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 | 39,072 | Δ1 bp | 6.5% | coding (44/1218 nt) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 48,330 | G→C | 6.7% | V188L (GTG→CTG) | kefC → | K(+) : H(+) antiporter KefC |
| RA | 78,206 | G→A | 5.6% | A196T (GCG→ACG) | setA → | sugar exporter SetA |
| RA | 82,607 | C→T | 5.4% | R308H (CGC→CAC) | leuA ← | 2‑isopropylmalate synthase |
| RA | 151,734 | A→C | 15.9% | V166V (GTT→GTG) | yadL ← | putative fimbrial protein YadL |
| RA | 205,561 | G→A | 7.0% | G146S (GGT→AGT) | dnaE → | DNA polymerase III subunit alpha |
| RA | 238,497 | G→T | 23.1% | I80I (ATC→ATA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,503 | G→T | 26.9% | F78L (TTC→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,507 | G→T | 15.4% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,523 | G→T | 36.2% | L72I (CTT→ATT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,532 | C→A | 29.2% | V69L (GTA→TTA) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,535 | G→T | 38.9% | H68N (CAT→AAT) | ykfM ← | uncharacterized protein YkfM |
| RA | 238,841 | T→C | 5.8% | pseudogene (244/339 nt) | yafU ← | putative inner membrane protein |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 269,266 | A→T | 5.9% | intergenic (‑306/+23) | ykfA ← / ← perR | CP4‑6 prophage; putative GTP‑binding protein YkfA/putative transcriptional regulator PerR |
| RA | 298,557 | A→C | 31.2% | L57R (CTC→CGC) | paoD ← | molybdenum cofactor insertion chaperone for PaoABC |
| RA | 366,097 | A→C | 24.6% | V70G (GTG→GGG) | lacZ ← | beta‑galactosidase |
| RA | 454,873 | C→G | 46.9% | intergenic (+84/‑260) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,877 | A→T | 40.6% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,883 | C→G | 26.8% | intergenic (+94/‑250) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,885 | C→T | 30.7% | intergenic (+96/‑248) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,924 | G→T | 26.2% | intergenic (+135/‑209) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,926 | G→T | 59.2% | intergenic (+137/‑207) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 497,585 | C→A | 29.7% | F137L (TTC→TTA) | adk → | adenylate kinase |
| RA | 497,588 | T→A | 39.0% | N138K (AAT→AAA) | adk → | adenylate kinase |
| RA | 587,191 | T→A | 6.9% | E264V (GAA→GTA) | ybcH ← | DUF4434 domain‑containing protein YbcH |
| RA | 621,321 | G→A | 56.5% | P290L (CCT→CTT) | fepD ← | ferric enterobactin ABC transporter membrane subunit FebD |
| RA | 621,523 | C→A | 23.5% | G223C (GGC→TGC) | fepD ← | ferric enterobactin ABC transporter membrane subunit FebD |
| RA | 693,037 | T→G | 18.0% | K114N (AAA→AAC) | ybeZ ← | PhoH‑like protein |
| MC JC | 710,218 | Δ411 bp | 100% | coding (19‑429/447 nt) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 729,372 | A→C | 35.1% | intergenic (+32/‑211) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 729,383 | T→G | 44.3% | intergenic (+43/‑200) | ybfA → / → rhsC | DUF2517 domain‑containing protein YbfA/rhs element protein RhsC |
| RA | 772,755 | C→T | 12.1% | P433L (CCG→CTG) | cydA → | cytochrome bd‑I ubiquinol oxidase subunit I |
| RA | 780,882 | C→A | 29.0% | noncoding (40/76 nt) | lysW → | tRNA‑Lys |
| RA | 872,765 | T→C | 6.8% | G292G (GGT→GGC) | gsiD → | glutathione ABC transporter membrane subunit GsiD |
| RA | 922,586 | T→C | 7.4% | E2G (GAA→GGA) | cspD ← | DNA replication inhibitor |
