breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
Predicted mutations | ||||||
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evidence | seq id | position | mutation | annotation | gene | description |
JC | Annotation_U21_Trimmed_contig_1 | 47 | +84 bp | coding (47/567 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 → | hypothetical protein |
RA | Annotation_U21_Trimmed_contig_1 | 64,267 | T→C | S371P (TCA→CCA) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 → | RNA polymerase sigma factor RpoD |
RA | Annotation_U21_Trimmed_contig_4 | 75,126 | T→C | C31R (TGC→CGC) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 → | Replication‑associated recombination protein RarA |
JC | Annotation_U21_Trimmed_contig_8 | 16 | +84 bp | coding (573/588 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 ← | hypothetical protein |
Unassigned missing coverage evidence | ||||||||||
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seq id | start | end | size | ←reads | reads→ | gene | description | |||
* | * | ÷ | Annotation_U21_Trimmed_contig_3 | 1 | 1 | 1 | NA [0] | [0] 1613 | –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | –/Integral membrane protein LafC, accessory function in glycolipid and LTA synthesis |
* | * | ÷ | Annotation_U21_Trimmed_contig_9 | 10580–10601 | 10661 | 61–82 | 1185 [1151] | [0] NA | rasttk_feature_annotation_tool=annotate_proteins_km er_v2/– | ORF9/– |
Unassigned new junction evidence | |||||||||||
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seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | Annotation_U21_Trimmed_contig_1 | 1 = | 0 (0.000) | 151 (0.560) | 57/256 | 1.7 | 100% | coding (1/567 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | hypothetical protein |
? | Annotation_U21_Trimmed_contig_8 | 1 = | 0 (0.000) | coding (588/588 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | hypothetical protein | |||||
* | ? | Annotation_U21_Trimmed_contig_1 | = 50 | 87 (0.320) | 37 (0.930) +109 bp |
7/38 | 1.1 | 69.5% | coding (50/567 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | hypothetical protein |
? | Annotation_U21_Trimmed_contig_1 | 76 = | 132 (0.490) | coding (76/567 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | hypothetical protein | |||||
* | ? | Annotation_U21_Trimmed_contig_10 | 1 = | 0 (0.000) | 450 (0.470) +GTTTATTCCGGCA |
62/230 | 0.5 | 84.4% | noncoding (117/117 nt) | rasttk_feature_creation_tool=RNA_reps_5S_rRNA | 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation |
? | Annotation_U21_Trimmed_contig_12 | = 910 | 185 (0.680) | noncoding (8/73 nt) | rasttk_feature_creation_tool=tRNAscan‑SE | tRNA‑Lys‑TTT | |||||
* | ? | Annotation_U21_Trimmed_contig_10 | 1 = | 0 (0.000) | 337 (0.310) | 96/256 | 0.0 | 100% | noncoding (117/117 nt) | rasttk_feature_creation_tool=RNA_reps_5S_rRNA | 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation |
? | Annotation_U21_Trimmed_contig_12 | = 1004 | 0 (0.000) | intergenic (‑5/–) | rasttk_feature_creation_tool=tRNAscan‑SE/– | tRNA‑Val‑TAC/– | |||||
* | ? | Annotation_U21_Trimmed_contig_10 | 1 = | 0 (0.000) | 353 (0.500) +46 bp |
70/164 | 0.0 | 100% | noncoding (117/117 nt) | rasttk_feature_creation_tool=RNA_reps_5S_rRNA | 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation |
