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 |
| RA | 38,805 | C→A | R104L (CGT→CTT) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 369,465 | C→A | F285L (TTC→TTA) | mhpA → | putative 3‑(3‑hydroxyphenyl)propanoate/3‑hydroxycinnamate hydroxylase |
| RA | 527,694 | (A)5→4 | coding (114/369 nt) | ybbC → | PF15631 family protein YbbC |
| RA | 578,333 | A→C | K76T (AAA→ACA) K3Q (AAG→CAG) |
rzpD → rzoD → |
DLP12 prophage; putative prophage endopeptidase RzpD DLP12 prophage; putative prophage lysis lipoprotein RzoD |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,087,644 | G→A | A68V (GCT→GTT) | pgaC ← | poly‑N‑acetyl‑D‑glucosamine synthase subunit PgaC |
| RA | 1,404,886 | C→G | A49G (GCG→GGG) | abgR → | putative LysR‑type DNA‑binding transcriptional regulator AbgR |
| RA | 1,432,529 | C→A | A40E (GCA→GAA) | tfaR → | Rac prophage; putative tail fiber assembly protein TfaR |
| RA | 1,437,374 | C→A | S1137S (TCG→TCT) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,649,933 | C→A | P47Q (CCG→CAG) | ydfD → | Qin prophage; lysis protein |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| 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 | 2,021,557 | G→A | L18L (CTG→CTA) | fliO → | flagellar biosynthesis protein FliO |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,511,277 | G→T | D93Y (GAT→TAT) | ypeC → | DUF2502 domain‑containing protein YpeC |
| RA | 3,147,848 | G→T | intergenic (‑108/‑49) | yqhI ← / → gpr | protein YqhI/L‑glyceraldehyde 3‑phosphate reductase |
| RA | 3,353,199 | G→T | V284V (GTC→GTA) | yhcC ← | radical SAM family oxidoreductase YhcC |
| 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 | 4,030,318 | C→A | K218N (AAG→AAT) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,182,494 | C→A | S417Y (TCC→TAC) | rpoB → | RNA polymerase subunit beta |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,348,011 | G→T | A245E (GCA→GAA) | dcuB ← | anaerobic C4‑dicarboxylate transporter DcuB |
| RA | 4,631,944 | C→A | S404R (AGC→AGA) | slt → | soluble lytic murein transglycosylase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102962 | 3104052 | 1091 | 38 [36] | [35] 37 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423751–3424540 | 3424540 | 1–790 | 37 [36] | [35] 37 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 47 (0.360) | 151 (1.290) | 67/244 | 0.2 | 80.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 30 (0.260) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 47 (0.360) | 64 (0.550) | 46/244 | 0.9 | 64.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 30 (0.260) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 170 (1.330) | 87/268 | 0.1 | 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 = | 207 (1.570) | 215 (1.640) | 77/274 | 0.2 | 67.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 163 (1.230) | 80/276 | 0.1 | 95.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 7 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||