mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
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 | 1,142,730 | A→C | P546P (CCT→CCG) | rne ← | ribonuclease E |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,400,497 | T→G | H426P (CAC→CCC) | abgT ← | p‑aminobenzoyl glutamate:H(+) symporter |
| MC JC | 1,586,443 | Δ555 bp | [ydeP]–[ydeQ] | [ydeP], [ydeQ] | |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,695,565 | C→T | G169G (GGG→GGA) | uidA ← | beta‑glucuronidase |
| RA | 1,699,275 | C→T | intergenic (‑95/‑80) | malI ← / → malX | DNA‑binding transcriptional repressor MalI/PTS enzyme IIBC component MalX |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| RA | 2,173,363 | Δ2 bp | intergenic (‑490/+918) | gatD ← / ← gatB | galactitol‑1‑phosphate 5‑dehydrogenase/galactitol‑specific PTS enzyme IIB component |
| RA | 2,823,288 | C→T | G161D (GGC→GAC) | recA ← | DNA recombination/repair protein RecA |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,893,294 | Δ1 bp | coding (638/1272 nt) | ygcN → | putative oxidoreductase with FAD/NAD(P)‑binding domain |
| MC JC | 3,090,238 | 688 bp→74 bp | [yggI]–[endA] | [yggI], [endA] | |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| JC JC | 3,806,046 | IS1 (+) +9 bp | coding (1014‑1022/1125 nt) | waaG ← | lipopolysaccharide glucosyltransferase I |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,585,480 | G→A | Q428* (CAA→TAA) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,602,509 | C→T | W117* (TGG→TAG) | yjjP ← | putative succinate exporter YjjP |
| RA | 4,616,669 | G→T | L133I (CTA→ATA) | yjjI ← | DUF3029 domain‑containing protein YjjI |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 275509 | 276408 | 900 | 26 [0] | [2] 3 | mmuP | S‑methyl‑L‑methionine transporter |
| * | * | ÷ | NC_000913 | 276648 | 277135 | 488 | 3 [2] | [2] 3 | [mmuP]–[mmuM] | [mmuP],[mmuM] |
| * | * | ÷ | NC_000913 | 277302 | 278363 | 1062 | 3 [2] | [2] 3 | [mmuM]–[afuC] | [mmuM],[afuC] |
| * | * | ÷ | NC_000913 | 278612 | 309899 | 31288 | 3 [2] | [2] 4 | [afuC]–[ecpB] | [afuC],insB2,insA2,yagB,yagA,yagE,yagF,yagG,yagH,xynR,argF,argL,ykgS,insB3,insA3,yagJ,yagK,yagL,yagM,ykgV,yagN,intF,yagP,paoD,paoC,paoB,paoA,yagU,ykgJ,ecpE,ecpD,ecpC,[ecpB] |
| * | * | ÷ | NC_000913 | 310053 | 322552 | 12500 | 4 [2] | [2] 3 | ecpA–[ykgF] | ecpA,matA,ykgL,ykgO,ykgM,ykgR,insE1,insF1,rclC,rclB,rclA,rclR,ykgE,[ykgF] |
| * | * | ÷ | NC_000913 | 322756 | 372740 | 49985 | 3 [2] | [2] 3 | [ykgF]–[mhpD] | [ykgF],ykgG,ykgH,betA,betB,betI,betT,yahV,pdeL,yahB,yahC,yahD,yahE,yahF,yahG,yahH,yahI,yahJ,yahK,yahL,yahM,yahN,yahO,prpR,prpB,prpC,prpD,prpE,codB,codA,cynR,cynT,cynS,cynX,lacA,lacY,lacZ,lacI,mhpR,mhpA,mhpB,mhpC,[mhpD] |
| * | * | ÷ | NC_000913 | 1694762 | 1695469 | 708 | 10 [1] | [0] 5 | uidA | beta‑glucuronidase |
| * | * | ÷ | NC_000913 | 3423903–3424234 | 3424415–3424238 | 5–513 | 3 [2] | [2] 5 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4628621 | 4629789 | 1169 | 29 [0] | [1] 3 | [ettA] | [ettA] |
| * | * | ÷ | NC_000913 | 4629841 | 4634846 | 5006 | 3 [2] | [1] 29 | [ettA]–[rob] | [ettA],slt,trpR,yjjX,ytjC,[rob] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 275508 | 0 (0.000) | 26 (0.470) | 25/462 | 0.8 | 96.3% | coding (184/1404 nt) | mmuP | S‑methyl‑L‑methionine transporter |
| ? | NC_000913 | 372749 = | 2 (0.040) | coding (635/810 nt) | mhpD | 2‑hydroxypentadienoate hydratase | |||||
| * | ? | NC_000913 | 1207790 = | 18 (0.310) | 19 (0.350) | 17/450 | 1.2 | 57.8% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 11 (0.210) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 15 (0.260) | 20 (0.370) | 19/450 | 1.1 | 61.5% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 11 (0.210) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 19 (0.340) | 18/474 | 1.2 | 100% | intergenic (+253/‑69) | ychE/insH21 | MarC family putative inner membrane protein YchE/IS5 family transposase and trans‑activator |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+151/‑484) | insH21/oppA | IS5 family transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 4628620 | 0 (0.000) | 28 (0.490) | 28/478 | 0.7 | 100% | intergenic (+73/+235) | nadR/ettA | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR/energy‑dependent translational throttle protein EttA |
| ? | NC_000913 | 4634847 = | 0 (0.000) | coding (464/870 nt) | rob | DNA‑binding transcriptional dual regulator Rob | |||||