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 | freq | annotation | gene | description |
| RA | 18,124 | C→G | 33.5% | G212G (GGC→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 18,126 | T→G | 29.5% | V213G (GTG→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 18,129 | T→G | 22.8% | V214G (GTG→GGG) | nhaA → | Na(+):H(+) antiporter NhaA |
| RA | 61,664 | A→G | 5.6% | F534S (TTC→TCC) | rapA ← | RNA polymerase‑binding ATPase and RNAP recycling factor |
| RA | 192,455 | G→A | 8.0% | D201N (GAC→AAC) | pyrH → | UMP kinase |
| RA | 207,086 | G→A | 7.7% | R654H (CGT→CAT) | dnaE → | DNA polymerase III subunit alpha |
| RA | 238,497 | G→T | 24.3% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 16.6% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 23.3% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 26.2% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 30.3% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 36.5% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 454,877 | A→T | 50.7% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 1,127,934 | T→A | 6.1% | F32L (TTT→TTA) | murJ → | putative lipid II flippase MurJ |
| RA | 1,157,593 | C→T | 100% | intergenic (+19/‑276) | ycfH → / → ptsG | putative metal‑dependent hydrolase YcfH/glucose‑specific PTS enzyme IIBC component |
| RA | 1,203,391 | A→C | 7.3% | N42H (AAC→CAC) | ymfL → | e14 prophage; uncharacterized protein YmfL |
| RA | 1,272,171 | C→T | 8.2% | P18L (CCG→CTG) | chaB → | putative cation transport regulator ChaB |
| RA | 1,309,233 | C→A | 5.3% | S346I (AGT→ATT) | kch ← | K(+) channel Kch |
| RA | 1,332,261 | C→A | 13.7% | P405Q (CCA→CAA) | topA → | DNA topoisomerase 1 |
| RA | 1,537,646 | A→T | 9.5% | L403Q (CTG→CAG) | narY ← | nitrate reductase Z subunit beta |
| RA | 1,592,961 | T→G | 24.8% | pseudogene (5126/5422 nt) | yneO ← | AIDA‑I family autotransporter YneO |
| RA | 1,602,320 | A→G | 9.1% | E277E (GAA→GAG) | lsrA → | Autoinducer‑2 ABC transporter ATP binding subunit |
| RA | 1,679,141 | A→C | 27.4% | T239P (ACC→CCC) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,779,850 | G→A | 11.7% | P78P (CCG→CCA) | ydiQ → | putative electron transfer flavoprotein subunit YdiQ |
| RA | 1,812,427 | C→T | 5.3% | D236N (GAC→AAC) | ydjO ← | protein YdjO |
| RA | 1,820,111 | C→T | 9.5% | L368L (CTG→CTA) | chbC ← | N,N'‑diacetylchitobiose‑specific PTS enzyme IIC component |
| RA | 1,958,736 | T→C | 6.8% | A177A (GCA→GCG) | cutC ← | protein CutC |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,061,667 | Δ1 bp | 8.0% | coding (267/918 nt) | nac ← | DNA‑binding transcriptional dual regulator Nac |
| RA | 2,121,696 | C→T | 7.7% | P428P (CCG→CCA) | cpsG ← | phosphomannomutase |
| RA | 2,139,598 | T→G | 47.2% | intergenic (+113/+161) | yegH → / ← asmA | inner membrane protein YegH/putative assembly protein AsmA |
| RA | 2,160,742 | C→T | 6.3% | P786L (CCG→CTG) | mdtC → | multidrug efflux pump RND permease subunit MdtC |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (917‑918/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,177,234 | C→A | 47.3% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 56.6% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,311,981 | C→T | 8.1% | A257T (GCT→ACT) | ompC ← | outer membrane porin C |
| RA | 2,470,427 | C→A | 43.2% | Q433K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 39.4% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,533,459 | T→A | 10.0% | intergenic (+79/‑305) | cysK → / → ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr |
