mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.29.0 revision 8f9c342918e4
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 | 443,040 | C→T | intergenic (+43/+11) | thiI → / ← yajL | tRNA s(4)U8 sulfurtransferase/oxidative‑stress‑resistance chaperone |
| RA | 660,573 | T→C | N269S (AAC→AGC) | ybeF ← | LysR family putative transcriptional regulator |
| RA | 701,381 | (C)5→4 | coding (214/1221 nt) | nagC ← | N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor |
| RA | 874,067 | G→A | R363R (CGG→CGA) | yliE → | putative membrane‑anchored cyclic‑di‑GMP phosphodiesterase |
| RA | 1,029,739 | (A)8→7 | coding (231/1191 nt) | rlmI ← | 23S rRNA m(5)C1962 methyltransferase, SAM‑dependent |
| RA | 1,187,352 | G→A | L297L (CTG→TTG) | roxA ← | 50S ribosomal protein L16 arginine hydroxylase; 2‑oxoglutarate oxygenase |
| RA | 1,728,884 | G→A | A180T (GCG→ACG) | rnt → | RNase T; exoribonuclease T; structured DNA 3' exonuclease; RNA processing; DNA repair |
| 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 | 2,262,665 | G→A | S277S (AGC→AGT) | fruB ← | fused fructose‑specific PTS enzymes: IIA component/HPr component |
| RA | 2,465,722 | Δ1 bp | coding (422/933 nt) | yfdC → | putative inner membrane protein |
| RA | 2,725,672 | (C)5→4 | coding (75/1299 nt) | kgtP ← | alpha‑ketoglutarate transporter |
| RA | 3,156,603 | T→C | intergenic (+85/‑20) | yqhD → / → dkgA | aldehyde reductase, NADPH‑dependent/2,5‑diketo‑D‑gluconate reductase A |
| RA | 3,263,200 | G→A | A154V (GCT→GTT) | tdcD ← | propionate kinase/acetate kinase C, anaerobic |
| RA | 3,378,539 | C→G | G38A (GGT→GCT) | rplM ← | 50S ribosomal subunit protein L13 |
| RA | 3,485,967 | A→G | intergenic (‑149/‑153) | yhfA ← / → crp | OsmC family protein/cAMP‑activated global transcription factor, mediator of catabolite repression |
| RA | 3,510,180 | T→C | N266S (AAC→AGC) | yhfX ← | putative pyridoxal 5'‑phosphate binding protein |
| 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 | 3,634,152 | T→C | pseudogene (307/1194 nt) | yhiL ← | pseudogene, DUF4049 family protein |
| RA | 3,779,384 | A→G | S111G (AGC→GGC) | lldR → | dual role activator/repressor for lldPRD operon |
| RA | 3,823,724 | C→T | T442I (ACC→ATC) | spoT → | bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| RA | 3,931,183 | (G)7→8 | intergenic (‑90/‑133) | ravA ← / → kup | hexameric AAA+ MoxR family ATPase, putative molecular chaperone/potassium transporter |
| RA | 3,943,892 | (G)5→4 | noncoding (189/2904 nt) | rrlC → | 23S ribosomal RNA of rrnC operon |
| RA | 3,999,387 | Δ1 bp | coding (1405/2163 nt) | uvrD → | DNA‑dependent ATPase I and helicase II |
| RA | 4,037,513 | T→C | intergenic (+178/‑6) | alaT → / → rrlA | tRNA‑Ala/23S ribosomal RNA of rrnA operon |
| RA | 4,219,696 | C→T | G367G (GGC→GGT) | aceK → | isocitrate dehydrogenase kinase/phosphatase |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,607,712 | C→T | intergenic (‑12/‑91) | rsmC ← / → holD | 16S rRNA m(2)G1207 methyltransferase, SAM‑dependent/DNA polymerase III, psi subunit |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 734301–734433 | 734766–734475 | 43–466 | 36 [35] | [34] 36 | rhsO | pseudogene, Rhs family |
| * | * | ÷ | NC_000913 | 3423718–3424234 | 3424579–3424238 | 5–862 | 36 [35] | [33] 36 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 75 (1.130) | 60/290 | 0.2 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||