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 | freq | annotation | gene | description |
| RA | 78,007 | G→T | 6.5% | R129R (CGG→CGT) | setA → | sugar exporter SetA |
| RA | 95,680 | T→C | 7.5% | V344A (GTC→GCC) | murF → | D‑alanyl‑D‑alanine‑adding enzyme |
| RA | 237,368 | T→A | 5.8% | L12I (TTA→ATA) | yafT → | lipoprotein YafT |
| RA | 238,497 | G→T | 21.1% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 24.6% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 25.5% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 298,557 | A→C | 33.3% | L57R (CTC→CGC) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 300,612 | T→A | 8.5% | Y108F (TAT→TTT) | paoC ← | aldehyde dehydrogenase: molybdenum cofactor‑binding subunit |
| RA | 454,877 | A→T | 32.0% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,885 | C→G | 28.4% | intergenic (+96/‑248) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,924 | G→T | 35.3% | intergenic (+135/‑209) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 563,122 | G→A | 5.8% | D263N (GAT→AAT) | sfmH → | putative fimbrial adhesin protein SfmH |
| RA | 630,246 | T→C | 5.4% | I118T (ATC→ACC) | cstA → | carbon starvation protein A |
| RA | 820,414 | C→G | 22.4% | V177V (GTC→GTG) | ybhL → | Bax1‑I family protein YbhL |
| RA | 860,560 | C→G | 14.9% | A683P (GCC→CCC) | ybiW ← | putative pyruvate formate lyase |
| RA | 997,452 | C→A | 6.4% | E21* (GAA→TAA) | ssuE ← | NADPH‑dependent FMN reductase |
| RA | 1,157,763 | G→A | 100% | intergenic (+189/‑106) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,281,986 | G→T | 8.2% | R708L (CGC→CTC) | narG → | nitrate reductase A subunit alpha |
| JC JC | 1,293,015 | IS1 (+) +8 bp | 100% | intergenic (‑93/‑505) | hns ← / → tdk | DNA‑binding transcriptional dual regulator H‑NS/thymidine/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,431,365 | A→T | 6.0% | T773S (ACC→TCC) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,434,972 | A→T | 20.2% | pseudogene (37/51 nt) | ttcC ← | putative tRNA 2‑thiocytidine (s(2)C32) synthase |
| RA | 1,708,758 | G→C | 19.2% | E614Q (GAA→CAA) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,723,914 | A→G | 8.7% | V598V (GTA→GTG) | ydhK → | putative transporter YdhK |
| RA | 1,742,319 | C→T | 6.7% | P303S (CCC→TCC) | cfa → | cyclopropane fatty acyl phospholipid synthase |
| RA | 1,974,504 | A→T | 6.9% | L274* (TTA→TAA) | cheA ← | chemotaxis protein CheA |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,023,051 | C→T | 6.9% | A53A (GCC→GCT) | fliR → | flagellar biosynthesis protein FliR |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,245 | G→T | 56.1% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,181,212 | T→A | 6.4% | R39R (CGT→CGA) | yegV → | putative sugar kinase YegV |
| RA | 2,274,988 | A→T | 6.7% | E270D (GAA→GAT) | yejB → | putative oligopeptide ABC transporter membrane subunit YejB |
| RA | 2,362,161 | G→A | 6.3% | L17L (CTC→CTT) | yfaX ← | putative DNA‑binding transcriptional regulator YfaX |
| RA | 2,433,826 | A→G | 5.6% | L34S (TTA→TCA) | accD ← | acetyl‑CoA carboxyltransferase subunit beta |
| RA | 2,533,567 | G→C | 100% | intergenic (+187/‑197) | cysK → / → ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr |
