mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 461,186 | C→A | L767M (CTG→ATG) | lon → | Lon protease |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 982,195 | C→A | A383A (GCC→GCA) | ldtD → | L,D‑transpeptidase LdtD |
| RA | 1,040,245 | G→T | S317I (AGC→ATC) | appB → | cytochrome bd‑II ubiquinol oxidase subunit II |
| RA | 1,139,960 | C→A | A528E (GCG→GAG) | flgK → | flagellar hook‑filament junction protein 1 |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,751,107 | C→A | W206C (TGG→TGT) | ydhW ← | protein YdhW |
| RA | 1,818,449 | G→T | P18T (CCG→ACG) | chbF ← | monoacetylchitobiose‑6‑phosphate hydrolase |
| RA | 1,876,651 | G→T | A327S (GCT→TCT) | nimT → | 2‑nitroimidazole exporter |
| JC JC | 1,879,829 | Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp | coding (115‑120/360 nt) | yeaR ← | DUF1971 domain‑containing protein YeaR |
| RA | 1,974,054 | C→A | G424V (GGG→GTG) | cheA ← | chemotaxis protein CheA |
| 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 | 2,537,862 | C→A | F38L (TTC→TTA) | yfeS → | conserved protein YfeS |
| RA | 2,618,576 | C→A | L67F (TTG→TTT) | hda ← | inibitor of reinitiation of DNA replication |
| RA | 2,737,242 | G→T | W30L (TGG→TTG) | raiA → | stationary phase translation inhibitor and ribosome stability factor |
| RA | 2,896,127 | G→T | G143G (GGC→GGA) | ygcR ← | putative flavoprotein |
| JC JC | 2,983,961 | IS5 (–) +4 bp | coding (161‑164/837 nt) | kduI ← | 5‑dehydro‑4‑deoxy‑D‑glucuronate isomerase |
| RA | 3,139,539 | G→T | E271D (GAG→GAT) | yghU → | disulfide reductase/organic hydroperoxide reductase |
| RA | 3,179,053 | G→T | P313P (CCG→CCT) | tolC → | outer membrane channel TolC |
| RA | 3,192,579 | C→A | P124P (CCC→CCA) | yqiJ → | putative inner membrane protein |
| 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 | 3,726,942 | C→A | Q140H (CAG→CAT) | yiaA ← | conserved inner membrane protein YiaA |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 4,045,403 | C→A | A402E (GCA→GAA) | yihF → | uncharacterized protein YihF |
| RA | 4,127,940 | C→A | intergenic (‑46/+138) | yiiX ← / ← metJ | putative lipid binding hydrolase/DNA‑binding transcriptional repressor MetJ |
| RA | 4,197,168 | C→A | A89E (GCG→GAG) | nudC → | NADH pyrophosphatase |
| 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 | 4,383,471 | C→T | H277Y (CAC→TAC) | epmA → | EF‑P‑lysine lysyltransferase |
| RA | 4,538,474 | C→T | E98K (GAG→AAG) | nanM ← | N‑acetylneuraminate mutarotase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3103000 | 3104051 | 1052 | 8 [6] | [7] 10 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423776–3424230 | 3424523–3424243 | 14–748 | 9 [6] | [5] 8 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 49 (1.050) | 32 (0.780) | 27/244 | 0.4 | 42.6% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 43 (1.040) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 49 (1.050) | 22 (0.530) | 18/244 | 1.0 | 33.8% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 43 (1.040) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | 3363001 = | 67 (1.430) | 65 (1.400) | 40/274 | 0.1 | 65.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 1 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 54 (1.160) | 42/276 | 0.1 | 96.4% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 2 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||