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 | 8,153 | G→T | intergenic (‑194/‑85) | yaaJ ← / → talB | putative transporter YaaJ/transaldolase B |
| RA | 43,228 | C→A | P14H (CCT→CAT) | fixB → | putative electron transfer flavoprotein FixB |
| RA | 62,769 | C→A | G166C (GGT→TGT) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 83,082 | C→A | D150Y (GAT→TAT) | leuA ← | 2‑isopropylmalate synthase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 278,654 | C→A | R50L (CGC→CTC) | afuC ← | CP4‑6 prophage; ABC transporter ATP‑binding protein AfuC |
| RA | 386,288 | G→T | E28* (GAG→TAG) | tauB → | taurine ABC transporter ATP binding subunit |
| RA | 402,964 | G→T | P406P (CCG→CCT) | phoA → | alkaline phosphatase |
| RA | 432,891 | G→T | intergenic (‑40/‑111) | yajI ← / → nrdR | putative lipoprotein YajI/NrdR transcriptional repressor |
| JC JC | 570,815 | IS2 (+) +5 bp | intergenic (+387/‑74) | ybcK → / → ybcL | DLP12 prophage; putative recombinase/DLP12 prophage; periplasmic protein YbcL |
| RA | 621,679 | G→T | L171M (CTG→ATG) | fepD ← | ferric enterobactin ABC transporter membrane subunit FebD |
| RA | 705,290 | G→C | V449V (GTG→GTC) | nagE → | N‑acetylglucosamine specific PTS enzyme IIABC component |
| RA | 707,343 | G→T | V417V (GTG→GTT) | glnS → | glutamine‑‑tRNA ligase |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 921,954 | C→A | G536G (GGC→GGA) | macB → | ABC‑type tripartite efflux pump ATP binding/membrane subunit |
| RA | 934,611 | C→A | P463Q (CCG→CAG) | ftsK → | cell division DNA translocase FtsK |
| RA | 1,066,854 | G→T | intergenic (+28/+10) | agp → / ← yccJ | glucose‑1‑phosphatase/PF13993 family protein YccJ |
| RA | 1,182,113 | C→A | A239A (GCG→GCT) | potD ← | spermidine preferential ABC transporter periplasmic binding protein |
| RA | 1,194,811 | G→T | P47P (CCC→CCA) | rluE ← | 23S rRNA pseudouridine(2457) synthase |
| RA | 1,246,496 | C→A | R294L (CGA→CTA) | treA ← | periplasmic trehalase |
| RA | 1,401,784 | C→A | intergenic (‑11/+26) | abgT ← / ← abgB | p‑aminobenzoyl glutamate:H(+) symporter/p‑aminobenzoyl‑glutamate hydrolase subunit B |
| RA | 1,447,126 | C→A | G53V (GGG→GTG) | feaR ← | DNA‑binding transcriptional activator FeaR |
| RA | 1,479,451 | G→T | G105V (GGA→GTA) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,515,515 | G→T | G252W (GGG→TGG) | ydcV → | putative ABC transporter membrane subunit YdcV |
| RA | 1,622,595 | G→T | intergenic (+76/‑51) | ydeE → / → mgtS | dipeptide exporter/small protein MgtS |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,688,613 | G→A | W13* (TGG→TAG) | manA → | mannose‑6‑phosphate isomerase |
| 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 | 2,025,940 | G→T | E144* (GAG→TAG) | yedP → | putative mannosyl‑3‑phosphoglycerate phosphatase |
| RA | 2,074,079 | C→A | T847T (ACC→ACA) | flu → | CP4‑44 prophage; self recognizing antigen 43 (Ag43) autotransporter |
| RA | 2,086,616 | C→G | L149L (CTG→CTC) | plaP ← | putrescine:H(+) symporter PlaP |
| RA | 2,126,824 | C→A | E123* (GAG→TAG) | fcl ← | GDP‑L‑fucose synthase |
| RA | 2,142,538 | Δ1 bp | coding (411/642 nt) | udk ← | uridine/cytidine kinase |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,257,566 | C→A | E268* (GAA→TAA) | psuG ← | pseudouridine‑5'‑phosphate glycosidase |
| RA | 2,296,197 | C→A | G42C (GGC→TGC) | ccmC ← | heme trafficking system membrane protein CcmC |
| RA | 2,379,570 | G→A | A358A (GCC→GCT) | menF ← | isochorismate synthase MenF |
| RA | 2,417,712 | C→A | P211Q (CCG→CAG) | yfcC → | putative transporter YfcC |
| RA | 2,509,783 | G→T | A52S (GCC→TCC) | yfeO → | putative transport protein YfeO |
| RA | 2,511,689 | G→T | L340M (CTG→ATG) | mntH ← | Mn(2(+))/Fe(2(+)): H(+) symporter MntH |
| RA | 2,558,577 | C→A | G35C (GGC→TGC) | eutB ← | ethanolamine ammonia‑lyase subunit alpha |
| RA | 2,565,828 | C→A | A353S (GCC→TCC) | eutA ← | reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,580,479 | C→A | P282T (CCA→ACA) | tktB → | transketolase 2 |
| RA | 2,674,658 | G→T | L11I (CTA→ATA) | yphB ← | putative aldose 1‑epimerase YphB |