| RA | 2,572,532 | G→T | 6.1% | T325K (ACA→AAA) | eutD ← | phosphate acetyltransferase EutD |
| RA | 2,575,651 | G→A | 8.2% | A52V (GCG→GTG) | eutS ← | putative structural protein, ethanolamine utilization microcompartment |
| RA | 2,584,693 | A→C | 11.6% | V278G (GTT→GGT) | aegA ← | putative oxidoreductase Fe‑S subunit AegA |
| RA | 2,632,143 | T→C | 7.7% | A131A (GCA→GCG) | guaA ← | GMP synthetase |
| RA | 2,978,292 | T→A | 7.3% | Q203L (CAG→CTG) | lysA ← | diaminopimelate decarboxylase |
| RA | 3,143,835 | C→A | 5.4% | V110V (GTG→GTT) | hybB ← | hydrogenase 2 membrane subunit |
| RA | 3,239,137 | C→T | 6.5% | T186T (ACC→ACT) | alx → | putative membrane‑bound redox modulator Alx |
| RA | 3,418,500 | T→A | 24.5% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,503,013 | A→G | 5.0% | K225R (AAA→AGA) | frlC → | fructoselysine 3‑epimerase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,561,665 | A→T | 5.2% | R53R (CGT→CGA) | glpE ← | thiosulfate sulfurtransferase GlpE |
| RA | 3,732,097 | G→T | 6.5% | G323* (GGA→TGA) | xylF → | xylose ABC transporter periplasmic binding protein |
| JC | 3,815,859 | Δ82 bp | 93.2% | [rph] | [rph] | |
| RA | 3,861,661 | T→C | 8.0% | E109E (GAA→GAG) | glvG ← | putative inactive phospho‑glucosidase |
| RA | 3,980,812 | A→C | 5.5% | intergenic (+116/‑75) | rffM → / → yifK | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase/putative transporter YifK |
| RA | 4,021,562 | T→G | 30.1% | L446R (CTG→CGG) | ubiB → | ubiquinone biosynthesis protein UbiB |
| JC JC | 4,118,284 | IS5 (–) +4 bp | 49.1% | intergenic (‑194/‑228) | glpF ← / → zapB | glycerol facilitator/cell division factor ZapB |
| RA | 4,132,213 | C→T | 5.8% | D793D (GAC→GAT) | metL → | fused aspartate kinase/homoserine dehydrogenase 2 |
| RA | 4,187,869 | G→A | 5.4% | L840L (CTG→CTA) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,215,525 | G→A | 7.8% | P16P (CCG→CCA) | aceB → | malate synthase A |
| RA | 4,250,535 | T→A | 5.3% | intergenic (+61/‑168) | malM → / → yjbI | maltose regulon periplasmic protein/pentapeptide repeats‑containing protein YjbI |
| RA | 4,253,953 | A→G | 7.8% | intergenic (+65/+90) | ubiA → / ← plsB | 4‑hydroxybenzoate octaprenyltransferase/glycerol‑3‑phosphate 1‑O‑acyltransferase |
| RA | 4,276,207 | C→T | 5.4% | A246V (GCG→GTG) | pdeC → | c‑di‑GMP phosphodiesterase PdeC |
| RA | 4,295,544 | C→G | 5.2% | A355G (GCT→GGT) | gltP → | glutamate/aspartate : H(+) symporter GltP |
| RA | 4,296,060 | C→T | 31.4% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,356,740 | T→A | 6.1% | K626N (AAA→AAT) | cadA ← | lysine decarboxylase 1 |
| RA | 4,424,210 | G→A | 5.6% | A171T (GCC→ACC) | ulaF → | L‑ribulose‑5‑phosphate 4‑epimerase UlaF |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423762–3424235 | 3424539–3424237 | 3–778 | 16 [15] | [15] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3486119 | 3486772 | 654 | 17 [8] | [14] 16 | crp | crp |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 26 (0.480) | 21 (0.450) | 16/204 | NT | 44.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 31 (0.670) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 28 (0.520) | 20 (0.430) | 15/204 | NT | 42.0% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 31 (0.670) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||