#=GENOME_DIFF	1.0
#=COMMAND	breseq -j 8 -r /data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk /data/pg-molgen/harma/2021_04/fastq/6A_S6_R1_001.fastq.gz -o /data/pg-molgen/harma/2021_04/results_breseq/HK3_r1t
#=REFSEQ	/data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk
#=READSEQ	/data/pg-molgen/harma/2021_04/fastq/6A_S6_R1_001.fastq.gz
#=CONVERTED-BASES	915585975
#=CONVERTED-READS	12207813
#=INPUT-BASES	915751950
#=INPUT-READS	12210026
#=MAPPED-BASES	141170
#=MAPPED-READS	2017
RA	1	.	NC_004302	1914	0	T	C	bias_e_value=33350	bias_p_value=1	consensus_reject=FREQUENCY_CUTOFF	consensus_score=17.9	fisher_strand_p_value=1	frequency=3.333e-01	gene_name=r1tp02/rro	gene_position=intergenic (-54/+7)	gene_product=ORF2/Repressor protein	gene_strand=</<	ks_quality_p_value=1	locus_tag=r1tp02/r1tp03	major_base=T	major_cov=0/20	major_frequency=6.667e-01	minor_base=C	minor_cov=0/10	new_cov=0/10	polymorphism_frequency=3.333e-01	polymorphism_score=14.8	prediction=polymorphism	ref_cov=0/20	snp_type=intergenic	total_cov=0/38
MC	2	.	NC_004302	1	91	0	0	gene_name=–/r1tp01	gene_position=intergenic (–/+3)	gene_product=–/Integrase	gene_strand=–/<	left_inside_cov=0	left_outside_cov=NA	locus_tag=–/r1tp01	right_inside_cov=1	right_outside_cov=2
MC	3	.	NC_004302	238	283	0	0	gene_name=r1tp01	gene_position=coding (936-981/1125 nt)	gene_product=Integrase	gene_strand=<	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp01	right_inside_cov=1	right_outside_cov=2
MC	4	.	NC_004302	382	446	0	0	gene_name=r1tp01	gene_position=coding (773-837/1125 nt)	gene_product=Integrase	gene_strand=<	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp01	right_inside_cov=0	right_outside_cov=2
MC	5	.	NC_004302	618	686	0	0	gene_name=r1tp01	gene_position=coding (533-601/1125 nt)	gene_product=Integrase	gene_strand=<	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp01	right_inside_cov=1	right_outside_cov=2
MC	6	.	NC_004302	948	991	0	0	gene_name=r1tp01	gene_position=coding (228-271/1125 nt)	gene_product=Integrase	gene_strand=<	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp01	right_inside_cov=1	right_outside_cov=2
MC	7	.	NC_004302	1063	1070	0	0	gene_name=r1tp01	gene_position=coding (149-156/1125 nt)	gene_product=Integrase	gene_strand=<	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp01	right_inside_cov=1	right_outside_cov=2
MC	8	.	NC_004302	1256	1333	0	0	gene_name=r1tp01/r1tp02	gene_position=intergenic (-38/+6)	gene_product=Integrase/ORF2	gene_strand=</<	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp01/r1tp02	right_inside_cov=1	right_outside_cov=3
MC	9	.	NC_004302	2766	2891	0	0	gene_name=rro/tec	gene_position=intergenic (-9/-96)	gene_product=Repressor protein/tec	gene_strand=</>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp03/r1tp04	right_inside_cov=1	right_outside_cov=2
MC	10	.	NC_004302	2966	3373	0	0	gene_name=tec–[r1tp05]	gene_product=tec,[r1tp05]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp04]–[r1tp05]	right_inside_cov=0	right_outside_cov=2
MC	11	.	NC_004302	3449	4421	0	0	gene_name=[r1tp05]–[r1tp07]	gene_product=[r1tp05],r1tp06,[r1tp07]	left_inside_cov=0	left_outside_cov=2	locus_tag=[r1tp05]–[r1tp07]	right_inside_cov=1	right_outside_cov=2
