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 | 275,065 | G→A | T18I (ACC→ATC) | insH1 ← | IS5 transposase and trans‑activator |
| RA | 285,318 | C→A | intergenic (+150/‑77) | yagF → / → yagG | CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter |
| RA | 389,925 | (T)6→7 | intergenic (‑198/‑326) | hemB ← / → yaiT | 5‑aminolevulinate dehydratase (porphobilinogen synthase)/pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein |
| RA | 482,230 | G→A | P725L (CCG→CTG) | acrB ← | multidrug efflux system protein |
| JC | 1,158,725 | Δ96 bp | coding (857‑952/1434 nt) | ptsG → | fused glucose‑specific PTS enzymes: IIB component/IIC component |
| RA | 1,544,022 | 1 bp→AA | coding (39/1389 nt) | narU ← | nitrate/nitrite transporter |
| RA | 1,726,378 | C→A | S119* (TCA→TAA) | nemR → | transcriptional repressor for the nemRA‑gloA operon, quinone‑, glyoxal‑, and HOCl‑activated |
| RA | 1,734,464 | G→C | T10T (ACG→ACC) | mepH → | murein DD‑endopeptidase, space‑maker hydrolase |
| RA | 1,757,058 | G→C | G454A (GGT→GCT) | pykF → | pyruvate kinase I |
| RA | 1,773,043 | G→T | V178L (GTA→TTA) | ydiN → | putative MFS transporter, membrane protein |
| RA | 1,774,576 | G→A | G263E (GGG→GAG) | ydiB → | quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding |
| 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 | 2,173,363 | 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 | 2,977,097 | Δ1 bp | coding (499/1032 nt) | galR → | galactose‑inducible d‑galactose regulon transcriptional repressor; autorepressor |
| 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 | 3,946,711 | C→A | noncoding (12/120 nt) | rrfC → | 5S ribosomal RNA of rrnC operon |
| RA | 4,183,195 | A→T | T657S (ACC→TCC) | rpoB → | RNA polymerase, beta subunit |
| RA | 4,296,363 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,604,698 | 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_hsa_tpiA | 1196219 | 1211471 | 15253 | 35 [30] | [30] 32 | [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_hsa_tpiA | 1394106 | 1397161–1396041 | 1936–3056 | 86 [5] | [31] 32 | [mppA]–insH1 | [mppA],ynaI,insH1 |
| * | * | ÷ | NC_000913_3_hsa_tpiA | 3423737–3424234 | 3424544–3424238 | 5–808 | 32 [30] | [31] 32 | [rrfD]–[rrlD] | [rrfD],[rrlD] |
| * | * | ÷ | NC_000913_3_hsa_tpiA | 3943479–3944053 | 3946537–3945915 | 1863–3059 | 32 [31] | [31] 32 | [gltU]–[rrlC] | [gltU],[rrlC] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913_3_hsa_tpiA | = 1299498 | 0 (0.000) | 57 (0.780) | 51/264 | 0.6 | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913_3_hsa_tpiA | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913_3_hsa_tpiA | = 1394105 | 5 (0.070) | 79 (1.040) | 67/272 | 0.2 | 94.0% | coding (879/1614 nt) | mppA | murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit |
| ? | NC_000913_3_hsa_tpiA | 1396044 = | NA (NA) | intergenic (‑122/‑32) | ynaI/insH1 | mechanosensitive channel protein, very small conductance/IS5 transposase and trans‑activator | |||||