| RA | 940,005 | A→T | 6.0% | N193I (AAC→ATC) | serS → | serine‑‑tRNA ligase |
| RA | 974,032 | G→T | 13.8% | D166Y (GAT→TAT) | cmoM → | tRNA cmo(5)U34 methyltransferase |
| RA | 1,142,628 | C→T | 8.7% | A580A (GCG→GCA) | rne ← | ribonuclease E |
| RA | 1,272,720 | G→A | 7.7% | V72I (GTT→ATT) | chaC → | glutathione‑specific gamma‑glutamylcyclotransferase |
| RA | 1,660,843 | T→A | 5.2% | V96V (GTT→GTA) | ynfF → | putative selenate reductase YnfF |
| RA | 1,672,479 | G→A | 6.7% | A174T (GCA→ACA) | ydgD → | putative serine protease YdgD |
| RA | 1,672,492 | C→T | 6.8% | A178V (GCA→GTA) | ydgD → | putative serine protease YdgD |
| RA | 1,708,758 | G→C | 18.8% | E614Q (GAA→CAA) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,708,901 | A→C | 15.4% | R661R (CGA→CGC) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,708,930 | C→A | 13.6% | P671Q (CCG→CAG) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,743,919 | G→A | 6.0% | A155T (GCA→ACA) | mdtK → | multidrug efflux pump MdtK |
| RA | 1,751,933 | A→G | 7.3% | V633A (GTA→GCA) | ydhV ← | putative oxidoreductase |
| RA | 1,852,707 | T→C | 5.6% | M425V (ATG→GTG) | ydjE ← | putative transporter YdjE |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,096,685 | A→G | 7.4% | Q24Q (CAA→CAG) | hisI → | putative bifunctional phosphoribosyl‑AMP cyclohydrolase/phosphoribosyl‑ATP pyrophosphatase |
| RA | 2,107,049 | G→T | 43.2% | L60I (CTA→ATA) | wbbH ← | putative O‑antigen polymerase |
| RA | 2,132,986 | G→A | 7.7% | P138S (CCG→TCG) | wcaA ← | putative colanic acid biosynthesis glycosyl transferase |
| 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 | 51.8% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,314,181 | G→T | 20.7% | D232Y (GAT→TAT) | rcsD → | RcsD phosphotransferase |
| RA | 2,413,920 | A→G | 15.5% | T151A (ACC→GCC) | ackA → | acetate kinase |
| RA | 2,414,402 | Δ1 bp | 31.4% | coding (933/1203 nt) | ackA → | acetate kinase |
| RA | 2,470,427 | C→A | 55.4% | Q433K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,431 | G→T | 50.4% | R434I (AGA→ATA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,436 | C→A | 45.2% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,459 | C→A | 29.5% | H443Q (CAC→CAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,463 | G→T | 26.1% | intergenic (+1/+614) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,499,833 | C→A | 37.9% | P388Q (CCG→CAG) | ypdA → | sensory histidine kinase YpdA |
| RA | 2,970,638 | G→A | 8.1% | L73L (CTG→CTA) | ygdQ → | UPF0053 inner membrane protein YgdQ |
| RA | 3,006,291 | G→A | 54.5% | K10K (AAG→AAA) | ygeW → | putative carbamoyltransferase YgeW |
| RA | 3,139,154 | C→A | 6.8% | T143K (ACG→AAG) | yghU → | disulfide reductase/organic hydroperoxide reductase |
| RA | 3,194,910 | Δ1 bp | 5.9% | intergenic (‑45/+187) | sibD ← / ← sibE | small RNA SibD/small RNA SibE |
| RA | 3,194,911 | Δ1 bp | 5.9% | intergenic (‑46/+186) | sibD ← / ← sibE | small RNA SibD/small RNA SibE |
| RA | 3,194,912 | Δ1 bp | 5.9% | intergenic (‑47/+185) | sibD ← / ← sibE | small RNA SibD/small RNA SibE |
| RA | 3,194,913 | Δ1 bp | 5.7% | intergenic (‑48/+184) | sibD ← / ← sibE | small RNA SibD/small RNA SibE |
| RA | 3,194,914 | Δ1 bp | 5.8% | intergenic (‑49/+183) | sibD ← / ← sibE | small RNA SibD/small RNA SibE |
| RA | 3,225,912 | G→A | 6.4% | R64H (CGC→CAC) | ebgC → | DUF386 domain‑containing evolved beta‑D‑galactosidase subunit beta |
