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 | 1,529,185 | C→T | pseudogene (1284/2037 nt) | rhsE → | pseudogene, Rhs family |
| 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 | 3,560,455 | +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 | 3,815,761 | G→T | P3Q (CCA→CAA) | pyrE ← | orotate phosphoribosyltransferase |
| RA | 4,159,160 | T→A | L224Q (CTG→CAG) | oxyR → | oxidative and nitrosative stress transcriptional regulator |
| RA | 4,186,605 | A→C | H419P (CAC→CCC) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,233,708 | C→T | intergenic (‑475/‑2199) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,233,772 | G→T | intergenic (‑539/‑2135) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,235,408 | Δ1 bp | intergenic (‑2175/‑499) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,296,382 | +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_bme_pgi | 3423732–3424234 | 3424564–3424238 | 5–833 | 53 [45] | [51] 53 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_bme_pgi | 1207790 = | 55 (0.520) | 46 (0.500) | 40/216 | 2.6 | 47.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | 1209619 = | 54 (0.580) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1207805 | 56 (0.530) | 46 (0.500) | 39/216 | 2.8 | 47.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | = 1209602 | 54 (0.580) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1299498 | 0 (0.000) | 104 (1.010) | 85/240 | 0.1 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_bme_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_bme_pgi | 3652037 = | NA (NA) | 108 (1.020) | 78/246 | 0.3 | 99.1% | intergenic (+6/+145) | yhiS/insH1 | pseudogene/IS5 transposase and trans‑activator |
| ? | NC_000913_3_bme_pgi | = 3992709 | 1 (0.010) | coding (1557/2547 nt) | cyaA | adenylate cyclase | |||||
| * | ? | NC_000913_3_bme_pgi | = 3653229 | NA (NA) | 118 (1.120) | 88/246 | 0.1 | 93.0% | intergenic (‑31/‑2) | insH1/yhiS | IS5 transposase and trans‑activator/pseudogene |
| ? | NC_000913_3_bme_pgi | 3992704 = | 9 (0.080) | coding (1552/2547 nt) | cyaA | adenylate cyclase | |||||