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 |
| JC JC | 153,986 | IS5 (–) +4 bp | coding (1438‑1441/2598 nt) | htrE ← | putative outer membrane usher protein |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 417,391 | G→C | A84P (GCC→CCC) | phoB → | response regulator in two‑component regulatory system with PhoR |
| RA | 702,066 | G→C | P229R (CCT→CGT) | nagA ← | N‑acetylglucosamine‑6‑phosphate deacetylase |
| RA | 1,158,384 | G→A | W172* (TGG→TGA) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| JC JC | 1,491,904 | IS186 (+) +3 bp | intergenic (+54/+16) | ydcA → / ← hokB | putative periplasmic protein/toxic polypeptide, small |
| RA | 1,726,507 | Δ1 bp | coding (485/600 nt) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| JC JC | 1,979,486 | IS5 (+) +4 bp | intergenic (‑271/‑264) | insA ← / → uspC | IS1 repressor TnpA/universal stress protein |
| RA | 2,132,787 | A→C | I204S (ATC→AGC) | wcaA ← | putative glycosyl transferase |
| 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 | 2,509,479 | C→T | intergenic (‑53/‑151) | glk ← / → yfeO | glucokinase/putative ion channel protein |
| RA | 2,977,596 | +C | coding (998/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| 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] | |
| MC JC | 3,909,312 | Δ774 bp | [pstA]–[pstC] | [pstA], [pstC] | |
| JC | 4,001,645 | Δ5 bp | coding (220‑224/951 nt) | corA → | magnesium/nickel/cobalt transporter |
| RA | 4,184,543 | C→A | P1100Q (CCG→CAG) | rpoB → | RNA polymerase, beta subunit |
| 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 | 1293040 | 1306931 | 13892 | 46 [0] | [1] 36 | tdk–[yciU] | tdk,insZ,insZ,insZ,adhE,ychE,oppA,oppB,oppC,oppD,oppF,[yciU] |
| * | * | ÷ | NC_000913 | 2726134–2729156 | 2729156 | 1–3023 | 20 [19] | [18] 20 | [rrfG]–[rrlG] | [rrfG],[rrlG] |
| * | * | ÷ | NC_000913 | 3423749–3424234 | 3424526–3424238 | 5–778 | 20 [19] | [18] 20 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913 | 4110733 | 4111546 | 814 | 20 [19] | [19] 20 | tpiA | tpiA |
| * | * | ÷ | NC_000913 | 4168677–4171676 | 4171676 | 1–3000 | 20 [19] | [18] 20 | [rrlB]–[rrfB] | [rrlB],[rrfB] |
| * | * | ÷ | NC_000913 | 4210103–4213075 | 4213075 | 1–2973 | 22 [19] | [19] 22 | [rrlE]–[rrfE] | [rrlE],[rrfE] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 257908 = | NA (NA) | 46 (0.960) | 41/282 | 0.1 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1293039 | 0 (0.000) | intergenic (‑117/‑488) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | = 258675 | NA (NA) | 35 (0.740) | 31/280 | 0.6 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 1306932 = | 0 (0.000) | coding (219/330 nt) | yciU | UPF0263 family protein | |||||
| * | ? | NC_000913 | 1207790 = | 10 (0.210) | 33 (0.780) | 29/250 | 0.5 | 76.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 11 (0.260) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.230) | 42 (0.990) | 34/250 | 0.2 | 80.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 11 (0.260) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||