_000913	809217	2	AG
SNP	14	125	NC_000913	968837	A
SNP	15	126	NC_000913	1040126	T
SNP	16	127	NC_000913	1042662	T
SNP	17	128	NC_000913	1061935	A
SNP	18	129	NC_000913	1069743	T
SNP	19	131	NC_000913	1098620	A
SUB	20	132,133	NC_000913	1111727	2	TT
SNP	21	134	NC_000913	1169836	G
SNP	22	135	NC_000913	1189980	G
SNP	23	136	NC_000913	1196220	T
SNP	24	137	NC_000913	1196232	T
SNP	25	138	NC_000913	1196245	C
SNP	26	139	NC_000913	1196247	G
SNP	27	149	NC_000913	1278428	G
SNP	28	151	NC_000913	1301992	T
SNP	29	152	NC_000913	1306736	G
SNP	30	153	NC_000913	1310770	G
SNP	31	154	NC_000913	1313379	G
SNP	32	155	NC_000913	1337394	G
SNP	33	156	NC_000913	1357202	T
SNP	34	157	NC_000913	1358859	C
INS	35	158	NC_000913	1437231	T	repeat_length=1	repeat_new_copies=10	repeat_ref_copies=9	repeat_seq=T
SNP	36	163	NC_000913	1643679	T
SNP	37	164	NC_000913	1652331	C
SNP	38	165	NC_000913	1721136	T
SNP	39	167	NC_000913	1776715	T
SNP	40	170	NC_000913	1894839	C
SNP	41	172	NC_000913	1964254	C
SNP	42	174	NC_000913	2040433	A
DEL	43	177,178	NC_000913	2173363	2
SNP	44	179	NC_000913	2188087	C
SNP	45	182	NC_000913	2384808	T
SNP	46	183	NC_000913	2410419	A
SNP	47	187	NC_000913	2484827	T
SNP	48	188	NC_000913	2564496	T
SNP	49	191	NC_000913	2803833	T
SNP	50	192	NC_000913	2825791	T
MOB	51	298,299	NC_000913	2913392	IS2	-1	5
SUB	52	194,195	NC_000913	3088010	2	TT
SNP	53	196	NC_000913	3137400	A
SUB	54	199,200	NC_000913	3336411	2	AT
SNP	55	201	NC_000913	3388041	G
SNP	56	203	NC_000913	3436697	A
SNP	57	204	NC_000913	3479685	T
INS	58	205	NC_000913	3560455	G
SNP	59	207	NC_000913	3682515	T
SNP	60	208	NC_000913	3707947	A
DEL	61	262,303	NC_000913	3708467	168
SNP	62	209	NC_000913	3725176	G
SNP	63	212	NC_000913	3771979	T
INS	64	213	NC_000913	3815883	C
INS	65	304	NC_000913	3822651	CAGGAT	repeat_length=6	repeat_new_copies=2	repeat_ref_copies=1	repeat_seq=CAGGAT
SNP	66	214	NC_000913	3823162	T
SNP	67	216	NC_000913	3869637	A
SNP	68	217	NC_000913	3878536	A
SNP	69	218	NC_000913	3888694	A
SNP	70	221	NC_000913	3993531	C
SNP	71	222	NC_000913	3996049	A
SNP	72	223	NC_000913	4011802	T
SNP	73	224	NC_000913	4084903	G
SNP	74	225	NC_000913	4092703	G
SNP	75	226	NC_000913	4113851	A
SNP	76	227	NC_000913	4143377	T
SNP	77	228	NC_000913	4161248	T
SNP	78	229	NC_000913	4164123	G
SNP	79	230	NC_000913	4193996	G
SNP	80	231	NC_000913	4196331	G
SNP	81	232	NC_000913	4215347	A
SNP	82	233	NC_000913	4223638	C
INS	83	235	NC_000913	4282332	A	repeat_length=1	repeat_new_copies=6	repeat_ref_copies=5	repeat_seq=A
SUB	84	236,237	NC_000913	4293781	2	AT
INS	85	239,240	NC_000913	4296381	GC
SNP	86	241	NC_000913	4325644	T
SNP	87	242	NC_000913	4343958	T
SNP	88	244	NC_000913	4392997	A
SNP	89	245	NC_000913	4393552	A
SNP	90	246	NC_000913	4396373	T
SNP	91	247	NC_000913	4396772	C
SNP	92	248	NC_000913	4425688	A
SNP	93	249	NC_000913	4425696	A
SNP	94	251	NC_000913	4510238	G
SNP	95	252	NC_000913	4532409	G
SNP	96	253	NC_000913	4546601	T
SNP	97	254	NC_000913	4576327	A
SNP	98	255	NC_000913	4636925	C
SNP	99	256	NC_000913	4638240	A
RA	100	.	NC_000913	141849	0	C	A	bias_e_value=0.000475048	bias_p_value=1.02345e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=226.9	fisher_strand_p_value=3.74753e-12	frequency=2.783e-01	ks_quality_p_value=1	major_base=C	major_cov=28/55	major_frequency=7.217e-01	minor_base=A	minor_cov=32/0	new_cov=32/0	polymorphism_frequency=2.783e-01	polymorphism_score=17.5	prediction=polymorphism	ref_cov=28/55	total_cov=60/55
RA	101	.	NC_000913	246747	0	G	T	bias_e_value=4640830	bias_p_value=0.999822	consensus_score=472.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.981213	major_base=T	major_cov=63/70	major_frequency=9.925e-01	minor_base=G	minor_cov=0/1	new_cov=63/70	polymorphism_frequency=9.925e-01	polymorphism_score=-4.7	prediction=consensus	ref_cov=0/1	total_cov=63/71
RA	102	.	NC_000913	284535	0	T	G	consensus_score=122.7	frequency=1	major_base=G	major_cov=17/19	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/19	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/19
RA	103	.	NC_000913	313543	0	G	A	consensus_score=375.2	frequency=1	major_base=A	major_cov=57/53	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=57/53	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=57/53
RA	104	.	NC_000913	332975	0	C	A	bias_e_value=0.00264097	bias_p_value=5.68973e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=210.5	fisher_strand_p_value=2.22891e-11	frequency=3.309e-01	ks_quality_p_value=1	major_base=C	major_cov=39/52	major_frequency=6.691e-01	minor_base=A	minor_cov=44/1	new_cov=44/1	polymorphism_frequency=3.309e-01	polymorphism_score=15.1	prediction=polymorphism	ref_cov=39/52	total_cov=83/53
RA	105	.	NC_000913	339935	0	C	T	consensus_score=80.8	frequency=1	major_base=T	major_cov=15/15	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=15/15	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=15/15
RA	106	.	NC_000913	339941	0	C	T	consensus_score=75.7	frequency=1	major_base=T	major_cov=15/15	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=15/15	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=15/15
RA	107	.	NC_000913	339958	0	G	A	consensus_score=77.4	frequency=1	major_base=A	major_cov=14/16	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=14/16	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=14/16
RA	108	.	NC_000913	339979	0	G	A	bias_e_value=4434580	bias_p_value=0.955389	consensus_reject=FREQUENCY_CUTOFF	consensus_score=42.4	fisher_strand_p_value=0.716574	frequency=6.765e-01	ks_quality_p_value=1	major_base=A	major_cov=13/10	major_frequency=6.765e-01	minor_base=G	minor_cov=5/6	new_cov=13/10	polymorphism_frequency=6.765e-01	polymorphism_score=17.2	prediction=polymorphism	ref_cov=5/6	total_cov=18/16
RA	109	.	NC_000913	339986	0	G	A	bias_e_value=2567140	bias_p_value=0.553067	consensus_reject=FREQUENCY_CUTOFF	consensus_score=47.6	fisher_strand_p_value=0.219973	frequency=7.500e-01	ks_quality_p_value=1	major_base=A	major_cov=14/10	major_frequency=7.500e-01	minor_base=G	minor_cov=2/6	new_cov=14/10	polymorphism_frequency=7.500e-01	polymorphism_score=13.3	prediction=polymorphism	ref_cov=2/6	total_cov=16/16
RA	110	.	NC_000913	339992	0	C	.	bias_e_value=1325410	bias_p_value=0.285546	consensus_reject=FREQUENCY_CUTOFF	consensus_score=73.8	fisher_strand_p_value=0.0829317	frequency=2.258e-01	ks_quality_p_value=0.981359	major_base=C	major_cov=14/10	major_frequency=7.742e-01	minor_base=.	minor_cov=1/6	new_cov=1/6	polymorphism_frequency=2.258e-01	polymorphism_score=22.8	prediction=polymorphism	ref_cov=14/10	total_cov=15/16
RA	111	.	NC_000913	430299	0	C	A	bias_e_value=61.1868	bias_p_value=1.31821e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=199.6	fisher_strand_p_value=8.82294e-07	frequency=2.549e-01	ks_quality_p_value=1	major_base=C	major_cov=39/37	major_frequency=7.451e-01	minor_base=A	minor_cov=26/0	new_cov=26/0	polymorphism_frequency=2.549e-01	polymorphism_score=13.2	prediction=polymorphism	ref_cov=39/37	total_cov=65/37
RA	112	.	NC_000913	442025	0	C	A	bias_e_value=0.00035805	bias_p_value=7.71386e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=200.4	fisher_strand_p_value=2.79454e-12	frequency=3.243e-01	ks_quality_p_value=1	major_base=C	major_cov=27/48	major_frequency=6.757e-01	minor_base=A	minor_cov=36/0	new_cov=36/0	polymorphism_frequency=3.243e-01	polymorphism_score=10.9	prediction=polymorphism	ref_cov=27/48	total_cov=63/48
RA	113	.	NC_000913	480295	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=594.0	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=82/85	major_frequency=9.940e-01	minor_base=C	minor_cov=0/1	new_cov=82/85	polymorphism_frequency=9.940e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=82/86
RA	114	.	NC_000913	480296	0	G	A	consensus_score=611.0	frequency=1	major_base=A	major_cov=82/86	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=82/86	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=82/86
RA	115	.	NC_000913	556023	0	C	T	consensus_score=284.6	frequency=1	major_base=T	major_cov=38/44	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=38/44	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=38/44
RA	116	.	NC_000913	571007	0	C	A	bias_e_value=6.01339e-05	bias_p_value=1.29553e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=338.4	fisher_strand_p_value=4.39873e-13	frequency=2.273e-01	ks_quality_p_value=1	major_base=C	major_cov=43/76	major_frequency=7.727e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=2.273e-01	polymorphism_score=12.7	prediction=polymorphism	ref_cov=43/76	total_cov=78/76
RA	117	.	NC_000913	657424	0	G	A	consensus_score=415.8	frequency=1	major_base=A	major_cov=54/64	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=54/64	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=54/64
RA	118	.	NC_000913	690948	0	G	A	consensus_score=321.7	frequency=1	major_base=A	major_cov=44/49	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=44/49	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=44/49
RA	119	.	NC_000913	700038	0	G	A	consensus_score=332.2	frequency=1	major_base=A	major_cov=54/36	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=54/36	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=54/36
RA	120	.	NC_000913	782194	0	T	G	bias_e_value=5.63179e-05	bias_p_value=1.21332e-11	consensus_reject=FREQUENCY_CUTOFF	consensus_score=281.4	fisher_strand_p_value=4.11013e-13	frequency=2.256e-01	ks_quality_p_value=1	major_base=T	major_cov=72/31	major_frequency=7.744e-01	minor_base=G	minor_cov=0/30	new_cov=0/30	polymorphism_frequency=2.256e-01	polymorphism_score=10.8	prediction=polymorphism	ref_cov=72/31	total_cov=72/61
RA	121	.	NC_000913	809217	0	C	A	consensus_score=288.1	frequency=1	major_base=A	major_cov=49/33	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=49/33	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=49/33
RA	122	.	NC_000913	809218	0	A	G	consensus_score=309.7	frequency=1	major_base=G	major_cov=49/33	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=49/33	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=49/33
RA	123	.	NC_000913	847955	0	G	A	bias_e_value=6.14732e-07	bias_p_value=1.32438e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=197.5	fisher_strand_p_value=3.87423e-15	frequency=3.165e-01	ks_quality_p_value=1	major_base=G	major_cov=64/44	major_frequency=6.835e-01	minor_base=A	minor_cov=0/50	new_cov=0/50	polymorphism_frequency=3.165e-01	polymorphism_score=64.7	prediction=polymorphism	ref_cov=64/44	total_cov=64/94
RA	124	.	NC_000913	848028	0	G	T	bias_e_value=0.00455925	bias_p_value=9.82248e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=274.0	fisher_strand_p_value=3.93554e-11	frequency=2.657e-01	ks_quality_p_value=1	major_base=G	major_cov=58/47	major_frequency=7.343e-01	minor_base=T	minor_cov=0/38	new_cov=0/38	polymorphism_frequency=2.657e-01	polymorphism_score=17.0	prediction=polymorphism	ref_cov=58/47	total_cov=58/85
RA	125	.	NC_000913	968837	0	G	A	bias_e_value=3773360	bias_p_value=0.812935	consensus_score=356.1	fisher_strand_p_value=0.454545	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=60/49	major_frequency=9.909e-01	minor_base=G	minor_cov=0/1	new_cov=60/49	polymorphism_frequency=9.909e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=60/50
RA	126	.	NC_000913	1040126	0	G	T	consensus_score=322.2	frequency=1	major_base=T	major_cov=52/38	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=52/38	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=52/38
RA	127	.	NC_000913	1042662	0	C	T	bias_e_value=1868760	bias_p_value=0.402606	consensus_score=292.6	fisher_strand_p_value=0.158523	frequency=1	ks_quality_p_value=0.843036	major_base=T	major_cov=38/61	major_frequency=8.115e-01	minor_base=C	minor_cov=13/10	new_cov=38/61	polymorphism_frequency=8.115e-01	polymorphism_score=58.7	prediction=consensus	ref_cov=13/10	total_cov=51/72
RA	128	.	NC_000913	1061935	0	G	A	consensus_score=321.0	frequency=1	major_base=A	major_cov=51/47	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=51/47	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=51/47
