#=GENOME_DIFF	1.0
#=CREATED	13:54:41 04 May 2021
#=PROGRAM	breseq 0.35.4 
#=COMMAND	breseq -j 8 -r /data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk /data/pg-molgen/harma/2021_04/fastq/8A_S8_R1_001.fastq.gz -o /data/pg-molgen/harma/2021_04/results_breseq/HK7_r1t
#=REFSEQ	/data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk
#=READSEQ	/data/pg-molgen/harma/2021_04/fastq/8A_S8_R1_001.fastq.gz
#=CONVERTED-BASES	1334109450
#=CONVERTED-READS	17788126
#=INPUT-BASES	1334309625
#=INPUT-READS	17790795
#=MAPPED-BASES	19754054
#=MAPPED-READS	282289
INS	1	12	NC_004302	3547	A
INS	2	13,14	NC_004302	3556	GT
SUB	3	15,16	NC_004302	5234	2	GC
SNP	4	17	NC_004302	5237	G
DEL	5	18,19,20,21,22,23	NC_004302	8712	6	repeat_length=6	repeat_new_copies=2	repeat_ref_copies=3	repeat_seq=TGAATT
SNP	6	24	NC_004302	9972	A
SNP	7	25	NC_004302	13763	C
SNP	8	27	NC_004302	23480	C
RA	9	.	NC_004302	1914	0	T	C	bias_e_value=29534.9	bias_p_value=0.885604	consensus_reject=FREQUENCY_CUTOFF	consensus_score=198.9	fisher_strand_p_value=0.573978	frequency=2.331e-01	ks_quality_p_value=0.978374	major_base=T	major_cov=4/121	major_frequency=7.669e-01	minor_base=C	minor_cov=0/38	new_cov=0/38	polymorphism_frequency=2.331e-01	polymorphism_score=69.9	prediction=polymorphism	ref_cov=4/121	total_cov=4/231
RA	10	.	NC_004302	2843	0	C	G	bias_e_value=12660.2	bias_p_value=0.379615	consensus_reject=SCORE_CUTOFF,FREQUENCY_CUTOFF	consensus_score=2.7	fisher_strand_p_value=1	frequency=4.667e-01	ks_quality_p_value=0.122456	major_base=C	major_cov=16/0	major_frequency=5.333e-01	minor_base=G	minor_cov=14/0	new_cov=14/0	polymorphism_frequency=4.667e-01	polymorphism_score=29.0	prediction=polymorphism	ref_cov=16/0	total_cov=40/0
RA	11	.	NC_004302	2995	1	.	A	bias_e_value=32935	bias_p_value=0.987555	consensus_reject=FREQUENCY_CUTOFF	consensus_score=302.4	fisher_strand_p_value=1	frequency=2.160e-01	ks_quality_p_value=0.846441	major_base=.	major_cov=126/1	major_frequency=7.840e-01	minor_base=A	minor_cov=35/0	new_cov=35/0	polymorphism_frequency=2.160e-01	polymorphism_score=69.6	prediction=polymorphism	ref_cov=126/1	total_cov=161/1
RA	12	.	NC_004302	3545	1	.	A	bias_e_value=33312	bias_p_value=0.998862	consensus_score=1096.9	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.952672	major_base=A	major_cov=427/5	major_frequency=9.818e-01	minor_base=.	minor_cov=8/0	new_cov=427/5	polymorphism_frequency=9.818e-01	polymorphism_score=5.6	prediction=consensus	ref_cov=8/0	total_cov=435/5
RA	13	.	NC_004302	3554	1	.	G	bias_e_value=33350	bias_p_value=1	consensus_score=1300.3	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=G	major_cov=447/5	major_frequency=9.168e-01	minor_base=.	minor_cov=41/0	new_cov=447/5	polymorphism_frequency=9.168e-01	polymorphism_score=67.8	prediction=consensus	ref_cov=41/0	total_cov=489/5
RA	14	.	NC_004302	3554	2	.	T	bias_e_value=33350	bias_p_value=1	consensus_score=1236.2	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=T	major_cov=448/5	major_frequency=9.170e-01	minor_base=.	minor_cov=41/0	new_cov=448/5	polymorphism_frequency=9.170e-01	polymorphism_score=72.1	prediction=consensus	ref_cov=41/0	total_cov=489/5
