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 | 211,834 | C→A | intergenic (+14/‑43) | ldcC → / → yaeR | lysine decarboxylase 2/VOC domain‑containing protein YaeR |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 772,568 | C→A | Q371K (CAG→AAG) | cydA → | cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 801,366 | C→A | A203D (GCT→GAT) | ybhH → | putative isomerase YbhH |
| RA | 812,765 | G→T | A166S (GCC→TCC) | bioD → | dethiobiotin synthetase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,069,376 | C→A | G155V (GGC→GTC) | rutG ← | pyrimidine:H(+) symporter |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,354,144 | G→T | G125G (GGC→GGA) | sapC ← | putrescine ABC exporter membrane protein SapC |
| RA | 1,430,448 | G→T | G467V (GGG→GTG) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,547,660 | G→T | S87I (AGC→ATC) | fdnG → | formate dehydrogenase N subunit alpha |
| 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 | 2,171,455 | Δ1 bp | pseudogene (273/299 nt) | gatR ← | DNA‑binding transcriptional repressor GatR, N‑terminal fragment |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,337,694 | T→C | D576G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,562,839 | G→T | A106S (GCC→TCC) | yffP → | CPZ‑55 prophage; uncharacterized protein YffP |
| RA | 2,817,985 | G→T | intergenic (‑125/+74) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,438,839 | C→A | A98S (GCC→TCC) | zntR ← | DNA‑binding transcriptional activator ZntR |
| RA | 3,479,225 | A→T | G461G (GGT→GGA) | kefB ← | K(+) : H(+) antiporter KefB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,580,017 | C→A | P263P (CCG→CCT) | yhhX ← | putative oxidoreductase YhhX |
| RA | 3,678,185 | G→T | L56M (CTG→ATG) | yhjG ← | AsmA family protein YhjG |
| RA | 3,772,095 | C→A | intergenic (‑351/‑186) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,949,114 | C→A | G286W (GGG→TGG) | yifB ← | putative magnesium chelatase YifB |
| RA | 4,037,062 | T→A | noncoding (1532/1542 nt) | rrsA → | 16S ribosomal RNA |
| RA | 4,085,935 | C→A | intergenic (‑113/‑81) | fdoG ← / → fdhD | formate dehydrogenase O subunit alpha/sulfurtransferase for molybdenum cofactor sulfuration |
| RA | 4,186,763 | C→A | L472M (CTG→ATG) | rpoC → | 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 | 4,577,317 | C→T | T214T (ACG→ACA) | mcrC ← | 5‑methylcytosine‑specific restriction enzyme subunit McrC |
| RA | 4,618,088 | Δ1 bp | coding (766/780 nt) | deoC → | deoxyribose‑phosphate aldolase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196288 | 1211431 | 15144 | 9 [7] | [7] 8 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913 | 3102976 | 3104050 | 1075 | 8 [7] | [7] 8 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423785–3424230 | 3424523–3424239 | 10–739 | 8 [6] | [5] 8 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 3363001 = | 65 (1.450) | 79 (1.780) | 48/274 | 0.0 | 70.4% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 39 (0.870) | 30/276 | 0.4 | 92.9% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.070) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 4542682 = | 27 (0.600) | 9 (0.220) | 9/258 | 2.3 | 23.9% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 32 (0.770) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||