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 |
| MC JC | 257,908 | Δ776 bp | [crl] | [crl] | |
| RA | 264,098 | G→T | L50L (CTC→CTA) | ykfH ← | uncharacterized protein |
| RA | 482,230 | G→A | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| RA | 1,196,220 | C→T | H366H (CAC→CAT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,232 | C→T | T370T (ACC→ACT) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,245 | T→C | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,196,247 | A→G | L375M (TTA→CTG) | icd → | isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase |
| RA | 1,544,022 | 1 bp→AA | coding (39/1389 nt) | narU ← | nitrate/nitrite transporter |
| MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
| RA | 2,106,741 | A→T | S162S (TCT→TCA) | wbbH ← | O‑antigen polymerase |
| RA | 2,111,423 | G→T | A185E (GCG→GAG) | rfbD ← | dTDP‑L‑rhamnose synthase, NAD(P)‑dependent dTDP‑4‑dehydrorhamnose reductase subunit |
| RA | 2,173,363 | Δ2 bp | intergenic (‑1/+1) | gatC ← / ← gatC | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,679,525 | G→T | A1074D (GCT→GAT) | yphG ← | DUF4380 domain‑containing TPR repeat protein |
| RA | 2,795,396 | C→A | Q382K (CAG→AAG) | gabP → | gamma‑aminobutyrate transporter |
| RA | 2,817,170 | C→A | E112* (GAA→TAA) | yqaB ← | fructose‑1‑P and 6‑phosphogluconate phosphatase |
| RA | 3,560,455 | +G | intergenic (‑2/+1) | glpR ← / ← glpR | pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon |
| RA | 3,815,810 | Δ1 bp | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
| RA | 4,296,411 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,746 | C→A | A186E (GCA→GAA) | bglJ → | bgl operon transcriptional activator |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913_3_vch_tpiA | 366237 | 366398 | 162 | 6 [4] | [5] 7 | [lacZ] | [lacZ] |
| * | * | ÷ | NC_000913_3_vch_tpiA | 1196270 | 1211448 | 15179 | 6 [5] | [5] 6 | [icd]–[icdC] | [icd],ymfD,ymfE,lit,intE,xisE,ymfI,ymfJ,cohE,croE,ymfL,ymfM,oweE,aaaE,ymfR,beeE,jayE,ymfQ,stfP,tfaP,tfaE,stfE,pinE,mcrA,[icdC] |
| * | * | ÷ | NC_000913_3_vch_tpiA | 3423775–3424542 | 3424542 | 1–768 | 6 [5] | [5] 6 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_vch_tpiA | 1096961 = | 13 (0.520) | 4 (0.240) +47 bp |
3/192 | 2.4 | 31.5% | noncoding (1096961/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 1097243 = | NA (NA) | noncoding (1097243/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | = 1299498 | 0 (0.000) | 20 (0.830) | 18/278 | 0.4 | 100% | noncoding (1299498/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 1300698 = | 0 (0.000) | noncoding (1300698/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | 1552101 = | NA (NA) | 7 (0.310) | 7/262 | 1.8 | NA | noncoding (31/97 nt) | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP120 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site |
| ? | NC_000913_3_vch_tpiA | 1552249 = | NA (NA) | noncoding (1/97 nt) | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | RIP121 (repetitive extragenic palindromic) element; contains 2 REP sequences and 1 IHF site | |||||
| * | ? | NC_000913_3_vch_tpiA | 2161648 = | 15 (0.600) | 5 (0.200) | 5/282 | 2.6 | 23.4% | noncoding (2161648/4641682 nt) | repeat_region | repeat region |
| ? | NC_000913_3_vch_tpiA | 2161675 = | 18 (0.730) | noncoding (2161675/4641682 nt) | repeat_region | repeat region | |||||
| * | ? | NC_000913_3_vch_tpiA | = 3674455 | NA (NA) | 4 (0.170) | 4/276 | 2.9 | NA | noncoding (75/93 nt) | REP263 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP263 (repetitive extragenic palindromic) element; contains 2 REP sequences |
| ? | NC_000913_3_vch_tpiA | = 3674459 | NA (NA) | noncoding (79/93 nt) | REP263 (repetitive extragenic palindromic) element; contains 2 REP sequences | REP263 (repetitive extragenic palindromic) element; contains 2 REP sequences | |||||