RA	129	.	NC_000913	1069743	0	C	T	bias_e_value=4641650	bias_p_value=1	consensus_score=246.3	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=33/43	major_frequency=9.870e-01	minor_base=G	minor_cov=0/1	new_cov=33/43	polymorphism_frequency=9.870e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=33/44
RA	130	.	NC_000913	1097118	0	C	A	bias_e_value=3397910	bias_p_value=0.732047	consensus_reject=FREQUENCY_CUTOFF	consensus_score=87.0	fisher_strand_p_value=0.364186	frequency=2.586e-01	ks_quality_p_value=1	major_base=C	major_cov=16/27	major_frequency=7.414e-01	minor_base=A	minor_cov=8/7	new_cov=8/7	polymorphism_frequency=2.586e-01	polymorphism_score=17.9	prediction=polymorphism	ref_cov=16/27	total_cov=24/34
RA	131	.	NC_000913	1098620	0	T	A	bias_e_value=3669330	bias_p_value=0.790522	consensus_score=375.7	fisher_strand_p_value=0.427184	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=43/59	major_frequency=9.903e-01	minor_base=C	minor_cov=1/0	new_cov=43/59	polymorphism_frequency=9.903e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=44/59
RA	132	.	NC_000913	1111727	0	C	T	bias_e_value=4641650	bias_p_value=1	consensus_score=333.9	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=51/47	major_frequency=9.899e-01	minor_base=C	minor_cov=1/0	new_cov=51/47	polymorphism_frequency=9.899e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=52/47
RA	133	.	NC_000913	1111728	0	C	T	bias_e_value=4641650	bias_p_value=1	consensus_score=350.2	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=51/47	major_frequency=9.899e-01	minor_base=C	minor_cov=1/0	new_cov=51/47	polymorphism_frequency=9.899e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=52/47
RA	134	.	NC_000913	1169836	0	A	G	consensus_score=391.0	frequency=1	major_base=G	major_cov=49/54	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=49/54	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=49/54
RA	135	.	NC_000913	1189980	0	A	G	consensus_score=462.8	frequency=1	major_base=G	major_cov=53/70	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=53/70	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=53/70
RA	136	.	NC_000913	1196220	0	C	T	bias_e_value=4641650	bias_p_value=1	consensus_score=128.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=19/27	major_frequency=9.787e-01	minor_base=G	minor_cov=0/1	new_cov=19/27	polymorphism_frequency=9.787e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=19/28
RA	137	.	NC_000913	1196232	0	C	T	consensus_score=123.6	frequency=1	major_base=T	major_cov=19/25	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=19/25	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=19/25
RA	138	.	NC_000913	1196245	0	T	C	consensus_score=122.1	frequency=1	major_base=C	major_cov=18/23	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=18/23	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=18/23
RA	139	.	NC_000913	1196247	0	A	G	consensus_score=123.6	frequency=1	major_base=G	major_cov=18/23	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=18/23	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=18/23
RA	140	.	NC_000913	1196277	0	C	T	bias_e_value=3879680	bias_p_value=0.835839	consensus_score=81.4	deleted=1	fisher_strand_p_value=0.484848	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=17/15	major_frequency=9.697e-01	minor_base=G	minor_cov=0/1	new_cov=17/15	polymorphism_frequency=9.697e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/16
RA	141	.	NC_000913	1196280	0	G	C	consensus_score=88.9	deleted=1	frequency=1	major_base=C	major_cov=17/16	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/16	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/16
RA	142	.	NC_000913	1196283	0	A	G	consensus_score=89.5	deleted=1	frequency=1	major_base=G	major_cov=17/16	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/16	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/16
RA	143	.	NC_000913	1196292	0	C	T	consensus_score=86.1	deleted=1	frequency=1	major_base=T	major_cov=17/16	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=17/16	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=17/16
RA	144	.	NC_000913	1196304	0	G	A	consensus_score=64.8	deleted=1	frequency=1	major_base=A	major_cov=12/15	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=12/15	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=12/15
RA	145	.	NC_000913	1196316	0	T	A	consensus_score=58.0	deleted=1	frequency=1	major_base=A	major_cov=12/13	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=12/13	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=12/13
RA	146	.	NC_000913	1196325	0	A	G	consensus_score=50.8	deleted=1	frequency=1	major_base=G	major_cov=12/11	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=12/11	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=12/11
RA	147	.	NC_000913	1196352	0	C	A	consensus_score=26.5	deleted=1	frequency=1	major_base=A	major_cov=9/5	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=9/5	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=9/5
RA	148	.	NC_000913	1272420	0	C	A	bias_e_value=7.00667	bias_p_value=1.50952e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=195.5	fisher_strand_p_value=8.75002e-08	frequency=2.793e-01	ks_quality_p_value=1	major_base=C	major_cov=41/39	major_frequency=7.207e-01	minor_base=A	minor_cov=31/0	new_cov=31/0	polymorphism_frequency=2.793e-01	polymorphism_score=12.7	prediction=polymorphism	ref_cov=41/39	total_cov=72/39
RA	149	.	NC_000913	1278428	0	T	G	bias_e_value=4641650	bias_p_value=1	consensus_score=259.9	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=32/37	major_frequency=9.857e-01	minor_base=A	minor_cov=0/1	new_cov=32/37	polymorphism_frequency=9.857e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=32/39
RA	150	.	NC_000913	1286870	0	C	A	bias_e_value=4641650	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=155.8	fisher_strand_p_value=1	frequency=2.125e-01	ks_quality_p_value=1	major_base=C	major_cov=33/30	major_frequency=7.875e-01	minor_base=A	minor_cov=9/8	new_cov=9/8	polymorphism_frequency=2.125e-01	polymorphism_score=16.6	prediction=polymorphism	ref_cov=33/30	total_cov=42/39
RA	151	.	NC_000913	1301992	0	A	T	consensus_score=465.9	frequency=1	major_base=T	major_cov=58/77	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=58/77	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=58/77
RA	152	.	NC_000913	1306736	0	T	G	bias_e_value=4641180	bias_p_value=0.999897	consensus_score=309.8	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.985704	major_base=G	major_cov=51/31	major_frequency=9.880e-01	minor_base=T	minor_cov=1/0	new_cov=51/31	polymorphism_frequency=9.880e-01	polymorphism_score=-3.2	prediction=consensus	ref_cov=1/0	total_cov=52/31
RA	153	.	NC_000913	1310770	0	A	G	consensus_score=521.8	frequency=1	major_base=G	major_cov=96/42	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=96/42	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=96/42
RA	154	.	NC_000913	1313379	0	A	G	bias_e_value=3858550	bias_p_value=0.831288	consensus_score=327.8	fisher_strand_p_value=0.649012	frequency=1	ks_quality_p_value=0.737454	major_base=G	major_cov=57/56	major_frequency=8.309e-01	minor_base=A	minor_cov=10/13	new_cov=57/56	polymorphism_frequency=8.309e-01	polymorphism_score=60.4	prediction=consensus	ref_cov=10/13	total_cov=67/69
RA	155	.	NC_000913	1337394	0	A	G	bias_e_value=3685060	bias_p_value=0.793912	consensus_score=396.3	fisher_strand_p_value=0.431193	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=62/46	major_frequency=9.908e-01	minor_base=T	minor_cov=0/1	new_cov=62/46	polymorphism_frequency=9.908e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=62/47
RA	156	.	NC_000913	1357202	0	C	T	consensus_score=480.0	frequency=1	major_base=T	major_cov=70/65	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=70/65	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=70/65
RA	157	.	NC_000913	1358859	0	T	C	consensus_score=389.7	frequency=1	major_base=C	major_cov=56/48	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=56/48	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=56/48
RA	158	.	NC_000913	1437231	1	.	T	bias_e_value=4024350	bias_p_value=0.867008	consensus_score=298.7	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.530824	major_base=T	major_cov=46/48	major_frequency=8.468e-01	minor_base=.	minor_cov=8/9	new_cov=46/48	polymorphism_frequency=8.468e-01	polymorphism_score=63.7	prediction=consensus	ref_cov=8/9	total_cov=55/57
RA	159	.	NC_000913	1466432	0	A	G	bias_e_value=2247360	bias_p_value=0.484173	consensus_reject=FREQUENCY_CUTOFF	consensus_score=177.4	fisher_strand_p_value=0.177393	frequency=2.073e-01	ks_quality_p_value=1	major_base=A	major_cov=29/36	major_frequency=7.927e-01	minor_base=G	minor_cov=11/6	new_cov=11/6	polymorphism_frequency=2.073e-01	polymorphism_score=24.8	prediction=polymorphism	ref_cov=29/36	total_cov=41/42
RA	160	.	NC_000913	1466438	0	T	G	bias_e_value=4641650	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=177.5	fisher_strand_p_value=1	frequency=2.048e-01	ks_quality_p_value=1	major_base=T	major_cov=33/33	major_frequency=7.952e-01	minor_base=G	minor_cov=8/9	new_cov=8/9	polymorphism_frequency=2.048e-01	polymorphism_score=24.9	prediction=polymorphism	ref_cov=33/33	total_cov=41/42
RA	161	.	NC_000913	1466604	0	G	A	bias_e_value=1325730	bias_p_value=0.285615	consensus_reject=FREQUENCY_CUTOFF	consensus_score=124.8	fisher_strand_p_value=0.0814132	frequency=2.206e-01	ks_quality_p_value=1	major_base=G	major_cov=18/35	major_frequency=7.794e-01	minor_base=A	minor_cov=9/6	new_cov=9/6	polymorphism_frequency=2.206e-01	polymorphism_score=20.8	prediction=polymorphism	ref_cov=18/35	total_cov=27/41
RA	162	.	NC_000913	1502770	0	T	C	bias_e_value=7.60032	bias_p_value=1.63742e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=266.9	fisher_strand_p_value=9.53912e-08	frequency=2.391e-01	ks_quality_p_value=1	major_base=T	major_cov=54/51	major_frequency=7.609e-01	minor_base=C	minor_cov=1/32	new_cov=1/32	polymorphism_frequency=2.391e-01	polymorphism_score=21.9	prediction=polymorphism	ref_cov=54/51	total_cov=55/83
RA	163	.	NC_000913	1643679	0	A	T	consensus_score=247.3	frequency=1	major_base=T	major_cov=28/44	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=28/44	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=28/44
RA	164	.	NC_000913	1652331	0	T	C	consensus_score=553.5	frequency=1	major_base=C	major_cov=71/75	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=71/75	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=71/75
RA	165	.	NC_000913	1721136	0	C	T	consensus_score=533.1	frequency=1	major_base=T	major_cov=70/88	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=70/88	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=70/88
RA	166	.	NC_000913	1756353	0	C	A	bias_e_value=0.00664149	bias_p_value=1.43085e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=218.6	fisher_strand_p_value=5.82441e-11	frequency=2.735e-01	ks_quality_p_value=1	major_base=C	major_cov=32/53	major_frequency=7.265e-01	minor_base=A	minor_cov=32/0	new_cov=32/0	polymorphism_frequency=2.735e-01	polymorphism_score=10.2	prediction=polymorphism	ref_cov=32/53	total_cov=64/53
RA	167	.	NC_000913	1776715	0	A	T	bias_e_value=2450770	bias_p_value=0.527995	consensus_score=437.3	fisher_strand_p_value=0.203817	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=65/52	major_frequency=9.832e-01	minor_base=G	minor_cov=0/2	new_cov=65/52	polymorphism_frequency=9.832e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=66/54
RA	168	.	NC_000913	1812509	0	G	T	bias_e_value=3.16805e-09	bias_p_value=6.82526e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=417.4	fisher_strand_p_value=1.72357e-17	frequency=2.350e-01	ks_quality_p_value=1	major_base=G	major_cov=95/45	major_frequency=7.650e-01	minor_base=T	minor_cov=0/43	new_cov=0/43	polymorphism_frequency=2.350e-01	polymorphism_score=15.4	prediction=polymorphism	ref_cov=95/45	total_cov=95/88
RA	169	.	NC_000913	1820763	0	G	T	bias_e_value=0.016787	bias_p_value=3.61661e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=153.9	fisher_strand_p_value=1.53253e-10	frequency=3.839e-01	ks_quality_p_value=1	major_base=G	major_cov=37/32	major_frequency=6.161e-01	minor_base=T	minor_cov=0/43	new_cov=0/43	polymorphism_frequency=3.839e-01	polymorphism_score=10.4	prediction=polymorphism	ref_cov=37/32	total_cov=37/75
