mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 51,382 | C→A | A75A (GCG→GCT) | apaG ← | DUF525 domain‑containing protein ApaG |
| RA | 250,252 | C→A | pseudogene (181/756 nt) | lafU → | flagellar system protein, promoterless fragment |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 334,247 | C→A | E63* (GAG→TAG) | yahB ← | putative LysR‑type DNA‑binding transcriptional regulator YahB |
| RA | 395,771 | G→T | L173M (CTG→ATG) | ampH ← | peptidoglycan DD‑carboxypeptidase/peptidoglycan DD‑endopeptidase |
| RA | 420,869 | G→T | D427Y (GAT→TAT) | brnQ → | branched chain amino acid transporter BrnQ |
| RA | 607,923 | G→T | E30* (GAG→TAG) | hokE → | protein HokE |
| RA | 660,058 | C→A | Q53H (CAG→CAT) | lipA ← | lipoyl synthase |
| RA | 745,017 | G→T | A259S (GCC→TCC) | pxpC → | 5‑oxoprolinase component C |
| RA | 780,725 | C→A | intergenic (+96/‑40) | lysT → / → valT | tRNA‑Lys/tRNA‑Val |
| RA | 854,717 | G→T | W357C (TGG→TGT) | ybiR → | putative transporter YbiR |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 979,782 | G→T | A1153S (GCG→TCG) | mukB → | chromosome partitioning protein MukB |
| RA | 1,056,307 | C→A | A16E (GCA→GAA) | torT → | periplasmic trimethylamine‑N‑oxide binding protein |
| RA | 1,059,971 | A→G | N239S (AAC→AGC) | torA → | trimethylamine N‑oxide reductase 1 |
| RA | 1,176,153 | G→T | G243C (GGC→TGC) | lolC → | lipoprotein release complex ‑ inner membrane subunit |
| 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 | 1,196,277 | C→T | N385N (AAC→AAT) | icd → | isocitrate dehydrogenase |
| RA | 1,196,280 | G→C | A386A (GCG→GCC) | icd → | isocitrate dehydrogenase |
| RA | 1,196,283 | A→G | K387K (AAA→AAG) | icd → | isocitrate dehydrogenase |
| RA | 1,295,628 | G→T | L832M (CTG→ATG) | adhE ← | aldehyde‑alcohol dehydrogenase |
| RA | 1,377,266 | G→T | V145V (GTG→GTT) | ycjS → | putative oxidoreductase YcjS |
| RA | 1,406,515 | G→T | W179C (TGG→TGT) | smrA → | DNA endonuclease SmrA |
| RA | 1,464,889 | C→A | A140E (GCG→GAG) | paaY → | 2‑hydroxycyclohepta‑1,4,6‑triene‑1‑carboxyl‑CoA thioesterase |
| 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 |
| RA | 1,956,590 | C→A | A140S (GCC→TCC) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,154,523 | G→T | A170S (GCG→TCG) | mdtA → | multidrug efflux pump membrane fusion protein MdtA |
| RA | 2,157,275 | C→A | S671R (AGC→AGA) | mdtB → | multidrug efflux pump RND permease subunit MdtB |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,314,956 | C→A | P490Q (CCG→CAG) | rcsD → | RcsD phosphotransferase |
| RA | 2,339,321 | G→T | L34M (CTG→ATG) | gyrA ← | DNA gyrase subunit A |
| RA | 2,413,248 | C→A | intergenic (‑116/‑222) | yfbV ← / → ackA | UPF0208 membrane protein YfbV/acetate kinase |
| RA | 2,445,132 | G→T | P143P (CCC→CCA) | yfcA ← | conserved inner membrane protein YfcA |
| RA | 2,476,474 | A→G | E55E (GAA→GAG) | torI → | CPS‑53 (KpLE1) prophage; prophage CPS‑53 recombination directionality factor and response regulator inhibitor |
| RA | 2,495,726 | C→A | L28I (CTT→ATT) | lpxP → | palmitoleoyl acyltransferase |
| RA | 2,734,900 | A→C | D45E (GAT→GAG) | pgeF ← | polyphenol oxidase YfiH |
| RA | 2,770,515 | G→T | S24I (AGC→ATC) | ypjK → | CP4‑57 prophage; uncharacterized protein YpjK |
| RA | 2,903,703 | C→A | intergenic (+329/+1044) | ygcE → / ← queE | putative sugar kinase YgcE/putative 7‑carboxy‑7‑deazaguanine synthase QueE |
| RA | 3,001,682 | G→T | W446C (TGG→TGT) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,047,636 | C→A | R469L (CGC→CTC) | gcvP ← | glycine decarboxylase |
