mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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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 | 96,456 | G→C | 21.6% | G152A (GGC→GCC) | mraY → | phospho‑N‑acetylmuramoyl‑pentapeptide‑ transferase |
| JC JC | 122,005 | IS5 (–) +4 bp | 12.3% | intergenic (‑454/‑84) | aroP ← / → pdhR | aromatic amino acid:H(+) symporter AroP/DNA‑binding transcriptional dual regulator PdhR |
| RA | 122,529 | A→G | 8.9% | E146E (GAA→GAG) | pdhR → | DNA‑binding transcriptional dual regulator PdhR |
| RA | 238,507 | G→T | 30.4% | S77* (TCA→TAA) | ykfM ← | uncharacterized protein YkfM |
| MC JC | 257,908 | Δ776 bp | 100% | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 282,510 | T→G | 29.3% | V78G (GTG→GGG) | yagE → | CP4‑6 prophage; putative 2‑keto‑3‑deoxygluconate aldolase |
| RA | 322,846 | A→G | 11.8% | H170R (CAC→CGC) | ykgF → | putative amino acid dehydrogenase with NAD(P)‑binding domain and ferridoxin‑like domain |
| RA | 454,873 | C→G | 49.9% | intergenic (+84/‑260) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,877 | A→T | 28.4% | intergenic (+88/‑256) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 454,896 | G→C | 28.4% | intergenic (+107/‑237) | bolA → / → tig | DNA‑binding transcriptional dual regulator BolA/trigger factor |
| RA | 550,996 | T→G | 8.7% | G186G (GGT→GGG) | ybcF → | putative carbamate kinase |
| RA | 578,399 | T→C | 10.0% | V98A (GTC→GCC) S25P (TCT→CCT) |
rzpD → rzoD → |
DLP12 prophage; putative prophage endopeptidase RzpD DLP12 prophage; putative prophage lysis lipoprotein RzoD |
| RA | 586,277 | T→A | 9.3% | K211I (AAA→ATA) | envY ← | DNA‑binding transcriptional activator EnvY |
| RA | 621,342 | G→A | 8.5% | P283L (CCC→CTC) | fepD ← | ferric enterobactin ABC transporter membrane subunit FebD |
| RA | 628,852 | C→A | 18.4% | A101E (GCG→GAG) | entA → | 2,3‑dihydro‑2,3‑dihydroxybenzoate dehydrogenase |
| MC JC | 710,218 | Δ411 bp | 100% | coding (19‑429/447 nt) | fur ← | DNA‑binding transcriptional dual regulator Fur |
| RA | 790,751 | G→A | 9.3% | H93H (CAC→CAT) | galT ← | galactose‑1‑phosphate uridylyltransferase |
| RA | 796,519 | G→T | 24.2% | A220S (GCC→TCC) | modB → | molybdate ABC transporter membrane subunit |
| RA | 798,922 | G→A | 10.2% | D113N (GAT→AAT) | pgl → | 6‑phosphogluconolactonase |
| RA | 1,031,023 | C→T | 7.7% | S132S (TCG→TCA) | yccA ← | modulator of FtsH protease |
| RA | 1,110,851 | A→T | 9.3% | Q506L (CAG→CTG) | opgG → | osmoregulated periplasmic glucans (OPGs) biosynthesis protein G |
| RA | 1,198,792 | A→G | 7.4% | D33G (GAC→GGC) | lit → | e14 prophage; cell death peptidase Lit |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | insH21 | insH21 | |
| RA | 1,408,102 | Δ1 bp | 7.0% | coding (53/984 nt) | zntB → | Zn(2(+)):H(+) symporter |
| RA | 1,408,103 | Δ1 bp | 7.0% | coding (54/984 nt) | zntB → | Zn(2(+)):H(+) symporter |
| RA | 1,439,405 | C→T | 10.2% | A460A (GCG→GCA) | ydbK ← | putative pyruvate‑flavodoxin oxidoreductase |
| RA | 1,480,865 | G→T | 8.3% | T576T (ACG→ACT) | ynbC → | hydrolase/methyltransferase domain‑containing protein YnbC |
