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 | 129,135 | G→T | V408V (GTG→GTT) | lpd → | lipoamide dehydrogenase |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 1,359,925 | G→T | N328K (AAC→AAA) | puuA ← | glutamate‑putrescine ligase |
| 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 | 2,015,254 | G→T | E125D (GAG→GAT) | fliG → | flagellar motor switch protein FliG |
| RA | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,425,329 | G→T | V196V (GTC→GTA) | hisQ ← | lysine/arginine/ornithine ABC transporter/histidine ABC transporter, membrane subunit HisQ |
| RA | 2,470,789 | G→T | intergenic (+327/+288) | yfdI → / ← yfdK | CPS‑53 (KpLE1) prophage; serotype specific glucosyl transferase/CPS‑53 (KpLE1) prophage; putative tail fiber assembly protein YfdK |
| RA | 2,547,948 | C→A | P426T (CCG→ACG) | murP → | N‑acetylmuramic acid‑specific PTS enzyme IICB component/anhydro‑N‑acetylmuramic acid transporter |
| RA | 2,611,955 | C→A | A19E (GCG→GAG) | hyfR → | DNA‑binding transcriptional activator HyfR |
| RA | 2,867,169 | A→G | I128T (ATC→ACC) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| RA | 2,974,644 | G→T | T457T (ACC→ACA) | aas ← | acyltransferase |
| RA | 3,008,155 | C→A | Q216K (CAA→AAA) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,232,125 | C→A | A154E (GCA→GAA) | fadH → | 2,4‑dienoyl‑CoA reductase |
| RA | 3,314,889 | C→A | A376S (GCG→TCG) | infB ← | translation initiation factor IF‑2 |
| RA | 3,354,487 | C→T | intergenic (‑437/‑238) | yhcC ← / → gltB | radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB |
| RA | 3,390,169 | G→T | R217I (AGA→ATA) | aaeR → | LysR‑type transcriptional regulator AaeR |
| RA | 3,560,455 | +G | pseudogene (151/758 nt) | glpR ← | DNA‑binding transcriptional repressor GlpR |
| RA | 3,604,429 | C→A | R13S (CGC→AGC) | rsmD → | 16S rRNA m(2)G966 methyltransferase |
| RA | 3,787,221 | C→A | G128G (GGC→GGA) | envC → | murein hydrolase activator EnvC |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,947,041 | C→A | intergenic (+9/+87) | trpT → / ← hdfR | tRNA‑Trp/DNA‑binding transcriptional dual regulator HdfR |
| RA | 3,993,027 | C→A | G625G (GGC→GGA) | cyaA → | adenylate cyclase |
| RA | 4,092,290 | G→T | A26D (GCC→GAC) | frvB ← | putative PTS enzyme IIBC component FrvB |
| 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 |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102944 | 3104055 | 1112 | 15 [13] | [13] 14 | [mutY] | [mutY] |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424525–3424239 | 6–756 | 15 [13] | [13] 16 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 22 (0.410) | 68 (1.450) | 45/246 | 0.1 | 78.4% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 18 (0.380) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 22 (0.410) | 30 (0.640) | 23/246 | 0.9 | 61.6% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 18 (0.380) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 69 (1.340) | 48/270 | 0.1 | 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 = | 64 (1.200) | 79 (1.500) | 56/276 | 0.0 | 70.7% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 2 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | 3583371 = | NA (NA) | 101 (1.900) | 66/278 | 0.0 | NA | pseudogene (334/390 nt) | yrhA | putative uncharacterized protein YrhA |
| ? | NC_000913 | = 3584195 | NA (NA) | noncoding (768/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 3583379 | 4 (0.080) | 69 (1.300) | 51/278 | 0.1 | 94.5% | pseudogene (342/390 nt) | yrhA | putative uncharacterized protein YrhA |
| ? | NC_000913 | 3583428 = | NA (NA) | noncoding (1/768 nt) | IS1 | repeat region | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 74 (1.390) | 49/278 | 0.1 | 100% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 0 (0.000) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||