| RA | 2,718,761 | G→T | Q9H (CAG→CAT) | trxC → | reduced thioredoxin 2 |
| RA | 2,751,990 | G→T | A66S (GCC→TCC) | recN → | DNA repair protein RecN |
| RA | 2,777,436 | A→T | intergenic (+4/‑17) | yfjZ → / → ypjF | CP4‑57 prophage; putative antitoxin of the YpjF‑YfjZ toxin‑antitoxin system/CP4‑57 prophage; toxin of the YpjF‑YfjZ toxin‑antitoxin system |
| RA | 2,781,522 | C→A | G402V (GGG→GTG) | ypjA ← | adhesin‑like autotransporter YpjA |
| RA | 2,804,070 | G→T | R190L (CGC→CTC) | nrdF → | ribonucleoside‑diphosphate reductase 2 subunit beta |
| RA | 2,898,991 | G→T | S143Y (TCT→TAT) | ygcU ← | putative FAD‑containing dehydrogenase |
| RA | 2,901,007 | G→T | W139L (TGG→TTG) | yqcE → | putative transport protein YqcE |
| RA | 2,983,675 | G→T | V150V (GTC→GTA) | kduI ← | 5‑dehydro‑4‑deoxy‑D‑glucuronate isomerase |
| RA | 2,998,609 | G→A | H74Y (CAC→TAC) | ygeQ ← | protein YgeQ |
| RA | 3,071,129 | C→A | G39V (GGT→GTT) | fbaA ← | fructose‑bisphosphate aldolase class II |
| RA | 3,330,424 | G→T | intergenic (+28/+158) | dacB → / ← obgE | peptidoglycan DD‑endopeptidase DacB/GTPase ObgE |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,382,156 | C→A | intergenic (+46/‑44) | degQ → / → degS | periplasmic serine endoprotease/serine endoprotease |
| RA | 3,468,244 | T→C | D537G (GAT→GGT) | chiA ← | endochitinase |
| RA | 3,503,120 | C→A | R261S (CGC→AGC) | frlC → | fructoselysine 3‑epimerase |
| RA | 3,509,349 | G→T | T155T (ACC→ACA) | yhfW ← | putative mutase YhfW |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,767,647 | C→A | pseudogene (427/702 nt) | yibJ → | putative RHS domain‑containing protein YibJ |
| RA | 3,789,526 | C→A | G186* (GGA→TGA) | waaH ← | UDP‑glucuronate:LPS(HepIII) glycosyltransferase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,952,677 | C→A | A65D (GCC→GAC) | ilvE → | branched‑chain‑amino‑acid aminotransferase |
| RA | 3,978,030 | C→A | P169H (CCT→CAT) | rffT → | 4‑acetamido‑4,6‑dideoxy‑D‑galactose transferase |
| RA | 4,058,356 | C→A | intergenic (‑322/‑51) | glnA ← / → bipA | glutamine synthetase/ribosome‑dependent GTPase, ribosome assembly factor |
| RA | 4,080,046 | C→T | intergenic (+77/+253) | yiiF → / ← fdhE | protein YiiF/formate dehydrogenase formation protein |
| RA | 4,084,861 | C→A | G321V (GGC→GTC) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,088,713 | A→T | R381R (CGT→CGA) | frvR ← | putative transcriptional regulator FrvR |
| RA | 4,090,345 | Δ1 bp | coding (581/1071 nt) | frvX ← | peptidase M42 family protein |
| RA | 4,157,275 | C→A | T142T (ACC→ACA) | argH → | argininosuccinate lyase |
| 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 | 4,312,208 | C→A | D262Y (GAC→TAC) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,516,077 | G→T | P201T (CCC→ACC) | fecA ← | ferric citrate outer membrane transporter |
| RA | 4,571,303 | C→A | W91L (TGG→TTG) | yjiR ← | fused putative DNA‑binding transcriptional regulator/putative aminotransferase YjiR |
| RA | 4,604,645 | C→A | R162R (CGC→CGA) | bglJ → | DNA‑binding transcriptional regulator BglJ |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102949 | 3104069 | 1121 | 24 [22] | [22] 25 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423766–3424234 | 3424528–3424239 | 6–763 | 25 [23] | [23] 24 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 27 (0.290) | 107 (1.290) | 55/246 | 0.1 | 83.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 20 (0.240) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 27 (0.290) | 62 (0.750) | 38/246 | 0.7 | 73.9% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 20 (0.240) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 142 (1.560) | 70/270 | 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 = | 167 (1.790) | 156 (1.680) | 76/276 | 0.0 | 64.6% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 5 (0.050) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 85 (0.910) | 54/278 | 0.3 | 93.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 6 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||