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 | annotation | gene | description |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 264,098 | G→T | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 275,065 | G→A | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 482,230 | G→A | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 1,197,502 | C→T | G11R (GGA→AGA) | ymfD ← | e14 prophage; putative SAM‑dependent methyltransferase |
| RA | 1,544,022 | 1 bp→AA | coding (39/1389 nt) | narU ← | nitrate/nitrite transporter |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,679,525 | G→T | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 3,431,411 | T→C | N2S (AAT→AGT) | tsaC ← | tRNA(ANN) t(6)A37 threonylcarbamoyladenosine modification protein, threonine‑dependent ADP‑forming ATPase |
| RA | 3,440,923 | C→T | G36D (GGC→GAC) | rpoA ← | RNA polymerase, alpha subunit |
| RA | 3,560,455 | +G | 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 | 4,111,596 | G→A | L179L (CTG→TTG) | yiiQ ← | DUF1454 family putative periplasmic protein |
| RA | 4,158,703 | A→G | T100A (ACA→GCA) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,296,297 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,632 | C→A | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_pae_tpiA | 3423732–3424596 | 3424596 | 1–865 | 124 [115] | [118] 121 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | 1207790 = | 25 (0.120) | 105 (0.590) | 78/210 | 2.3 | 85.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | 1209619 = | 14 (0.080) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1207805 | 25 (0.120) | 160 (0.890) | 107/210 | 0.3 | 90.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_pae_tpiA | = 1209602 | 14 (0.080) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1299498 | 0 (0.000) | 211 (1.060) | 140/234 | 0.0 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_pae_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1397238 | NA (NA) | 203 (0.980) | 117/242 | 0.5 | 84.9% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | NC_000913_3_pae_tpiA | = 1757085 | 36 (0.170) | coding (1388/1413 nt) | pykF | pyruvate kinase I | |||||
| * | ? | NC_000913_3_pae_tpiA | 1757082 = | 34 (0.160) | 192 (0.930) | 120/242 | 0.4 | 85.0% | coding (1385/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913_3_pae_tpiA | = 2102943 | NA (NA) | intergenic (‑32/+1) | insH1/wbbL | IS5 transposase and trans‑activator/pseudogene, lipopolysaccharide biosynthesis protein | |||||