#=GENOME_DIFF	1.0
#=TITLE	D53
#=CREATED	15:53:52 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 D53 -o /var/www/ngs/solomon/breseq/D53 --no-junction-prediction /var/ngs/rnaseq/raw/solomon/RNAseq_USA300_Eleni/OtA1608_D53A0.5_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/OtA1608_D53A0.5_R1_.fastq
#=CONVERTED-BASES	643385100
#=CONVERTED-READS	6433851
#=INPUT-BASES	643391100
#=INPUT-READS	6433911
#=MAPPED-BASES	476714597
#=MAPPED-READS	4807467
DEL	1	12	NC_007790	1	3125
DEL	2	13	NC_007791	1	4439
DEL	3	16	NC_007792	1916	22120	between=repeat_region
DEL	4	18	NC_007793	1	2872769
RA	5	.	NC_007792	23889	0	C	T	consensus_score=10.6	deleted=1	frequency=1	major_base=T	major_cov=6/4	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/4	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/4
RA	6	.	NC_007792	23891	0	C	A	consensus_score=10.6	deleted=1	frequency=1	major_base=A	major_cov=6/4	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/4	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/4
RA	7	.	NC_007792	23892	0	T	A	consensus_score=10.6	deleted=1	frequency=1	major_base=A	major_cov=6/4	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/4	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/4
RA	8	.	NC_007792	23931	0	A	G	consensus_score=10.5	deleted=1	frequency=1	major_base=G	major_cov=6/4	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/4	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/4
RA	9	.	NC_007792	23945	0	A	G	consensus_score=10.6	deleted=1	frequency=1	major_base=G	major_cov=6/4	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/4	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/4
RA	10	.	NC_007792	23946	0	C	T	consensus_score=10.4	deleted=1	frequency=1	major_base=T	major_cov=6/4	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/4	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/4
RA	11	.	NC_007792	23948	0	A	T	consensus_score=10.4	deleted=1	frequency=1	major_base=T	major_cov=6/4	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=6/4	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=6/4
MC	12	.	NC_007790	1	3125	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
MC	13	.	NC_007791	1	4439	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
MC	14	.	NC_007792	1	1663	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=1
MC	15	.	NC_007792	1801	1806	0	0	left_inside_cov=0	left_outside_cov=1	right_inside_cov=0	right_outside_cov=1
MC	16	.	NC_007792	1907	23870	0	0	left_inside_cov=0	left_outside_cov=1	right_inside_cov=0	right_outside_cov=6
MC	17	.	NC_007792	23974	37136	34	0	left_inside_cov=0	left_outside_cov=3	right_inside_cov=0	right_outside_cov=NA
MC	18	.	NC_007793	1	2872769	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=NA
UN	19	.	NC_007792	1	23882
UN	20	.	NC_007792	23905	23905
UN	21	.	NC_007792	23909	23909
UN	22	.	NC_007792	23915	23915
UN	23	.	NC_007792	23925	23925
UN	24	.	NC_007792	23927	23927
UN	25	.	NC_007792	23930	23930
UN	26	.	NC_007792	23938	23938
UN	27	.	NC_007792	23944	23944
UN	28	.	NC_007792	23955	37136