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 | 668,742 | C→G | E99Q (GAA→CAA) | rsfS ← | ribosomal silencing factor |
| 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 | 2,513,351 | C→A | L104M (CTG→ATG) | nupC → | nucleoside (except guanosine) transporter |
| RA | 3,440,135 | A→C | S299A (TCT→GCT) | rpoA ← | RNA polymerase, alpha subunit |
| 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 |
| JC | 4,233,757 | +46 bp | intergenic (‑524/‑583) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| JC | 4,233,840 | +46 bp | intergenic (‑607/‑500) | lysC ← / → yjbE | lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein |
| RA | 4,294,815 | +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_KO_pgi | 1403767 | 1408659 | 4893 | 13 [12] | [12] 13 | [abgA]–[ydaN] | [abgA],abgR,mcaS,smrA,ydaM,[ydaN] |
| * | * | ÷ | NC_000913_3_KO_pgi | 1411908 | 1417222 | 5315 | 13 [11] | [11] 13 | [ttcA]–[recE] | [ttcA],intR,ydaQ,ydaC,ralR,recT,[recE] |
| * | * | ÷ | NC_000913_3_KO_pgi | 1417227 | 1419921 | 2695 | 13 [12] | [12] 13 | [recE]–[racR] | [recE],racC,ydaE,kilR,sieB,ydaF,ydaG,[racR] |
| * | * | ÷ | NC_000913_3_KO_pgi | 1419927 | 1426674 | 6748 | 13 [12] | [12] 13 | [racR]–[tmpR] | [racR],ydaS,ydaT,ydaU,ydaV,ydaW,rzpR,rzoR,trkG,ynaK,ydaY,[tmpR] |
| * | * | ÷ | NC_000913_3_KO_pgi | 3423757–3424234 | 3424561–3424239 | 6–805 | 13 [12] | [12] 13 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_KO_pgi | 1207790 = | 4 (0.100) | 32 (0.930) | 27/248 | 0.4 | 85.9% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_KO_pgi | 1209619 = | 7 (0.200) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_KO_pgi | = 1207805 | 4 (0.100) | 33 (0.960) | 32/248 | 0.2 | 86.2% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913_3_KO_pgi | = 1209602 | 7 (0.200) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913_3_KO_pgi | = 1395541 | 9 (0.230) | 43 (1.110) | 39/280 | 0.1 | 82.7% | coding (382/1032 nt) | ynaI | mechanosensitive channel protein, very small conductance |
| ? | NC_000913_3_KO_pgi | 1427777 = | 9 (0.230) | coding (950/981 nt) | insH1 | IS5 transposase and trans‑activator | |||||