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 | 1,842 | T→C | G502G (GGT→GGC) | thrA → | fused aspartate kinase/homoserine dehydrogenase 1 |
| RA | 45,885 | C→T | P27S (CCG→TCG) | yaaU → | putative transporter YaaU |
| RA | 231,834 | A→G | N238S (AAC→AGC) | yafD → | endonuclease/exonuclease/phosphatase domain‑containing protein YafD |
| RA | 234,047 | A→G | S246P (TCA→CCA) | gloB ← | hydroxyacylglutathione hydrolase GloB |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 293,042 | A→G | intergenic (‑94/+178) | yagK ← / ← yagL | CP4‑6 prophage; uncharacterized protein YagK/CP4‑6 prophage; resolvase‑like catalytic domain‑containing protein YagL |
| RA | 326,693 | A→G | G185G (GGT→GGC) | betA ← | choline dehydrogenase |
| RA | 447,883 | A→G | V55A (GTG→GCG) | cyoD ← | cytochrome bo3 ubiquinol oxidase subunit 4 |
| RA | 522,495 | T→C | L694L (TTG→CTG) | ybbP → | putative ABC transporter membrane subunit YbbP |
| RA | 527,577 | T→C | intergenic (+36/‑4) | rhsD → / → ybbC | protein RhsD/PF15631 family protein YbbC |
| RA | 531,868 | A→G | R118R (CGT→CGC) | allS ← | DNA‑binding transcriptional activator AllS |
| RA | 554,180 | T→C | A86A (GCA→GCG) | ppiB ← | peptidyl‑prolyl cis‑trans isomerase B |
| MC JC | 634,250 | Δ13 bp | coding (665‑677/1161 nt) | ybdL → | methionine‑oxo‑acid transaminase, PLP‑dependent |
| RA | 635,915 | A→G | Y219H (TAT→CAT) | ybdN ← | putative PAPS reductase/DUF3440 domain‑containing protein YbdN |
| RA | 695,690 | A→G | N197S (AAC→AGC) | ubiF → | 2‑octaprenyl‑3‑methyl‑6‑methoxy‑1,4‑benzoquinol hydroxylase |
| RA | 758,773 | T→C | I23T (ATA→ACA) | sucA → | subunit of E1(0) component of 2‑oxoglutarate dehydrogenase |
| RA | 790,924 | C→T | A36T (GCG→ACG) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 885,013 | A→G | V73A (GTT→GCT) | ybjH ← | uncharacterized protein YbjH |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 902,828 | A→G | L54P (CTG→CCG) | artI ← | putative ABC transporter periplasmic binding protein ArtI |
| RA | 909,556 | A→G | G498G (GGT→GGC) | poxB ← | pyruvate oxidase |
| RA | 926,229 | C→T | R72H (CGC→CAC) | infA ← | translation initiation factor IF‑1 |
| RA | 932,340 | (A)8→7 | intergenic (‑290/‑255) | trxB ← / → lrp | thioredoxin reductase/DNA‑binding transcriptional dual regulator Lrp |
| RA | 992,903 | T→C | V761A (GTG→GCG) | pepN → | aminopeptidase N |
| RA | 999,709 | (C)6→7 | coding (494/2601 nt) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,010,898 | C→T | A312V (GCC→GTC) | uup → | ATP‑binding protein with possible role in replication |
| RA | 1,051,733 | A→G | Y17C (TAC→TGC) | ymcF → | protein YmcF |
| RA | 1,061,940 | C→T | P48S (CCG→TCG) | torD → | trimethylamine‑N‑oxide reductase‑specific chaperone |
| RA | 1,143,140 | T→C | T410A (ACT→GCT) | rne ← | ribonuclease E |
| RA | 1,195,769 | A→G | Y216C (TAC→TGC) | icd → | isocitrate dehydrogenase |
| RA | 1,207,942 | (G)7→8 | coding (442/630 nt) | ycfK → | e14 prophage; protein StfP |
| RA | 1,220,971 | G→A | pseudogene (1371/2648 nt) | ycgH → | putative transporter component, N‑terminal fragment |
| RA | 1,336,072 | A→G | Y81C (TAC→TGC) | acnA → | aconitate hydratase 1 |
| RA | 1,344,674 | T→C | intergenic (‑65/+83) | yciZ ← / ← pdeR | UPF0509 protein YciZ/cyclic di‑GMP phosphodiesterase PdeR |
| RA | 1,385,070 | T→C | R318R (CGT→CGC) | ycjX → | DUF463 domain‑containing protein YcjX |
