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 | 9,558 | C→A | P85T (CCC→ACC) | mog → | molybdopterin adenylyltransferase |
| RA | 23,199 | C→T | A270V (GCC→GTC) | ileS → | isoleucine‑‑tRNA ligase |
| RA | 91,791 | C→A | R127S (CGC→AGC) | ftsI → | peptidoglycan DD‑transpeptidase FtsI |
| RA | 99,715 | G→T | A24A (GCG→GCT) | murG → | N‑acetylglucosaminyl transferase |
| RA | 123,007 | G→T | intergenic (+151/‑10) | pdhR → / → aceE | DNA‑binding transcriptional dual regulator PdhR/pyruvate dehydrogenase E1 component |
| RA | 173,699 | G→A | P395L (CCG→CTG) | hemL ← | glutamate‑1‑semialdehyde aminotransferase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 371,618 | G→T | W127L (TGG→TTG) | mhpC → | 2‑hydroxy‑6‑ketonona‑2,4‑dienedioate hydrolase |
| RA | 603,786 | G→T | P293H (CCT→CAT) | ybdG ← | miniconductance mechanosensitive channel YbdG |
| RA | 634,400 | C→A | P272Q (CCG→CAG) | ybdL → | methionine‑oxo‑acid transaminase, PLP‑dependent |
| RA | 636,335 | G→T | L79M (CTG→ATG) | ybdN ← | putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 668,620 | G→T | P32P (CCC→CCA) | rlmH ← | 23S rRNA m(3)psi1915 methyltransferase |
| RA | 731,731 | C→A | R717R (CGG→AGG) | rhsC → | rhs element protein RhsC |
| RA | 751,168 | G→T | P334P (CCC→CCA) | ybgQ ← | putative fimbrial usher protein YbgQ |
| RA | 867,888 | G→T | V123V (GTG→GTT) | gsiA → | glutathione ABC transporter ATP binding subunit GsiA |
| RA | 871,236 | G→T | E90D (GAG→GAT) | gsiC → | glutathione ABC transporter membrane subunit GsiC |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 922,231 | G→T | G629C (GGC→TGC) | macB → | ABC‑type tripartite efflux pump ATP binding/membrane subunit |
| RA | 938,930 | G→C | V313L (GTG→CTG) | rarA → | recombination factor |
| RA | 1,105,202 | C→A | P81Q (CCG→CAG) | csgC → | inhibitor of CsgA amyloid formation |
| 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 |
| RA | 1,429,994 | G→T | A316S (GCC→TCC) | stfR → | Rac prophage; putative membrane protein |
| RA | 1,533,572 | G→T | R94S (CGT→AGT) | yddH ← | flavin reductase‑like protein YddH |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,686,461 | G→T | S43* (TCA→TAA) | fumC ← | fumarase C |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,941,820 | G→C | A255G (GCT→GGT) | znuA ← | Zn(2(+)) ABC transporter periplasmic binding protein |
| RA | 1,943,179 | G→C | G173A (GGC→GCC) | znuC → | Zn(2(+)) ABC transporter ATP binding subunit |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,003,389 | G→T | S73Y (TCC→TAC) | fliC ← | flagellar filament structural protein |
| RA | 2,138,644 | G→T | R248L (CGG→CTG) | yegH → | inner membrane protein YegH |
| RA | 2,173,361 | +C | pseudogene (918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| JC | 2,173,362 | Δ3 bp | pseudogene (915‑917/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,176,687 | G→T | A173E (GCG→GAG) | gatY ← | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY |
| RA | 2,357,917 | C→A | pseudogene (102/186 nt) | ypaA → | protein YpaA |
| RA | 2,686,972 | G→A | V380M (GTG→ATG) | hmp → | nitric oxide dioxygenase |
| RA | 2,770,738 | G→T | A20S (GCC→TCC) | yfjS → | CP4‑57 prophage; inner membrane lipoprotein YfjS |
| RA | 2,905,112 | G→T | P103T (CCA→ACA) | queE ← | putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 2,972,063 | C→A | S156* (TCG→TAG) | tas → | putative NADP(H)‑dependent aldo‑keto reductase Tas |
| RA | 3,017,295 | 2 bp→CT | coding (1236‑1237/3099 nt) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,083,215 | C→A | G195C (GGC→TGC) | speB ← | agmatinase |
| RA | 3,160,189 | G→T | P320T (CCA→ACA) | ygiQ ← | radical SAM superfamily protein YgiQ |
| RA | 3,169,742 | G→A | intergenic (‑66/‑86) | ygiW ← / → qseB | BOF family protein YgiW/DNA‑binding transcriptional activator QseB |
| RA | 3,185,169 | C→A | intergenic (+39/‑245) | ubiK → / → ygiL | ubiquinone biosynthesis accessory factor UbiK/putative fimbrial protein YgiL |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,559,527 | G→T | T420T (ACG→ACT) | rtcR → | DNA‑binding transcriptional activator RtcR |
| 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 | 3,857,480 | G→C | P309A (CCG→GCG) | yidJ ← | putative sulfatase/phosphatase |
| RA | 3,870,554 | C→A | G393W (GGG→TGG) | dgoT ← | putative D‑galactonate transporter |
| RA | 4,054,314 | G→T | A322E (GCG→GAG) | glnG ← | DNA‑binding transcriptional dual regulator NtrC |
| RA | 4,059,732 | G→T | V442V (GTG→GTT) | bipA → | ribosome‑dependent GTPase, ribosome assembly factor |
| RA | 4,223,261 | G→T | A123E (GCG→GAG) | iclR ← | DNA‑binding transcriptional repressor IclR |
| RA | 4,228,109 | G→T | A127S (GCC→TCC) | yjbB → | putative inorganic phosphate export protein |
| RA | 4,231,855 | C→A | intergenic (‑224/+29) | yjbD ← / ← lysC | conserved protein YjbD/aspartate kinase III |
| 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 | 4,311,497 | G→T | F182L (TTC→TTA) | alsB ← | D‑allose ABC transporter periplasmic binding protein |
| RA | 4,500,378 | C→A | pseudogene (414/1199 nt) | yjgX ← | KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196277 | 1211437 | 15161 | 47 [43] | [39] 47 | [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 | 3102949 | 3104069 | 1121 | 46 [43] | [43] 44 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423764–3424234 | 3424538–3424238 | 5–775 | 44 [43] | [43] 47 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3619335–3621083 | 3622194–3621086 | 4–2860 | 47 [42] | [43] 44 | rhsB | rhs element protein RhsB |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 198 (1.370) | 88/270 | 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 | 3363001 = | 268 (1.800) | 215 (1.450) | 85/276 | 0.1 | 61.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 7 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 179 (1.200) | 91/278 | 0.1 | 95.2% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 9 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||