#=GENOME_DIFF 1.0 #=COMMAND breseq -j 8 -r /data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk /data/pg-molgen/harma/2021_04/fastq/7A_S7_R1_001.fastq.gz -o /data/pg-molgen/harma/2021_04/results_breseq/HK5_r1t #=REFSEQ /data/pg-molgen/harma/genomes/Bacteriophage_r1t.gbk #=READSEQ /data/pg-molgen/harma/2021_04/fastq/7A_S7_R1_001.fastq.gz #=CONVERTED-BASES 1294282275 #=CONVERTED-READS 17257097 #=INPUT-BASES 1294485375 #=INPUT-READS 17259805 #=MAPPED-BASES 2393233 #=MAPPED-READS 34175 INS 1 12 NC_004302 3547 A gene_name=r1tp05 gene_position=coding (307/798 nt) gene_product=ORF5 gene_strand=> genes_inactivated=r1tp05 locus_tag=r1tp05 locus_tags_inactivated=r1tp05 mutation_category=small_indel position_end=3547 position_start=3547 ref_seq=A INS 2 13,14 NC_004302 3556 GT gene_name=r1tp05 gene_position=coding (316/798 nt) gene_product=ORF5 gene_strand=> genes_inactivated=r1tp05 locus_tag=r1tp05 locus_tags_inactivated=r1tp05 mutation_category=small_indel position_end=3556 position_start=3556 ref_seq=T SUB 3 15,16 NC_004302 5234 2 GC gene_name=r1tp09 gene_position=coding (325-326/834 nt) gene_product=ORF9 gene_strand=> genes_inactivated=r1tp09 locus_tag=r1tp09 locus_tags_inactivated=r1tp09 mutation_category=small_indel position_end=5235 position_start=5234 ref_seq=CG SNP 4 17 NC_004302 5237 G aa_new_seq=V aa_position=110 aa_ref_seq=L codon_new_seq=GTT codon_number=110 codon_position=1 codon_ref_seq=CTT gene_name=r1tp09 gene_position=328 gene_product=ORF9 gene_strand=> genes_overlapping=r1tp09 locus_tag=r1tp09 locus_tags_overlapping=r1tp09 mutation_category=snp_nonsynonymous position_end=5237 position_start=5237 ref_seq=C snp_type=nonsynonymous transl_table=11 DEL 5 27,29 NC_004302 8712 6 gene_name=r1tp14 gene_position=coding (21-26/396 nt) gene_product=ORF14 gene_strand=> genes_inactivated=r1tp14 locus_tag=r1tp14 locus_tags_inactivated=r1tp14 mutation_category=small_indel position_end=8717 position_start=8712 ref_seq=TGAATT repeat_length=6 repeat_new_copies=2 repeat_ref_copies=3 repeat_seq=TGAATT SNP 6 21 NC_004302 9972 A aa_new_seq=E aa_position=59 aa_ref_seq=A codon_new_seq=GAA codon_number=59 codon_position=2 codon_ref_seq=GCA gene_name=r1tp18 gene_position=176 gene_product=ORF18 gene_strand=> genes_overlapping=r1tp18 locus_tag=r1tp18 locus_tags_overlapping=r1tp18 mutation_category=snp_nonsynonymous position_end=9972 position_start=9972 ref_seq=C snp_type=nonsynonymous transl_table=11 SNP 7 22 NC_004302 13763 C aa_new_seq=A aa_position=122 aa_ref_seq=V codon_new_seq=GCT codon_number=122 codon_position=2 codon_ref_seq=GTT gene_name=r1tp24 gene_position=365 gene_product=ORF24 gene_strand=> genes_overlapping=r1tp24 locus_tag=r1tp24 locus_tags_overlapping=r1tp24 mutation_category=snp_nonsynonymous position_end=13763 position_start=13763 ref_seq=T snp_type=nonsynonymous transl_table=11 SNP 8 24 NC_004302 23480 C aa_new_seq=A aa_position=213 aa_ref_seq=E codon_new_seq=GCA codon_number=213 codon_position=2 codon_ref_seq=GAA gene_name=r1tp40 gene_position=638 gene_product=ORF40 gene_strand=> genes_overlapping=r1tp40 locus_tag=r1tp40 locus_tags_overlapping=r1tp40 mutation_category=snp_nonsynonymous position_end=23480 position_start=23480 ref_seq=A snp_type=nonsynonymous transl_table=11 RA 9 . NC_004302 1914 0 T C bias_e_value=33346.8 bias_p_value=0.999904 