MC	12	.	NC_004302	4496	5203	0	0	gene_name=[r1tp07]–[r1tp09]	gene_product=[r1tp07],r1tp08,[r1tp09]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp07]–[r1tp09]	right_inside_cov=0	right_outside_cov=2
MC	13	.	NC_004302	5273	6189	0	0	gene_name=[r1tp09]–[r1tp10]	gene_product=[r1tp09],[r1tp10]	left_inside_cov=0	left_outside_cov=2	locus_tag=[r1tp09]–[r1tp10]	right_inside_cov=1	right_outside_cov=2
MC	14	.	NC_004302	6256	7788	0	0	gene_name=[r1tp10]–[r1tp12]	gene_product=[r1tp10],r1tp11,[r1tp12]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp10]–[r1tp12]	right_inside_cov=0	right_outside_cov=2
MC	15	.	NC_004302	7859	7886	0	0	gene_name=r1tp12	gene_position=coding (221-248/891 nt)	gene_product=ATP-binding protein	gene_strand=>	left_inside_cov=0	left_outside_cov=2	locus_tag=r1tp12	right_inside_cov=0	right_outside_cov=2
MC	16	.	NC_004302	8038	8071	0	0	gene_name=r1tp12	gene_position=coding (400-433/891 nt)	gene_product=ATP-binding protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp12	right_inside_cov=0	right_outside_cov=2
MC	17	.	NC_004302	8143	8384	0	0	gene_name=r1tp12	gene_position=coding (505-746/891 nt)	gene_product=ATP-binding protein	gene_strand=>	left_inside_cov=0	left_outside_cov=2	locus_tag=r1tp12	right_inside_cov=1	right_outside_cov=2
MC	18	.	NC_004302	8418	8514	0	0	gene_name=r1tp12	gene_position=coding (780-876/891 nt)	gene_product=ATP-binding protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp12	right_inside_cov=1	right_outside_cov=3
MC	19	.	NC_004302	8583	10407	0	0	gene_name=[r1tp13]–r1tp18	gene_product=[r1tp13],r1tp14,r1tp15,r1tp16,r1tp17,r1tp18	left_inside_cov=0	left_outside_cov=2	locus_tag=[r1tp13]–[r1tp18]	right_inside_cov=1	right_outside_cov=2
MC	20	.	NC_004302	10447	11202	0	0	gene_name=[r1tp19]–[r1tp20]	gene_product=[r1tp19],[r1tp20]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp19]–[r1tp20]	right_inside_cov=1	right_outside_cov=2
MC	21	.	NC_004302	11325	11493	0	0	gene_name=[r1tp20]–[r1tp21]	gene_product=[r1tp20],[r1tp21]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp20]–[r1tp21]	right_inside_cov=1	right_outside_cov=3
MC	22	.	NC_004302	11561	11719	0	0	gene_name=r1tp21	gene_position=coding (82-240/252 nt)	gene_product=ORF21	gene_strand=>	left_inside_cov=0	left_outside_cov=2	locus_tag=r1tp21	right_inside_cov=1	right_outside_cov=2
MC	23	.	NC_004302	11787	13463	0	0	gene_name=[r1tp22]–[r1tp24]	gene_product=[r1tp22],r1tp23,[r1tp24]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp22]–[r1tp24]	right_inside_cov=1	right_outside_cov=3
MC	24	.	NC_004302	13532	14022	0	0	gene_name=[r1tp24]–[r1tp25]	gene_product=[r1tp24],[r1tp25]	left_inside_cov=0	left_outside_cov=2	locus_tag=[r1tp24]–[r1tp25]	right_inside_cov=0	right_outside_cov=2
MC	25	.	NC_004302	14096	15591	0	0	gene_name=[r1tp25]–[r1tp27]	gene_product=[r1tp25],r1tp26,[r1tp27]	left_inside_cov=0	left_outside_cov=2	locus_tag=[r1tp25]–[r1tp27]	right_inside_cov=1	right_outside_cov=2
MC	26	.	NC_004302	15666	15990	0	0	gene_name=r1tp27	gene_position=coding (613-937/1230 nt)	gene_product=Structural protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp27	right_inside_cov=1	right_outside_cov=2
MC	27	.	NC_004302	16030	16148	0	0	gene_name=r1tp27	gene_position=coding (977-1095/1230 nt)	gene_product=Structural protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp27	right_inside_cov=1	right_outside_cov=2