? | Annotation_U21_Trimmed_contig_3 | = 367983 | 0 (0.000) | intergenic (‑70/–) | rasttk_feature_creation_tool=tRNAscan‑SE/– | tRNA‑Thr‑GGT/– | |||||
* | ? | Annotation_U21_Trimmed_contig_10 | 1 = | 0 (0.000) | 342 (0.460) +46 bp |
69/164 | 0.1 | 100% | noncoding (117/117 nt) | rasttk_feature_creation_tool=RNA_reps_5S_rRNA | 5S rRNA # 5S ribosomal RNA ‑ 3 prime truncation |
? | Annotation_U21_Trimmed_contig_5 | = 139689 | 0 (0.000) | intergenic (+108/–) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2/– | Uncharacterized deacetylase/– | |||||
* | ? | Annotation_U21_Trimmed_contig_10 | = 3297 | 0 (0.000) | 986 (0.580) +TTGAGAGTAA |
113/236 | 1.4 | 100% | intergenic (‑160/–) | rasttk_feature_creation_tool=RNA_reps_LSU_rRNA/– | LSU rRNA ## 23S rRNA, large subunit ribosomal RNA/– |
? | Annotation_U21_Trimmed_contig_11 | = 1711 | 0 (0.000) | intergenic (+53/–) | rasttk_feature_creation_tool=RNA_reps_SSU_rRNA/– | SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/– | |||||
* | ? | Annotation_U21_Trimmed_contig_11 | 1 = | 0 (0.000) | 1612 (1.490) +C |
130/254 | 0.0 | 100% | intergenic (–/‑74) | –/rasttk_feature_creation_tool=RNA_reps_SSU_rRNA | –/SSU rRNA ## 16S rRNA, small subunit ribosomal RNA |
? | Annotation_U21_Trimmed_contig_3 | 2 = | 0 (0.000) | intergenic (–/+370) | –/rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | –/Integral membrane protein LafC, accessory function in glycolipid and LTA synthesis | |||||
* | ? | Annotation_U21_Trimmed_contig_11 | = 1711 | 0 (0.000) | 356 (0.400) +22 bp |
67/212 | 0.0 | 73.6% | intergenic (+53/–) | rasttk_feature_creation_tool=RNA_reps_SSU_rRNA/– | SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/– |
? | Annotation_U21_Trimmed_contig_13 | 191 = | 309 (0.980) | noncoding (1/75 nt) | rasttk_feature_creation_tool=tRNAscan‑SE | tRNA‑Ile‑GAT | |||||
* | ? | Annotation_U21_Trimmed_contig_13 | 1 = | 0 (0.000) | 162 (0.550) | 49/256 | 1.5 | 58.3% | intergenic (–/‑4) | –/rasttk_feature_creation_tool=tRNAscan‑SE | –/tRNA‑Phe‑GAA |
? | Annotation_U21_Trimmed_contig_8 | 48167 = | 232 (0.860) | intergenic (‑22/+1) | rasttk_feature_creation_tool=tRNAscan‑SE/rasttk_feature_creation_tool=tRNAscan‑SE | tRNA‑Phe‑GAA/tRNA‑Asp‑GTC | |||||
* | ? | Annotation_U21_Trimmed_contig_2 | = 374547 | 465 (1.060) | 487 (1.090) | 82/252 | 0.7 | 68.0% | coding (3920/5343 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Predicted cell‑wall‑anchored protein SasA (LPXTG motif) |
? | Annotation_U21_Trimmed_contig_7 | = 60417 | 0 (0.000) | coding (3/753 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Predicted cell‑wall‑anchored protein SasA (LPXTG motif) | |||||
* | ? | Annotation_U21_Trimmed_contig_2 | = 375970 | 0 (0.000) | 228 (0.500) | 58/256 | 2.6 | 100% | coding (5343/5343 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Predicted cell‑wall‑anchored protein SasA (LPXTG motif) |
? | Annotation_U21_Trimmed_contig_7 | = 60419 | 0 (0.000) | coding (1/753 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Predicted cell‑wall‑anchored protein SasA (LPXTG motif) | |||||
* | ? | Annotation_U21_Trimmed_contig_9 | 1 = | 0 (0.000) | 1412 (0.850) | 135/256 | 0.7 | 100% | coding (1/936 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Plasmid replication initiation protein |
? | Annotation_U21_Trimmed_contig_9 | = 10661 | NA (NA) | intergenic (+719/–) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2/– | ORF9/– |