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 |
| RA | 38,537 | G→T | G193G (GGC→GGA) | caiB ← | gamma‑butyrobetainyl‑CoA:carnitine CoA transferase |
| RA | 47,579 | C→A | H112N (CAT→AAT) | kefF → | regulator of KefC‑mediated potassium transport and quinone oxidoreductase |
| RA | 79,715 | C→A | A384S (GCC→TCC) | leuC ← | 3‑isopropylmalate dehydratase subunit LeuC |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 549,560 | C→A | L402M (CTG→ATG) | ylbE → | DUF1116 domain‑containing protein YlbE |
| RA | 671,960 | C→A | R76L (CGT→CTT) | lptE ← | lipopolysaccharide assembly protein LptE |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 963,290 | C→A | G432G (GGC→GGA) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,274,353 | G→T | A190A (GCG→GCT) | ychO → | putative invasin YchO |
| RA | 1,483,411 | G→T | L117L (CTG→CTT) | hrpA → | ATP‑dependent RNA helicase HrpA |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| MC JC | 1,978,503 | Δ776 bp | insB‑5–insA‑5 | insB‑5, insA‑5 | |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,485,750 | G→T | S459S (TCG→TCT) | evgS → | sensory histidine kinase EvgS |
| RA | 2,587,586 | C→A | intergenic (+155/‑9) | narQ → / → acrD | sensory histidine kinase NarQ/multidrug efflux pump RND permease AcrD |
| RA | 2,771,492 | G→T | M115I (ATG→ATT) | yfjT → | CP4‑57 prophage; uncharacterized protein YfjT |
| RA | 2,951,529 | G→T | G311G (GGC→GGA) | recD ← | exodeoxyribonuclease V subunit RecD |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,622,185 | C→A | G998G (GGC→GGA) | rhsB → | rhs element protein RhsB |
| RA | 3,649,990 | G→T | T352T (ACG→ACT) | arsB → | arsenite/antimonite:H(+) antiporter |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 4,030,852 | G→T | G40G (GGC→GGA) | fadB ← | dodecenoyl‑CoA delta‑isomerase, enoyl‑CoA hydratase, 3‑hydroxybutyryl‑CoA epimerase, 3‑hydroxyacyl‑CoA dehydrogenase |
| RA | 4,085,456 | G→T | Q123K (CAA→AAA) | fdoG ← | formate dehydrogenase O subunit alpha |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,505,167 | C→A | G370G (GGC→GGA) | yjhB → | putative sialic acid transporter |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102965 | 3104050 | 1086 | 11 [10] | [10] 11 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423785–3424234 | 3424542–3424238 | 5–758 | 11 [8] | [10] 11 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 11 (0.250) | 49 (1.250) | 31/246 | 0.2 | 84.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 9 (0.230) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 11 (0.250) | 29 (0.740) | 24/246 | 0.5 | 75.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 9 (0.230) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 61 (1.410) | 46/270 | 0.0 | 100% | intergenic (+253/‑33) | ychE/insH21 | putative inner membrane protein/IS5 transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | 3363001 = | 69 (1.550) | 82 (1.860) | 48/276 | 0.0 | 70.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 0 (0.000) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 64 (1.440) | 45/278 | 0.1 | 98.5% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 1 (0.020) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||