#=GENOME_DIFF	1.0
#=TITLE	D69
#=CREATED	15:53:20 03 Mar 2017
#=PROGRAM	breseq 0.29.0 
#=COMMAND	breseq -j 2 -r /var/genomes/g2d_mirror/Staphylococcus_aureus_subsp_aureus_USA300_FPR3757/ASM1346v1_genomic.gbff -n D69 -o /var/www/ngs/solomon/breseq/D69 --no-junction-prediction /var/ngs/rnaseq/raw/solomon/RNAseq_USA300_Eleni/OtA1620_D69A0.5_R1_.fastq
#=REFSEQ	/var/genomes/g2d_mirror/Staphylococcus_aureus_subsp_aureus_USA300_FPR3757/ASM1346v1_genomic.gbff
#=READSEQ	/var/ngs/rnaseq/raw/solomon/RNAseq_USA300_Eleni/OtA1620_D69A0.5_R1_.fastq
#=CONVERTED-BASES	609505000
#=CONVERTED-READS	6095050
#=INPUT-BASES	609515200
#=INPUT-READS	6095152
#=MAPPED-BASES	453115473
#=MAPPED-READS	4567166
DEL	1	19	NC_007791	1	4439
DEL	2	20	NC_007792	1	37136
DEL	3	21	NC_007793	1	2872769
RA	4	.	NC_007790	849	0	A	G	bias_e_value=916061	bias_p_value=0.313992	consensus_score=1433.6	fisher_strand_p_value=0.108587	frequency=2.885e-01	ks_quality_p_value=0.856854	major_base=A	major_cov=801/40	major_frequency=7.115e-01	minor_base=G	minor_cov=332/9	new_cov=332/9	polymorphism_frequency=2.885e-01	polymorphism_score=inf	prediction=polymorphism	ref_cov=801/40	total_cov=1134/49
RA	5	.	NC_007790	875	0	T	C	bias_e_value=854970	bias_p_value=0.293052	consensus_score=1418.6	fisher_strand_p_value=0.0843997	frequency=2.605e-01	ks_quality_p_value=1	major_base=T	major_cov=589/47	major_frequency=7.395e-01	minor_base=C	minor_cov=215/9	new_cov=215/9	polymorphism_frequency=2.605e-01	polymorphism_score=inf	prediction=polymorphism	ref_cov=589/47	total_cov=806/56
RA	6	.	NC_007790	898	0	G	A	bias_e_value=41921.1	bias_p_value=0.014369	consensus_score=763.7	fisher_strand_p_value=0.00276661	frequency=2.658e-01	ks_quality_p_value=0.719405	major_base=G	major_cov=341/43	major_frequency=7.342e-01	minor_base=A	minor_cov=135/4	new_cov=135/4	polymorphism_frequency=2.658e-01	polymorphism_score=270.6	prediction=polymorphism	ref_cov=341/43	total_cov=476/47
RA	7	.	NC_007790	918	0	A	G	bias_e_value=35725.3	bias_p_value=0.0122453	consensus_score=250.6	fisher_strand_p_value=0.00165372	frequency=3.200e-01	ks_quality_p_value=1	major_base=A	major_cov=131/22	major_frequency=6.800e-01	minor_base=G	minor_cov=71/1	new_cov=71/1	polymorphism_frequency=3.200e-01	polymorphism_score=139.1	prediction=polymorphism	ref_cov=131/22	total_cov=204/23
RA	8	.	NC_007790	931	0	G	.	bias_e_value=41930.4	bias_p_value=0.0143722	consensus_score=232.2	fisher_strand_p_value=0.00199082	frequency=3.120e-01	ks_quality_p_value=1	major_base=G	major_cov=65/21	major_frequency=6.880e-01	minor_base=.	minor_cov=38/1	new_cov=38/1	polymorphism_frequency=3.120e-01	polymorphism_score=144.3	prediction=polymorphism	ref_cov=65/21	total_cov=103/22
RA	9	.	NC_007790	1243	0	A	T	bias_e_value=2434180	bias_p_value=0.834348	consensus_score=107.0	fisher_strand_p_value=0.506214	frequency=2.105e-01	ks_quality_p_value=0.953736	major_base=A	major_cov=29/16	major_frequency=7.895e-01	minor_base=T	minor_cov=6/6	new_cov=6/6	polymorphism_frequency=2.105e-01	polymorphism_score=24.0	prediction=polymorphism	ref_cov=29/16	total_cov=35/23
RA	10	.	NC_007790	1244	0	A	T	bias_e_value=2396150	bias_p_value=0.821312	consensus_score=107.2	fisher_strand_p_value=0.506214	frequency=2.105e-01	ks_quality_p_value=0.919238	major_base=A	major_cov=29/16	major_frequency=7.895e-01	minor_base=T	minor_cov=6/6	new_cov=6/6	polymorphism_frequency=2.105e-01	polymorphism_score=24.9	prediction=polymorphism	ref_cov=29/16	total_cov=35/23
