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 | 204,575 | T→C | V28A (GTC→GCC) | rnhB → | RNase HII |
| MC JC | 257,908 | Δ776 bp | insB9–[crl] | insB9, insA9, [crl] | |
| RA | 327,128 | G→T | R40R (CGC→CGA) | betA ← | choline dehydrogenase |
| RA | 404,797 | C→T | N365N (AAC→AAT) | dgcC → | diguanylate cyclase DgcC |
| RA | 675,005 | G→T | intergenic (‑222/‑13) | leuS ← / → ybeL | leucine‑‑tRNA ligase/DUF1451 domain‑containing protein YbeL |
| RA | 889,923 | A→G | intergenic (‑104/‑166) | ybjL ← / → ybjM | putative transport protein YbjL/putative inner membrane protein |
| RA | 922,467 | G→T | L42I (CTA→ATA) | cspD ← | DNA replication inhibitor |
| RA | 924,668 | G→T | A469S (GCG→TCG) | clpA → | ATP‑dependent Clp protease ATP‑binding subunit ClpA |
| RA | 1,071,813 | G→T | A116E (GCG→GAG) | rutC ← | putative aminoacrylate peracid reductase |
| RA | 1,091,827 | G→T | L155I (CTT→ATT) | pgaA ← | partially deacetylated poly‑beta‑1,6‑N‑acetyl‑D‑glucosamine outer membrane porin |
| RA | 1,477,029 | C→T | A629V (GCG→GTG) | ydbD → | DUF2773 domain‑containing protein YdbD |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,754,268 | A→G | G70G (GGT→GGC) | ydhY ← | putative 4Fe‑4S ferredoxin‑type protein |
| 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 | 2,173,363 | Δ2 bp | pseudogene (915‑916/1358 nt) | gatC ← | galactitol‑specific PTS enzyme IIC component |
| RA | 2,513,328 | G→T | C96F (TGC→TTC) | nupC → | nucleoside:H(+) symporter NupC |
| RA | 2,534,731 | C→A | A222A (GCC→GCA) | ptsI → | PTS enzyme I |
| RA | 2,566,134 | G→T | P251T (CCC→ACC) | eutA ← | reactivating factor for ethanolamine ammonia‑lyase EutBC |
| RA | 2,640,043 | C→A | R178L (CGC→CTC) | hisS ← | histidine‑‑tRNA ligase |
| RA | 2,753,321 | C→A | T509T (ACC→ACA) | recN → | DNA repair protein RecN |
| RA | 2,962,730 | C→A | S12I (AGC→ATC) | ppdC ← | putative YgdA |
| RA | 3,019,683 | C→A | R175S (CGT→AGT) | ssnA → | putative aminohydrolase |
| RA | 3,322,290 | G→T | N72K (AAC→AAA) | secG ← | Sec translocon subunit SecG |
| 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 | 3,700,153 | G→T | noncoding (18/64 nt) | rdlD → | antisense regulatory RNA RdlD |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 4,261,710 | C→A | S14R (AGC→AGA) | dusA → | tRNA‑dihydrouridine synthase A |
| RA | 4,270,214 | G→T | intergenic (+87/‑24) | aphA → / → yjbQ | acid phosphatase/phosphotransferase/UPF0047 protein YjbQ |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,158 | G→T | T3K (ACG→AAG) | phnC ← | phosphonate ABC transporter ATP binding subunit |
| RA | 4,497,190 | G→T | pseudogene (441/1191 nt) | intB → | KpLE2 phage‑like element; putative integrase |
| RA | 4,524,734 | G→T | H93N (CAT→AAT) | yjhH ← | KpLE2 phage‑like element; putative 2‑dehydro‑3‑deoxy‑D‑pentonate aldolase |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 3102970 | 3104069 | 1100 | 32 [30] | [27] 31 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423770–3424234 | 3424526–3424239 | 6–757 | 31 [26] | [30] 35 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 82 (0.700) | 77 (0.740) | 56/244 | 0.3 | 50.1% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 81 (0.780) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 133 (1.160) | 78/268 | 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 = | 212 (1.800) | 210 (1.800) | 94/274 | 0.0 | 66.2% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 4 (0.030) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 145 (1.230) | 67/276 | 0.3 | 96.7% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 5 (0.040) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||