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 | 230,984 | C→A | intergenic (‑103/‑138) | yafC ← / → yafD | putative LysR family transcriptional regulator YafC/endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 757,112 | C→A | G402G (GGC→GGA) | sdhA → | succinate:quinone oxidoreductase, FAD binding protein |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 947,146 | T→C | intergenic (+127/‑83) | ycaD → / → ycaM | putative transporter YcaD/putative transporter YcaM |
| RA | 990,178 | G→T | A60E (GCG→GAG) | pncB ← | nicotinate phosphoribosyltransferase |
| RA | 1,572,262 | T→C | intergenic (‑217/+145) | gadB ← / ← pqqL | glutamate decarboxylase B/putative zinc peptidase |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,789,666 | G→T | K18N (AAG→AAT) | ydiE → | PF10636 family protein YdiE |
| 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 | 2,039,387 | G→T | intergenic (+18/‑91) | yedX → / → msrP | hydroxyisourate hydrolase/transthyretin‑related protein/periplasmic protein‑L‑methionine sulfoxide reductase catalytic subunit |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,198,532 | G→T | intergenic (+1234/‑1747) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,282,209 | G→T | P526P (CCG→CCT) | radD → | putative DNA repair helicase RadD |
| RA | 2,291,850 | C→A | L187F (TTG→TTT) | ccmH ← | holocytochrome c synthetase ‑ thiol:disulfide oxidoreductase CcmH |
| RA | 3,007,402 | G→T | G381C (GGT→TGT) | ygeW → | putative carbamoyltransferase YgeW |
| RA | 3,238,222 | C→T | R304R (CGC→CGT) | ygjR → | putative oxidoreductase YgjR |
| 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 | 3,771,593 | C→A | S51I (AGC→ATC) | yibI ← | DUF3302 domain‑containing protein YibI |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,868,172 | C→A | E380* (GAA→TAA) | yidR ← | DUF3748 domain‑containing galacturonate catabolism protein YidR |
| RA | 4,227,781 | G→T | G17G (GGG→GGT) | yjbB → | putative inorganic phosphate export protein |
| 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 | 4,304,229 | G→T | R59R (CGA→AGA) | ytcA ← | putative lipoprotein YtcA |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1287146–1287147 | 1287457 | 311–312 | 64 [63] | [63] 69 | [rttR]–tyrV | [rttR],[tpr],tyrV |
| * | * | ÷ | NC_000913 | 3102973 | 3104054 | 1082 | 64 [61] | [61] 64 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423752–3424234 | 3424546–3424238 | 5–795 | 66 [63] | [63] 65 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 46 (0.210) | 327 (1.700) | 109/244 | 0.0 | 88.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 43 (0.220) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 46 (0.210) | 167 (0.870) | 76/244 | 0.4 | 80.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 43 (0.220) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 339 (1.600) | 116/268 | 0.0 | 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 = | 359 (1.650) | 418 (1.930) | 126/274 | 0.0 | 69.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 6 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 235 (1.080) | 101/276 | 0.2 | 95.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 11 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||