RA	15	.	NC_004302	5234	0	C	G	bias_e_value=33349.5	bias_p_value=0.999985	consensus_score=64.5	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.994521	major_base=G	major_cov=25/1	major_frequency=9.286e-01	minor_base=C	minor_cov=2/0	new_cov=25/1	polymorphism_frequency=9.286e-01	polymorphism_score=-0.3	prediction=consensus	ref_cov=2/0	total_cov=27/1
RA	16	.	NC_004302	5235	0	G	C	bias_e_value=33350	bias_p_value=1	consensus_score=66.7	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=1	major_base=C	major_cov=25/1	major_frequency=9.286e-01	minor_base=A	minor_cov=2/0	new_cov=25/1	polymorphism_frequency=9.286e-01	polymorphism_score=-0.9	prediction=consensus	ref_cov=1/0	total_cov=28/1
RA	17	.	NC_004302	5237	0	C	G	bias_e_value=33349.5	bias_p_value=0.999985	consensus_score=64.4	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.994521	major_base=G	major_cov=25/1	major_frequency=9.286e-01	minor_base=T	minor_cov=2/0	new_cov=25/1	polymorphism_frequency=9.286e-01	polymorphism_score=-1.1	prediction=consensus	ref_cov=1/0	total_cov=28/1
RA	18	.	NC_004302	8696	0	A	.	consensus_score=20.9	frequency=1	major_base=.	major_cov=7/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=7/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=7/1
RA	19	.	NC_004302	8697	0	A	.	consensus_score=20.9	frequency=1	major_base=.	major_cov=7/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=7/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=7/1
RA	20	.	NC_004302	8698	0	T	.	consensus_score=20.9	frequency=1	major_base=.	major_cov=7/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=7/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=7/1
RA	21	.	NC_004302	8699	0	T	.	consensus_score=20.9	frequency=1	major_base=.	major_cov=7/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=7/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=7/1
RA	22	.	NC_004302	8700	0	T	.	consensus_score=20.9	frequency=1	major_base=.	major_cov=7/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=7/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=7/1
RA	23	.	NC_004302	8701	0	G	.	consensus_score=20.9	frequency=1	major_base=.	major_cov=7/1	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=7/1	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=7/1
RA	24	.	NC_004302	9972	0	C	A	consensus_score=92.3	frequency=1	major_base=A	major_cov=38/0	major_frequency=1.000e+00	minor_base=N	minor_cov=0/0	new_cov=38/0	polymorphism_frequency=1.000e+00	polymorphism_score=NA	prediction=consensus	ref_cov=0/0	total_cov=38/0
RA	25	.	NC_004302	13763	0	T	C	bias_e_value=33345.9	bias_p_value=0.999876	consensus_score=53.0	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.984314	major_base=C	major_cov=19/3	major_frequency=9.565e-01	minor_base=T	minor_cov=1/0	new_cov=19/3	polymorphism_frequency=9.565e-01	polymorphism_score=-2.6	prediction=consensus	ref_cov=1/0	total_cov=20/3
RA	26	.	NC_004302	15047	1	.	A	bias_e_value=26975.4	bias_p_value=0.808858	consensus_reject=FREQUENCY_CUTOFF	consensus_score=485.9	fisher_strand_p_value=0.587123	frequency=2.103e-01	ks_quality_p_value=0.765446	major_base=.	major_cov=194/5	major_frequency=7.897e-01	minor_base=A	minor_cov=53/0	new_cov=53/0	polymorphism_frequency=2.103e-01	polymorphism_score=106.2	prediction=polymorphism	ref_cov=194/5	total_cov=247/5