| RA | 1,418,524 | A→G | intergenic (‑295/‑147) | kilR ← / → sieB | Rac prophage; inhibitor of FtsZ, killing protein/Rac prophage; phage superinfection exclusion protein |
| RA | 1,421,856 | C→T | S246S (AGC→AGT) | ydaU → | Rac prophage; DUF1376 domain‑containing protein YdaU |
| RA | 1,497,929 | A→G | K358K (AAA→AAG) | opgD → | glucan biosynthesis protein D |
| RA | 1,541,351 | C→T | E414K (GAA→AAA) | narZ ← | nitrate reductase Z subunit alpha |
| RA | 1,594,132 | (C)8→9 | pseudogene (3955/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,611,174 | A→G | A227A (GCT→GCC) | dgcF ← | putative diguanylate cyclase DgcF |
| RA | 1,631,586 | T→C | T234A (ACT→GCT) | ydfJ ← | putative transporter YdfJ |
| RA | 1,634,642 | C→T | G82S (GGC→AGC) | tfaQ ← | Qin prophage; putative tail fiber assembly protein TfaQ |
| RA | 1,656,477 | T→C | G98G (GGT→GGC) | speG → | spermidine N‑acetyltransferase |
| RA | 1,685,542 | (C)6→5 | coding (1047/1404 nt) | fumC ← | fumarase C |
| RA | 1,695,409 | T→C | Q221Q (CAA→CAG) | uidA ← | beta‑glucuronidase |
| RA | 1,717,792 | T→C | K72K (AAA→AAG) | pdxH ← | pyridoxal 5‑phosphate synthase |
| RA | 1,735,220 | T→C | R262R (CGT→CGC) | mepH → | peptidoglycan DD‑endopeptidase MepH |
| RA | 1,746,557 | T→C | noncoding (42/77 nt) | valW → | tRNA‑Val |
| RA | 1,774,533 | G→A | G249S (GGT→AGT) | ydiB → | shikimate dehydrogenase/quinate dehydrogenase |
| RA | 1,784,424 | T→C | V483A (GTT→GCT) | fadK → | short chain acyl‑CoA synthetase |
| RA | 1,850,562 | T→C | F576L (TTC→CTC) | sppA → | protease IV, a signal peptide peptidase |
| RA | 1,873,384 | A→G | K448K (AAA→AAG) | dgcJ → | putative diguanylate cyclase DgcJ |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,913,124 | T→C | T565A (ACG→GCG) | prc ← | tail‑specific protease |
| RA | 1,955,000 | A→G | L670L (TTA→CTA) | torZ ← | trimethylamine N‑oxide reductase 2 |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 1,996,183 | T→C | N217S (AAC→AGC) | sdiA ← | DNA‑binding transcriptional dual regulator SdiA |
| RA | 2,022,646 | A→G | T11A (ACT→GCT) | fliQ → | flagellar biosynthesis protein FliQ |
| RA | 2,059,421 | (A)7→6 | coding (426/1644 nt) | yeeO ← | FMN/FAD exporter |
| RA | 2,078,657 | A→G | Y28C (TAC→TGC) | yoeF → | CP4‑44 prophage; putative uncharacterized protein YoeF |
| RA | 2,165,573 | (C)6→5 | intergenic (+52/‑95) | yegP → / → yegQ | DUF1508 domain‑containing protein YegP/putative peptidase YegQ |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,196,901 | T→C | V143A (GTT→GCT) | yehF → | putative protein YehF |
| RA | 2,264,292 | T→C | F144L (TTC→CTC) | setB → | sugar exporter SetB |
| RA | 2,304,635 | 2 bp→GG | intergenic (+242/+472) | eco → / ← mqo | serine protease inhibitor ecotin/malate:quinone oxidoreductase |
| RA | 2,305,722 | C→T | A345T (GCC→ACC) | mqo ← | malate:quinone oxidoreductase |
| RA | 2,339,161 | T→C | D87G (GAC→GGC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,360,919 | A→G | F166L (TTC→CTC) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,364,181 | T→C | Y32C (TAC→TGC) | yfaZ ← | putative porin YfaZ |
| RA | 2,408,980 | T→C | V40A (GTC→GCC) | yfbR → | dCMP phosphohydrolase |
| RA | 2,411,793 | A→G | G99G (GGT→GGC) | hxpA ← | hexitol phosphatase A |
| RA | 2,446,579 | T→C | T299A (ACC→GCC) | aroC ← | chorismate synthase |
| RA | 2,462,889 | (C)9→10 | intergenic (+243/‑123) | fadL → / → yfdF | long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF |
| RA | 2,527,823 | T→C | V293A (GTG→GCG) | yfeH → | putative solute:Na(+) symporter |
