mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
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 | 76,544 | C→A | P252P (CCG→CCT) | sgrR ← | DNA‑binding transcriptional dual regulator SgrR |
| RA | 243,989 | C→A | G149G (GGC→GGA) | lpcA → | D‑sedoheptulose 7‑phosphate isomerase |
| 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 | 963,186 | T→G | W398G (TGG→GGG) | rpsA → | 30S ribosomal subunit protein S1 |
| RA | 1,143,885 | C→A | P161P (CCG→CCT) | rne ← | ribonuclease E |
| RA | 1,333,004 | A→G | T653A (ACC→GCC) | topA → | DNA topoisomerase 1 |
| RA | 1,653,515 | G→T | A134E (GCA→GAA) | rspB ← | putative zinc‑binding dehydrogenase RspB |
| RA | 1,678,604 | G→T | A60S (GCA→TCA) | ydgH → | DUF1471 domain‑containing protein YdgH |
| RA | 1,701,775 | G→T | A273A (GCG→GCT) | malY → | negative regulator of MalT activity/cystathionine beta‑lyase |
| 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 | 2,199,672 | C→A | intergenic (+2374/‑607) | yehF → / → yehI | putative protein YehF/DUF4132 domain‑containing protein YehI |
| RA | 2,209,519 | G→T | P140P (CCG→CCT) | yehQ → | SWIM zinc finger domains‑containing protein YehQ |
| RA | 2,486,822 | C→A | P817T (CCT→ACT) | evgS → | sensory histidine kinase EvgS |
| RA | 2,574,798 | C→A | S69I (AGC→ATC) | eutQ ← | putative ethanolamine utilization protein EutQ |
| RA | 2,791,449 | C→A | R59R (CGC→CGA) | gabD → | NADP(+)‑dependent succinate‑semialdehyde dehydrogenase |
| RA | 2,798,603 | G→T | intergenic (‑108/‑561) | stpA ← / → alaE | DNA‑binding transcriptional repressor StpA with RNA chaperone activity/L‑alanine exporter |
| RA | 2,837,167 | C→A | E87* (GAG→TAG) | hypF ← | carbamoyltransferase HypF |
| RA | 3,008,372 | G→T | G288V (GGC→GTC) | ygeX → | 2,3‑diaminopropionate ammonia‑lyase |
| RA | 3,288,195 | G→T | D36Y (GAT→TAT) | yraI → | putative fimbrial chaperone YraI |
| 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 | 3,566,204 | C→A | L126L (CTG→CTT) | glgP ← | glycogen phosphorylase |
| RA | 3,636,973 | G→T | N146K (AAC→AAA) | yhiN ← | putative oxidoreductase YhiN |
| RA | 3,733,471 | C→A | P424Q (CCG→CAG) | xylG → | xylose ABC transporter ATP binding subunit |
| RA | 3,771,784 | C→A | intergenic (‑40/‑497) | yibI ← / → mtlA | DUF3302 domain‑containing protein YibI/mannitol‑specific PTS enzyme IICBA component |
| RA | 3,794,055 | C→A | G23G (GGC→GGA) | rfaD → | ADP‑L‑glycero‑D‑mannoheptose 6‑epimerase |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,912,052 | C→A | A539A (GCG→GCT) | glmS ← | L‑glutamine‑‑D‑fructose‑6‑phosphate aminotransferase |
| RA | 4,014,242 | C→A | A397E (GCG→GAG) | metE → | cobalamin‑independent homocysteine transmethylase |
| RA | 4,071,820 | G→T | Q278K (CAA→AAA) | yihT ← | 6‑deoxy‑6‑sulfofructose‑1‑phosphate aldolase |
| RA | 4,103,942 | C→A | G345V (GGC→GTC) | cpxA ← | sensory histidine kinase CpxA |
| RA | 4,157,191 | G→T | A114A (GCG→GCT) | argH → | argininosuccinate lyase |
| 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 | 3102949 | 3104072 | 1124 | 47 [40] | [43] 44 | mutY | mutY |
| * | * | ÷ | NC_000913 | 3423757–3424545 | 3424545 | 1–789 | 44 [43] | [40] 44 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | 1207790 = | 43 (0.270) | 193 (1.380) | 85/246 | 0.1 | 85.2% | coding (290/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | 1209619 = | 29 (0.210) | pseudogene (37/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1207805 | 42 (0.270) | 106 (0.760) | 61/246 | 0.5 | 76.2% | coding (305/630 nt) | ycfK | e14 prophage; protein StfP |
| ? | NC_000913 | = 1209602 | 29 (0.210) | pseudogene (54/537 nt) | stfE | e14 prophage; putative side tail fiber protein fragment | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 247 (1.610) | 101/270 | 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 = | 315 (1.990) | 303 (1.930) | 98/276 | 0.1 | 65.5% | coding (195/2382 nt) | yhcD | putative fimbrial usher protein YhcD |
| ? | NC_000913 | 3766087 = | 6 (0.040) | coding (3905/4134 nt) | rhsA | rhs element protein RhsA | |||||
| * | ? | NC_000913 | = 3653230 | NA (NA) | 196 (1.240) | 88/278 | 0.1 | 95.6% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3766089 | 9 (0.060) | coding (3907/4134 nt) | rhsA | rhs element protein RhsA | |||||