mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
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] | |
| JC JC | 564,107 | IS2 (+) +5 bp | coding (370‑374/633 nt) | sfmZ ← | response regulator family protein |
| RA | 756,119 | C→A | D71E (GAC→GAA) | sdhA → | succinate dehydrogenase, flavoprotein subunit |
| MC JC | 1,299,499 | Δ1,199 bp | intergenic (+254/‑485) | ychE → / → oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| 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 | 2,284,630 | G→A | L85L (CTG→CTA) | yejM → | essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor |
| 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 |
| JC JC | 4,543,608 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (494‑499/549 nt) | fimA → | major type 1 subunit fimbrin (pilin) |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 761509 | 762718 | 1210 | 4 [2] | [0] 4 | [sucB] | [sucB] |
| * | * | ÷ | NC_000913 | 3423798–3424234 | 3424551–3424240 | 7–754 | 4 [2] | [3] 4 | [rrlD] | [rrlD] |
| * | * | ÷ | NC_000913 | 3875496 | 3875546 | 51 | 4 [3] | [3] 4 | yidX | putative lipoprotein |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 274347 = | NA (NA) | 7 (0.300) | 7/256 | 1.8 | NA | noncoding (803/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 274410 = | NA (NA) | noncoding (740/1195 nt) | IS5 | repeat region | |||||
| * | ? | NC_000913 | = 316201 | NA (NA) | 4 (0.170) | 4/252 | 2.6 | NA | noncoding (973/1255 nt) | IS3 | repeat region |
| ? | NC_000913 | = 316220 | NA (NA) | noncoding (992/1255 nt) | IS3 | repeat region | |||||
| * | ? | NC_000913 | 1207790 = | 6 (0.240) | 20 (0.910) | 19/238 | 0.3 | 81.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 4 (0.180) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.240) | 22 (1.000) | 21/238 | 0.2 | 82.6% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 4 (0.180) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1378468 | 12 (0.480) | 4 (0.170) | 4/258 | 2.7 | 31.4% | coding (585/2268 nt) | ycjT | putative family 65 glycosyl hydrolase |
| ? | NC_000913 | = 1378524 | 6 (0.250) | coding (641/2268 nt) | ycjT | putative family 65 glycosyl hydrolase | |||||
| * | ? | NC_000913 | = 4480959 | NA (NA) | 6 (0.290) | 6/222 | 1.7 | NA | intergenic (+33/+23) | yjgN/valS | DUF898 family inner membrane protein/valyl‑tRNA synthetase |
| ? | NC_000913 | = 4480935 | NA (NA) | intergenic (+9/+47) | yjgN/valS | DUF898 family inner membrane protein/valyl‑tRNA synthetase | |||||