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 | position | mutation | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| MC | 279,931 | Δ11,471 bp | between IS1 | yagB–insA‑3 | yagB, yagA, yagE, yagF, yagG, yagH, xynR, argF, ykgS, insB‑3, insA‑3 |
| RA | 505,107 | G→T | G65V (GGT→GTT) | ushA → | 5'‑nucleotidase/UDP‑sugar hydrolase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 947,685 | C→A | L153M (CTG→ATG) | ycaM → | putative transporter YcaM |
| RA | 1,068,941 | C→G | G300A (GGC→GCC) | rutG ← | pyrimidine:H(+) symporter |
| RA | 1,605,984 | T→G | Y312D (TAT→GAT) | lsrB → | Autoinducer‑2 ABC transporter periplasmic binding protein |
| RA | 1,606,332 | T→G | L78R (CTG→CGG) | lsrF → | 3‑hydroxy‑2,4‑pentadione 5‑phosphate thiolase |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| JC | 2,921,717 | Δ10 bp | coding (375‑384/1353 nt) | gudP ← | galactarate/glucarate/glycerate transporter GudP |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2033815 | 2033942 | 128 | 34 [22] | [25] 30 | rseX/yedS | small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment |
| * | * | ÷ | NC_000913 | 3423759–3424234 | 3424544–3424239 | 6–786 | 26 [25] | [24] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 16 (0.190) | 65 (0.890) | 46/244 | 0.3 | 80.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 17 (0.230) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.190) | 43 (0.590) | 32/244 | 1.1 | 73.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 17 (0.230) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 79 (0.990) | 50/268 | 0.4 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 119 (1.440) | 109 (1.330) | 68/274 | 0.1 | 64.1% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 90 (1.090) | 59/276 | 0.2 | 96.8% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||