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 | 67,887:1 | +G | 66.4% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| RA | 67,887:2 | +T | 66.4% | coding (451/1503 nt) | araA ← | L‑arabinose isomerase |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| JC JC | 1,293,032 | IS1 (–) +8 bp | 100% | intergenic (‑110/‑488) | hns ← / → tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase |
| MC JC | 1,299,499 | Δ1,199 bp | 100% | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| JC | 1,326,599 | Δ36 bp | 8.0% | coding (1854‑1889/1896 nt) | yciQ → | enhancer of membrane protein expression; putative inner membrane protein |
| RA | 1,708,820 | G→A | 7.9% | K634K (AAG→AAA) | rsxC → | SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex |
| MC JC | 1,978,503 | Δ776 bp | 100% | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | 100% | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| JC | 2,023,796 | Δ5 bp | 71.2% | intergenic (+118/‑168) | fliR → / → rcsA | flagellar export pore protein/transcriptional regulator of colanic acid capsular biosynthesis |
| JC JC | 2,024,155 | IS5 (–) +4 bp | 7.4% | coding (188‑191/624 nt) | rcsA → | transcriptional regulator of colanic acid capsular biosynthesis |
| RA | 2,132,787 | A→C | 100% | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,316,681 | A→G | 100% | T169A (ACC→GCC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,533,666 | C→T | 6.2% | intergenic (+286/‑98) | cysK → / → ptsH | cysteine synthase A, O‑acetylserine sulfhydrolase A subunit/phosphohistidinoprotein‑hexose phosphotransferase component of PTS system (Hpr) |
| RA | 3,495,038 | C→A | 8.3% | A343E (GCA→GAA) | nirB → | nitrite reductase, large subunit, NAD(P)H‑binding |
| RA | 3,527,591 | C→T | 100% | Q375* (CAG→TAG) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,560,455:1 | +G | 100% | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,805,981 | T→C | 6.4% | K363E (AAA→GAA) | waaG ← | UDP‑glucose:(heptosyl)lipopolysaccharide alpha‑1,3‑glucosyltransferase; lipopolysaccharide core biosynthesis protein; lipopolysaccharide glucosyltransferase I |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| JC JC | 3,992,705 | IS5 (+) +4 bp | 100% | coding (1553‑1556/2547 nt) | cyaA → | adenylate cyclase |
| MC JC | 4,001,645 | Δ5 bp | 100% | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | 100% | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,060 | C→T | 11.9% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,190 | A→G | 30.4% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 34.2% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 22.8% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533720 | 2536376 | 2657 | 44 [41] | [38] 45 | ptsH–crr | ptsH,ptsI,crr |
| * | * | ÷ | NC_000913 | 3423837–3424438 | 3424438 | 1–602 | 42 [41] | [41] 42 | [rrlD] | [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 51 (0.440) | 62 (0.570) | 51/472 | NT | 60.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 32 (0.290) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 48 (0.410) | 62 (0.570) | 48/472 | NT | 61.7% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 32 (0.290) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1616905 | 78 (0.670) | 4 (0.040) | 4/484 | NT | 5.0% | intergenic (+27/‑123) | yneK/ydeA | uncharacterized protein/arabinose efflux transporter, arabinose‑inducible |
| ? | NC_000913 | = 1616917 | 77 (0.690) | intergenic (+39/‑111) | yneK/ydeA | uncharacterized protein/arabinose efflux transporter, arabinose‑inducible | |||||
| * | ? | NC_000913 | = 3636853 | 80 (0.690) | 4 (0.040) | 4/476 | NT | 5.1% | coding (558/1203 nt) | yhiN | putative oxidoreductase |
| ? | NC_000913 | = 3636839 | 74 (0.670) | coding (572/1203 nt) | yhiN | putative oxidoreductase | |||||