consensus_reject=FREQUENCY_CUTOFF consensus_score=217.4 fisher_strand_p_value=1 frequency=2.731e-01 gene_name=r1tp02/rro gene_position=intergenic (-54/+7) gene_product=ORF2/Repressor protein gene_strand= ks_quality_p_value=1 locus_tag=r1tp03/r1tp04 major_base=C major_cov=0/24 major_frequency=6.667e-01 minor_base=T minor_cov=0/12 new_cov=0/12 polymorphism_frequency=3.333e-01 polymorphism_score=17.5 prediction=polymorphism ref_cov=0/24 snp_type=intergenic total_cov=0/37 RA 11 . NC_004302 2843 0 C G bias_e_value=33334.3 bias_p_value=0.99953 consensus_reject=FREQUENCY_CUTOFF consensus_score=16.1 fisher_strand_p_value=1 frequency=4.906e-01 gene_name=rro/tec gene_position=intergenic (-86/-144) gene_product=Repressor protein/tec gene_strand= ks_quality_p_value=0.969512 locus_tag=r1tp03/r1tp04 major_base=C major_cov=27/0 major_frequency=5.094e-01 minor_base=G minor_cov=26/0 new_cov=26/0 polymorphism_frequency=4.906e-01 polymorphism_score=47.1 prediction=polymorphism ref_cov=27/0 snp_type=intergenic total_cov=80/0 RA 12 . NC_004302 3545 1 . A bias_e_value=33349.9 bias_p_value=0.999996 consensus_score=1095.2 fisher_strand_p_value=1 frequency=1 gene_name=r1tp05 gene_position=coding (305/798 nt) gene_product=ORF5 gene_strand=> ks_quality_p_value=0.997285 locus_tag=r1tp05 major_base=A major_cov=426/6 major_frequency=9.908e-01 minor_base=. minor_cov=4/0 new_cov=426/6 polymorphism_frequency=9.908e-01 polymorphism_score=-0.0 prediction=consensus ref_cov=4/0 total_cov=430/6 RA 13 . NC_004302 3554 1 . G bias_e_value=26193.5 bias_p_value=0.785411 consensus_score=1136.3 fisher_strand_p_value=0.464749 frequency=1 gene_name=r1tp05 gene_position=coding (314/798 nt) gene_product=ORF5 gene_strand=> ks_quality_p_value=0.90635 locus_tag=r1tp05 major_base=G major_cov=436/6 major_frequency=9.151e-01 minor_base=. minor_cov=40/1 new_cov=436/6 polymorphism_frequency=9.151e-01 polymorphism_score=68.2 prediction=consensus ref_cov=40/1 total_cov=481/7 RA 14 . NC_004302 3554 2 . T bias_e_value=25994.1 bias_p_value=0.779432 consensus_score=1128.6 fisher_strand_p_value=0.469569 frequency=1 gene_name=r1tp05 gene_position=coding (314/798 nt) gene_product=ORF5 gene_strand=> ks_quality_p_value=0.882456 locus_tag=r1tp05 major_base=T major_cov=440/6 major_frequency=9.139e-01 minor_base=. minor_cov=41/1 new_cov=440/6 polymorphism_frequency=9.139e-01 polymorphism_score=71.6 prediction=consensus ref_cov=41/1 total_cov=481/7 RA 15 . NC_004302 5234 0 C G aa_new_seq=A aa_position=109 aa_ref_seq=R bias_e_value=33350 bias_p_value=1 codon_new_seq=GCA codon_number=109 codon_position=1 codon_ref_seq=CGA consensus_score=153.7 fisher_strand_p_value=1 frequency=1 gene_name=r1tp09 gene_position=325 gene_product=ORF9 gene_strand=> ks_quality_p_value=1 locus_tag=r1tp09 major_base=G major_cov=62/1 major_frequency=9.692e-01 minor_base=C minor_cov=2/0 new_cov=62/1 new_seq=G polymorphism_frequency=9.692e-01 polymorphism_score=-2.6 prediction=consensus ref_cov=2/0 ref_seq=C snp_type=nonsynonymous total_cov=64/1 transl_table=11 RA 16 . NC_004302 5235 0 G C aa_new_seq=A aa_position=109 aa_ref_seq=R bias_e_value=33350 bias_p_value=1 codon_new_seq=GCA codon_number=109 codon_position=2 codon_ref_seq=CGA consensus_score=167.8 fisher_strand_p_value=1 frequency=1 gene_name=r1tp09 gene_position=326 gene_product=ORF9 