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] | |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| JC JC | 1,434,361 | IS2 (–) +5 bp | intergenic (‑137/+593) | ynaE ← / ← ttcC | cold shock protein, Rac prophage/pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related |
| RA | 1,662,350 | C→T | P599S (CCC→TCC) | ynfF → | S‑ and N‑oxide reductase, A subunit, periplasmic |
| RA | 1,806,319 | C→T | intergenic (‑236/‑51) | ydiY ← / → pfkB | acid‑inducible putative outer membrane protein/6‑phosphofructokinase II |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| 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 | 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 | 4,296,381 | +GC | intergenic (+587/+55) | 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 | 3423755–3424234 | 3424530–3424239 | 6–776 | 9 [8] | [7] 9 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4107529 | 4108511 | 983 | 11 [7] | [8] 9 | [pfkA] | [pfkA] |
| * | * | ÷ | NC_000913 | 4144033 | 4147088 | 3056 | 9 [8] | [7] 9 | [pflD]–[pflC] | [pflD],[pflC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 37 (1.010) | 12 (0.370) | 12/234 | 1.8 | 29.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 24 (0.750) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | 3583428 = | NA (NA) | 19 (0.520) | 14/266 | 1.8 | 38.0% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3986004 | 31 (0.850) | coding (4/1656 nt) | aslA | putative Ser‑type periplasmic non‑aryl sulfatase | |||||
| * | ? | NC_000913 | = 3584195 | NA (NA) | 20 (0.550) | 19/266 | 1.1 | 39.2% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 3731482 | 31 (0.850) | coding (352/993 nt) | xylF | D‑xylose transporter subunit | |||||
| * | ? | NC_000913 | 3721219 = | 37 (1.010) | 20 (0.550) | 19/264 | 1.1 | 37.1% | noncoding (587/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | 3731475 = | 31 (0.860) | coding (345/993 nt) | xylF | D‑xylose transporter subunit | |||||