mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.35.4 revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| 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 |
| JC | Annotation_U21_Trimmed_contig_1 | 51 | 25 bp→109 bp | coding (51‑75/567 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 new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | Annotation_U21_Trimmed_contig_1 | 1 = | 0 (0.000) | 210 (0.670) | 70/258 | 1.0 | 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_10 | 1 = | 0 (0.000) | 487 (0.440) +GTTTATTCCGGCA |
54/232 | 2.1 | 82.6% | 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 | 228 (0.700) | noncoding (8/73 nt) | rasttk_feature_creation_tool=tRNAscan‑SE | tRNA‑Lys‑TTT | |||||
| * | ? | Annotation_U21_Trimmed_contig_10 | 1 = | 0 (0.000) | 354 (0.290) | 96/258 | 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_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) | 365 (0.450) +46 bp |
83/166 | 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) | 407 (0.480) +46 bp |
77/166 | 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_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) | 1085 (0.550) +TTGAGAGTAA |
113/238 | 1.8 | 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) | 1934 (1.530) +C |
131/256 | 0.0 | 100.0% | intergenic (–/‑74) | –/rasttk_feature_creation_tool=RNA_reps_SSU_rRNA | –/SSU rRNA ## 16S rRNA, small subunit ribosomal RNA |
| ? | Annotation_U21_Trimmed_contig_3 | 2 = | 1 (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) | 422 (0.400) +22 bp |
77/214 | 0.0 | 73.7% | intergenic (+53/–) | rasttk_feature_creation_tool=RNA_reps_SSU_rRNA/– | SSU rRNA ## 16S rRNA, small subunit ribosomal RNA/– |
| ? | Annotation_U21_Trimmed_contig_13 | 191 = | 363 (0.970) | noncoding (1/75 nt) | rasttk_feature_creation_tool=tRNAscan‑SE | tRNA‑Ile‑GAT | |||||
| * | ? | Annotation_U21_Trimmed_contig_13 | 1 = | 0 (0.000) | 196 (0.570) | 52/258 | 1.4 | 59.0% | intergenic (–/‑4) | –/rasttk_feature_creation_tool=tRNAscan‑SE | –/tRNA‑Phe‑GAA |
| ? | Annotation_U21_Trimmed_contig_8 | 48167 = | 273 (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 | = 373842 | 493 (1.020) | 441 (1.170) +28 bp |
60/202 | 1.2 | 53.6% | coding (3215/5343 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Predicted cell‑wall‑anchored protein SasA (LPXTG motif) |
| ? | Annotation_U21_Trimmed_contig_2 | 374858 = | 485 (1.000) | coding (4231/5343 nt) | rasttk_feature_annotation_tool=annotate_proteins_km er_v2 | Predicted cell‑wall‑anchored protein SasA (LPXTG motif) | |||||
| * | ? | Annotation_U21_Trimmed_contig_2 | = 374547 | 524 (1.080) | 451 (0.910) | 69/254 | 1.7 | 63.6% | 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) | 243 (0.480) | 58/258 | 2.9 | 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) | 1965 (0.860) | 151/258 | 0.5 | 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/– | |||||