RA	170	.	NC_000913	1894839	0	T	C	consensus_score=386.3	frequency=1	major_base=C	major_cov=51/52	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=51/52	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=51/52
RA	171	.	NC_000913	1922815	0	C	A	bias_e_value=147.613	bias_p_value=3.18019e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=223.1	fisher_strand_p_value=2.27243e-06	frequency=2.893e-01	ks_quality_p_value=1	major_base=C	major_cov=28/58	major_frequency=7.107e-01	minor_base=A	minor_cov=28/7	new_cov=28/7	polymorphism_frequency=2.893e-01	polymorphism_score=12.1	prediction=polymorphism	ref_cov=28/58	total_cov=56/65
RA	172	.	NC_000913	1964254	0	A	C	consensus_score=294.3	frequency=1	major_base=C	major_cov=49/30	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=49/30	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=49/30
RA	173	.	NC_000913	2013023	0	C	A	bias_e_value=33.4075	bias_p_value=7.19732e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=205.7	fisher_strand_p_value=4.61713e-07	frequency=2.286e-01	ks_quality_p_value=1	major_base=C	major_cov=38/43	major_frequency=7.714e-01	minor_base=A	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=2.286e-01	polymorphism_score=14.1	prediction=polymorphism	ref_cov=38/43	total_cov=62/43
RA	174	.	NC_000913	2040433	0	C	A	bias_e_value=4641650	bias_p_value=1	consensus_score=317.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=45/45	major_frequency=9.890e-01	minor_base=C	minor_cov=1/0	new_cov=45/45	polymorphism_frequency=9.890e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=46/45
RA	175	.	NC_000913	2159413	0	C	T	bias_e_value=9594.1	bias_p_value=0.00206696	consensus_reject=FREQUENCY_CUTOFF	consensus_score=140.3	fisher_strand_p_value=0.000219305	frequency=2.254e-01	ks_quality_p_value=1	major_base=C	major_cov=28/27	major_frequency=7.746e-01	minor_base=T	minor_cov=16/0	new_cov=16/0	polymorphism_frequency=2.254e-01	polymorphism_score=12.8	prediction=polymorphism	ref_cov=28/27	total_cov=44/27
RA	176	.	NC_000913	2171384	0	A	C	bias_e_value=3136350	bias_p_value=0.675697	consensus_reject=SCORE_CUTOFF,FREQUENCY_CUTOFF	consensus_score=0.0	fisher_strand_p_value=0.312253	frequency=6.400e-01	ks_quality_p_value=1	major_base=C	major_cov=2/14	major_frequency=6.400e-01	minor_base=A	minor_cov=3/6	new_cov=2/14	polymorphism_frequency=6.400e-01	polymorphism_score=18.6	prediction=polymorphism	ref_cov=3/6	total_cov=5/20
RA	177	.	NC_000913	2173363	0	C	.	consensus_score=81.3	frequency=1	major_base=.	major_cov=8/10	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=8/10	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=8/10
RA	178	.	NC_000913	2173364	0	C	.	consensus_score=81.3	frequency=1	major_base=.	major_cov=8/10	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=8/10	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=8/10
RA	179	.	NC_000913	2188087	0	T	C	bias_e_value=3917700	bias_p_value=0.844031	consensus_score=518.5	fisher_strand_p_value=0.49635	frequency=1	ks_quality_p_value=1	major_base=C	major_cov=67/69	major_frequency=9.927e-01	minor_base=A	minor_cov=1/0	new_cov=67/69	polymorphism_frequency=9.927e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=68/69
RA	180	.	NC_000913	2288418	0	G	T	bias_e_value=2.6104e-11	bias_p_value=5.62385e-18	consensus_reject=FREQUENCY_CUTOFF	consensus_score=235.4	fisher_strand_p_value=1.26335e-19	frequency=3.660e-01	ks_quality_p_value=1	major_base=G	major_cov=66/31	major_frequency=6.340e-01	minor_base=T	minor_cov=0/56	new_cov=0/56	polymorphism_frequency=3.660e-01	polymorphism_score=39.0	prediction=polymorphism	ref_cov=66/31	total_cov=67/88
RA	181	.	NC_000913	2326713	0	C	A	bias_e_value=0.0133453	bias_p_value=2.87512e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=190.6	fisher_strand_p_value=1.20608e-10	frequency=3.182e-01	ks_quality_p_value=1	major_base=C	major_cov=31/44	major_frequency=6.818e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=3.182e-01	polymorphism_score=14.2	prediction=polymorphism	ref_cov=31/44	total_cov=66/44
RA	182	.	NC_000913	2384808	0	C	T	bias_e_value=392630	bias_p_value=0.0845884	consensus_score=424.6	fisher_strand_p_value=0.0165892	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=61/68	major_frequency=9.485e-01	minor_base=C	minor_cov=0/7	new_cov=61/68	polymorphism_frequency=9.485e-01	polymorphism_score=-5.2	prediction=consensus	ref_cov=0/7	total_cov=61/75
RA	183	.	NC_000913	2410419	0	G	A	consensus_score=416.1	frequency=1	major_base=A	major_cov=71/46	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=71/46	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=71/46
RA	184	.	NC_000913	2466633	0	C	A	bias_e_value=0.339937	bias_p_value=7.32361e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=276.0	fisher_strand_p_value=3.58168e-09	frequency=2.180e-01	ks_quality_p_value=1	major_base=C	major_cov=46/58	major_frequency=7.820e-01	minor_base=A	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=2.180e-01	polymorphism_score=11.1	prediction=polymorphism	ref_cov=46/58	total_cov=75/58
RA	185	.	NC_000913	2477258	0	G	A	bias_e_value=12.9097	bias_p_value=2.78128e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=185.6	fisher_strand_p_value=1.67525e-07	frequency=2.118e-01	ks_quality_p_value=1	major_base=G	major_cov=23/44	major_frequency=7.882e-01	minor_base=A	minor_cov=18/0	new_cov=18/0	polymorphism_frequency=2.118e-01	polymorphism_score=13.0	prediction=polymorphism	ref_cov=23/44	total_cov=41/44
RA	186	.	NC_000913	2477265	0	A	C	bias_e_value=0.000466046	bias_p_value=1.00405e-10	consensus_reject=FREQUENCY_CUTOFF	consensus_score=134.0	fisher_strand_p_value=3.67384e-12	frequency=3.038e-01	ks_quality_p_value=1	major_base=A	major_cov=11/44	major_frequency=6.962e-01	minor_base=C	minor_cov=24/0	new_cov=24/0	polymorphism_frequency=3.038e-01	polymorphism_score=17.9	prediction=polymorphism	ref_cov=11/44	total_cov=35/44
RA	187	.	NC_000913	2484827	0	C	T	consensus_score=483.3	frequency=1	major_base=T	major_cov=59/85	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=59/85	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=59/85
RA	188	.	NC_000913	2564496	0	G	T	bias_e_value=4641650	bias_p_value=1	consensus_score=458.5	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=59/72	major_frequency=9.924e-01	minor_base=G	minor_cov=0/1	new_cov=59/72	polymorphism_frequency=9.924e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=60/73
RA	189	.	NC_000913	2704512	0	C	A	bias_e_value=1.24261	bias_p_value=2.67709e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=185.0	fisher_strand_p_value=1.40293e-08	frequency=2.737e-01	ks_quality_p_value=1	major_base=C	major_cov=28/41	major_frequency=7.263e-01	minor_base=A	minor_cov=26/0	new_cov=26/0	polymorphism_frequency=2.737e-01	polymorphism_score=14.1	prediction=polymorphism	ref_cov=28/41	total_cov=54/41
RA	190	.	NC_000913	2767444	0	C	A	bias_e_value=3.44376e-09	bias_p_value=7.41926e-16	consensus_reject=FREQUENCY_CUTOFF	consensus_score=238.2	fisher_strand_p_value=1.87763e-17	frequency=2.816e-01	ks_quality_p_value=1	major_base=C	major_cov=10/64	major_frequency=7.184e-01	minor_base=A	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=2.816e-01	polymorphism_score=14.2	prediction=polymorphism	ref_cov=10/64	total_cov=39/64
RA	191	.	NC_000913	2803833	0	C	T	consensus_score=418.5	frequency=1	major_base=T	major_cov=67/54	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=67/54	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=67/54
RA	192	.	NC_000913	2825791	0	G	T	consensus_score=558.8	frequency=1	major_base=T	major_cov=73/85	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=73/85	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=73/85
RA	193	.	NC_000913	2856087	0	G	T	bias_e_value=0.0232944	bias_p_value=5.01855e-09	consensus_reject=FREQUENCY_CUTOFF	consensus_score=171.4	fisher_strand_p_value=2.15789e-10	frequency=3.204e-01	ks_quality_p_value=1	major_base=G	major_cov=42/28	major_frequency=6.796e-01	minor_base=T	minor_cov=0/33	new_cov=0/33	polymorphism_frequency=3.204e-01	polymorphism_score=10.9	prediction=polymorphism	ref_cov=42/28	total_cov=42/61
RA	194	.	NC_000913	3088010	0	C	T	bias_e_value=2757500	bias_p_value=0.594078	consensus_score=540.3	fisher_strand_p_value=0.248204	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=77/84	major_frequency=9.817e-01	minor_base=G	minor_cov=0/3	new_cov=77/84	polymorphism_frequency=9.817e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=77/87
RA	195	.	NC_000913	3088011	0	C	T	bias_e_value=3925640	bias_p_value=0.845742	consensus_score=545.7	fisher_strand_p_value=0.498803	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=77/85	major_frequency=9.878e-01	minor_base=G	minor_cov=0/2	new_cov=77/85	polymorphism_frequency=9.878e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=77/87
RA	196	.	NC_000913	3137400	0	G	A	bias_e_value=3264650	bias_p_value=0.703338	consensus_score=257.6	fisher_strand_p_value=0.336809	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=36/40	major_frequency=8.837e-01	minor_base=G	minor_cov=3/7	new_cov=36/40	polymorphism_frequency=8.837e-01	polymorphism_score=18.7	prediction=consensus	ref_cov=3/7	total_cov=39/47
RA	197	.	NC_000913	3191376	0	G	T	bias_e_value=2.81878	bias_p_value=6.07278e-07	consensus_reject=FREQUENCY_CUTOFF	consensus_score=307.5	fisher_strand_p_value=3.33365e-08	frequency=2.147e-01	ks_quality_p_value=1	major_base=G	major_cov=58/70	major_frequency=7.853e-01	minor_base=T	minor_cov=0/35	new_cov=0/35	polymorphism_frequency=2.147e-01	polymorphism_score=14.6	prediction=polymorphism	ref_cov=58/70	total_cov=58/105
RA	198	.	NC_000913	3268247	0	G	T	bias_e_value=1.11115e-05	bias_p_value=2.39386e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=376.0	fisher_strand_p_value=7.67299e-14	frequency=2.013e-01	ks_quality_p_value=1	major_base=G	major_cov=87/40	major_frequency=7.987e-01	minor_base=T	minor_cov=0/32	new_cov=0/32	polymorphism_frequency=2.013e-01	polymorphism_score=14.8	prediction=polymorphism	ref_cov=87/40	total_cov=87/72
RA	199	.	NC_000913	3336411	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=386.1	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=52/53	major_frequency=9.906e-01	minor_base=G	minor_cov=0/1	new_cov=52/53	polymorphism_frequency=9.906e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=52/54
RA	200	.	NC_000913	3336412	0	A	T	consensus_score=369.6	frequency=1	major_base=T	major_cov=52/54	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=52/54	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=52/54
RA	201	.	NC_000913	3388041	0	T	G	consensus_score=411.0	frequency=1	major_base=G	major_cov=57/52	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=57/52	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=57/52
RA	202	.	NC_000913	3433680	0	C	A	bias_e_value=0.124631	bias_p_value=2.68506e-08	consensus_reject=FREQUENCY_CUTOFF	consensus_score=239.5	fisher_strand_p_value=1.2488e-09	frequency=2.657e-01	ks_quality_p_value=1	major_base=C	major_cov=53/52	major_frequency=7.343e-01	minor_base=A	minor_cov=38/0	new_cov=38/0	polymorphism_frequency=2.657e-01	polymorphism_score=17.8	prediction=polymorphism	ref_cov=53/52	total_cov=91/52
RA	203	.	NC_000913	3436697	0	G	A	bias_e_value=3845240	bias_p_value=0.828421	consensus_score=350.8	fisher_strand_p_value=0.474747	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=52/46	major_frequency=9.899e-01	minor_base=G	minor_cov=0/1	new_cov=52/46	polymorphism_frequency=9.899e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=52/47
RA	204	.	NC_000913	3479685	0	A	T	bias_e_value=4641650	bias_p_value=1	consensus_score=246.0	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=24/51	major_frequency=9.868e-01	minor_base=G	minor_cov=0/1	new_cov=24/51	polymorphism_frequency=9.868e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=24/52
RA	205	.	NC_000913	3560455	1	.	G	bias_e_value=3596640	bias_p_value=0.774862	consensus_score=355.1	fisher_strand_p_value=0.434343	frequency=1	ks_quality_p_value=0.942165	major_base=G	major_cov=42/56	major_frequency=9.899e-01	minor_base=.	minor_cov=1/0	new_cov=42/56	polymorphism_frequency=9.899e-01	polymorphism_score=-2.3	prediction=consensus	ref_cov=1/0	total_cov=43/56
