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 |
| RA | 1,399,451 | T→G | S26R (AGC→CGC) | fnr ← | oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor |
| 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 | 2,662,004 | T→A | E43V (GAA→GTA) | iscR ← | isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor |
| RA | 2,664,591 | C→A | P68T (CCT→ACT) | yfhR → | putative S9 family prolyl oligopeptidase |
| RA | 3,486,594 | A→C | T159P (ACT→CCT) | crp → | cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,552,719 | G→T | intergenic (‑246/‑366) | malP ← / → malT | maltodextrin phosphorylase/mal regulon transcriptional activator |
| 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 | 4,015,910 | Δ1 bp | coding (260/816 nt) | ysgA ← | putative carboxymethylenebutenolidase |
| 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 | 2101364 | 2102890–2101747 | 384–1527 | 194 [0] | [84] 86 | wbbL–[insH1] | wbbL,[insH1] |
| * | * | ÷ | NC_000913_3_KO_pgi | 3423723–3424234 | 3424591–3424238 | 5–869 | 89 [85] | [85] 86 | [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 | = 1299498 | 1 (0.010) | 171 (1.160) | 110/266 | 0.1 | 99.7% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_KO_pgi | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_KO_pgi | = 2101363 | 0 (0.000) | 188 (1.240) | 110/274 | 0.2 | 100% | intergenic (‑95/+33) | gnd/wbbL | 6‑phosphogluconate dehydrogenase, decarboxylating/pseudogene, lipopolysaccharide biosynthesis protein |
| ? | NC_000913_3_KO_pgi | 2101749 = | NA (NA) | intergenic (‑5/+146) | wbbL/insH1 | pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator | |||||