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 |
| RA | 1,726,004 | G→A | intergenic (‑84/‑19) | ydhL ← / → nemR | DUF1289 family protein/transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| 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 | 3,560,455 | +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 | 4,110,747 | G→T | intergenic (+62/+784) | cdh → / ← yiiQ | CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein |
| RA | 4,159,112 | G→A | G236E (GGG→GAG) | 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 | 3423755–3424234 | 3424547–3424238 | 5–793 | 22 [21] | [21] 25 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 4035283–4036990 | 4036990 | 1–1708 | 22 [21] | [20] 22 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | 273955 = | NA (NA) | 80 (1.380) | 45/278 | 0.4 | 95.2% | intergenic (+1/+146) | ykfC/insH1 | CP4‑6 prophage; conserved protein;Phage or Prophage Related/IS5 transposase and trans‑activator |
| ? | NC_000913_3_pae_tpiA | 344918 = | 4 (0.070) | coding (743/816 nt) | yahL | uncharacterized protein | |||||
| * | ? | NC_000913_3_pae_tpiA | = 275149 | NA (NA) | 62 (1.070) | 42/278 | 0.6 | 96.9% | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage; putative S‑methylmethionine transporter |
| ? | NC_000913_3_pae_tpiA | = 344921 | 2 (0.030) | coding (746/816 nt) | yahL | uncharacterized protein | |||||
| * | ? | NC_000913_3_pae_tpiA | 1263650 = | 69 (1.190) | 24 (0.420) | 23/272 | 2.4 | 26.9% | intergenic (‑150/‑64) | lolB/hemA | lipoprotein localization factor/glutamyl tRNA reductase |
| ? | NC_000913_3_pae_tpiA | = 1263818 | 63 (1.110) | coding (105/1257 nt) | hemA | glutamyl tRNA reductase | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1299498 | 0 (0.000) | 61 (1.080) | 54/270 | 0.1 | 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) | 64 (1.100) | 50/278 | 0.2 | 100% | intergenic (+146/‑127) | insH1/ynaJ | IS5 transposase and trans‑activator/DUF2534 family putative inner membrane protein |
| ? | NC_000913_3_pae_tpiA | = 2042468 | 0 (0.000) | coding (101/531 nt) | yodB | cytochrome b561 homolog | |||||
| * | ? | NC_000913_3_pae_tpiA | 1757082 = | 5 (0.090) | 49 (0.840) | 45/278 | 0.4 | 90.7% | coding (1385/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913_3_pae_tpiA | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||
| * | ? | NC_000913_3_pae_tpiA | = 1757085 | 1 (0.020) | 46 (0.790) | 35/278 | 1.0 | 97.9% | coding (1388/1413 nt) | pykF | pyruvate kinase I |
| ? | NC_000913_3_pae_tpiA | = 2290113 | NA (NA) | intergenic (‑32/+1) | insH1/yejO | IS5 transposase and trans‑activator/pseudogene, autotransporter outer membrane homology;putative transport; Not classified; putative ATP‑binding component of a transport system | |||||
| * | ? | NC_000913_3_pae_tpiA | 2042464 = | 1 (0.020) | 56 (0.970) | 46/276 | 0.4 | 98.3% | coding (97/531 nt) | yodB | cytochrome b561 homolog |
| ? | NC_000913_3_pae_tpiA | = 2102942 | NA (NA) | intergenic (‑31/+2) | insH1/wbbL | IS5 transposase and trans‑activator/pseudogene, lipopolysaccharide biosynthesis protein | |||||