| RA | 3,277,377 | C→A | 10.6% | A14D (GCT→GAT) | yhaV → | ribosome‑dependent mRNA interferase toxin YhaV |
| RA | 3,364,921 | A→T | 7.0% | G705G (GGA→GGT) | yhcD → | putative fimbrial usher protein YhcD |
| RA | 3,408,000 | C→G | 28.7% | L132V (CTG→GTG) | panF → | pantothenate:Na(+) symporter |
| RA | 3,418,500 | T→A | 24.8% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,454,069 | G→T | 26.0% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,465,025 | G→A | 5.0% | M368I (ATG→ATA) | gspL → | Type II secretion system protein GspL |
| RA | 3,543,808 | T→A | 7.6% | N214K (AAT→AAA) | rpnA → | recombination‑promoting nuclease RpnA |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,580,935 | G→T | 5.3% | noncoding (82/90 nt) | ryhB ← | small regulatory RNA RyhB |
| RA | 3,782,858 | A→C | 18.6% | G268G (GGT→GGG) | gpsA ← | glycerol‑3‑phosphate dehydrogenase |
| RA | 4,121,703 | C→A | 6.5% | K15N (AAG→AAT) | hslU ← | ATPase component of the HslVU protease |
| RA | 4,147,699 | G→T | 20.3% | Q207K (CAA→AAA) | yijO ← | putative DNA‑binding transcriptional regulator YijO |
| RA | 4,162,530 | A→G | 6.9% | A247A (GCT→GCC) | trmA ← | tRNA m(5)U54 methyltransferase |
| RA | 4,182,929 | A→T | 100% | E562V (GAA→GTA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,296,060 | C→T | 24.2% | 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 | 4,359,969 | C→A | 13.6% | M21I (ATG→ATT) | cadB ← | lysine:cadaverine antiporter |
| RA | 4,363,802 | C→A | 5.3% | R414L (CGT→CTT) | dsbD ← | protein disulfide oxidoreductase ‑ DsbDreduced |
| RA | 4,400,313 | A→C | 100% | D9A (GAT→GCT) | hfq → | RNA‑binding protein Hfq |
| RA | 4,587,327 | G→C | 17.8% | A127P (GCC→CCC) | mrr → | methylated adenine and cytosine restriction protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423782–3424234 | 3424543–3424238 | 5–762 | 19 [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 | 1207790 = | 29 (0.500) | 44 (0.880) | 31/204 | NT | 67.7% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 17 (0.340) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 29 (0.500) | 36 (0.720) | 24/204 | NT | 63.1% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 17 (0.340) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 1 (0.020) | 57 (1.020) | 34/228 | NT | 99.2% | 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 | = 2290113 | NA (NA) | 7 (0.120) | 7/236 | NT | 14.3% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 2615844 | 42 (0.720) | coding (38/1062 nt) | yfgO | putative transporter YfgO | |||||
| * | ? | NC_000913 | = 2585835 | 56 (0.970) | 3 (0.050) | 3/234 | NT | 5.3% | coding (105/1701 nt) | narQ | sensory histidine kinase NarQ |
| ? | NC_000913 | = 3838178 | 52 (0.900) | intergenic (+41/‑70) | setC/yicL | putative arabinose exporter/putative inner membrane protein | |||||
| * | ? | NC_000913 | 4498180 = | NA (NA) | 11 (0.190) | 11/236 | NT | NA | intergenic (+240/‑92) | intB/insC‑6 | KpLE2 phage‑like element; putative integrase/KpLE2 phage‑like element; IS2 insertion element repressor InsA |
| ? | NC_000913 | = 4499511 | NA (NA) | noncoding (1331/1331 nt) | IS2 | repeat region | |||||
| * | ? | NC_000913 | 4542682 = | 32 (0.550) | 6 (0.110) | 6/218 | NT | 13.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 46 (0.860) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 35 (0.600) | 10 (0.190) | 9/218 | NT | 20.3% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 46 (0.860) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||