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 | 1,529,203 | 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 | 4,187,215 | C→G | D622E (GAC→GAG) | rpoC → | RNA polymerase, beta prime subunit |
| RA | 4,233,746 | A→G | intergenic (‑513/‑2161) | 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 | 3423741–3424545 | 3424545 | 1–805 | 18 [17] | [17] 18 | [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 | 19797 = | NA (NA) | 53 (1.180) | 39/288 | 0.2 | 94.7% | intergenic (+177/+14) | nhaR/insB1 | transcriptional activator of nhaA/IS1 transposase B |
| ? | NC_000913_3_bme_pgi | 61481 = | 3 (0.070) | coding (1784/2907 nt) | rapA | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase | |||||
| * | ? | NC_000913_3_bme_pgi | = 20563 | NA (NA) | 40 (0.880) | 34/290 | 0.4 | 88.9% | intergenic (‑55/+252) | insA/rpsT | IS1 repressor TnpA/30S ribosomal subunit protein S20 |
| ? | NC_000913_3_bme_pgi | = 61489 | 5 (0.110) | coding (1776/2907 nt) | rapA | RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase | |||||
| * | ? | NC_000913_3_bme_pgi | = 275149 | NA (NA) | 44 (0.970) | 32/290 | 0.5 | 100% | intergenic (‑32/‑176) | insH1/mmuP | IS5 transposase and trans‑activator/CP4‑6 prophage; putative S‑methylmethionine transporter |
| ? | NC_000913_3_bme_pgi | = 869877 | 0 (0.000) | coding (467/1539 nt) | gsiB | glutathione ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_bme_pgi | 687851 = | NA (NA) | 50 (1.100) | 44/290 | 0.1 | 100% | intergenic (‑104/+146) | gltI/insH1 | glutamate/aspartate periplasmic binding protein/IS5 transposase and trans‑activator |
| ? | NC_000913_3_bme_pgi | 869874 = | 0 (0.000) | coding (464/1539 nt) | gsiB | glutathione ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_bme_pgi | 1207790 = | 8 (0.180) | 33 (0.820) | 29/258 | 0.4 | 78.5% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | 1209619 = | 11 (0.270) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_bme_pgi | = 1207805 | 9 (0.200) | 46 (1.140) | 39/258 | 0.1 | 82.9% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_bme_pgi | = 1209602 | 11 (0.270) | 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) | 47 (1.070) | 44/282 | 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 | |||||