gene_strand=> ks_quality_p_value=0.999504 locus_tag=r1tp09 major_base=C major_cov=62/1 major_frequency=9.844e-01 minor_base=G minor_cov=1/0 new_cov=62/1 new_seq=C polymorphism_frequency=9.844e-01 polymorphism_score=-3.6 prediction=consensus ref_cov=1/0 ref_seq=G snp_type=nonsynonymous total_cov=63/1 transl_table=11 RA 17 . NC_004302 5237 0 C G aa_new_seq=V aa_position=110 aa_ref_seq=L codon_new_seq=GTT codon_number=110 codon_position=1 codon_ref_seq=CTT consensus_score=160.6 frequency=1 gene_name=r1tp09 gene_position=328 gene_product=ORF9 gene_strand=> locus_tag=r1tp09 major_base=G major_cov=63/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=63/1 new_seq=G polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 ref_seq=C snp_type=nonsynonymous total_cov=63/1 transl_table=11 RA 18 . NC_004302 5716 1 . A bias_e_value=29483 bias_p_value=0.884049 consensus_reject=FREQUENCY_CUTOFF consensus_score=107.6 fisher_strand_p_value=1 frequency=2.000e-01 gene_name=r1tp09 gene_position=coding (807/834 nt) gene_product=ORF9 gene_strand=> ks_quality_p_value=0.558881 locus_tag=r1tp09 major_base=. major_cov=42/2 major_frequency=8.000e-01 minor_base=A minor_cov=11/0 new_cov=11/0 polymorphism_frequency=2.000e-01 polymorphism_score=18.6 prediction=polymorphism ref_cov=42/2 total_cov=53/2 RA 19 . NC_004302 6967 0 C T aa_new_seq=* aa_position=25 aa_ref_seq=Q bias_e_value=33029.6 bias_p_value=0.990393 codon_new_seq=TAG codon_number=25 codon_position=1 codon_ref_seq=CAG consensus_reject=FREQUENCY_CUTOFF consensus_score=87.8 fisher_strand_p_value=1 frequency=2.000e-01 gene_name=r1tp11 gene_position=73 gene_product=ORF11 gene_strand=> ks_quality_p_value=0.864629 locus_tag=r1tp11 major_base=C major_cov=44/0 major_frequency=8.000e-01 minor_base=T minor_cov=11/0 new_cov=11/0 new_seq=T polymorphism_frequency=2.000e-01 polymorphism_score=12.6 prediction=polymorphism ref_cov=44/0 ref_seq=C snp_type=nonsense total_cov=57/0 transl_table=11 RA 20 . NC_004302 7392 1 . A bias_e_value=10924.6 bias_p_value=0.327573 consensus_reject=FREQUENCY_CUTOFF consensus_score=138.4 fisher_strand_p_value=1 frequency=2.000e-01 gene_name=r1tp11 gene_position=coding (498/735 nt) gene_product=ORF11 gene_strand=> ks_quality_p_value=0.0988368 locus_tag=r1tp11 major_base=. major_cov=56/0 major_frequency=8.000e-01 minor_base=A minor_cov=14/0 new_cov=14/0 polymorphism_frequency=2.000e-01 polymorphism_score=24.7 prediction=polymorphism ref_cov=56/0 total_cov=70/0 RA 21 . NC_004302 9972 0 C A aa_new_seq=E aa_position=59 aa_ref_seq=A bias_e_value=4383.76 bias_p_value=0.131447 codon_new_seq=GAA codon_number=59 codon_position=2 codon_ref_seq=GCA consensus_score=168.5 fisher_strand_p_value=0.0289855 frequency=1 gene_name=r1tp18 gene_position=176 gene_product=ORF18 gene_strand=> ks_quality_p_value=0.998296 locus_tag=r1tp18 major_base=A major_cov=67/1 major_frequency=9.855e-01 minor_base=T minor_cov=0/1 new_cov=67/1 new_seq=A polymorphism_frequency=9.855e-01 polymorphism_score=-3.3 prediction=consensus ref_cov=0/0 ref_seq=C snp_type=nonsynonymous total_cov=67/2 transl_table=11 RA 22 . NC_004302 13763 0 T C aa_new_seq=A aa_position=122 aa_ref_seq=V bias_e_value=33350 bias_p_value=1 codon_new_seq=GCT codon_number=122 codon_position=2 codon_ref_seq=GTT consensus_score=200.1 fisher_strand_p_value=1 frequency=1 gene_name=r1tp24 gene_position=365 