| RA | 1,550,264 | G→A | 8.7% | R955H (CGT→CAT) | fdnG → | formate dehydrogenase N subunit alpha |
| RA | 1,584,043 | G→A | 6.7% | intergenic (‑84/+164) | safA ← / ← ydeP | two‑component system connector SafA/putative oxidoreductase YdeP |
| RA | 1,700,529 | G→A | 11.1% | G392D (GGT→GAT) | malX → | PTS enzyme IIBC component MalX |
| RA | 1,708,930 | C→A | 24.6% | P671Q (CCG→CAG) | rsxC → | SoxR [2Fe‑2S] reducing system protein RsxC |
| RA | 1,895,683 | G→A | 11.1% | L293L (CTG→CTA) | pabB → | aminodeoxychorismate synthase subunit 1 |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| 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 | 52.5% | intergenic (‑30/+278) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,177,245 | G→T | 44.7% | intergenic (‑41/+267) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2 subunit GatY/fructose‑bisphosphate aldolase class I |
| RA | 2,223,749 | G→A | 12.9% | G522D (GGC→GAC) | dld → | D‑lactate dehydrogenase |
| RA | 2,247,646 | G→A | 7.0% | A296V (GCG→GTG) | lysP ← | lysine:H(+) symporter |
| RA | 2,303,782 | C→A | 38.3% | intergenic (+12/‑123) | yojO → / → eco | uncharacterized protein YojO/serine protease inhibitor ecotin |
| RA | 2,311,863 | A→T | 43.1% | L296Q (CTG→CAG) | ompC ← | outer membrane porin C |
| RA | 2,321,136 | T→C | 7.9% | V365A (GTG→GCG) | atoS → | sensory histidine kinase AtoS |
| RA | 2,470,435 | T→A | 28.4% | N435K (AAT→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,470,436 | C→A | 49.6% | Q436K (CAA→AAA) | yfdI → | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase |
| RA | 2,633,560 | C→G | 60.0% | V171L (GTG→CTG) | guaB ← | inosine 5'‑monophosphate dehydrogenase |
| RA | 2,920,258 | A→T | 12.1% | Y163* (TAT→TAA) | gudX ← | glucarate dehydratase‑related protein |
| RA | 3,151,453 | G→T | 55.8% | L178M (CTG→ATG) | exbB ← | Ton complex subunit ExbB |
| RA | 3,188,337 | A→G | 6.9% | pseudogene (906/2434 nt) | yqiG → | putative outer membrane usher protein YqiG |
| RA | 3,270,479 | T→G | 24.4% | noncoding (114/377 nt) | rnpB ← | RNase P catalytic RNA component |
| RA | 3,301,431 | A→G | 9.7% | intergenic (‑155/‑54) | yhbT ← / → yhbU | SCP2 domain‑containing protein YhbT/putative peptidase YhbU |
| RA | 3,363,237 | C→T | 7.4% | T144I (ACA→ATA) | yhcD → | putative fimbrial usher protein YhcD |
| RA | 3,377,202 | G→T | 9.3% | R73R (CGC→CGA) | sspA ← | stringent starvation protein A |
| RA | 3,418,500 | T→A | 27.7% | N37K (AAT→AAA) | yhdV → | lipoprotein YhdV |
| RA | 3,445,780 | T→C | 7.0% | I121V (ATC→GTC) | rplF ← | 50S ribosomal subunit protein L6 |
| RA | 3,454,069 | G→T | 30.7% | Q444K (CAA→AAA) | gspA ← | Type II secretion system protein GspA |
| RA | 3,454,767 | G→T | 10.6% | A211D (GCC→GAC) | gspA ← | Type II secretion system protein GspA |
| RA | 3,548,364 | C→T | 8.9% | L569L (CTG→CTA) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,549,335 | C→A | 10.8% | D246Y (GAT→TAT) | malQ ← | 4‑alpha‑glucanotransferase |
