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 |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 614,751 | G→T | E199* (GAA→TAA) | entF → | apo‑serine activating enzyme |
| RA | 622,465 | C→A | L56I (CTT→ATT) | entS → | enterobactin exporter EntS |
| RA | 730,644 | A→G | R354R (CGA→CGG) | rhsC → | rhs element protein RhsC |
| RA | 766,899 | C→T | L306L (CTG→TTG) | mngA → | 2‑O‑alpha‑mannosyl‑D‑glycerate specific PTS enzyme II |
| RA | 885,020 | G→T | P71T (CCT→ACT) | ybjH ← | uncharacterized protein YbjH |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,020,937 | T→C | intergenic (‑18/‑201) | sulA ← / → sxy | cell division inhibitor SulA/transcriptional coactivator for CRP |
| 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 | 1,242,292 | Δ5 bp | coding (785‑789/915 nt) | ldcA ← | murein L,D‑carboxypeptidase |
| RA | 1,269,117 | C→G | intergenic (+98/+51) | kdsA → / ← ldrA | 3‑deoxy‑D‑manno‑octulosonate 8‑phosphate synthase/small toxic polypeptide LdrA |
| RA | 1,351,376 | G→T | intergenic (‑337/+31) | fabI ← / ← ycjD | enoyl‑[acyl‑carrier‑protein] reductase/DUF559 domain‑containing protein YcjD |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,703,301 | G→T | S336S (TCC→TCA) | ydgJ ← | putative oxidoreductase YdgJ |
| RA | 1,727,199 | C→T | L181F (CTC→TTC) | nemA → | N‑ethylmaleimide reductase |
| 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 | 2,053,832 | C→A | L64I (CTC→ATC) | shiA → | shikimate:H(+) symporter |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,630,356 | G→T | A11S (GCC→TCC) | yfgI → | nalidixic acid resistance protein YfgI |
| RA | 2,998,998 | G→T | noncoding (60/74 nt) | glyU ← | tRNA‑Gly |
| RA | 3,110,533 | G→A | intergenic (+92/+57) | pheV → / ← yghD | tRNA‑Phe/putative type II secretion system M‑type protein |
| RA | 3,309,282 | C→A | V629V (GTG→GTT) | pnp ← | polynucleotide phosphorylase |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,453,657 | C→A | E91* (GAA→TAA) | gspB ← | putative general secretion pathway protein B |
| JC JC | 3,455,388 | IS1 (+) +9 bp | coding (3‑11/1470 nt) | gspA ← | Type II secretion system protein GspA |
| JC JC | 3,465,602 | IS1 (–) +9 bp | coding (60‑68/678 nt) | gspO → | Type II secretion system prepilin peptidase |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,604,784 | G→T | R131L (CGC→CTC) | rsmD → | 16S rRNA m(2)G966 methyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,926,265 | T→C | D64G (GAC→GGC) | mioC ← | flavoprotein MioC |
| RA | 3,941,541 | G→T | intergenic (‑214/‑267) | yieP ← / → rrsC | putative transcriptional regulator YieP/16S ribosomal RNA |
| RA | 3,942,012 | A→G | noncoding (205/1542 nt) | rrsC → | 16S ribosomal RNA |
| RA | 4,149,878 | C→A | A130S (GCC→TCC) | eptC ← | phosphoethanolamine transferase EptC |
| RA | 4,189,902 | G→T | E39D (GAG→GAT) | yjaZ → | conserved protein YjaZ |
| 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 |
| JC JC | 4,573,173 | IS5 (–) +4 bp | coding (760‑763/1518 nt) | yjiT → | putative uncharacterized protein YjiT |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196277 | 1211433 | 15157 | 17 [13] | [10] 17 | [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 | 3103000 | 3104084 | 1085 | 17 [16] | [13] 17 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423768–3424234 | 3424525–3424242 | 9–758 | 17 [16] | [15] 19 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 608010 = | NA (NA) | 56 (0.840) | 40/274 | 0.5 | 94.9% | noncoding (4/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | = 1503204 | 3 (0.050) | noncoding (44/1748 nt) | IS609 | repeat region | |||||
| * | ? | NC_000913 | = 609351 | NA (NA) | 67 (1.030) | 43/268 | 0.3 | NA | noncoding (1345/1345 nt) | IS186 | repeat region |
| ? | NC_000913 | 1503198 = | NA (NA) | noncoding (38/1748 nt) | IS609 | repeat region | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 80 (1.230) | 56/268 | 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 | 2904195 = | 22 (0.330) | 29 (0.550) | 22/216 | 1.1 | 65.0% | intergenic (+821/+552) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| ? | NC_000913 | = 2904255 | 14 (0.270) | intergenic (+881/+492) | ygcE/queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE | |||||
| * | ? | NC_000913 | 3363001 = | 91 (1.360) | 113 (1.700) | 58/274 | 0.1 | 71.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 73 (1.090) | 46/276 | 0.3 | 96.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 3 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||