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 | 1,195,445 | G→A | G108D (GGT→GAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,529,203 | C→A | pseudogene (1302/2037 nt) | rhsE → | pseudogene, Rhs family |
| RA | 1,529,218 | C→T | pseudogene (1317/2037 nt) | rhsE → | pseudogene, Rhs family |
| 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 | 3,397,306 | C→A | E164* (GAG→TAG) | rng ← | ribonuclease G |
| 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 | 3,578,650 | A→C | L26* (TTA→TGA) | gntR ← | d‑gluconate inducible gluconate regulon transcriptional repressor |
| RA | 3,815,824 | G→T | intergenic (‑56/+10) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 4,235,435 | Δ1 bp | intergenic (‑2202/‑499) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,296,409 | +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_3_hsa_pgi | 2947446 | 2947624 | 179 | 30 [28] | [28] 30 | [metZ]–[metV] | [metZ],metW,[metV] |
| * | * | ÷ | NC_000913_3_hsa_pgi | 3423750–3424234 | 3424571–3424238 | 5–822 | 31 [29] | [29] 30 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_pgi | 1207790 = | 1 (0.010) | 41 (0.600) | 36/264 | 1.1 | 91.2% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | 1209619 = | 7 (0.100) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1207805 | 3 (0.040) | 59 (0.870) | 47/264 | 0.4 | 92.4% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_hsa_pgi | = 1209602 | 7 (0.100) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_hsa_pgi | = 1299498 | 0 (0.000) | 102 (1.380) | 81/288 | 0.0 | 99.5% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_pgi | 1300698 = | 1 (0.010) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_hsa_pgi | 2514277 = | NA (NA) | 65 (0.870) | 56/290 | 0.3 | 91.7% | intergenic (+33/‑54) | nupC/insL1 | nucleoside (except guanosine) transporter/IS186 transposase |
| ? | NC_000913_3_hsa_pgi | 4543633 = | 6 (0.080) | coding (491/549 nt) | fimA | major type 1 subunit fimbrin (pilin) | |||||
| * | ? | NC_000913_3_hsa_pgi | = 2515613 | NA (NA) | 61 (0.820) | 51/290 | 0.5 | 91.2% | intergenic (+170/+30) | insL1/yfeA | IS186 transposase/putative diguanylate cyclase |
| ? | NC_000913_3_hsa_pgi | = 4543644 | 6 (0.080) | coding (502/549 nt) | fimA | major type 1 subunit fimbrin (pilin) | |||||