| RA | 2,530,484 | T→C | K250K (AAA→AAG) | zipA ← | cell division protein ZipA |
| RA | 2,572,295 | A→G | C52C (TGT→TGC) | eutM ← | putative structural protein, ethanolamine utilization microcompartment |
| RA | 2,622,952 | (T)7→6 | intergenic (+80/‑92) | purN → / → ppk | phosphoribosylglycinamide formyltransferase 1/polyphosphate kinase |
| RA | 2,695,848 | G→A | L16L (CTG→CTA) | mltF → | membrane‑bound lytic murein transglycosylase F |
| RA | 2,745,602 | T→C | Y106C (TAC→TGC) | rimM ← | ribosome maturation factor RimM |
| RA | 2,787,472 | T→C | pseudogene (1076/2253 nt) | ygaQ → | putative uncharacterized protein YgaQ |
| RA | 2,794,536 | G→A | G95D (GGC→GAC) | gabP → | 4‑aminobutyrate:H(+) symporter |
| RA | 2,811,134 | A→G | H122R (CAC→CGC) | mprA → | DNA‑binding transcriptional repressor MprA |
| RA | 2,818,018 | T→C | intergenic (‑158/+41) | argQ ← / ← argZ | tRNA‑Arg/tRNA‑Arg |
| RA | 2,854,287 | T→C | intergenic (+23/‑51) | hypE → / → fhlA | hydrogenase maturation protein, carbamoyl dehydratase/DNA‑binding transcriptional activator FhlA |
| MC JC | 2,857,096 | Δ2,538 bp | coding (4‑2541/2562 nt) | mutS → | DNA mismatch repair protein MutS |
| RA | 2,861,530 | Δ1 bp | coding (101/909 nt) | ygbJ → | putative L‑threonate dehydrogenase |
| RA | 2,902,161 | T→C | L89S (TTA→TCA) | ygcE → | putative sugar kinase YgcE |
| RA | 2,917,723 | T→C | G889G (GGT→GGC) | barA → | sensory histidine kinase BarA |
| RA | 2,949,993 | (T)5→6 | coding (752/1332 nt) | argA → | N‑acetylglutamate synthase |
| RA | 2,996,070 | T→C | pseudogene (291/399 nt) | ygeO ← | putative uncharacterized protein YgeO |
| RA | 3,001,304 | (G)7→9 | coding (960/2259 nt) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,016,485 | T→C | G142G (GGT→GGC) | ygfK → | putative oxidoreductase, Fe‑S subunit |
| RA | 3,034,537 | A→G | V213A (GTG→GCG) | lysS ← | lysine‑‑tRNA ligase, constitutive |
| RA | 3,042,574 | T→C | Y192C (TAC→TGC) | yqfA ← | hemolysin‑III family protein |
| RA | 3,068,157 | T→C | intergenic (‑77/+16) | yggE ← / ← argO | uncharacterized protein YggE/L‑arginine exporter |
| RA | 3,077,201 | (T)6→5 | coding (256/1278 nt) | yggP ← | putative zinc‑binding dehydrogenase YggP |
| RA | 3,102,762 | T→C | T31A (ACC→GCC) | trmI ← | tRNA m(7)G46 methyltransferase |
| RA | 3,156,525 | (T)5→4 | intergenic (+7/‑98) | yqhD → / → dkgA | NADPH‑dependent aldehyde reductase YqhD/methylglyoxal reductase DkgA |
| RA | 3,192,017 | T→C | intergenic (‑78/‑191) | glgS ← / → yqiJ | surface composition regulator/putative inner membrane protein |
| RA | 3,211,245 | A→G | T47A (ACC→GCC) | dnaG → | DNA primase |
| RA | 3,211,964 | T→C | G286G (GGT→GGC) | dnaG → | DNA primase |
| RA | 3,236,703 | T→C | V55A (GTT→GCT) | ygjQ → | DUF218 domain‑containing protein YgjQ |
| RA | 3,247,179 | G→A | W176* (TGG→TGA) | exuR → | DNA‑binding transcriptional repressor ExuR |
| RA | 3,264,994 | T→C | V8V (GTA→GTG) | tdcC ← | threonine/serine:H(+) symporter |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,388,726 | A→G | V134A (GTT→GCT) | aaeA ← | aromatic carboxylic acid efflux pump membrane fusion protein |
| RA | 3,484,293 | A→G | T26A (ACC→GCC) | yheU → | UPF0270 family protein YheU |
| RA | 3,535,847 | G→A | P8S (CCA→TCA) | envZ ← | sensory histidine kinase EnvZ |
| RA | 3,537,063 | A→G | K84K (AAA→AAG) | greB → | transcription elongation factor GreB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,587,525 | Δ1 bp | coding (589/744 nt) | ugpQ ← | glycerophosphodiester phosphodiesterase |