RA	206	.	NC_000913	3622422	0	C	G	bias_e_value=4225420	bias_p_value=0.910327	consensus_reject=FREQUENCY_CUTOFF	consensus_score=33.8	fisher_strand_p_value=0.62406	frequency=7.727e-01	ks_quality_p_value=0.973616	major_base=G	major_cov=7/10	major_frequency=7.727e-01	minor_base=C	minor_cov=3/2	new_cov=7/10	polymorphism_frequency=7.727e-01	polymorphism_score=12.3	prediction=polymorphism	ref_cov=3/2	total_cov=11/12
RA	207	.	NC_000913	3682515	0	C	T	consensus_score=323.9	frequency=1	major_base=T	major_cov=52/39	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=52/39	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=52/39
RA	208	.	NC_000913	3707947	0	C	A	bias_e_value=4641650	bias_p_value=1	consensus_score=482.4	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=90/49	major_frequency=9.929e-01	minor_base=C	minor_cov=1/0	new_cov=90/49	polymorphism_frequency=9.929e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=91/49
RA	209	.	NC_000913	3725176	0	T	G	bias_e_value=3785330	bias_p_value=0.815514	consensus_score=299.6	fisher_strand_p_value=0.457831	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=45/37	major_frequency=9.880e-01	minor_base=A	minor_cov=0/1	new_cov=45/37	polymorphism_frequency=9.880e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=45/38
RA	210	.	NC_000913	3741871	0	G	T	bias_e_value=51.8266	bias_p_value=1.11656e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=176.2	fisher_strand_p_value=7.38531e-07	frequency=2.759e-01	ks_quality_p_value=1	major_base=G	major_cov=36/48	major_frequency=7.241e-01	minor_base=T	minor_cov=0/32	new_cov=0/32	polymorphism_frequency=2.759e-01	polymorphism_score=10.7	prediction=polymorphism	ref_cov=36/48	total_cov=36/80
RA	211	.	NC_000913	3768435	0	C	A	bias_e_value=3.24186e-05	bias_p_value=6.98429e-12	consensus_reject=FREQUENCY_CUTOFF	consensus_score=425.3	fisher_strand_p_value=2.32101e-13	frequency=2.021e-01	ks_quality_p_value=1	major_base=C	major_cov=62/92	major_frequency=7.979e-01	minor_base=A	minor_cov=39/0	new_cov=39/0	polymorphism_frequency=2.021e-01	polymorphism_score=11.5	prediction=polymorphism	ref_cov=62/92	total_cov=101/92
RA	212	.	NC_000913	3771979	0	G	T	bias_e_value=3901460	bias_p_value=0.840532	consensus_score=416.7	fisher_strand_p_value=0.491667	frequency=1	ks_quality_p_value=0.99944	major_base=T	major_cov=61/58	major_frequency=9.917e-01	minor_base=G	minor_cov=0/1	new_cov=61/58	polymorphism_frequency=9.917e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=61/59
RA	213	.	NC_000913	3815883	1	.	C	bias_e_value=2585760	bias_p_value=0.557077	consensus_score=424.7	fisher_strand_p_value=0.226138	frequency=1	ks_quality_p_value=0.984495	major_base=C	major_cov=52/59	major_frequency=9.823e-01	minor_base=.	minor_cov=2/0	new_cov=52/59	polymorphism_frequency=9.823e-01	polymorphism_score=-1.0	prediction=consensus	ref_cov=2/0	total_cov=54/59
RA	214	.	NC_000913	3823162	0	C	T	consensus_score=322.3	frequency=1	major_base=T	major_cov=33/59	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=33/59	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=33/59
RA	215	.	NC_000913	3843750	0	C	A	bias_e_value=8.85771	bias_p_value=1.90831e-06	consensus_reject=FREQUENCY_CUTOFF	consensus_score=255.4	fisher_strand_p_value=1.12236e-07	frequency=2.781e-01	ks_quality_p_value=1	major_base=C	major_cov=73/49	major_frequency=7.219e-01	minor_base=A	minor_cov=46/1	new_cov=46/1	polymorphism_frequency=2.781e-01	polymorphism_score=16.7	prediction=polymorphism	ref_cov=73/49	total_cov=119/50
RA	216	.	NC_000913	3869637	0	C	A	consensus_score=358.1	frequency=1	major_base=A	major_cov=40/60	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=40/60	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=40/60
RA	217	.	NC_000913	3878536	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=239.9	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=30/40	major_frequency=9.859e-01	minor_base=G	minor_cov=0/1	new_cov=30/40	polymorphism_frequency=9.859e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=30/41
RA	218	.	NC_000913	3888694	0	G	A	bias_e_value=1817880	bias_p_value=0.391646	consensus_score=491.9	fisher_strand_p_value=0.12825	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=72/74	major_frequency=8.588e-01	minor_base=G	minor_cov=16/8	new_cov=72/74	polymorphism_frequency=8.588e-01	polymorphism_score=52.8	prediction=consensus	ref_cov=16/8	total_cov=88/82
RA	219	.	NC_000913	3896780	0	C	A	bias_e_value=1.08624e-07	bias_p_value=2.3402e-14	consensus_reject=FREQUENCY_CUTOFF	consensus_score=346.8	fisher_strand_p_value=6.50623e-16	frequency=2.405e-01	ks_quality_p_value=1	major_base=C	major_cov=37/83	major_frequency=7.595e-01	minor_base=A	minor_cov=38/0	new_cov=38/0	polymorphism_frequency=2.405e-01	polymorphism_score=15.9	prediction=polymorphism	ref_cov=37/83	total_cov=75/84
RA	220	.	NC_000913	3911533	0	C	A	bias_e_value=8.18425e-07	bias_p_value=1.76322e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=211.8	fisher_strand_p_value=5.20283e-15	frequency=3.435e-01	ks_quality_p_value=1	major_base=C	major_cov=30/56	major_frequency=6.565e-01	minor_base=A	minor_cov=45/0	new_cov=45/0	polymorphism_frequency=3.435e-01	polymorphism_score=23.2	prediction=polymorphism	ref_cov=30/56	total_cov=75/56
RA	221	.	NC_000913	3993531	0	T	C	consensus_score=395.2	frequency=1	major_base=C	major_cov=64/39	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=64/39	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=64/39
RA	222	.	NC_000913	3996049	0	T	A	consensus_score=278.0	frequency=1	major_base=A	major_cov=36/42	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=36/42	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=36/42
RA	223	.	NC_000913	4011802	0	C	T	consensus_score=353.5	frequency=1	major_base=T	major_cov=35/65	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=35/65	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=35/65
RA	224	.	NC_000913	4084903	0	T	G	bias_e_value=2718200	bias_p_value=0.585611	consensus_score=297.0	fisher_strand_p_value=0.242181	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=42/42	major_frequency=9.655e-01	minor_base=T	minor_cov=0/3	new_cov=42/42	polymorphism_frequency=9.655e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/3	total_cov=43/45
RA	225	.	NC_000913	4092703	0	A	G	consensus_score=366.5	frequency=1	major_base=G	major_cov=46/53	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=46/53	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=46/53
RA	226	.	NC_000913	4113851	0	G	A	consensus_score=339.2	frequency=1	major_base=A	major_cov=58/39	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=58/39	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=58/39
RA	227	.	NC_000913	4143377	0	C	T	consensus_score=293.1	frequency=1	major_base=T	major_cov=47/32	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=47/32	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=47/32
RA	228	.	NC_000913	4161248	0	G	T	bias_e_value=4641650	bias_p_value=1	consensus_score=336.0	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.999224	major_base=T	major_cov=46/55	major_frequency=9.902e-01	minor_base=G	minor_cov=0/1	new_cov=46/55	polymorphism_frequency=9.902e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=46/56
RA	229	.	NC_000913	4164123	0	C	G	bias_e_value=1685730	bias_p_value=0.363174	consensus_score=390.4	fisher_strand_p_value=0.114746	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=55/50	major_frequency=9.722e-01	minor_base=T	minor_cov=0/3	new_cov=55/50	polymorphism_frequency=9.722e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=55/53
RA	230	.	NC_000913	4193996	0	T	G	consensus_score=294.5	frequency=1	major_base=G	major_cov=35/41	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=35/41	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=35/41
RA	231	.	NC_000913	4196331	0	C	G	consensus_score=463.6	frequency=1	major_base=G	major_cov=67/55	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=67/55	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=67/55
RA	232	.	NC_000913	4215347	0	T	A	consensus_score=428.5	frequency=1	major_base=A	major_cov=59/67	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=59/67	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=59/67
RA	233	.	NC_000913	4223638	0	T	C	bias_e_value=4641650	bias_p_value=1	consensus_score=544.2	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=C	major_cov=65/83	major_frequency=9.933e-01	minor_base=T	minor_cov=0/1	new_cov=65/83	polymorphism_frequency=9.933e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/1	total_cov=66/84
RA	234	.	NC_000913	4226614	0	C	A	bias_e_value=220.118	bias_p_value=4.74223e-05	consensus_reject=FREQUENCY_CUTOFF	consensus_score=129.4	fisher_strand_p_value=3.49623e-06	frequency=2.658e-01	ks_quality_p_value=1	major_base=C	major_cov=27/31	major_frequency=7.342e-01	minor_base=A	minor_cov=21/0	new_cov=21/0	polymorphism_frequency=2.658e-01	polymorphism_score=14.4	prediction=polymorphism	ref_cov=27/31	total_cov=48/31
RA	235	.	NC_000913	4282332	1	.	A	consensus_score=482.4	frequency=1	major_base=A	major_cov=74/63	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=74/63	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=74/63
RA	236	.	NC_000913	4293781	0	G	A	consensus_score=303.4	frequency=1	major_base=A	major_cov=30/52	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=30/52	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=30/52
RA	237	.	NC_000913	4293782	0	C	T	consensus_score=284.3	frequency=1	major_base=T	major_cov=30/52	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=30/52	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=30/52
RA	238	.	NC_000913	4296268	0	T	C	bias_e_value=1489200	bias_p_value=0.320834	consensus_reject=FREQUENCY_CUTOFF	consensus_score=36.4	fisher_strand_p_value=0.0987241	frequency=2.857e-01	ks_quality_p_value=0.971833	major_base=T	major_cov=10/10	major_frequency=7.143e-01	minor_base=C	minor_cov=7/1	new_cov=7/1	polymorphism_frequency=2.857e-01	polymorphism_score=15.2	prediction=polymorphism	ref_cov=10/10	total_cov=17/11
RA	239	.	NC_000913	4296380	1	.	C	bias_e_value=4636170	bias_p_value=0.998819	consensus_score=179.5	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.951801	major_base=C	major_cov=34/19	major_frequency=9.636e-01	minor_base=T	minor_cov=1/1	new_cov=34/19	polymorphism_frequency=9.636e-01	polymorphism_score=-1.0	prediction=consensus	ref_cov=2/0	total_cov=38/20
RA	240	.	NC_000913	4296380	2	.	G	bias_e_value=4032490	bias_p_value=0.868763	consensus_score=194.1	fisher_strand_p_value=0.533606	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=36/21	major_frequency=9.661e-01	minor_base=.	minor_cov=2/0	new_cov=36/21	polymorphism_frequency=9.661e-01	polymorphism_score=-1.2	prediction=consensus	ref_cov=2/0	total_cov=38/21
RA	241	.	NC_000913	4325644	0	C	T	consensus_score=329.6	frequency=1	major_base=T	major_cov=40/58	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=40/58	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=40/58
RA	242	.	NC_000913	4343958	0	C	T	bias_e_value=3527210	bias_p_value=0.759903	consensus_score=347.7	fisher_strand_p_value=0.392853	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=60/56	major_frequency=8.169e-01	minor_base=C	minor_cov=16/10	new_cov=60/56	polymorphism_frequency=8.169e-01	polymorphism_score=50.1	prediction=consensus	ref_cov=16/10	total_cov=76/67
RA	243	.	NC_000913	4360965	0	C	A	bias_e_value=1.55933e-11	bias_p_value=3.35944e-18	consensus_reject=FREQUENCY_CUTOFF	consensus_score=308.9	fisher_strand_p_value=7.45839e-20	frequency=3.086e-01	ks_quality_p_value=1	major_base=C	major_cov=33/79	major_frequency=6.914e-01	minor_base=A	minor_cov=50/0	new_cov=50/0	polymorphism_frequency=3.086e-01	polymorphism_score=29.8	prediction=polymorphism	ref_cov=33/79	total_cov=83/79
RA	244	.	NC_000913	4392997	0	G	A	bias_e_value=3132790	bias_p_value=0.67493	consensus_score=525.8	fisher_strand_p_value=0.311594	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=42/95	major_frequency=9.928e-01	minor_base=G	minor_cov=1/0	new_cov=42/95	polymorphism_frequency=9.928e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=43/95