| RA | 3,560,455:1 | +G | 100% | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,576,177 | A→T | 18.3% | I295I (ATT→ATA) | gntU ← | low‑affinity gluconate transporter |
| RA | 3,580,947 | C→G | 67.6% | noncoding (70/90 nt) | ryhB ← | small regulatory RNA RyhB |
| RA | 3,581,027 | T→C | 19.1% | intergenic (‑11/‑111) | ryhB ← / → yhhY | small regulatory RNA RyhB/N‑acetyltransferase YhhY |
| RA | 3,630,606 | C→T | 10.2% | intergenic (‑4/+362) | yhiI ← / ← yhiJ | putative membrane fusion protein YhiI/DUF4049 domain‑containing protein YhiJ |
| RA | 3,654,882 | T→C | 6.2% | V67A (GTC→GCC) | dctR → | putative DNA‑binding transcriptional regulator DctR |
| RA | 3,839,637 | G→T | 26.8% | S119S (TCC→TCA) | nlpA ← | lipoprotein‑28 |
| RA | 3,845,081 | A→T | 8.3% | E373V (GAG→GTG) | adeD → | adenine deaminase |
| RA | 3,869,601 | T→C | 13.3% | I75I (ATT→ATC) | cbrA → | colicin M resistance protein |
| RA | 3,929,961 | A→T | 12.6% | V378D (GTT→GAT) | ravA ← | regulatory ATPase RavA |
| RA | 4,093,466 | G→T | 10.8% | A269A (GCC→GCA) | rhaD ← | rhamnulose‑1‑phosphate aldolase |
| RA | 4,143,320 | C→T | 9.5% | A264V (GCG→GTG) | frwC → | putative PTS enzyme IIC component FrwC |
| RA | 4,182,929 | A→T | 25.0% | E562V (GAA→GTA) | rpoB → | RNA polymerase subunit beta |
| RA | 4,188,572 | C→T | 67.6% | R1075C (CGT→TGT) | rpoC → | RNA polymerase subunit beta' |
| RA | 4,296,060 | C→T | 34.3% | 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 | 4,304,579 | T→C | 16.7% | intergenic (‑176/+33) | ytcA ← / ← yjcS | putative lipoprotein YtcA/alkyl sulfatase |
| RA | 4,619,583 | G→C | 8.9% | intergenic (+32/‑20) | deoA → / → deoB | thymidine phosphorylase/phosphopentomutase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3423779–3424234 | 3424533–3424238 | 5–755 | 9 [8] | [8] 9 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4070468 | 4070484 | 17 | 19 [8] | [3] 9 | yihR/yihS | putative aldose 1‑epimerase YihR/sulfoquinovose isomerase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 612665 | 32 (0.870) | 6 (0.170) | 5/228 | NT | 19.0% | intergenic (‑171/‑72) | fepA/fes | ferric enterobactin outer membrane transporter/enterochelin esterase |
| ? | NC_000913 | 612949 = | 20 (0.560) | coding (213/1203 nt) | fes | enterochelin esterase | |||||
| * | ? | NC_000913 | 1207790 = | 48 (1.310) | 9 (0.280) | 5/202 | NT | 20.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 29 (0.920) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 1467910 = | NA (NA) | 20 (0.550) | 18/234 | NT | NA | noncoding (1331/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 1469241 | NA (NA) | intergenic (‑92/‑5) | insC‑2/ydbA | IS2 insertion element repressor InsA/putative outer membrane protein, N‑terminal fragment | |||||
| * | ? | NC_000913 | 4498181 = | NA (NA) | 16 (0.440) | 12/234 | NT | NA | noncoding (1/1331 nt) | IS2 | repeat region |
| ? | NC_000913 | = 4499512 | NA (NA) | intergenic (+12/+81) | insD‑6/yjgX | KpLE2 phage‑like element; IS2 insertion element protein InsB/KpLE2 phage‑like element; putative phosphoethanolamine transferase YjgX, N‑terminal fragment | |||||