RA	27	.	NC_004302	23480	0	A	C	bias_e_value=33347.5	bias_p_value=0.999924	consensus_score=296.0	fisher_strand_p_value=1	frequency=1	ks_quality_p_value=0.9877	major_base=C	major_cov=110/0	major_frequency=9.244e-01	minor_base=A	minor_cov=9/0	new_cov=110/0	polymorphism_frequency=9.244e-01	polymorphism_score=9.0	prediction=consensus	ref_cov=9/0	total_cov=120/0
RA	28	.	NC_004302	24164	1	.	T	bias_e_value=32086.8	bias_p_value=0.962122	consensus_reject=FREQUENCY_CUTOFF	consensus_score=65.0	fisher_strand_p_value=1	frequency=3.671e-01	ks_quality_p_value=0.737701	major_base=.	major_cov=50/0	major_frequency=6.329e-01	minor_base=T	minor_cov=29/0	new_cov=29/0	polymorphism_frequency=3.671e-01	polymorphism_score=72.2	prediction=polymorphism	ref_cov=50/0	total_cov=79/0
MC	29	.	NC_004302	1	11	0	0	left_inside_cov=0	left_outside_cov=NA	right_inside_cov=0	right_outside_cov=2
MC	30	.	NC_004302	33195	33350	0	0	left_inside_cov=1	left_outside_cov=2	right_inside_cov=0	right_outside_cov=NA
JC	31	.	NC_004302	23379	-1	NC_004302	24308	1	0	alignment_overlap=0	coverage_minus=32	coverage_plus=1	flanking_left=75	flanking_right=75	frequency=1	junction_possible_overlap_registers=74	key=NC_004302__23379__-1__NC_004302__24308__1__0____75__75__0__0	max_left=73	max_left_minus=73	max_left_plus=43	max_min_left=29	max_min_left_minus=29	max_min_left_plus=0	max_min_right=32	max_min_right_minus=31	max_min_right_plus=32	max_pos_hash_score=148	max_right=73	max_right_minus=73	max_right_plus=32	neg_log10_pos_hash_p_value=0.2	new_junction_coverage=0.81	new_junction_read_count=475	polymorphism_frequency=9.143e-01	pos_hash_score=19	prediction=consensus	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=0.05	side_1_overlap=0	side_1_possible_overlap_registers=74	side_1_read_count=27	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=0.11	side_2_overlap=0	side_2_possible_overlap_registers=74	side_2_read_count=62	side_2_redundant=0	total_non_overlap_reads=33
JC	32	.	NC_004302	32569	1	NC_004302	32599	1	0	alignment_overlap=5	coverage_minus=0	coverage_plus=10	flanking_left=75	flanking_right=75	frequency=1.000e-01	junction_possible_overlap_registers=69	key=NC_004302__32569__1__NC_004302__32594__1__5____75__75__0__0	max_left=68	max_left_minus=0	max_left_plus=68	max_min_left=0	max_min_left_minus=0	max_min_left_plus=0	max_min_right=20	max_min_right_minus=0	max_min_right_plus=20	max_pos_hash_score=138	max_right=20	max_right_minus=0	max_right_plus=20	neg_log10_pos_hash_p_value=0.4	new_junction_coverage=0.66	new_junction_read_count=359	polymorphism_frequency=1.000e-01	pos_hash_score=8	prediction=polymorphism	reject=FREQUENCY_CUTOFF	side_1_annotate_key=gene	side_1_continuation=0	side_1_coverage=6.74	side_1_overlap=5	side_1_possible_overlap_registers=74	side_1_read_count=3957	side_1_redundant=0	side_2_annotate_key=gene	side_2_continuation=0	side_2_coverage=5.06	side_2_overlap=0	side_2_possible_overlap_registers=69	side_2_read_count=2770	side_2_redundant=0	total_non_overlap_reads=10
UN	33	.	NC_004302	1	36
UN	34	.	NC_004302	148	157
UN	35	.	NC_004302	332	332
UN	36	.	NC_004302	334	334
UN	37	.	NC_004302	468	468
UN	38	.	NC_004302	641	650
UN	39	.	NC_004302	658	658
UN	40	.	NC_004302	1034	1034
UN	41	.	NC_004302	1217	1220
UN	42	.	NC_004302	1225	1225
UN	43	.	NC_004302	1253	1316
UN	44	.	NC_004302	2843	2843
UN	45	.	NC_004302	4782	4819
UN	46	.	NC_004302	7255	7255
UN	47	.	NC_004302	7258	7291
UN	48	.	NC_004302	7714	7752
UN	49	.	NC_004302	14523	14523
UN	50	.	NC_004302	33030	33350