| RA | 3,050,444 | G→T | A75E (GCG→GAG) | gcvT ← | aminomethyltransferase |
| RA | 3,150,826 | C→A | A140S (GCG→TCG) | exbD ← | Ton complex subunit ExbD |
| RA | 3,338,167 | G→T | L99M (CTG→ATG) | mlaD ← | intermembrane phospholipid transport system, substrate binding protein MlaD |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,484,227 | C→A | P4T (CCG→ACG) | yheU → | UPF0270 family protein YheU |
| RA | 3,520,577 | G→T | Q43K (CAG→AAG) | hofQ ← | DNA utilization protein HofQ |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,689,494 | G→T | D256E (GAC→GAA) | bcsZ ← | endo‑1,4‑D‑glucanase |
| RA | 3,780,649 | C→A | H275N (CAC→AAC) | lldD → | L‑lactate dehydrogenase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,896,216 | C→A | V132F (GTT→TTT) | adeP ← | adenine:H(+) symporter |
| RA | 3,961,560 | C→A | P295Q (CCG→CAG) | rep → | ATP‑dependent DNA helicase Rep |
| RA | 4,096,922 | T→A | Y176F (TAT→TTT) | rhaB ← | rhamnulokinase |
| RA | 4,107,457 | T→A | intergenic (+86/‑95) | fieF → / → pfkA | Zn(2(+))/Fe(2(+))/Cd(2(+)) exporter/6‑phosphofructokinase I |
| RA | 4,147,763 | C→A | A185A (GCG→GCT) | 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 | 4,370,152 | G→T | V87V (GTC→GTA) | yjeH ← | L‑methionine/branched chain amino acid exporter |
| RA | 4,464,988 | G→T | P398Q (CCG→CAG) | treB ← | trehalose‑specific PTS enzyme IIBC component |
| RA | 4,567,901 | C→A | D207Y (GAT→TAT) | mdtM ← | multidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter |
| RA | 4,634,129 | C→A | T111T (ACC→ACA) | ytjC → | putative phosphatase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196287 | 1211428 | 15142 | 28 [23] | [22] 28 | [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 | 3102952 | 3104069 | 1118 | 27 [26] | [26] 27 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424525–3424238 | 5–756 | 27 [20] | [22] 27 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 136 (1.340) | 71/278 | 0.1 | NA | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 270549 = | NA (NA) | noncoding (9/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | = 258676 | NA (NA) | 125 (1.230) | 58/278 | 0.3 | NA | pseudogene (1/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl |
| ? | NC_000913 | = 270556 | NA (NA) | noncoding (16/1221 nt) | IS30 | repeat region | |||||
| * | ? | NC_000913 | 374921 = | NA (NA) | 65 (0.930) | 13/192 | 2.8 | NA | intergenic (+40/‑538) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377531 = | NA (NA) | intergenic (+220/+4) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 374922 = | NA (NA) | 96 (1.000) | 23/262 | 2.3 | NA | intergenic (+41/‑537) | mhpE/mhpT | 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter |
| ? | NC_000913 | 377329 = | NA (NA) | intergenic (+18/+206) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | = 374963 | NA (NA) | 38 (0.540) | 18/192 | 1.9 | NA | noncoding (33/34 nt) | other | REP31a |
| ? | NC_000913 | = 377487 | NA (NA) | intergenic (+176/+48) | yaiL/frmB | DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB | |||||
| * | ? | NC_000913 | 375304 = | NA (NA) | 39 (0.460) | 20/234 | 2.3 | NA | noncoding (17/36 nt) | other | REP31h |
| ? | NC_000913 | 377351 = | NA (NA) | noncoding (16/37 nt) | other | REP32a | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 142 (1.440) | 77/270 | 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 = | 158 (1.560) | 153 (1.520) | 76/276 | 0.0 | 65.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 112 (1.100) | 63/278 | 0.2 | 95.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||