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 | 225,805 | C→A | noncoding (47/2904 nt) | rrlH → | 23S ribosomal RNA |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 415,660 | G→T | L32M (CTG→ATG) | sbcC ← | ATP dependent, structure specific DNA nuclease ‑ SbcC subunit |
| RA | 561,422 | G→T | D576Y (GAT→TAT) | sfmD → | putative fimbrial usher protein SfmD |
| RA | 717,257 | C→A | A337S (GCA→TCA) | potE ← | putrescine:H(+) symporter/putrescine:ornithine antiporter PotE |
| RA | 846,090 | C→A | G125V (GGT→GTT) | glnQ ← | L‑glutamine ABC transporter ATP binding subunit |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 974,255 | C→T | P240L (CCG→CTG) | cmoM → | tRNA cmo(5)U34 methyltransferase |
| RA | 1,089,912 | C→A | R793I (AGA→ATA) | pgaA ← | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine outer membrane porin |
| MC JC | 1,233,317 | Δ10 bp | coding (1392‑1401/1542 nt) | nhaB ← | Na(+):H(+) antiporter NhaB |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,727,994 | C→A | A53E (GCG→GAG) | gloA → | glyoxalase I |
| RA | 1,817,420 | G→T | L361M (CTG→ATG) | chbF ← | monoacetylchitobiose‑6‑phosphate hydrolase |
| RA | 1,822,260 | C→A | intergenic (‑4/‑198) | osmE ← / → nadE | osmotically‑inducible lipoprotein OsmE/NAD synthetase, NH3‑dependent |
| 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 | 2,011,090 | G→T | intergenic (+11/+133) | yedL → / ← yedN | putative acetyltransferase YedL/putative type III secreted effector, N‑terminal fragment |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,260,694 | C→A | P239P (CCG→CCT) | fruA ← | fructose‑specific PTS multiphosphoryl transfer protein FruA |
| RA | 2,441,238 | G→T | P123Q (CCG→CAG) | fabB ← | beta‑ketoacyl‑[acyl carrier protein] synthase I |
| RA | 3,000,624 | C→A | R94S (CGT→AGT) | xdhA → | putative xanthine dehydrogenase molybdenum‑binding subunit XdhA |
| RA | 3,141,233 | G→T | I18I (ATC→ATA) | hybD ← | putative hydrogenase 2 maturation protease |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,538,065 | C→A | F227L (TTC→TTA) | yhgF → | putative RNA‑binding protein YhgF |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,791,325 | C→A | L7L (CTG→CTT) | tdh ← | threonine dehydrogenase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,927,437 | C→A | H95N (CAC→AAC) | asnA → | asparagine synthetase A |
| RA | 4,018,140 | G→T | A270S (GCC→TCC) | rmuC → | putative recombination limiting protein RmuC |
| 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 | 4,354,654 | G→T | R22S (CGC→AGC) | lysU ← | lysine‑‑tRNA ligase/Ap4A synthetase/Ap3A synthetase |
| JC | 4,527,042 | +GCA | coding (496/633 nt) | sgcE ← | KpLE2 phage‑like element; putative epimerase SgcE |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102972 | 3104072 | 1101 | 51 [47] | [50] 52 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423754–3424233 | 3424527–3424239 | 7–774 | 51 [49] | [50] 51 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 80 (0.460) | 225 (1.460) | 85/244 | 0.1 | 75.0% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 79 (0.510) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 80 (0.460) | 120 (0.780) | 69/244 | 0.4 | 61.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 79 (0.510) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 257 (1.510) | 105/268 | 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 = | 250 (1.430) | 265 (1.530) | 101/274 | 0.1 | 67.8% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.020) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 254 (1.450) | 96/276 | 0.1 | 96.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 9 (0.050) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||