gene_product=ORF24 gene_strand=> ks_quality_p_value=1 locus_tag=r1tp24 major_base=C major_cov=73/2 major_frequency=9.868e-01 minor_base=G minor_cov=1/0 new_cov=73/2 new_seq=C polymorphism_frequency=9.868e-01 polymorphism_score=-4.1 prediction=consensus ref_cov=0/0 ref_seq=T snp_type=nonsynonymous total_cov=74/2 transl_table=11 RA 23 . NC_004302 15047 1 . A bias_e_value=31135.7 bias_p_value=0.933605 consensus_reject=FREQUENCY_CUTOFF consensus_score=101.5 fisher_strand_p_value=1 frequency=2.182e-01 gene_name=r1tp26/r1tp27 gene_position=intergenic (+140/-7) gene_product=HNH endonuclease/Structural protein gene_strand=>/> ks_quality_p_value=0.658475 locus_tag=r1tp26/r1tp27 major_base=. major_cov=41/2 major_frequency=7.818e-01 minor_base=A minor_cov=12/0 new_cov=12/0 polymorphism_frequency=2.182e-01 polymorphism_score=21.2 prediction=polymorphism ref_cov=41/2 snp_type=intergenic total_cov=53/2 RA 24 . NC_004302 23480 0 A C aa_new_seq=A aa_position=213 aa_ref_seq=E codon_new_seq=GCA codon_number=213 codon_position=2 codon_ref_seq=GAA consensus_score=11.9 frequency=1 gene_name=r1tp40 gene_position=638 gene_product=ORF40 gene_strand=> locus_tag=r1tp40 major_base=C major_cov=5/1 major_frequency=1.000e+00 minor_base=N minor_cov=0/0 new_cov=5/1 new_seq=C polymorphism_frequency=1.000e+00 polymorphism_score=NA prediction=consensus ref_cov=0/0 ref_seq=A snp_type=nonsynonymous total_cov=5/1 transl_table=11 MC 25 . NC_004302 1 52 0 0 gene_name=–/r1tp01 gene_position=intergenic (–/+42) 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 26 . NC_004302 2766 2834 0 0 gene_name=rro/tec gene_position=intergenic (-9/-153) 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=6 MC 27 . NC_004302 8696 8701 0 0 gene_name=r1tp13|r1tp14 gene_position=coding (159-164/165 nt)|coding (5-10/396 nt) gene_product=ORF13|ORF14 gene_strand=>|> left_inside_cov=0 left_outside_cov=117 locus_tag=r1tp13|r1tp14 right_inside_cov=0 right_outside_cov=114 snp_type=| MC 28 . NC_004302 33336 33350 0 0 gene_name=r1tp50/– gene_position=intergenic (+113/–) gene_product=ORF50/– gene_strand=>/– left_inside_cov=1 left_outside_cov=2 locus_tag=r1tp50/– right_inside_cov=0 right_outside_cov=NA JC 29 . NC_004302 8702 1 NC_004302 8695 -1 0 alignment_overlap=16 coverage_minus=1 coverage_plus=5 flanking_left=75 flanking_right=75 frequency=1 junction_possible_overlap_registers=58 key=NC_004302__8702__1__NC_004302__8711__-1__16____75__75__0__0 max_left=42 max_left_minus=31 max_left_plus=42 max_min_left=28 max_min_left_minus=0 max_min_left_plus=28 max_min_right=28 max_min_right_minus=28 max_min_right_plus=15 max_pos_hash_score=116 max_right=42 max_right_minus=28 max_right_plus=42 neg_log10_pos_hash_p_value=0.2 new_junction_coverage=1.74 new_junction_read_count=97 polymorphism_frequency=1.000e+00 pos_hash_score=5 prediction=consensus side_1_annotate_key=gene side_1_continuation=0 side_1_coverage=0.00 side_1_overlap=16 side_1_possible_overlap_registers=74 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=58 side_2_read_count=0 side_2_redundant=0 total_non_overlap_reads=6 UN 30 . NC_004302 1 99 UN 31 . NC_004302 105 127 UN 32 . NC_004302 159 159 UN 33 . NC_004302 162 170 UN 34 . NC_004302 193 196 UN 35 . NC_004302 198 198 UN 36 . NC_004302 383 424 UN 37 . NC_004302 429 430 UN 38 . NC_004302 642 669 UN 39 . NC_004302 674 687 UN 40 . NC_004302 690 742 UN 41 . NC_004302 748 748 UN 42 . NC_004302 844 847 UN 43 . NC_004302 1030 1037 UN 44 . NC_004302 1054 1054 UN 45 . NC_004302 1278 1316 UN 46 . NC_004302 2763 2842 UN 47 . NC_004302 8696 8701 UN 48 . NC_004302 14501 14501 UN 49 . NC_004302 14509 14520 UN 50 . NC_004302 14524 14524 UN 51 . NC_004302 21078 21078 UN 52 . NC_004302 21172 21248 UN 53 . NC_004302 22200 22200 UN 54 . NC_004302 22207 22207 UN 55 . NC_004302 22290 22290 UN 56 . NC_004302 22403 22415 UN 57 . NC_004302 22417 22419 UN 58 . NC_004302 22501 22585 UN 59 . NC_004302 22647 22648 UN 60 . NC_004302 22652 22652 UN 61 . NC_004302 23332 23332 UN 62 . NC_004302 23368 23382 UN 63 . NC_004302 23462 23462 UN 64 . NC_004302 23470 23476 UN 65 . NC_004302 24125 24175 UN 66 . NC_004302 24184 24184 UN 67 . NC_004302 24193 24193 UN 68 . NC_004302 24275 24357 UN 69 . NC_004302 24400 24405 UN 70 . NC_004302 24829 24848 UN 71 . NC_004302 24961 24961 UN 72 . NC_004302 24968 24974 UN 73 . NC_004302 24977 25031 UN 74 . NC_004302 25039 25044 UN 75 . NC_004302 25065 25074 UN 76 . NC_004302 25089 25089 UN 77 . NC_004302 25093 25167 UN 78 . NC_004302 25177 25177 UN 79 . NC_004302 25328 25330 UN 80 . NC_004302 25337 25337 UN 81 . NC_004302 25342 25342 UN 82 . NC_004302 25992 26022 UN 83 . NC_004302 26024 26025 UN 84 . NC_004302 26052 26052 UN 85 . NC_004302 26072 26106 UN 86 . NC_004302 26110 26110 UN 87 . NC_004302 26247 26256 UN 88 . NC_004302 26280 26284 UN 89 . NC_004302 26307 26307 UN 90 . NC_004302 26310 26405 UN 91 . NC_004302 26413 26413 UN 92 . NC_004302 26477 26514 UN 93 . NC_004302 26538 26543 UN 94 . NC_004302 26556 26576 UN 95 . NC_004302 26821 26834 UN 96 . NC_004302 26840 26844 UN 97 . NC_004302 26849 26865 UN 98 . NC_004302 27012 27034 UN 99 . NC_004302 27038 27050 UN 100 . NC_004302 27055 27061 UN 101 . NC_004302 27145 27146 UN 102 . NC_004302 27155 27156 UN 103 . NC_004302 27183 27183 UN 104 . NC_004302 27193 27195 UN 105 . NC_004302 27198 27250 UN 106 . NC_004302 27282 27487 UN 107 . NC_004302 27492 27492 UN 108 . NC_004302 27496 27505 UN 109 . NC_004302 27569 27569 UN 110 . NC_004302 27571 27688 UN 111 . NC_004302 27733 27733 UN 112 . NC_004302 27738 27738 UN 113 . NC_004302 28417 28418 UN 114 . NC_004302 28760 28760 UN 115 . NC_004302 28764 28834 UN 116 . NC_004302 28849 28858 UN 117 . NC_004302 28865 28865 UN 118 . NC_004302 28938 28939 UN 119 . NC_004302 28943 28943 UN 120 . NC_004302 28956 29007 UN 121 . NC_004302 29010 29025 UN 122 . NC_004302 29033 29033 UN 123 . NC_004302 29101 29110 UN 124 . NC_004302 29185 29190 UN 125 . NC_004302 29582 29582 UN 126 . NC_004302 29659 29670 UN 127 . NC_004302 29672 29696 UN 128 . NC_004302 29700 29700 UN 129 . NC_004302 29702 29703 UN 130 . NC_004302 29825 29825 UN 131 . NC_004302 29911 30022 UN 132 . NC_004302 30034 30054 UN 133 . NC_004302 30564 30572 UN 134 . NC_004302 30586 30606 UN 135 . NC_004302 30613 30660 UN 136 . NC_004302 30701 30750 UN 137 . NC_004302 31026 31048 UN 138 . NC_004302 31351 31351 UN 139 . NC_004302 31353 31376 UN 140 . NC_004302 32799 32799 UN 141 . NC_004302 32862 32862 UN 142 . NC_004302 32864 32916 UN 143 . NC_004302 32936 32953 UN 144 . NC_004302 32977 32977 UN 145 . NC_004302 32979 33199 UN 146 . NC_004302 33201 33213 UN 147 . NC_004302 33218 33245 UN 148 . NC_004302 33248 33350