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 |
| 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 |
| 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 |
| 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 | 2,316,565 | C→T | 32.0% | T130I (ACC→ATC) | rcsB → | response regulator in two‑component regulatory system with RcsC and YojN |
| RA | 2,976,996 | C→A | 9.4% | S133* (TCA→TAA) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| RA | 2,977,092 | G→A | 10.9% | W165* (TGG→TAG) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| JC | 3,523,578 | +CAA | 5.6% | coding (708/2553 nt) | mrcA → | penicillin‑binding protein 1a, murein transglycosylase and transpeptidase |
| JC JC | 3,526,449 | IS5 (+) +4 bp | 46.1% | intergenic (‑300/‑17) | nudE ← / → yrfF | adenosine nucleotide hydrolase; Ap3A/Ap2A/ADP‑ribose/NADH hydrolase/putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,527,606 | Δ1 bp | 30.6% | coding (1138/2136 nt) | yrfF → | putative RcsCDB‑response attenuator, inner membrane protein |
| RA | 3,528,603 | Δ1 bp | 11.3% | coding (2135/2136 nt) | 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 |
| MC JC | 3,815,859 | Δ82 bp | 100% | [rph]–[rph] | [rph], [rph] | |
| RA | 3,992,438 | T→G | 20.8% | L429* (TTA→TGA) | cyaA → | adenylate cyclase |
| JC | 3,992,469 | Δ4 bp | 8.3% | coding (1317‑1320/2547 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 | 4,296,190 | A→G | 21.2% | intergenic (+396/+246) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,191 | A→C | 23.4% | intergenic (+397/+245) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 18.7% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,286 | C→T | 10.2% | intergenic (+492/+150) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,303 | A→G | 6.2% | intergenic (+509/+133) | 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 |
| RA | 4,326,088 | T→G | 7.5% | intergenic (‑347/+311) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| RA | 4,326,147 | T→C | 6.5% | intergenic (‑406/+252) | yjdN ← / ← yjdM | metalloprotein superfamily protein/zinc‑ribbon family protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 2533672 | 2536468 | 2797 | 81 [79] | [79] 82 | ptsH–[pdxK] | ptsH,ptsI,crr,[pdxK] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 66 (0.410) | 76 (0.500) | 60/486 | NT | 55.7% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 59 (0.390) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 61 (0.380) | 92 (0.610) | 66/486 | NT | 61.3% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 59 (0.390) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1979270 | NA (NA) | 10 (0.060) | 8/516 | NT | 5.6% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 3527247 = | 169 (1.050) | coding (779/2136 nt) | yrfF | putative RcsCDB‑response attenuator, inner membrane protein | |||||
| * | ? | NC_000913 | = 2024339 | 174 (1.080) | 12 (0.070) | 12/518 | NT | 6.5% | coding (372/624 nt) | rcsA | transcriptional regulator of colanic acid capsular biosynthesis |
| ? | NC_000913 | 2025115 = | 172 (1.070) | coding (130/228 nt) | yodD | uncharacterized protein | |||||
| * | ? | NC_000913 | 3845531 = | 126 (0.780) | 77 (0.500) | 51/498 | NT | 36.0% | coding (1568/1767 nt) | adeD | cryptic adenine deaminase |
| ? | NC_000913 | = 3992760 | 153 (0.990) | coding (1608/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913 | 4295832 = | NA (NA) | 6 (0.040) | 3/440 | NT | NA | intergenic (+38/+604) | gltP/yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| ? | NC_000913 | = 4296394 | NA (NA) | noncoding (560/600 nt) | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | RIP321 (repetitive extragenic palindromic) element; contains 11 REP sequences and 4 IHF sites | |||||