| RA | 3,679,687 | T→C | I90T (ATT→ACT) | kdgK → | 2‑dehydro‑3‑deoxygluconokinase |
| RA | 3,681,333 | T→C | E203G (GAA→GGA) | yhjJ ← | peptidase M16 family protein |
| RA | 3,740,106 | A→G | A134A (GCA→GCG) | avtA → | valine‑‑pyruvate aminotransferase |
| RA | 3,803,685 | Δ1 bp | coding (453/1080 nt) | waaB ← | UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,827,726 | T→C | T314A (ACC→GCC) | gltS ← | glutamate:sodium symporter |
| RA | 3,854,055 | T→C | V45A (GTG→GCG) | emrD → | multidrug efflux pump EmrD |
| RA | 3,860,630 | (C)5→4 | coding (348/894 nt) | yidL → | putative DNA‑binding transcriptional regulator YidL |
| RA | 3,932,741 | A→G | T476A (ACC→GCC) | kup → | K(+):H(+) symporter Kup |
| RA | 3,934,952 | C→T | A392V (GCA→GTA) | rbsA → | ribose ABC transporter ATP binding subunit |
| RA | 3,956,019 | T→C | V230A (GTT→GCT) | ilvA → | threonine deaminase |
| RA | 3,956,685 | A→G | N452S (AAC→AGC) | ilvA → | threonine deaminase |
| RA | 3,969,424 | A→G | S132G (AGC→GGC) | wzzE → | enterobacterial common antigen polysaccharide co‑polymerase |
| RA | 3,973,620 | A→G | I5V (ATC→GTC) | rffH → | dTDP‑glucose pyrophosphorylase 2 |
| RA | 4,165,198 | A→G | K520K (AAA→AAG) | btuB → | cobalamin/cobinamide outer membrane transporter |
| RA | 4,234,854 | A→G | N366S (AAC→AGC) | pgi → | glucose‑6‑phosphate isomerase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,305,347 | A→G | G417G (GGT→GGC) | yjcS ← | alkyl sulfatase |
| RA | 4,336,521 | A→G | F171L (TTC→CTC) | adiC ← | arginine:agmatine antiporter |
| RA | 4,351,440 | (T)6→7 | coding (223/1632 nt) | dcuS ← | sensory histidine kinase DcuS |
| RA | 4,421,823 | T→C | V39A (GTA→GCA) | ulaC → | L‑ascorbate specific PTS enzyme IIA component |
| RA | 4,445,549 | A→G | T480A (ACC→GCC) | tamB → | translocation and assembly module subunit TamB |
| RA | 4,451,008 | A→G | intergenic (+90/‑50) | ytfQ → / → ytfR | galactofuranose ABC transporter periplasmic binding protein/galactofuranose ABC transporter putative ATP binding subunit |
| RA | 4,458,059 | A→G | D34G (GAC→GGC) | pmbA → | metalloprotease PmbA |
| RA | 4,474,275 | (C)6→8 | coding (152/594 nt) | bdcR → | putative transcriptional regulator BdcR |
| RA | 4,512,341 | A→G | V25A (GTG→GCG) | fecD ← | ferric citrate ABC transporter membrane subunit FecD |
| RA | 4,523,881 | C→T | G72S (GGC→AGC) | yjhG ← | KpLE2 phage‑like element; D‑xylonate dehydratase |
| RA | 4,573,154 | G→A | T247T (ACG→ACA) | yjiT → | putative uncharacterized protein YjiT |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423768–3424234 | 3424534–3424239 | 6–767 | 15 [14] | [14] 15 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 374922 = | NA (NA) | 19 (0.340) | 12/260 | 3.0 | 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 | 1207790 = | 59 (1.000) | 18 (0.350) | 15/244 | 2.2 | 27.3% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 44 (0.850) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 59 (1.000) | 13 (0.250) | 13/244 | 2.6 | 21.3% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 44 (0.850) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 53 (0.930) | 38/268 | 0.4 | 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 = | 77 (1.310) | 97 (1.660) | 56/274 | 0.1 | 71.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 70 (1.190) | 47/276 | 0.2 | 98.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||