RA	245	.	NC_000913	4393552	0	G	A	bias_e_value=4641650	bias_p_value=1	consensus_score=287.8	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=46/39	major_frequency=9.884e-01	minor_base=C	minor_cov=1/0	new_cov=46/39	polymorphism_frequency=9.884e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=47/39
RA	246	.	NC_000913	4396373	0	C	T	consensus_score=298.5	frequency=1	major_base=T	major_cov=45/36	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=45/36	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=45/36
RA	247	.	NC_000913	4396772	0	T	C	consensus_score=255.6	frequency=1	major_base=C	major_cov=33/37	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=33/37	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=33/37
RA	248	.	NC_000913	4425688	0	C	A	consensus_score=318.9	frequency=1	major_base=A	major_cov=41/44	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=41/44	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=41/44
RA	249	.	NC_000913	4425696	0	C	A	bias_e_value=4641650	bias_p_value=1	consensus_score=309.7	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=40/43	major_frequency=9.881e-01	minor_base=G	minor_cov=0/1	new_cov=40/43	polymorphism_frequency=9.881e-01	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=40/44
RA	250	.	NC_000913	4427822	0	C	A	bias_e_value=7.35673e-07	bias_p_value=1.58494e-13	consensus_reject=FREQUENCY_CUTOFF	consensus_score=301.4	fisher_strand_p_value=4.66167e-15	frequency=2.927e-01	ks_quality_p_value=1	major_base=C	major_cov=47/69	major_frequency=7.073e-01	minor_base=A	minor_cov=48/0	new_cov=48/0	polymorphism_frequency=2.927e-01	polymorphism_score=15.1	prediction=polymorphism	ref_cov=47/69	total_cov=95/69
RA	251	.	NC_000913	4510238	0	T	G	bias_e_value=218068	bias_p_value=0.0469806	consensus_score=485.1	fisher_strand_p_value=0.0080734	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=77/59	major_frequency=9.577e-01	minor_base=T	minor_cov=0/6	new_cov=77/59	polymorphism_frequency=9.577e-01	polymorphism_score=-5.1	prediction=consensus	ref_cov=0/6	total_cov=78/65
RA	252	.	NC_000913	4532409	0	T	G	consensus_score=278.5	frequency=1	major_base=G	major_cov=33/41	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=33/41	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=33/41
RA	253	.	NC_000913	4546601	0	C	T	bias_e_value=4641650	bias_p_value=1	consensus_score=470.5	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=78/57	major_frequency=9.926e-01	minor_base=C	minor_cov=1/0	new_cov=78/57	polymorphism_frequency=9.926e-01	polymorphism_score=NA	prediction=consensus	ref_cov=1/0	total_cov=79/57
RA	254	.	NC_000913	4576327	0	G	A	bias_e_value=4318700	bias_p_value=0.930423	consensus_score=294.7	fisher_strand_p_value=0.650962	frequency=1	ks_quality_p_value=1	major_base=A	major_cov=47/52	major_frequency=8.049e-01	minor_base=G	minor_cov=13/11	new_cov=47/52	polymorphism_frequency=8.049e-01	polymorphism_score=54.2	prediction=consensus	ref_cov=13/11	total_cov=60/63
RA	255	.	NC_000913	4636925	0	G	C	consensus_score=306.8	frequency=1	major_base=C	major_cov=45/34	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=45/34	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=45/34
RA	256	.	NC_000913	4638240	0	G	A	consensus_score=328.4	frequency=1	major_base=A	major_cov=54/45	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=54/45	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=54/45
MC	257	.	NC_000913	257908	258683	0	0	left_inside_cov=0	left_outside_cov=151	right_inside_cov=3	right_outside_cov=156
MC	258	.	NC_000913	1196277	1211453	0	0	left_inside_cov=33	left_outside_cov=36	right_inside_cov=34	right_outside_cov=35
MC	259	.	NC_000913	1978495	1979270	0	768	left_inside_cov=0	left_outside_cov=132	right_inside_cov=0	right_outside_cov=155
MC	260	.	NC_000913	2066397	2067091	694	0	left_inside_cov=33	left_outside_cov=36	right_inside_cov=33	right_outside_cov=35
MC	261	.	NC_000913	3423887	3424492	345	253	left_inside_cov=33	left_outside_cov=35	right_inside_cov=34	right_outside_cov=38
MC	262	.	NC_000913	3708467	3708634	0	0	left_inside_cov=0	left_outside_cov=36	right_inside_cov=28	right_outside_cov=64
JC	263	.	NC_000913	1	1	NC_000913	4641652	-1	0	alignment_overlap=0	coverage_minus=91	coverage_plus=77	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=295	max_left_minus=295	max_left_plus=271	max_min_left=149	max_min_left_minus=149	max_min_left_plus=147	max_min_right=144	max_min_right_minus=139	max_min_right_plus=144	max_pos_hash_score=590	max_right=289	max_right_minus=287	max_right_plus=289	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.63	new_junction_read_count=172	polymorphism_frequency=1.000e+00	pos_hash_score=92	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=168
JC	264	.	NC_000913	3588	-1	NC_000913	3990	1	0	alignment_overlap=10	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.491e-02	junction_possible_overlap_registers=284	key=NC_000913__3588__-1__NC_000913__3980__1__10____300__300__0__0	max_left=114	max_left_minus=114	max_left_plus=114	max_min_left=1	max_min_left_minus=0	max_min_left_plus=1	max_min_right=88	max_min_right_minus=88	max_min_right_plus=88	max_pos_hash_score=570	max_right=96	max_right_minus=88	max_right_plus=96	neg_log10_pos_hash_p_value=8.8	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.491e-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=0.80	side_1_overlap=10	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=1.38	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=140	side_2_redundant=0	total_non_overlap_reads=4
JC	265	.	NC_000913	257907	-1	NC_000913	258684	1	0	alignment_overlap=8	coverage_minus=60	coverage_plus=88	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=291	max_left_minus=291	max_left_plus=282	max_min_left=143	max_min_left_minus=140	max_min_left_plus=143	max_min_right=144	max_min_right_minus=136	max_min_right_plus=144	max_pos_hash_score=574	max_right=287	max_right_minus=287	max_right_plus=267	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.47	new_junction_read_count=151	polymorphism_frequency=1.000e+00	pos_hash_score=76	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=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=148
JC	266	.	NC_000913	268317	-1	NC_000913	268750	1	0	alignment_overlap=8	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.031e-02	junction_possible_overlap_registers=286	key=NC_000913__268317__-1__NC_000913__268742__1__8____300__300__0__0	max_left=158	max_left_minus=158	max_left_plus=158	max_min_left=61	max_min_left_minus=61	max_min_left_plus=60	max_min_right=8	max_min_right_minus=8	max_min_right_plus=8	max_pos_hash_score=574	max_right=166	max_right_minus=166	max_right_plus=166	neg_log10_pos_hash_p_value=8.9	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=5.031e-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=0.69	side_1_overlap=8	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=0.78	side_2_overlap=0	side_2_possible_overlap_registers=286	side_2_read_count=80	side_2_redundant=0	total_non_overlap_reads=4
JC	267	.	NC_000913	271761	-1	NC_000913	4640419	-1	0	alignment_overlap=3	coverage_minus=3	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.018e-02	junction_possible_overlap_registers=291	key=NC_000913__271762__-1__NC_000913__4640421__-1__3____300__300__0__0	max_left=139	max_left_minus=121	max_left_plus=139	max_min_left=139	max_min_left_minus=121	max_min_left_plus=139	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=584	max_right=255	max_right_minus=255	max_right_plus=158	neg_log10_pos_hash_p_value=9.0	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.018e-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=2	side_1_read_count=NA	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.23	side_2_overlap=1	side_2_possible_overlap_registers=292	side_2_read_count=129	side_2_redundant=0	total_non_overlap_reads=4
JC	268	.	NC_000913	273955	1	NC_000913	1102451	-1	0	alignment_overlap=0	coverage_minus=13	coverage_plus=10	flanking_left=300	flanking_right=300	frequency=1.633e-01	junction_possible_overlap_registers=294	key=NC_000913__273955__1__NC_000913__1102451__-1__0____300__300__1__0	max_left=281	max_left_minus=273	max_left_plus=281	max_min_left=146	max_min_left_minus=146	max_min_left_plus=112	max_min_right=139	max_min_right_minus=124	max_min_right_plus=139	max_pos_hash_score=590	max_right=296	max_right_minus=296	max_right_plus=272	neg_log10_pos_hash_p_value=4.7	new_junction_coverage=0.23	new_junction_read_count=24	polymorphism_frequency=1.633e-01	pos_hash_score=16	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=1.17	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=123	side_2_redundant=0	total_non_overlap_reads=23
JC	269	.	NC_000913	280111	-1	NC_000913	4640419	-1	0	alignment_overlap=2	coverage_minus=3	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.008e-02	junction_possible_overlap_registers=292	key=NC_000913__280111__-1__NC_000913__4640421__-1__2____300__300__0__0	max_left=139	max_left_minus=121	max_left_plus=139	max_min_left=139	max_min_left_minus=121	max_min_left_plus=139	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=586	max_right=256	max_right_minus=256	max_right_plus=159	neg_log10_pos_hash_p_value=9.0	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.008e-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=2	side_1_read_count=NA	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.23	side_2_overlap=0	side_2_possible_overlap_registers=292	side_2_read_count=129	side_2_redundant=0	total_non_overlap_reads=4
JC	270	.	NC_000913	282063	-1	NC_000913	282179	1	0	alignment_overlap=3	coverage_minus=2	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=8.419e-02	junction_possible_overlap_registers=291	key=NC_000913__282063__-1__NC_000913__282176__1__3____300__300__0__0	max_left=261	max_left_minus=100	max_left_plus=261	max_min_left=100	max_min_left_minus=100	max_min_left_plus=88	max_min_right=35	max_min_right_minus=0	max_min_right_plus=35	max_pos_hash_score=584	max_right=294	max_right_minus=249	max_right_plus=294	neg_log10_pos_hash_p_value=7.5	new_junction_coverage=0.07	new_junction_read_count=7	polymorphism_frequency=8.419e-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=0.66	side_1_overlap=3	side_1_possible_overlap_registers=294	side_1_read_count=70	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.80	side_2_overlap=0	side_2_possible_overlap_registers=291	side_2_read_count=83	side_2_redundant=0	total_non_overlap_reads=7
JC	271	.	NC_000913	381260	1	NC_000913	572000	1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.846e-02	junction_possible_overlap_registers=294	key=NC_000913__381260__1__NC_000913__572000__1__0____300__300__1__0	max_left=296	max_left_minus=135	max_left_plus=296	max_min_left=135	max_min_left_minus=135	max_min_left_plus=0	max_min_right=123	max_min_right_minus=0	max_min_right_plus=123	max_pos_hash_score=590	max_right=292	max_right_minus=292	max_right_plus=123	neg_log10_pos_hash_p_value=8.5	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=3.846e-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=1.19	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=125	side_2_redundant=0	total_non_overlap_reads=5
JC	272	.	NC_000913	572004	-1	NC_000913	1467910	1	0	alignment_overlap=2	coverage_minus=1	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=3.200e-02	junction_possible_overlap_registers=292	key=NC_000913__572006__-1__NC_000913__1467910__1__2____300__300__0__1	max_left=210	max_left_minus=207	max_left_plus=210	max_min_left=3	max_min_left_minus=0	max_min_left_plus=3	max_min_right=88	max_min_right_minus=75	max_min_right_plus=88	max_pos_hash_score=586	max_right=291	max_right_minus=75	max_right_plus=291	neg_log10_pos_hash_p_value=9.0	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.200e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.16	side_1_overlap=0	side_1_possible_overlap_registers=292	side_1_read_count=121	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=2	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=4