MC	28	.	NC_004302	16219	16331	0	0	gene_name=[r1tp27]–[r1tp28]	gene_product=[r1tp27],[r1tp28]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp27]–[r1tp28]	right_inside_cov=1	right_outside_cov=2
MC	29	.	NC_004302	16379	17219	0	0	gene_name=[r1tp28]–[r1tp29]	gene_product=[r1tp28],[r1tp29]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp28]–[r1tp29]	right_inside_cov=1	right_outside_cov=2
MC	30	.	NC_004302	17837	17913	0	0	gene_name=r1tp29	gene_position=coding (740-816/1410 nt)	gene_product=putative terminase	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp29	right_inside_cov=1	right_outside_cov=2
MC	31	.	NC_004302	17982	18029	0	0	gene_name=r1tp29	gene_position=coding (885-932/1410 nt)	gene_product=putative terminase	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp29	right_inside_cov=1	right_outside_cov=2
MC	32	.	NC_004302	18363	18565	0	0	gene_name=[r1tp29]	gene_product=[r1tp29]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp29]	right_inside_cov=1	right_outside_cov=2
MC	33	.	NC_004302	18869	18994	0	0	gene_name=r1tp30	gene_position=coding (290-415/465 nt)	gene_product=DUF4355 domain-containing protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp30	right_inside_cov=1	right_outside_cov=2
MC	34	.	NC_004302	19109	19184	0	0	gene_name=r1tp31	gene_position=coding (62-137/897 nt)	gene_product=Structural protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp31	right_inside_cov=1	right_outside_cov=2
MC	35	.	NC_004302	19858	20026	0	0	gene_name=[r1tp31]–[r1tp32]	gene_product=[r1tp31],[r1tp32]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp31]–[r1tp32]	right_inside_cov=1	right_outside_cov=2
MC	36	.	NC_004302	20297	20369	0	0	gene_name=r1tp33	gene_position=coding (38-110/399 nt)	gene_product=ORF33	gene_strand=>	left_inside_cov=0	left_outside_cov=2	locus_tag=r1tp33	right_inside_cov=1	right_outside_cov=2
MC	37	.	NC_004302	20455	20559	0	0	gene_name=r1tp33	gene_position=coding (196-300/399 nt)	gene_product=ORF33	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp33	right_inside_cov=1	right_outside_cov=2
MC	38	.	NC_004302	20565	20694	0	0	gene_name=[r1tp33]–[r1tp34]	gene_product=[r1tp33],[r1tp34]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp33]–[r1tp34]	right_inside_cov=1	right_outside_cov=3
MC	39	.	NC_004302	20764	20923	0	0	gene_name=r1tp34	gene_position=coding (129-288/348 nt)	gene_product=ORF34	gene_strand=>	left_inside_cov=0	left_outside_cov=2	locus_tag=r1tp34	right_inside_cov=1	right_outside_cov=2
MC	40	.	NC_004302	21032	21091	0	0	gene_name=r1tp35	gene_position=coding (57-116/237 nt)	gene_product=ORF35	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp35	right_inside_cov=1	right_outside_cov=2
MC	41	.	NC_004302	21166	21413	0	0	gene_name=[r1tp35]–[r1tp36]	gene_product=[r1tp35],[r1tp36]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp35]–[r1tp36]	right_inside_cov=0	right_outside_cov=2
MC	42	.	NC_004302	21544	21554	0	0	gene_name=[r1tp36]	gene_product=[r1tp36]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp36]	right_inside_cov=1	right_outside_cov=2
MC	43	.	NC_004302	21618	21626	0	0	gene_name=r1tp37	gene_position=coding (60-68/558 nt)	gene_product=Structural protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp37	right_inside_cov=1	right_outside_cov=2
