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 | 34,841 | C→A | R177S (AGG→AGT) | caiE ← | putative transferase CaiE |
| RA | 89,103 | G→T | intergenic (+71/‑531) | cra → / → mraZ | DNA‑binding transcriptional dual regulator Cra/DNA‑binding transcriptional repressor MraZ |
| RA | 194,803 | G→T | intergenic (+86/‑100) | dxr → / → ispU | 1‑deoxy‑D‑xylulose 5‑phosphate reductoisomerase/undecaprenyl diphosphate synthase |
| RA | 225,735 | G→A | intergenic (+160/‑24) | alaV → / → rrlH | tRNA‑Ala/23S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 403,595 | C→A | A105A (GCC→GCA) | psiF → | PsiF family protein |
| RA | 442,633 | C→A | A362E (GCG→GAG) | thiI → | tRNA uridine 4‑sulfurtransferase |
| RA | 508,513 | C→A | A99D (GCT→GAT) | ybaQ → | putative DNA‑binding transcriptional regulator YbaQ |
| RA | 578,922 | C→A | intergenic (‑29/+262) | borD ← / ← ybcV | DLP12 prophage; prophage lipoprotein BorD/DLP12 prophage; protein YbcV |
| RA | 658,955 | G→T | E3D (GAG→GAT) | tatE → | twin arginine protein translocation system ‑ TatE protein |
| RA | 663,900 | C→A | A22S (GCC→TCC) | dacA ← | D‑alanyl‑D‑alanine carboxypeptidase DacA |
| RA | 720,535 | C→A | intergenic (‑75/‑48) | speF ← / → ybfK | ornithine decarboxylase, degradative/uncharacterized protein YbfK |
| RA | 843,669 | C→A | G604G (GGG→GGT) | ybiO ← | moderate conductance mechanosensitive channel |
| RA | 853,995 | G→T | E117* (GAG→TAG) | ybiR → | putative transporter YbiR |
| RA | 885,091 | G→T | A47E (GCG→GAG) | ybjH ← | uncharacterized protein YbjH |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 903,112 | G→T | A208D (GCC→GAC) | artP ← | L‑arginine ABC transporter ATP binding subunit |
| RA | 987,380 | G→T | intergenic (‑398/+205) | ompF ← / ← asnS | outer membrane porin F/asparagine‑‑tRNA ligase |
| RA | 1,013,784 | G→T | V176L (GTG→TTG) | pqiB → | intermembrane transport protein PqiB |
| RA | 1,087,862 | C→A | A666S (GCC→TCC) | pgaB ← | poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine N‑deacetylase and beta‑1,6 glycoside hydrolase |
| 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 | 1,214,191 | G→T | intergenic (‑132/+73) | bluR ← / ← bluF | DNA‑binding transcriptional repressor BluR/blue light‑responsive regulator of BluR |
| RA | 1,215,288 | C→A | R63L (CGG→CTG) | bluF ← | blue light‑responsive regulator of BluR |
| RA | 1,266,847 | C→A | L252I (CTC→ATC) | prmC → | protein‑(glutamine‑N(5)) methyltransferase |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,419,861 | G→T | R127R (CGC→CGA) | racR ← | Rac prophage; DNA‑binding transcriptional repressor RacR |
| RA | 1,467,681 | G→T | pseudogene (2290/2518 nt) | ydbA → | putative outer membrane protein, N‑terminal fragment |
| RA | 1,589,990 | G→T | Y4* (TAC→TAA) | ydeT ← | fimbrial usher domain‑containing protein YdeT |
| RA | 1,614,296 | C→A | W136C (TGG→TGT) | sad ← | NAD(+)‑dependent succinate semialdehyde dehydrogenase |
| RA | 1,635,676 | G→C | H58D (CAT→GAT) | ydfN ← | Qin prophage; putative side tail fiber assembly protein |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,713,746 | G→C | P326P (CCG→CCC) | dtpA → | dipeptide/tripeptide:H(+) symporter DtpA |
| 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 | 2,005,898 | G→T | E62D (GAG→GAT) | fliT → | flagellar biosynthesis protein FliT |
| RA | 2,059,940 | C→A | intergenic (+14/+24) | asnU → / ← cbl | tRNA‑Asn/DNA‑binding transcriptional activator Cbl |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,222,739 | G→A | L185L (CTG→CTA) | dld → | D‑lactate dehydrogenase |
| RA | 2,225,068 | C→A | W188C (TGG→TGT) | yohC ← | putative inner membrane protein |
| RA | 2,277,088 | C→A | G263G (GGC→GGA) | yejF → | putative oligopeptide ABC transporter ATP binding subunit |
