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 | 149,470 | G→T | G44G (GGC→GGA) | panB ← | 3‑methyl‑2‑oxobutanoate hydroxymethyltransferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 309,451 | C→A | P192P (CCG→CCT) | ecpB ← | putative fimbrial chaperone EcpB |
| RA | 435,206 | C→A | Q24K (CAG→AAG) | nusB → | transcription antitermination protein NusB |
| RA | 643,960 | C→A | R3I (AGA→ATA) | rnk ← | nucleoside diphosphate kinase regulator |
| RA | 877,023 | G→T | P338Q (CCG→CAG) | rimO ← | ribosomal protein S12 methylthiotransferase RimO |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| JC JC | 1,092,683 | IS5 (–) +4 bp | intergenic (‑394/‑190) | pgaA ← / → dgcT | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine outer membrane porin/putative diguanylate cyclase DgcT |
| RA | 1,660,686 | G→T | R44L (CGG→CTG) | ynfF → | putative selenate reductase YnfF |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,715,011 | C→A | intergenic (+29/+15) | gstA → / ← pdxY | glutathione S‑transferase GstA/pyridoxal kinase 2 |
| 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 | 2,039,191 | C→A | T79N (ACT→AAT) | yedX → | hydroxyisourate hydrolase/transthyretin‑related protein |
| RA | 2,068,083 | G→T | intergenic (‑762/‑552) | insH‑6 ← / → yoeA | CP4‑44 prophage; IS5 transposase and trans‑activator/CP4‑44 prophage; TonB‑dependent receptor plug domain‑containing protein YoeA |
| RA | 2,078,265 | C→A | intergenic (+131/‑310) | yeeW → / → yoeF | CP4‑44 prophage; putative uncharacterized protein YeeW/CP4‑44 prophage; putative uncharacterized protein YoeF |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,560,093 | G→T | intergenic (+27/‑164) | intZ → / → yffL | CPZ‑55 prophage; putative phage integrase IntZ/CPZ‑55 prophage; uncharacterized protein YffL |
| RA | 2,561,159 | C→A | intergenic (+261/‑209) | yffL → / → yffM | CPZ‑55 prophage; uncharacterized protein YffL/CPZ‑55 prophage; uncharacterized protein YffM |
| RA | 2,610,205 | G→T | A14A (GCG→GCT) | hyfH → | hydrogenase 4 component H |
| RA | 3,270,858 | G→T | P305T (CCG→ACG) | garK ← | glycerate 2‑kinase 1 |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,416,802 | G→T | L590F (TTG→TTT) | acrF → | multidrug efflux pump RND permease AcrF |
| RA | 3,459,294 | A→G | E319G (GAA→GGA) | gspE → | Type II secretion system protein GspE |
| 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 | 3,834,980 | G→T | A317D (GCC→GAC) | yicJ ← | putative xyloside transporter YicJ |
| RA | 3,963,226 | G→T | A335D (GCT→GAT) | gpp ← | guanosine‑5'‑triphosphate,3'‑diphosphate phosphatase |
| RA | 4,135,618 | T→G | L595R (CTG→CGG) | katG → | hydroperoxidase I |
| RA | 4,147,953 | C→A | G122V (GGT→GTT) | yijO ← | putative DNA‑binding transcriptional regulator YijO |
| 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 | 4,529,836 | G→T | T136T (ACC→ACA) | sgcC ← | putative PTS enzyme IIC component SgcC |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102965 | 3104047 | 1083 | 3 [2] | [2] 3 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423264 | 3423353 | 90 | 3 [2] | [2] 3 | yhdZ/rrfF | putative ABC transporter ATP‑binding subunit YhdZ/5S ribosomal RNA |
| * | * | ÷ | NC_000913 | 3423791–3424233 | 3424525–3424238 | 6–735 | 4 [2] | [2] 8 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3802382 | 3802455 | 74 | 3 [2] | [1] 4 | waaO | UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase |
| * | * | ÷ | NC_000913 | 3802700 | 3802788 | 89 | 4 [2] | [2] 3 | waaO | UDP‑D‑glucose:(glucosyl)LPS alpha‑1,3‑glucosyltransferase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 37 (1.520) | 9 (0.420) | 8/244 | 1.1 | 24.8% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 22 (1.030) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 40 (1.700) | 31/268 | 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 = | 23 (0.950) | 30 (1.240) | 21/274 | 0.2 | 71.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 26 (1.070) | 25/276 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||