MC	44	.	NC_004302	21695	21761	0	0	gene_name=r1tp37	gene_position=coding (137-203/558 nt)	gene_product=Structural protein	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp37	right_inside_cov=1	right_outside_cov=2
MC	45	.	NC_004302	22079	22280	0	0	gene_name=[r1tp37]–[r1tp38]	gene_product=[r1tp37],[r1tp38]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp37]–[r1tp38]	right_inside_cov=1	right_outside_cov=2
MC	46	.	NC_004302	22284	22587	0	0	gene_name=[r1tp38]	gene_product=[r1tp38]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp38]	right_inside_cov=1	right_outside_cov=2
MC	47	.	NC_004302	22996	23012	0	0	gene_name=r1tp40	gene_position=coding (154-170/642 nt)	gene_product=ORF40	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp40	right_inside_cov=0	right_outside_cov=2
MC	48	.	NC_004302	24102	24139	0	0	gene_name=[r1tp41]	gene_product=[r1tp41]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp41]	right_inside_cov=1	right_outside_cov=2
MC	49	.	NC_004302	24208	24230	0	0	gene_name=r1tp41/r1tp42	gene_position=intergenic (+98/-99)	gene_product=ORF41/ORF42	gene_strand=>/>	left_inside_cov=0	left_outside_cov=2	locus_tag=r1tp41/r1tp42	right_inside_cov=1	right_outside_cov=2
MC	50	.	NC_004302	24293	24316	0	0	gene_name=r1tp41/r1tp42	gene_position=intergenic (+183/-13)	gene_product=ORF41/ORF42	gene_strand=>/>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp41/r1tp42	right_inside_cov=1	right_outside_cov=2
MC	51	.	NC_004302	24382	24510	0	0	gene_name=r1tp42	gene_position=coding (54-182/1974 nt)	gene_product=ORF42	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp42	right_inside_cov=1	right_outside_cov=2
MC	52	.	NC_004302	24673	24716	0	0	gene_name=r1tp42	gene_position=coding (345-388/1974 nt)	gene_product=ORF42	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp42	right_inside_cov=0	right_outside_cov=2
MC	53	.	NC_004302	24797	25087	0	0	gene_name=r1tp42	gene_position=coding (469-759/1974 nt)	gene_product=ORF42	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp42	right_inside_cov=1	right_outside_cov=2
MC	54	.	NC_004302	25275	25352	0	0	gene_name=r1tp42	gene_position=coding (947-1024/1974 nt)	gene_product=ORF42	gene_strand=>	left_inside_cov=1	left_outside_cov=3	locus_tag=r1tp42	right_inside_cov=0	right_outside_cov=2
MC	55	.	NC_004302	25426	25521	0	0	gene_name=r1tp42	gene_position=coding (1098-1193/1974 nt)	gene_product=ORF42	gene_strand=>	left_inside_cov=1	left_outside_cov=3	locus_tag=r1tp42	right_inside_cov=1	right_outside_cov=2
MC	56	.	NC_004302	25746	25816	0	0	gene_name=r1tp42	gene_position=coding (1418-1488/1974 nt)	gene_product=ORF42	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp42	right_inside_cov=1	right_outside_cov=2
MC	57	.	NC_004302	25922	26167	0	0	gene_name=r1tp42	gene_position=coding (1594-1839/1974 nt)	gene_product=ORF42	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp42	right_inside_cov=1	right_outside_cov=2
MC	58	.	NC_004302	26241	26446	0	0	gene_name=[r1tp42]–[r1tp43]	gene_product=[r1tp42],[r1tp43]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp42]–[r1tp43]	right_inside_cov=1	right_outside_cov=2
MC	59	.	NC_004302	27099	27166	0	0	gene_name=r1tp43	gene_position=coding (785-852/897 nt)	gene_product=ORF43	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp43	right_inside_cov=1	right_outside_cov=2
