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 | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| 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 | 2,880,635 | T→C | L138L (TTA→TTG) | casD ← | type I‑E CRISPR system Cascade subunit CasD |
| 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] | |
| MC JC | 3,131,341 | Δ128 bp | IS5‑mediated | yghQ ← | putative transport protein YghQ |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| JC JC | 3,807,520 | IS1 (–) +8 bp | coding (572‑579/1035 nt) | waaQ ← | lipopolysaccharide core heptosyltransferase 3 |
| 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 |
| MC JC | 4,628,621 | Δ6,226 bp | ettA–[rob] | ettA, slt, trpR, yjjX, ytjC, [rob] | |
| 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 | 257908–258676 | 258682 | 7–775 | 23 [0] | [0] 3 | insB9–[crl] | insB9,insA9,[crl] |
| * | * | ÷ | NC_000913 | 275509 | 321802 | 46294 | 32 [0] | [2] 3 | [mmuP]–[ykgE] | [mmuP],mmuM,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,ecpA,matA,ykgL,ykgO,ykgM,ykgR,insE1,insF1,rclC,rclB,rclA,rclR,[ykgE] |
| * | * | ÷ | NC_000913 | 321859 | 348973 | 27115 | 3 [1] | [2] 3 | [ykgE]–[prpB] | [ykgE],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] |
| * | * | ÷ | NC_000913 | 348977 | 372744 | 23768 | 3 [2] | [2] 4 | [prpB]–[mhpD] | [prpB],prpC,prpD,prpE,codB,codA,cynR,cynT,cynS,cynX,lacA,lacY,lacZ,lacI,mhpR,mhpA,mhpB,mhpC,[mhpD] |
| * | * | ÷ | NC_000913 | 1694762 | 1695469 | 708 | 4 [0] | [0] 3 | uidA | beta‑glucuronidase |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 257907 | 0 (0.000) | 23 (0.520) | 22/460 | 0.7 | 100% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 275508 | 0 (0.000) | 32 (0.730) | 30/456 | 0.4 | 98.5% | coding (184/1404 nt) | mmuP | S‑methyl‑L‑methionine transporter |
| ? | NC_000913 | 372749 = | 1 (0.020) | coding (635/810 nt) | mhpD | 2‑hydroxypentadienoate hydratase | |||||
| * | ? | NC_000913 | 1207790 = | 19 (0.410) | 12 (0.280) | 12/444 | 1.4 | 43.9% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 13 (0.300) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 16 (0.350) | 23 (0.540) | 22/444 | 0.7 | 62.2% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 13 (0.300) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||