JC	273	.	NC_000913	599805	-1	NC_000913	600187	1	0	alignment_overlap=8	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.528e-02	junction_possible_overlap_registers=286	key=NC_000913__599805__-1__NC_000913__600179__1__8____300__300__0__0	max_left=115	max_left_minus=115	max_left_plus=115	max_min_left=115	max_min_left_minus=115	max_min_left_plus=115	max_min_right=40	max_min_right_minus=40	max_min_right_plus=40	max_pos_hash_score=574	max_right=119	max_right_minus=119	max_right_plus=119	neg_log10_pos_hash_p_value=8.9	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.528e-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=0.82	side_1_overlap=8	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=0.83	side_2_overlap=0	side_2_possible_overlap_registers=286	side_2_read_count=85	side_2_redundant=0	total_non_overlap_reads=4
JC	274	.	NC_000913	655901	1	NC_000913	687851	1	0	alignment_overlap=0	coverage_minus=3	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=8.943e-02	junction_possible_overlap_registers=294	key=NC_000913__655901__1__NC_000913__687851__1__0____300__300__0__1	max_left=296	max_left_minus=270	max_left_plus=296	max_min_left=61	max_min_left_minus=61	max_min_left_plus=61	max_min_right=133	max_min_right_minus=30	max_min_right_plus=133	max_pos_hash_score=590	max_right=293	max_right_minus=293	max_right_plus=253	neg_log10_pos_hash_p_value=6.7	new_junction_coverage=0.10	new_junction_read_count=11	polymorphism_frequency=8.943e-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=1.06	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=112	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=10
JC	275	.	NC_000913	676306	-1	NC_000913	687851	1	0	alignment_overlap=0	coverage_minus=14	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.615e-01	junction_possible_overlap_registers=294	key=NC_000913__676306__-1__NC_000913__687851__1__0____300__300__0__1	max_left=212	max_left_minus=212	max_left_plus=212	max_min_left=143	max_min_left_minus=143	max_min_left_plus=118	max_min_right=132	max_min_right_minus=132	max_min_right_plus=55	max_pos_hash_score=590	max_right=294	max_right_minus=254	max_right_plus=294	neg_log10_pos_hash_p_value=5.2	new_junction_coverage=0.20	new_junction_read_count=21	polymorphism_frequency=1.615e-01	pos_hash_score=14	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.04	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=109	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=21
JC	276	.	NC_000913	696506	-1	NC_000913	696619	1	0	alignment_overlap=77	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.102e-02	junction_possible_overlap_registers=217	key=NC_000913__696506__-1__NC_000913__696542__1__77____300__300__0__0	max_left=119	max_left_minus=119	max_left_plus=116	max_min_left=71	max_min_left_minus=0	max_min_left_plus=71	max_min_right=69	max_min_right_minus=69	max_min_right_plus=69	max_pos_hash_score=436	max_right=152	max_right_minus=69	max_right_plus=152	neg_log10_pos_hash_p_value=7.4	new_junction_coverage=0.05	new_junction_read_count=4	polymorphism_frequency=5.102e-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=0.95	side_1_overlap=77	side_1_possible_overlap_registers=294	side_1_read_count=100	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.97	side_2_overlap=0	side_2_possible_overlap_registers=217	side_2_read_count=75	side_2_redundant=0	total_non_overlap_reads=4
JC	277	.	NC_000913	696741	-1	NC_000913	697135	1	0	alignment_overlap=78	coverage_minus=9	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=2.215e-01	junction_possible_overlap_registers=216	key=NC_000913__696741__-1__NC_000913__697057__1__78____300__300__0__0	max_left=182	max_left_minus=182	max_left_plus=171	max_min_left=10	max_min_left_minus=10	max_min_left_plus=10	max_min_right=56	max_min_right_minus=56	max_min_right_plus=55	max_pos_hash_score=434	max_right=56	max_right_minus=56	max_right_plus=55	neg_log10_pos_hash_p_value=4.2	new_junction_coverage=0.21	new_junction_read_count=16	polymorphism_frequency=2.215e-01	pos_hash_score=12	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.63	side_1_overlap=78	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=0.83	side_2_overlap=0	side_2_possible_overlap_registers=216	side_2_read_count=64	side_2_redundant=0	total_non_overlap_reads=16
JC	278	.	NC_000913	781016	-1	NC_000913	781577	1	-48	alignment_overlap=-48	coverage_minus=3	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=1.016e-01	junction_possible_overlap_registers=246	key=NC_000913__781016__-1__NC_000913__781577__1__-48__ATCTTAAAGATTGGCCCCGAGTAAAAATCTTTCAGGTAACACCCGTAT__300__300__0__0	max_left=248	max_left_minus=223	max_left_plus=248	max_min_left=65	max_min_left_minus=65	max_min_left_plus=64	max_min_right=121	max_min_right_minus=5	max_min_right_plus=121	max_pos_hash_score=494	max_right=207	max_right_minus=207	max_right_plus=157	neg_log10_pos_hash_p_value=6.6	new_junction_coverage=0.08	new_junction_read_count=7	polymorphism_frequency=1.016e-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=0.72	side_1_overlap=0	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=0.68	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=72	side_2_redundant=0	total_non_overlap_reads=7	unique_read_sequence=ATCTTAAAGATTGGCCCCGAGTAAAAATCTTTCAGGTAACACCCGTAT
JC	279	.	NC_000913	781016	-1	NC_000913	2521253	1	-48	alignment_overlap=-48	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.094e-02	junction_possible_overlap_registers=246	key=NC_000913__781016__-1__NC_000913__2521253__1__-48__ATCTTAAAGATTGGCCCCGAGTAAAAATCTTTCAGGTAACACCCGTAT__300__300__0__0	max_left=248	max_left_minus=223	max_left_plus=248	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=5	max_min_right_minus=5	max_min_right_plus=5	max_pos_hash_score=494	max_right=5	max_right_minus=5	max_right_plus=5	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=4.094e-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=0	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=0.87	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=92	side_2_redundant=0	total_non_overlap_reads=3	unique_read_sequence=ATCTTAAAGATTGGCCCCGAGTAAAAATCTTTCAGGTAACACCCGTAT
JC	280	.	NC_000913	781282	-1	NC_000913	781771	1	0	alignment_overlap=8	coverage_minus=2	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=6.269e-02	junction_possible_overlap_registers=286	key=NC_000913__781282__-1__NC_000913__781763__1__8____300__300__0__0	max_left=178	max_left_minus=60	max_left_plus=178	max_min_left=60	max_min_left_minus=60	max_min_left_plus=41	max_min_right=78	max_min_right_minus=0	max_min_right_plus=78	max_pos_hash_score=574	max_right=145	max_right_minus=111	max_right_plus=145	neg_log10_pos_hash_p_value=7.8	new_junction_coverage=0.06	new_junction_read_count=6	polymorphism_frequency=6.269e-02	pos_hash_score=6	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.90	side_1_overlap=8	side_1_possible_overlap_registers=294	side_1_read_count=95	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.85	side_2_overlap=0	side_2_possible_overlap_registers=286	side_2_read_count=87	side_2_redundant=0	total_non_overlap_reads=6
JC	281	.	NC_000913	781543	-1	NC_000913	781809	1	0	alignment_overlap=24	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=4.859e-02	junction_possible_overlap_registers=270	key=NC_000913__781543__-1__NC_000913__781785__1__24____300__300__0__0	max_left=165	max_left_minus=165	max_left_plus=143	max_min_left=103	max_min_left_minus=0	max_min_left_plus=103	max_min_right=133	max_min_right_minus=128	max_min_right_plus=133	max_pos_hash_score=542	max_right=155	max_right_minus=128	max_right_plus=155	neg_log10_pos_hash_p_value=8.6	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=4.859e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.85	side_1_overlap=24	side_1_possible_overlap_registers=294	side_1_read_count=90	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.77	side_2_overlap=0	side_2_possible_overlap_registers=270	side_2_read_count=74	side_2_redundant=0	total_non_overlap_reads=4
JC	282	.	NC_000913	1102448	1	NC_000913	1396044	1	0	alignment_overlap=5	coverage_minus=6	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=7.697e-02	junction_possible_overlap_registers=289	key=NC_000913__1102448__1__NC_000913__1396039__1__5____300__300__0__1	max_left=291	max_left_minus=291	max_left_plus=268	max_min_left=70	max_min_left_minus=70	max_min_left_plus=46	max_min_right=58	max_min_right_minus=58	max_min_right_plus=27	max_pos_hash_score=580	max_right=283	max_right_minus=283	max_right_plus=282	neg_log10_pos_hash_p_value=6.3	new_junction_coverage=0.10	new_junction_read_count=10	polymorphism_frequency=7.697e-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=1.16	side_1_overlap=5	side_1_possible_overlap_registers=294	side_1_read_count=122	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=10
JC	283	.	NC_000913	1166125	-1	NC_000913	1166621	1	0	alignment_overlap=15	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.650e-02	junction_possible_overlap_registers=279	key=NC_000913__1166125__-1__NC_000913__1166606__1__15____300__300__0__0	max_left=127	max_left_minus=127	max_left_plus=127	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=69	max_min_right_minus=39	max_min_right_plus=69	max_pos_hash_score=560	max_right=69	max_right_minus=39	max_right_plus=69	neg_log10_pos_hash_p_value=8.7	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=3.650e-02	pos_hash_score=4	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.27	side_1_overlap=15	side_1_possible_overlap_registers=294	side_1_read_count=134	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.84	side_2_overlap=0	side_2_possible_overlap_registers=279	side_2_read_count=84	side_2_redundant=0	total_non_overlap_reads=4
JC	284	.	NC_000913	1287084	-1	NC_000913	1287557	1	0	alignment_overlap=20	coverage_minus=6	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=1.341e-01	junction_possible_overlap_registers=274	key=NC_000913__1287084__-1__NC_000913__1287537__1__20____300__300__0__0	max_left=242	max_left_minus=242	max_left_plus=163	max_min_left=23	max_min_left_minus=21	max_min_left_plus=23	max_min_right=103	max_min_right_minus=103	max_min_right_plus=103	max_pos_hash_score=550	max_right=103	max_right_minus=103	max_right_plus=103	neg_log10_pos_hash_p_value=7.1	new_junction_coverage=0.10	new_junction_read_count=10	polymorphism_frequency=1.341e-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=0.82	side_1_overlap=20	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=0.50	side_2_overlap=0	side_2_possible_overlap_registers=274	side_2_read_count=49	side_2_redundant=0	total_non_overlap_reads=8
JC	285	.	NC_000913	1287262	-1	NC_000913	1287382	1	0	alignment_overlap=21	coverage_minus=2	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=9.844e-02	junction_possible_overlap_registers=273	key=NC_000913__1287262__-1__NC_000913__1287361__1__21____300__300__0__0	max_left=91	max_left_minus=91	max_left_plus=91	max_min_left=91	max_min_left_minus=91	max_min_left_plus=91	max_min_right=0	max_min_right_minus=0	max_min_right_plus=0	max_pos_hash_score=548	max_right=211	max_right_minus=211	max_right_plus=211	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.07	new_junction_read_count=7	polymorphism_frequency=9.844e-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=0.77	side_1_overlap=21	side_1_possible_overlap_registers=294	side_1_read_count=81	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=273	side_2_read_count=53	side_2_redundant=0	total_non_overlap_reads=6
JC	286	.	NC_000913	1293196	1	NC_000913	1300693	-1	0	alignment_overlap=0	coverage_minus=9	coverage_plus=6	flanking_left=300	flanking_right=300	frequency=1.042e-01	junction_possible_overlap_registers=294	key=NC_000913__1293196__1__NC_000913__1300693__-1__0____300__300__0__1	max_left=261	max_left_minus=261	max_left_plus=189	max_min_left=135	max_min_left_minus=116	max_min_left_plus=135	max_min_right=148	max_min_right_minus=148	max_min_right_plus=127	max_pos_hash_score=590	max_right=294	max_right_minus=294	max_right_plus=294	neg_log10_pos_hash_p_value=5.4	new_junction_coverage=0.14	new_junction_read_count=15	polymorphism_frequency=1.042e-01	pos_hash_score=13	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.23	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=129	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=15
