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 | 147,727 | Δ12 bp | coding (760‑771/903 nt) | rpnC → | recombination‑promoting nuclease RpnC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 1,049,443 | C→A | R101L (CGC→CTC) | gfcA ← | threonine‑rich inner membrane protein GfcA |
| RA | 1,143,998 | C→T | G124S (GGT→AGT) | rne ← | ribonuclease E |
| JC JC | 1,293,033 | IS1 (+) +9 bp | intergenic (‑111/‑486) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA‑5 ← / → uspC | IS1 protein InsA/universal stress protein C |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,917,345 | G→A | G763G (GGG→GGA) | barA → | sensory histidine kinase BarA |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,566,544 | C→A | S13I (AGC→ATC) | glgP ← | glycogen phosphorylase |
| MC JC | 3,815,859 | Δ82 bp | [rph] | [rph] | |
| RA | 4,215,147 | A→C | N290H (AAC→CAC) | metA → | homoserine O‑succinyltransferase |
| 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 | 3423810–3424234 | 3424504–3424238 | 5–695 | 3 [0] | [0] 2 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274347 = | NA (NA) | 13 (0.100) | 6/282 | 2.4 | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274410 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274384 = | NA (NA) | 3 (0.020) | 3/290 | 2.9 | NA | noncoding (766/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274422 = | NA (NA) | noncoding (728/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 274620 = | NA (NA) | 17 (0.140) | 6/278 | 2.4 | NA | noncoding (530/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274663 = | NA (NA) | noncoding (487/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 279564 | NA (NA) | 5 (0.040) | 4/284 | 2.7 | NA | noncoding (367/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 279590 | NA (NA) | noncoding (341/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | 315781 = | NA (NA) | 3 (0.020) | 3/286 | 2.9 | NA | noncoding (553/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315875 = | NA (NA) | noncoding (647/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 315844 = | NA (NA) | 4 (0.030) | 3/288 | 2.9 | NA | noncoding (616/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | 315925 = | NA (NA) | noncoding (697/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | = 316201 | NA (NA) | 14 (0.110) | 6/278 | 2.4 | NA | noncoding (973/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316220 | NA (NA) | noncoding (992/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 3 (0.020) | 34 (0.290) | 28/264 | 1.0 | 93.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 2 (0.020) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 3 (0.020) | 93 (0.790) | 66/264 | 0.3 | 97.5% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 2 (0.020) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 82 (0.630) | 52/288 | 0.5 | 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 | 1396531 = | NA (NA) | 48 (0.380) | 4/284 | 2.7 | NA | noncoding (488/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 1428264 | NA (NA) | noncoding (531/1196 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | 2822705 = | 77 (0.580) | 140 (1.290) +27 bp |
66/242 | 0.2 | 67.9% | intergenic (‑66/+3) | recX/recA | RecA inhibitor RecX/DNA recombination/repair protein RecA |
| ? | NC_000913 | 4171753 = | 85 (0.640) | noncoding (117/120 nt) | rrfB | 5S ribosomal RNA | |||||
| * | ? | NC_000913 | = 3620116 | NA (NA) | 11 (0.090) | 5/284 | 2.5 | 100% | coding (925/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3620152 | 0 (0.000) | coding (961/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 3620119 = | NA (NA) | 4 (0.030) | 3/284 | 2.9 | 100% | coding (928/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620146 = | 0 (0.000) | coding (955/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 3620123 = | NA (NA) | 3 (0.020) | 3/284 | 2.9 | 100% | coding (932/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | 3620147 = | 0 (0.000) | coding (956/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 3620350 | NA (NA) | 7 (0.050) | 6/284 | 2.4 | 100% | coding (1159/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3620425 | 0 (0.000) | coding (1234/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 3621583 | NA (NA) | 9 (0.070) | 4/284 | 2.7 | 100% | coding (2392/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3621667 | 0 (0.000) | coding (2476/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | = 3621980 | NA (NA) | 5 (0.040) | 4/280 | 2.7 | 100% | coding (2789/4236 nt) | rhsB | rhs element protein RhsB |
| ? | NC_000913 | = 3622019 | 0 (0.000) | coding (2828/4236 nt) | rhsB | rhs element protein RhsB | |||||
| * | ? | NC_000913 | 4027497 = | NA (NA) | 4 (0.030) | 3/280 | 2.9 | NA | noncoding (8/34 nt) | other | REP291d |
| ? | NC_000913 | 4027567 = | NA (NA) | intergenic (+339/+42) | fre/fadA | flavin reductase/3‑ketoacyl‑CoA thiolase | |||||
| * | ? | NC_000913 | = 4633089 | NA (NA) | 3 (0.020) | 3/280 | 2.9 | NA | intergenic (+3/+144) | trpR/yjjX | DNA‑binding transcriptional repressor TrpR/ITPase/XTPase |
| ? | NC_000913 | = 4633169 | NA (NA) | noncoding (34/34 nt) | other | REP355b | |||||