| RA | 2,397,622 | C→A | A848A (GCG→GCT) | nuoG ← | NADH:quinone oxidoreductase subunit G |
| RA | 2,411,514 | C→A | E192D (GAG→GAT) | hxpA ← | hexitol phosphatase A |
| RA | 2,456,361 | C→A | S151I (AGC→ATC) | sixA ← | phosphohistidine phosphatase |
| RA | 2,498,573 | C→A | intergenic (‑278/‑98) | alaC ← / → ypdA | glutamate‑‑pyruvate aminotransferase AlaC/sensory histidine kinase YpdA |
| RA | 2,554,087 | C→A | A288E (GCG→GAG) | hemF → | coproporphyrinogen III oxidase |
| RA | 2,652,663 | C→A | A57E (GCG→GAG) | sseA → | 3‑mercaptopyruvate sulfurtransferase |
| RA | 2,748,046 | G→T | G29C (GGC→TGC) | ypjD → | cytochrome c assembly family protein |
| RA | 2,898,778 | C→A | C214F (TGC→TTC) | ygcU ← | putative FAD‑containing dehydrogenase |
| RA | 2,961,386 | C→A | R348L (CGC→CTC) | recC ← | exodeoxyribonuclease V subunit RecC |
| RA | 3,107,849 | G→T | P436Q (CCG→CAG) | speC ← | ornithine decarboxylase, biosynthetic |
| RA | 3,173,948 | G→T | G483G (GGC→GGA) | parE ← | DNA topoisomerase IV subunit B |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| MC JC | 3,366,751 | Δ3,335 bp | IS5‑mediated | yhcE–[nanK] | yhcE, yhcF, yhcG, yhcH, [nanK] |
| RA | 3,387,360 | G→T | P277T (CCG→ACG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| JC JC | 3,582,685 | IS5 (–) +4 bp | coding (823‑826/1179 nt) | yhhZ → | putative endonuclease YhhZ |
| RA | 3,728,455 | C→A | G306V (GGC→GTC) | xylB ← | xylulokinase |
| RA | 3,744,201 | G→T | A153A (GCG→GCT) | yiaL → | DUF386 domain‑containing protein YiaL |
| RA | 3,746,165 | G→T | A24A (GCG→GCT) | yiaO → | 2,3‑diketo‑L‑gulonate:Na(+) symporter ‑ periplasmic binding protein |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,892,208 | G→T | S198S (TCG→TCT) | mdtL → | efflux pump MdtL |
| RA | 3,945,594 | G→T | noncoding (1891/2904 nt) | rrlC → | 23S ribosomal RNA |
| RA | 3,996,486 | G→T | G67V (GGG→GTG) | xerC → | site‑specific tyrosine recombinase |
| RA | 4,082,827 | G→T | A999E (GCG→GAG) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,203,242 | G→T | Q439H (CAG→CAT) | zraS → | sensory histidine kinase ZraS |
| RA | 4,246,357 | G→T | S21S (TCC→TCA) | malE ← | maltose ABC transporter periplasmic binding protein |
| 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 | 4,311,556 | C→A | E163* (GAG→TAG) | alsB ← | D‑allose ABC transporter periplasmic binding protein |
| RA | 4,312,710 | C→A | L94F (TTG→TTT) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,386,140 | C→A | P1077P (CCG→CCT) | mscM ← | miniconductance mechanosensitive channel MscM |
| RA | 4,438,249 | G→T | R181R (CGG→CGT) | ytfI → | protein YtfI |
| RA | 4,580,991 | G→T | P158T (CCA→ACA) | hsdS ← | type I restriction enzyme EcoKI specificity protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 1196273 | 1211428 | 15156 | 18 [17] | [17] 21 | [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 | 2521130 | 2521289–2521254 | 125–160 | 76 [0] | [17] 18 | valY–[lysV] | valY,[lysV] |
| * | * | ÷ | NC_000913 | 3102972 | 3104060 | 1089 | 18 [17] | [17] 19 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424533–3424238 | 5–764 | 18 [14] | [17] 18 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 781577 = | 68 (0.910) | 75 (1.010) +G |
27/276 | 1.3 | 69.0% | noncoding (1/76 nt) | lysQ | tRNA‑Lys |
| ? | NC_000913 | = 2521129 | 0 (0.000) | intergenic (+3/‑44) | valX/valY | tRNA‑Val/tRNA‑Val | |||||
| * | ? | NC_000913 | 3363001 = | 110 (1.470) | 122 (1.640) | 62/276 | 0.1 | 68.3% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 71 (0.950) | 45/278 | 0.3 | 97.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.030) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||