| RA | 2,533,482 | A→T | 19.7% | intergenic (+102/‑282) | cysK → / → ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr |
| RA | 2,533,495 | C→T | 17.6% | intergenic (+115/‑269) | cysK → / → ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr |
| RA | 2,533,567 | G→C | 6.6% | intergenic (+187/‑197) | cysK → / → ptsH | O‑acetylserine sulfhydrylase A/phosphocarrier protein HPr |
| RA | 2,743,035 | A→T | 7.7% | H218L (CAC→CTC) | dgcN → | diguanylate cyclase DgcN |
| RA | 2,977,323 | C→T | 6.7% | A242V (GCC→GTC) | galR → | DNA‑binding transcriptional dual regulator GalR |
| RA | 3,140,231 | A→C | 21.9% | W30G (TGG→GGG) | hybF ← | hydrogenase maturation protein HybF |
| RA | 3,276,362 | A→C | 26.0% | T361P (ACC→CCC) | garD → | galactarate dehydratase |
| RA | 3,375,097 | G→A | 7.0% | G77R (GGG→AGG) | dcuD → | putative transporter DcuD |
| RA | 3,407,983 | T→G | 34.4% | L126R (CTG→CGG) | panF → | pantothenate:Na(+) symporter |
| RA | 3,418,500 | T→A | 27.0% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,453,757 | A→T | 8.1% | L57L (CTT→CTA) | gspB ← | putative general secretion pathway protein B |
| RA | 3,454,069 | G→T | 35.7% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,734,546 | A→G | 9.8% | E276G (GAA→GGA) | xylH → | xylose ABC transporter membrane subunit |
| RA | 3,761,839 | G→A | 8.7% | G39G (GGC→GGT) | yibF ← | glutathione transferase‑like protein YibF |
| RA | 3,815,823 | C→T | 64.5% | intergenic (‑55/+40) | pyrE ← / ← rph | orotate phosphoribosyltransferase/truncated RNase PH |
| JC | 3,815,859 | Δ82 bp | 9.2% | [rph] | [rph] | |
| RA | 3,889,713 | C→T | 6.3% | L328L (CTC→CTT) | tnaA → | tryptophanase |
| RA | 3,970,424 | A→G | 5.8% | T98A (ACG→GCG) | wecB → | UDP‑N‑acetylglucosamine 2‑epimerase |
| RA | 4,088,438 | A→T | 10.3% | V473D (GTC→GAC) | frvR ← | putative transcriptional regulator FrvR |
| RA | 4,185,501 | C→T | 100% | P51L (CCA→CTA) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,241,608 | A→G | 11.8% | L216P (CTG→CCG) | xylE ← | D‑xylose:H(+) symporter |
| RA | 4,246,419 | T→A | 9.1% | M1M (ATG→TTG) † | malE ← | maltose ABC transporter periplasmic binding protein |
| RA | 4,265,672 | T→A | 8.5% | F453L (TTT→TTA) | dnaB → | replicative DNA helicase |
| RA | 4,283,228 | T→G | 43.4% | intergenic (‑153/+25) | yjcF ← / ← actP | pentapeptide repeat‑containing protein YjcF/acetate/glycolate:cation symporter |
| RA | 4,296,060 | C→T | 22.6% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,312,924 | T→C | 5.3% | K23R (AAG→AGG) | alsR ← | DNA‑binding transcriptional repressor AlsR |
| RA | 4,591,897 | A→G | 8.3% | I81V (ATT→GTT) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423750–3424234 | 3424546–3424239 | 6–797 | 13 [12] | [12] 13 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 3486111 | 3486759 | 649 | 16 [12] | [11] 16 | crp | crp |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 16 (0.330) | 31 (0.750) | 26/202 | NT | 64.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 20 (0.480) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.330) | 28 (0.680) | 23/202 | NT | 62.4% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 20 (0.480) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 52 (1.120) | 29/226 | NT | 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 | = 4542690 | 45 (0.940) | 10 (0.230) | 9/216 | NT | 18.1% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 49 (1.110) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||