MC	60	.	NC_004302	27333	27363	0	0	gene_name=r1tp44	gene_position=coding (118-148/1158 nt)	gene_product=ORF44	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp44	right_inside_cov=1	right_outside_cov=2
MC	61	.	NC_004302	27422	27517	0	0	gene_name=r1tp44	gene_position=coding (207-302/1158 nt)	gene_product=ORF44	gene_strand=>	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp44	right_inside_cov=1	right_outside_cov=2
MC	62	.	NC_004302	33008	33071	0	0	gene_name=[r1tp50]	gene_product=[r1tp50]	left_inside_cov=1	left_outside_cov=2	locus_tag=[r1tp50]	right_inside_cov=1	right_outside_cov=2
MC	63	.	NC_004302	33286	33350	0	0	gene_name=r1tp50/–	gene_position=intergenic (+63/–)	gene_product=ORF50/–	gene_strand=>/–	left_inside_cov=1	left_outside_cov=2	locus_tag=r1tp50/–	right_inside_cov=0	right_outside_cov=NA
UN	64	.	NC_004302	1	778
UN	65	.	NC_004302	888	888
UN	66	.	NC_004302	911	1112
UN	67	.	NC_004302	1119	1119
UN	68	.	NC_004302	1121	1121
UN	69	.	NC_004302	1132	1133
UN	70	.	NC_004302	1135	1359
UN	71	.	NC_004302	1948	1948
UN	72	.	NC_004302	1961	1968
UN	73	.	NC_004302	1970	1974
UN	74	.	NC_004302	2000	2000
UN	75	.	NC_004302	2002	2002
UN	76	.	NC_004302	2004	2004
UN	77	.	NC_004302	2006	2007
UN	78	.	NC_004302	2754	2754
UN	79	.	NC_004302	2757	17405
UN	80	.	NC_004302	17414	17414
UN	81	.	NC_004302	17424	17424
UN	82	.	NC_004302	17431	17431
UN	83	.	NC_004302	17435	17490
UN	84	.	NC_004302	17492	17492
UN	85	.	NC_004302	17529	17529
UN	86	.	NC_004302	17538	17538
UN	87	.	NC_004302	17545	17545
UN	88	.	NC_004302	17552	19564
UN	89	.	NC_004302	19574	19574
UN	90	.	NC_004302	19576	22837
UN	91	.	NC_004302	22852	22852
UN	92	.	NC_004302	22866	22866
UN	93	.	NC_004302	22887	23073
UN	94	.	NC_004302	23076	23076
UN	95	.	NC_004302	23083	23088
UN	96	.	NC_004302	23096	23096
UN	97	.	NC_004302	23098	23098
UN	98	.	NC_004302	23109	23109
UN	99	.	NC_004302	23112	23112
UN	100	.	NC_004302	23127	23127
UN	101	.	NC_004302	23137	23343
UN	102	.	NC_004302	23345	23624
UN	103	.	NC_004302	23626	23629
UN	104	.	NC_004302	23632	23633
UN	105	.	NC_004302	23741	23746
UN	106	.	NC_004302	23767	23767
UN	107	.	NC_004302	23770	23770
UN	108	.	NC_004302	23827	23942
UN	109	.	NC_004302	23999	23999
UN	110	.	NC_004302	24007	24007
UN	111	.	NC_004302	24013	24032
UN	112	.	NC_004302	24036	24038
UN	113	.	NC_004302	24052	24052
UN	114	.	NC_004302	24062	24063
UN	115	.	NC_004302	24069	24561
UN	116	.	NC_004302	24575	24575
UN	117	.	NC_004302	24578	24578
UN	118	.	NC_004302	24582	24605
UN	119	.	NC_004302	24608	24608
UN	120	.	NC_004302	24612	24612
UN	121	.	NC_004302	24616	24616
UN	122	.	NC_004302	24620	24620
UN	123	.	NC_004302	24622	24622
UN	124	.	NC_004302	24626	26501
UN	125	.	NC_004302	26508	26508
UN	126	.	NC_004302	26511	26515
UN	127	.	NC_004302	26518	26956
UN	128	.	NC_004302	26958	26958
UN	129	.	NC_004302	26960	26961
UN	130	.	NC_004302	26965	26965
UN	131	.	NC_004302	26972	26972
UN	132	.	NC_004302	26996	26996
UN	133	.	NC_004302	27005	27013
UN	134	.	NC_004302	27015	27015
UN	135	.	NC_004302	27017	27017
UN	136	.	NC_004302	27024	27031
UN	137	.	NC_004302	27034	27216
UN	138	.	NC_004302	27224	27224
UN	139	.	NC_004302	27295	27295
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