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 | [crl] | [crl] | |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,019,460 | G→A | V359I (GTC→ATC) | fliK → | flagellar hook‑length control protein |
| JC JC | 2,099,835 | IS1 (+) +8 bp | intergenic (‑222/+20) | ugd ← / ← gnd | UDP‑glucose 6‑dehydrogenase/6‑phosphogluconate dehydrogenase, decarboxylating |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,317,667 | T→G | E737A (GAA→GCA) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,632,046 | G→T | P164T (CCG→ACG) | guaA ← | GMP synthetase (glutamine aminotransferase) |
| JC JC | 2,868,098 | IS5 (+) +4 bp | coding (653‑656/1140 nt) | nlpD ← | activator of AmiC murein hydrolase activity, lipoprotein |
| RA | 3,002,530 | G→A | G729D (GGT→GAT) | xdhA → | xanthine dehydrogenase, molybdenum binding subunit |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| JC JC | 3,890,075 | IS5 (–) +4 bp | coding (1346‑1349/1416 nt) | tnaA → | tryptophanase/L‑cysteine desulfhydrase, PLP‑dependent |
| RA | 4,186,607 | C→T | P420S (CCG→TCG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| MC JC | 4,309,624 | Δ3,364 bp | [alsA]–[alsR] | [alsA], alsB, [alsR] | |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423755–3424560 | 3424560 | 1–806 | 47 [46] | [43] 47 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3514354 | 3515093 | 740 | 48 [46] | [42] 48 | [gph]–[dam] | [gph],rpe,[dam] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 88 (0.740) | 46 (0.440) | 39/248 | 2.5 | 36.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 84 (0.800) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 153 (1.320) | 112/272 | 0.0 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||