JC	287	.	NC_000913	1293199	-1	NC_000913	1299499	1	0	alignment_overlap=0	coverage_minus=10	coverage_plus=14	flanking_left=300	flanking_right=300	frequency=1.690e-01	junction_possible_overlap_registers=294	key=NC_000913__1293199__-1__NC_000913__1299499__1__0____300__300__0__1	max_left=298	max_left_minus=297	max_left_plus=298	max_min_left=148	max_min_left_minus=36	max_min_left_plus=148	max_min_right=107	max_min_right_minus=95	max_min_right_plus=107	max_pos_hash_score=590	max_right=293	max_right_minus=293	max_right_plus=272	neg_log10_pos_hash_p_value=3.5	new_junction_coverage=0.23	new_junction_read_count=24	polymorphism_frequency=1.690e-01	pos_hash_score=22	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.12	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=118	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=24
JC	288	.	NC_000913	1293199	-1	NC_000913	2067353	-1	0	alignment_overlap=3	coverage_minus=5	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=7.154e-02	junction_possible_overlap_registers=291	key=NC_000913__1293199__-1__NC_000913__2067356__-1__3____300__300__0__0	max_left=295	max_left_minus=294	max_left_plus=295	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=88	max_min_right_minus=88	max_min_right_plus=30	max_pos_hash_score=584	max_right=88	max_right_minus=88	max_right_plus=30	neg_log10_pos_hash_p_value=7.0	new_junction_coverage=0.09	new_junction_read_count=9	polymorphism_frequency=7.154e-02	pos_hash_score=8	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.12	side_1_overlap=3	side_1_possible_overlap_registers=294	side_1_read_count=118	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=0	total_non_overlap_reads=9
JC	289	.	NC_000913	1299498	-1	NC_000913	1300698	1	0	alignment_overlap=4	coverage_minus=68	coverage_plus=78	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=290	max_left_plus=294	max_min_left=146	max_min_left_minus=143	max_min_left_plus=146	max_min_right=140	max_min_right_minus=139	max_min_right_plus=140	max_pos_hash_score=582	max_right=295	max_right_minus=283	max_right_plus=295	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.44	new_junction_read_count=150	polymorphism_frequency=9.902e-01	pos_hash_score=89	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.03	side_1_overlap=4	side_1_possible_overlap_registers=294	side_1_read_count=3	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=146
JC	290	.	NC_000913	1397238	-1	NC_000913	1978494	-1	0	alignment_overlap=0	coverage_minus=66	coverage_plus=63	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=294	key=NC_000913__1397238__-1__NC_000913__1978494__-1__0____300__300__1__0	max_left=294	max_left_minus=284	max_left_plus=294	max_min_left=146	max_min_left_minus=146	max_min_left_plus=146	max_min_right=148	max_min_right_minus=148	max_min_right_plus=138	max_pos_hash_score=590	max_right=298	max_right_minus=298	max_right_plus=296	neg_log10_pos_hash_p_value=0.1	new_junction_coverage=1.25	new_junction_read_count=132	polymorphism_frequency=1.000e+00	pos_hash_score=78	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=294	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=129
JC	291	.	NC_000913	1979271	1	NC_000913	2102947	-1	0	alignment_overlap=0	coverage_minus=68	coverage_plus=80	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=294	key=NC_000913__1979271__1__NC_000913__2102947__-1__0____300__300__0__1	max_left=299	max_left_minus=294	max_left_plus=299	max_min_left=145	max_min_left_minus=127	max_min_left_plus=145	max_min_right=150	max_min_right_minus=145	max_min_right_plus=150	max_pos_hash_score=590	max_right=292	max_right_minus=291	max_right_plus=292	neg_log10_pos_hash_p_value=0.0	new_junction_coverage=1.47	new_junction_read_count=155	polymorphism_frequency=1.000e+00	pos_hash_score=89	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=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=148
JC	292	.	NC_000913	2163497	-1	NC_000913	2178436	1	0	alignment_overlap=11	coverage_minus=33	coverage_plus=41	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=283	key=NC_000913__2163497__-1__NC_000913__2178425__1__11____300__300__0__0	max_left=277	max_left_minus=274	max_left_plus=277	max_min_left=142	max_min_left_minus=113	max_min_left_plus=142	max_min_right=139	max_min_right_minus=133	max_min_right_plus=139	max_pos_hash_score=568	max_right=286	max_right_minus=286	max_right_plus=285	neg_log10_pos_hash_p_value=0.8	new_junction_coverage=0.76	new_junction_read_count=77	polymorphism_frequency=8.540e-01	pos_hash_score=47	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.17	side_1_overlap=11	side_1_possible_overlap_registers=294	side_1_read_count=18	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.09	side_2_overlap=0	side_2_possible_overlap_registers=283	side_2_read_count=9	side_2_redundant=0	total_non_overlap_reads=74
JC	293	.	NC_000913	2558698	-1	NC_000913	2565489	1	0	alignment_overlap=8	coverage_minus=2	coverage_plus=11	flanking_left=300	flanking_right=300	frequency=1.438e-01	junction_possible_overlap_registers=286	key=NC_000913__2558698__-1__NC_000913__2565481__1__8____300__300__0__0	max_left=290	max_left_minus=57	max_left_plus=290	max_min_left=141	max_min_left_minus=57	max_min_left_plus=141	max_min_right=140	max_min_right_minus=0	max_min_right_plus=140	max_pos_hash_score=574	max_right=279	max_right_minus=235	max_right_plus=279	neg_log10_pos_hash_p_value=5.3	new_junction_coverage=0.14	new_junction_read_count=14	polymorphism_frequency=1.438e-01	pos_hash_score=13	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.78	side_1_overlap=8	side_1_possible_overlap_registers=294	side_1_read_count=82	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.85	side_2_overlap=0	side_2_possible_overlap_registers=286	side_2_read_count=87	side_2_redundant=0	total_non_overlap_reads=13
JC	294	.	NC_000913	2653419	-1	NC_000913	2653746	1	0	alignment_overlap=25	coverage_minus=6	coverage_plus=7	flanking_left=300	flanking_right=300	frequency=1.154e-01	junction_possible_overlap_registers=269	key=NC_000913__2653419__-1__NC_000913__2653721__1__25____300__300__0__0	max_left=181	max_left_minus=181	max_left_plus=159	max_min_left=110	max_min_left_minus=110	max_min_left_plus=42	max_min_right=108	max_min_right_minus=108	max_min_right_plus=108	max_pos_hash_score=540	max_right=233	max_right_minus=225	max_right_plus=233	neg_log10_pos_hash_p_value=5.0	new_junction_coverage=0.13	new_junction_read_count=13	polymorphism_frequency=1.154e-01	pos_hash_score=13	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.97	side_1_overlap=25	side_1_possible_overlap_registers=294	side_1_read_count=102	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=269	side_2_read_count=106	side_2_redundant=0	total_non_overlap_reads=13
JC	295	.	NC_000913	2653549	-1	NC_000913	2653872	1	0	alignment_overlap=16	coverage_minus=6	coverage_plus=4	flanking_left=300	flanking_right=300	frequency=8.980e-02	junction_possible_overlap_registers=278	key=NC_000913__2653549__-1__NC_000913__2653856__1__16____300__300__0__0	max_left=260	max_left_minus=260	max_left_plus=222	max_min_left=129	max_min_left_minus=129	max_min_left_plus=129	max_min_right=66	max_min_right_minus=66	max_min_right_plus=66	max_pos_hash_score=558	max_right=157	max_right_minus=157	max_right_plus=157	neg_log10_pos_hash_p_value=6.1	new_junction_coverage=0.10	new_junction_read_count=10	polymorphism_frequency=8.980e-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=0.92	side_1_overlap=16	side_1_possible_overlap_registers=294	side_1_read_count=97	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.11	side_2_overlap=0	side_2_possible_overlap_registers=278	side_2_read_count=111	side_2_redundant=0	total_non_overlap_reads=10
JC	296	.	NC_000913	2817942	-1	NC_000913	2818492	1	0	alignment_overlap=20	coverage_minus=2	coverage_plus=5	flanking_left=300	flanking_right=300	frequency=7.535e-02	junction_possible_overlap_registers=274	key=NC_000913__2817942__-1__NC_000913__2818472__1__20____300__300__0__0	max_left=259	max_left_minus=257	max_left_plus=259	max_min_left=38	max_min_left_minus=0	max_min_left_plus=38	max_min_right=44	max_min_right_minus=41	max_min_right_plus=44	max_pos_hash_score=550	max_right=44	max_right_minus=41	max_right_plus=44	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.07	new_junction_read_count=7	polymorphism_frequency=7.535e-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=0.86	side_1_overlap=20	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=0.89	side_2_overlap=0	side_2_possible_overlap_registers=274	side_2_read_count=87	side_2_redundant=0	total_non_overlap_reads=7
JC	297	.	NC_000913	2877792	-1	NC_000913	2878283	1	0	alignment_overlap=19	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.983e-02	junction_possible_overlap_registers=275	key=NC_000913__2877792__-1__NC_000913__2878264__1__19____300__300__0__0	max_left=90	max_left_minus=90	max_left_plus=90	max_min_left=6	max_min_left_minus=0	max_min_left_plus=6	max_min_right=62	max_min_right_minus=62	max_min_right_plus=62	max_pos_hash_score=552	max_right=118	max_right_minus=62	max_right_plus=118	neg_log10_pos_hash_p_value=9.3	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.983e-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=19	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=0.68	side_2_overlap=0	side_2_possible_overlap_registers=275	side_2_read_count=67	side_2_redundant=0	total_non_overlap_reads=3
JC	298	.	NC_000913	2913392	1	NC_000913	2997691	-1	0	alignment_overlap=0	coverage_minus=47	coverage_plus=63	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=294	key=NC_000913__2913392__1__NC_000913__2997691__-1__0____300__300__0__1	max_left=295	max_left_minus=284	max_left_plus=295	max_min_left=144	max_min_left_minus=144	max_min_left_plus=137	max_min_right=147	max_min_right_minus=143	max_min_right_plus=147	max_pos_hash_score=590	max_right=296	max_right_minus=296	max_right_plus=296	neg_log10_pos_hash_p_value=0.3	new_junction_coverage=1.21	new_junction_read_count=127	polymorphism_frequency=1.000e+00	pos_hash_score=64	prediction=consensus	read_count_offset=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=289	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=110
JC	299	.	NC_000913	2913396	-1	NC_000913	2996361	1	0	alignment_overlap=0	coverage_minus=60	coverage_plus=47	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=294	key=NC_000913__2913396__-1__NC_000913__2996361__1__0____300__300__0__1	max_left=295	max_left_minus=295	max_left_plus=275	max_min_left=148	max_min_left_minus=148	max_min_left_plus=140	max_min_right=145	max_min_right_minus=145	max_min_right_plus=142	max_pos_hash_score=590	max_right=297	max_right_minus=297	max_right_plus=293	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=1.04	new_junction_read_count=109	polymorphism_frequency=1.000e+00	pos_hash_score=68	prediction=consensus	read_count_offset=5	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=0	side_1_possible_overlap_registers=289	side_1_read_count=0	side_1_redundant=0	side_2_annotate_key=repeat	side_2_continuation=0	side_2_coverage=NA	side_2_overlap=0	side_2_possible_overlap_registers=NA	side_2_read_count=NA	side_2_redundant=1	total_non_overlap_reads=107
JC	300	.	NC_000913	2944325	-1	NC_000913	2944820	1	0	alignment_overlap=10	coverage_minus=2	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=5.436e-02	junction_possible_overlap_registers=284	key=NC_000913__2944325__-1__NC_000913__2944810__1__10____300__300__0__0	max_left=72	max_left_minus=72	max_left_plus=72	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=55	max_min_right_minus=55	max_min_right_plus=55	max_pos_hash_score=570	max_right=55	max_right_minus=55	max_right_plus=55	neg_log10_pos_hash_p_value=9.5	new_junction_coverage=0.04	new_junction_read_count=4	polymorphism_frequency=5.436e-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=10	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=0.58	side_2_overlap=0	side_2_possible_overlap_registers=284	side_2_read_count=59	side_2_redundant=0	total_non_overlap_reads=4