RA	11	.	NC_007790	1254	0	A	T	bias_e_value=2154980	bias_p_value=0.738648	consensus_score=104.3	fisher_strand_p_value=0.512575	frequency=2.069e-01	ks_quality_p_value=0.723367	major_base=A	major_cov=29/17	major_frequency=7.931e-01	minor_base=T	minor_cov=6/6	new_cov=6/6	polymorphism_frequency=2.069e-01	polymorphism_score=25.1	prediction=polymorphism	ref_cov=29/17	total_cov=35/23
RA	12	.	NC_007790	1259	0	C	A	bias_e_value=960695	bias_p_value=0.32929	consensus_score=100.7	fisher_strand_p_value=0.745248	frequency=2.182e-01	ks_quality_p_value=0.13362	major_base=C	major_cov=18/25	major_frequency=7.818e-01	minor_base=A	minor_cov=6/6	new_cov=6/6	polymorphism_frequency=2.182e-01	polymorphism_score=24.9	prediction=polymorphism	ref_cov=18/25	total_cov=24/31
RA	13	.	NC_007790	1272	0	A	G	bias_e_value=433445	bias_p_value=0.148569	consensus_score=166.9	fisher_strand_p_value=0.809765	frequency=2.547e-01	ks_quality_p_value=0.041842	major_base=A	major_cov=23/56	major_frequency=7.453e-01	minor_base=G	minor_cov=7/20	new_cov=7/20	polymorphism_frequency=2.547e-01	polymorphism_score=47.5	prediction=polymorphism	ref_cov=23/56	total_cov=30/76
RA	14	.	NC_007790	1276	0	C	A	bias_e_value=7132.75	bias_p_value=0.00244484	consensus_score=176.3	fisher_strand_p_value=0.808539	frequency=2.477e-01	ks_quality_p_value=0.000327355	major_base=C	major_cov=25/57	major_frequency=7.523e-01	minor_base=A	minor_cov=7/20	new_cov=7/20	polymorphism_frequency=2.477e-01	polymorphism_score=69.2	prediction=polymorphism	ref_cov=25/57	total_cov=32/77
RA	15	.	NC_007790	1303	0	T	G	bias_e_value=1584380	bias_p_value=0.543068	consensus_score=85.4	fisher_strand_p_value=0.234843	frequency=3.984e-01	ks_quality_p_value=0.908838	major_base=T	major_cov=20/54	major_frequency=6.016e-01	minor_base=G	minor_cov=19/30	new_cov=19/30	polymorphism_frequency=3.984e-01	polymorphism_score=142.0	prediction=polymorphism	ref_cov=20/54	total_cov=39/84
RA	16	.	NC_007790	1317	0	G	T	bias_e_value=2351960	bias_p_value=0.806164	consensus_score=153.8	fisher_strand_p_value=0.448881	frequency=2.523e-01	ks_quality_p_value=0.993711	major_base=G	major_cov=18/62	major_frequency=7.477e-01	minor_base=T	minor_cov=8/19	new_cov=8/19	polymorphism_frequency=2.523e-01	polymorphism_score=65.8	prediction=polymorphism	ref_cov=18/62	total_cov=35/94
RA	17	.	NC_007790	2451	0	G	C	bias_e_value=5.84467	bias_p_value=2.00334e-06	consensus_score=1251.7	fisher_strand_p_value=8.35792e-07	frequency=3.386e-01	ks_quality_p_value=0.141403	major_base=G	major_cov=34/556	major_frequency=6.614e-01	minor_base=C	minor_cov=0/302	new_cov=0/302	polymorphism_frequency=3.386e-01	polymorphism_score=inf	prediction=polymorphism	ref_cov=34/556	total_cov=34/858
RA	18	.	NC_007790	2456	1	.	A	bias_e_value=0.12722	bias_p_value=4.36064e-08	consensus_score=832.7	fisher_strand_p_value=5.40073e-07	frequency=3.370e-01	ks_quality_p_value=0.00384626	major_base=.	major_cov=36/562	major_frequency=6.630e-01	minor_base=A	minor_cov=0/304	new_cov=0/304	polymorphism_frequency=3.370e-01	polymorphism_score=inf	prediction=polymorphism	ref_cov=36/562	total_cov=36/866
MC	19	.	NC_007791	1	4439	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
MC	20	.	NC_007792	1	37136	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
MC	21	.	NC_007793	1	2872769	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
UN	22	.	NC_007790	1	1
UN	23	.	NC_007790	3125	3125