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 |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| 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 | 3,560,455 | +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 |
| MC JC | 3,815,859 | Δ82 bp | [rph]–[rph] | [rph], [rph] | |
| RA | 4,111,596 | G→A | L179L (CTG→TTG) | yiiQ ← | DUF1454 family putative periplasmic protein |
| 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 | 326096 | 326125 | 30 | 2 [0] | [1] 2 | betA | choline dehydrogenase, a flavoprotein |
| * | * | ÷ | NC_000913_3_pae_tpiA | 345778 | 345835 | 58 | 2 [1] | [1] 2 | yahN | amino acid exporter for proline, lysine, glutamate, homoserine |
| * | * | ÷ | NC_000913_3_pae_tpiA | 366254 | 366381 | 128 | 2 [1] | [1] 2 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1071836 | 1071891 | 56 | 2 [1] | [1] 3 | rutC | putative aminoacrylate deaminase, reactive intermediate detoxification; weak enamine/imine deaminase activity |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1311186 | 1311210 | 25 | 2 [0] | [1] 2 | tonB | membrane spanning protein in TonB‑ExbB‑ExbD transport complex |
| * | * | ÷ | NC_000913_3_pae_tpiA | 1344743 | 1344780 | 38 | 2 [0] | [1] 2 | [gmr] | [gmr] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 2039440 | 2039508 | 69 | 2 [1] | [1] 2 | [yedY] | [yedY] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 2182972 | 2183024 | 53 | 2 [1] | [0] 2 | yegX | putative family 25 glycosyl hydrolase |
| * | * | ÷ | NC_000913_3_pae_tpiA | 2802065 | 2802081 | 17 | 2 [0] | [1] 3 | nrdE | ribonucleoside‑diphosphate reductase 2, alpha subunit |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3314901 | 3314939 | 39 | 2 [0] | [1] 2 | infB | translation initiation factor IF‑2 |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3423768–3424532 | 3424532 | 1–765 | 2 [1] | [1] 2 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3803830 | 3803883 | 54 | 3 [1] | [1] 2 | waaB | lipopolysaccharide 1,6‑galactosyltransferase; UDP‑D‑galactose:(glucosyl)lipopolysaccharide‑1, 6‑D‑galactosyltransferase |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3836042 | 3836086 | 45 | 2 [1] | [1] 3 | yicJ/selC | putative transporter/tRNA‑Sec |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3878290 | 3878339 | 50 | 3 [1] | [1] 2 | gyrB | DNA gyrase, subunit B |
| * | * | ÷ | NC_000913_3_pae_tpiA | 3980499 | 3980531 | 33 | 2 [1] | [1] 2 | wecG | UDP‑N‑acetyl‑D‑mannosaminuronic acid transferase |
| * | * | ÷ | NC_000913_3_pae_tpiA | 4005914 | 4005946 | 33 | 2 [1] | [1] 2 | recQ | ATP‑dependent DNA helicase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_pae_tpiA | 228016 = | NA (NA) | 3 (0.240) | 3/236 | 1.4 | NA | noncoding (2258/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon |
| ? | NC_000913_3_pae_tpiA | 228041 = | NA (NA) | noncoding (2283/2904 nt) | rrlH | 23S ribosomal RNA of rrnH operon | |||||
| * | ? | NC_000913_3_pae_tpiA | 2726200 = | NA (NA) | 4 (0.320) | 4/238 | 1.1 | NA | intergenic (‑12/+81) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon |
| ? | NC_000913_3_pae_tpiA | 2726224 = | NA (NA) | intergenic (‑36/+57) | rrfG/rrlG | 5S ribosomal RNA of rrnG operon/23S ribosomal RNA of rrnG operon | |||||
| * | ? | NC_000913_3_pae_tpiA | = 3285741 | 3 (0.230) | 3 (0.240) | 3/244 | 1.4 | 35.4% | coding (264/792 nt) | agaD | N‑acetylgalactosamine‑specific enzyme IID component of PTS |
| ? | NC_000913_3_pae_tpiA | = 3285798 | 8 (0.630) | coding (321/792 nt) | agaD | N‑acetylgalactosamine‑specific enzyme IID component of PTS | |||||