JC	301	.	NC_000913	3129975	-1	NC_000913	3130146	1	0	alignment_overlap=0	coverage_minus=35	coverage_plus=30	flanking_left=300	flanking_right=300	frequency=7.765e-01	junction_possible_overlap_registers=294	key=NC_000913__3129975__-1__NC_000913__3130146__1__0____300__300__0__1	max_left=297	max_left_minus=297	max_left_plus=296	max_min_left=148	max_min_left_minus=133	max_min_left_plus=148	max_min_right=146	max_min_right_minus=140	max_min_right_plus=146	max_pos_hash_score=590	max_right=288	max_right_minus=270	max_right_plus=288	neg_log10_pos_hash_p_value=0.9	new_junction_coverage=0.63	new_junction_read_count=66	polymorphism_frequency=7.765e-01	pos_hash_score=48	prediction=polymorphism	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.18	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=19	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=65
JC	302	.	NC_000913	3269872	-1	NC_000913	3270212	1	0	alignment_overlap=7	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=2.892e-02	junction_possible_overlap_registers=287	key=NC_000913__3269872__-1__NC_000913__3270205__1__7____300__300__0__0	max_left=282	max_left_minus=282	max_left_plus=83	max_min_left=83	max_min_left_minus=83	max_min_left_plus=83	max_min_right=8	max_min_right_minus=8	max_min_right_plus=0	max_pos_hash_score=576	max_right=113	max_right_minus=113	max_right_plus=113	neg_log10_pos_hash_p_value=9.5	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.892e-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=1.01	side_1_overlap=7	side_1_possible_overlap_registers=294	side_1_read_count=106	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.95	side_2_overlap=0	side_2_possible_overlap_registers=287	side_2_read_count=98	side_2_redundant=0	total_non_overlap_reads=3
JC	303	.	NC_000913	3708466	-1	NC_000913	3708635	1	0	alignment_overlap=108	coverage_minus=14	coverage_plus=22	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=186	key=NC_000913__3708466__-1__NC_000913__3708527__1__108____300__300__0__0	max_left=184	max_left_minus=162	max_left_plus=184	max_min_left=95	max_min_left_minus=90	max_min_left_plus=95	max_min_right=87	max_min_right_minus=63	max_min_right_plus=87	max_pos_hash_score=374	max_right=184	max_right_minus=184	max_right_plus=161	neg_log10_pos_hash_p_value=1.9	new_junction_coverage=0.54	new_junction_read_count=36	polymorphism_frequency=1.000e+00	pos_hash_score=20	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.00	side_1_overlap=108	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=186	side_2_read_count=0	side_2_redundant=0	total_non_overlap_reads=36
JC	304	.	NC_000913	3822646	1	NC_000913	3822651	-1	0	alignment_overlap=0	coverage_minus=42	coverage_plus=49	flanking_left=300	flanking_right=300	frequency=1	junction_possible_overlap_registers=294	key=NC_000913__3822646__1__NC_000913__3822651__-1__0____300__300__0__0	max_left=296	max_left_minus=293	max_left_plus=296	max_min_left=146	max_min_left_minus=146	max_min_left_plus=131	max_min_right=147	max_min_right_minus=137	max_min_right_plus=147	max_pos_hash_score=590	max_right=294	max_right_minus=294	max_right_plus=288	neg_log10_pos_hash_p_value=0.6	new_junction_coverage=0.87	new_junction_read_count=92	polymorphism_frequency=9.634e-01	pos_hash_score=54	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.02	side_1_overlap=0	side_1_possible_overlap_registers=294	side_1_read_count=2	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.05	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=5	side_2_redundant=0	total_non_overlap_reads=91
JC	305	.	NC_000913	4226134	-1	NC_000913	4226429	1	0	alignment_overlap=13	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.189e-02	junction_possible_overlap_registers=281	key=NC_000913__4226134__-1__NC_000913__4226416__1__13____300__300__0__0	max_left=151	max_left_minus=151	max_left_plus=151	max_min_left=3	max_min_left_minus=0	max_min_left_plus=3	max_min_right=121	max_min_right_minus=121	max_min_right_plus=121	max_pos_hash_score=564	max_right=121	max_right_minus=121	max_right_plus=121	neg_log10_pos_hash_p_value=9.4	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.189e-02	pos_hash_score=3	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=1.04	side_1_overlap=13	side_1_possible_overlap_registers=294	side_1_read_count=110	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.77	side_2_overlap=0	side_2_possible_overlap_registers=281	side_2_read_count=77	side_2_redundant=0	total_non_overlap_reads=3
JC	306	.	NC_000913	4385536	1	NC_000913	4385538	-1	0	alignment_overlap=0	coverage_minus=1	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=3.333e-02	junction_possible_overlap_registers=294	key=NC_000913__4385536__1__NC_000913__4385538__-1__0____300__300__0__0	max_left=290	max_left_minus=158	max_left_plus=290	max_min_left=109	max_min_left_minus=0	max_min_left_plus=109	max_min_right=142	max_min_right_minus=142	max_min_right_plus=5	max_pos_hash_score=590	max_right=191	max_right_minus=142	max_right_plus=191	neg_log10_pos_hash_p_value=9.6	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=3.333e-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=0	side_1_possible_overlap_registers=294	side_1_read_count=85	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.85	side_2_overlap=0	side_2_possible_overlap_registers=294	side_2_read_count=89	side_2_redundant=0	total_non_overlap_reads=3
JC	307	.	NC_000913	4507459	1	NC_000913	4640419	-1	0	alignment_overlap=2	coverage_minus=4	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=3.731e-02	junction_possible_overlap_registers=292	key=NC_000913__4507459__1__NC_000913__4640421__-1__2____300__300__1__0	max_left=202	max_left_minus=202	max_left_plus=139	max_min_left=139	max_min_left_minus=121	max_min_left_plus=139	max_min_right=94	max_min_right_minus=94	max_min_right_plus=0	max_pos_hash_score=586	max_right=256	max_right_minus=256	max_right_plus=159	neg_log10_pos_hash_p_value=8.4	new_junction_coverage=0.05	new_junction_read_count=5	polymorphism_frequency=3.731e-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=2	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.23	side_2_overlap=0	side_2_possible_overlap_registers=292	side_2_read_count=129	side_2_redundant=0	total_non_overlap_reads=5
JC	308	.	NC_000913	4508679	-1	NC_000913	4640418	1	0	alignment_overlap=1	coverage_minus=6	coverage_plus=8	flanking_left=300	flanking_right=300	frequency=9.722e-02	junction_possible_overlap_registers=293	key=NC_000913__4508679__-1__NC_000913__4640417__1__1____300__300__1__0	max_left=237	max_left_minus=177	max_left_plus=237	max_min_left=110	max_min_left_minus=26	max_min_left_plus=110	max_min_right=107	max_min_right_minus=10	max_min_right_plus=107	max_pos_hash_score=588	max_right=285	max_right_minus=285	max_right_plus=187	neg_log10_pos_hash_p_value=7.5	new_junction_coverage=0.13	new_junction_read_count=14	polymorphism_frequency=9.722e-02	pos_hash_score=7	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=repeat	side_1_continuation=0	side_1_coverage=NA	side_1_overlap=1	side_1_read_count=NA	side_1_redundant=1	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.24	side_2_overlap=0	side_2_possible_overlap_registers=293	side_2_read_count=130	side_2_redundant=0	total_non_overlap_reads=14
JC	309	.	NC_000913	4542690	-1	NC_000913	4542986	-1	0	alignment_overlap=9	coverage_minus=2	coverage_plus=1	flanking_left=300	flanking_right=300	frequency=2.021e-02	junction_possible_overlap_registers=285	key=NC_000913__4542690__-1__NC_000913__4542995__-1__9____300__300__0__0	max_left=200	max_left_minus=200	max_left_plus=161	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=130	max_min_right_minus=115	max_min_right_plus=130	max_pos_hash_score=572	max_right=130	max_right_minus=115	max_right_plus=130	neg_log10_pos_hash_p_value=9.5	new_junction_coverage=0.03	new_junction_read_count=3	polymorphism_frequency=2.021e-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=1.57	side_1_overlap=9	side_1_possible_overlap_registers=294	side_1_read_count=165	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=1.28	side_2_overlap=0	side_2_possible_overlap_registers=285	side_2_read_count=131	side_2_redundant=0	total_non_overlap_reads=3
JC	310	.	NC_000913	4606165	-1	NC_000913	4606287	1	0	alignment_overlap=47	coverage_minus=1	coverage_plus=3	flanking_left=300	flanking_right=300	frequency=5.734e-02	junction_possible_overlap_registers=247	key=NC_000913__4606165__-1__NC_000913__4606240__1__47____300__300__0__0	max_left=237	max_left_minus=175	max_left_plus=237	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=78	max_min_right_minus=78	max_min_right_plus=78	max_pos_hash_score=496	max_right=78	max_right_minus=78	max_right_plus=78	neg_log10_pos_hash_p_value=8.1	new_junction_coverage=0.05	new_junction_read_count=4	polymorphism_frequency=5.734e-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=0.74	side_1_overlap=47	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=247	side_2_read_count=66	side_2_redundant=0	total_non_overlap_reads=4
JC	311	.	NC_000913	4606166	-1	NC_000913	4606403	1	0	alignment_overlap=89	coverage_minus=3	coverage_plus=2	flanking_left=300	flanking_right=300	frequency=7.789e-02	junction_possible_overlap_registers=205	key=NC_000913__4606166__-1__NC_000913__4606314__1__89____300__300__0__0	max_left=142	max_left_minus=142	max_left_plus=73	max_min_left=73	max_min_left_minus=65	max_min_left_plus=73	max_min_right=69	max_min_right_minus=69	max_min_right_plus=0	max_pos_hash_score=412	max_right=203	max_right_minus=145	max_right_plus=203	neg_log10_pos_hash_p_value=6.5	new_junction_coverage=0.07	new_junction_read_count=5	polymorphism_frequency=7.789e-02	pos_hash_score=5	prediction=polymorphism	reject=COVERAGE_EVENNESS_SKEW,FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.74	side_1_overlap=89	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=205	side_2_read_count=64	side_2_redundant=0	total_non_overlap_reads=5
UN	312	.	NC_000913	15663	16465
UN	313	.	NC_000913	16467	16467
UN	314	.	NC_000913	20071	20071
UN	315	.	NC_000913	20074	20074
UN	316	.	NC_000913	20077	20077
UN	317	.	NC_000913	20079	20281
UN	318	.	NC_000913	224019	224517
UN	319	.	NC_000913	225164	225300
UN	320	.	NC_000913	227266	227267
UN	321	.	NC_000913	227269	228412
UN	322	.	NC_000913	257908	258683
UN	323	.	NC_000913	270808	271031
UN	324	.	NC_000913	271035	271035
UN	325	.	NC_000913	274245	274245
UN	326	.	NC_000913	274248	274864
UN	327	.	NC_000913	279434	279434
UN	328	.	NC_000913	279436	279661
UN	329	.	NC_000913	290909	290910
UN	330	.	NC_000913	290913	291141
UN	331	.	NC_000913	315510	316227
UN	332	.	NC_000913	316230	316231
UN	333	.	NC_000913	316233	316233
UN	334	.	NC_000913	381534	382314
UN	335	.	NC_000913	382316	382318
UN	336	.	NC_000913	382320	382320
UN	337	.	NC_000913	391973	392690
UN	338	.	NC_000913	392699	392700
UN	339	.	NC_000913	392703	392703
UN	340	.	NC_000913	526057	526057
UN	341	.	NC_000913	526066	526432
UN	342	.	NC_000913	526434	526434
UN	343	.	NC_000913	567055	567770
UN	344	.	NC_000913	574867	575505
UN	345	.	NC_000913	608283	609087
UN	346	.	NC_000913	688129	688129
UN	347	.	NC_000913	688131	688768
UN	348	.	NC_000913	1094493	1095222
UN	349	.	NC_000913	1196373	1211413
UN	350	.	NC_000913	1299499	1300697
UN	351	.	NC_000913	1396324	1396966
UN	352	.	NC_000913	1468165	1468165
UN	353	.	NC_000913	1468170	1468170
UN	354	.	NC_000913	1468173	1468959
UN	355	.	NC_000913	1469550	1470228
UN	356	.	NC_000913	1528562	1528562
UN	357	.	NC_000913	1528564	1528564
UN	358	.	NC_000913	1528583	1528584
UN	359	.	NC_000913	1528586	1528587
UN	360	.	NC_000913	1528589	1528590
UN	361	.	NC_000913	1528592	1528886
UN	362	.	NC_000913	1528890	1528890
UN	363	.	NC_000913	1528893	1528893
UN	364	.	NC_000913	1528896	1528896
UN	365	.	NC_000913	1528900	1528901
UN	366	.	NC_000913	1651118	1651119
UN	367	.	NC_000913	1651122	1651265
UN	368	.	NC_000913	1651276	1651276
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