mutation predictions | marginal predictions | summary statistics | genome diff | command line log
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breseq version 0.33.1 revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | ||||||
|---|---|---|---|---|---|---|
| evidence | position | mutation | freq | annotation | gene | description |
| RA | 70,657:1 | +G | 5.3% | coding (271/879 nt) | araC → | ara regulon transcriptional activator; autorepressor |
| MC JC | 257,908 | Δ776 bp | 100% | [crl] | [crl] | |
| RA | 693,453 | A→G | 5.2% | intergenic (‑75/+78) | ybeZ ← / ← miaB | heat shock protein, putative NTPase; PhoH‑like protein/tRNA‑i(6)A37 methylthiotransferase |
| RA | 1,685,527 | A→G | 100% | G354G (GGT→GGC) | fumC ← | fumarate hydratase (fumarase C),aerobic Class II |
| RA | 2,053,561 | A→T | 6.1% | intergenic (‑233/‑82) | yeeL ← / → shiA | pseudogene, glycosyltransferase homology/shikimate transporter |
| RA | 2,131,769 | T→C | 7.2% | H101R (CAT→CGT) | wcaC ← | putative glycosyl transferase |
| RA | 2,145,313 | C→A | 100% | S683Y (TCC→TAC) | yegE → | putative diguanylate cyclase |
| RA | 2,173,361 | Δ2 bp | 100% | pseudogene (1‑2/442 nt) | gatC ← | pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC |
| RA | 2,318,095 | C→G | 100% | L594F (TTG→TTC) | rcsC ← | hybrid sensory kinase in two‑component regulatory system with RcsB and YojN |
| RA | 2,535,934 | T→C | 100% | I34T (ATC→ACC) | crr → | glucose‑specific enzyme IIA component of PTS |
| RA | 2,750,922 | G→A | 5.1% | C31Y (TGC→TAC) | nadK → | NAD kinase |
| RA | 2,966,420 | G→T | 33.8% | A672E (GCG→GAG) | ptsP ← | PEP‑protein phosphotransferase enzyme I; GAF domain containing protein |
| RA | 3,307,900 | A→G | 5.0% | C12R (TGT→CGT) | yrbN ← | uncharacterized protein |
| RA | 3,560,455:1 | +G | 100% | 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 | 4,115,770 | C→T | 6.3% | A485T (GCA→ACA) | glpK ← | glycerol kinase |
| RA | 4,116,538 | T→G | 93.8% | N229H (AAC→CAC) | glpK ← | glycerol kinase |
| RA | 4,296,060 | C→T | 27.7% | intergenic (+266/+376) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,268 | T→C | 15.3% | intergenic (+474/+168) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| RA | 4,296,380:1 | +CG | 100% | intergenic (+586/+56) | gltP → / ← yjcO | glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 384723 | 385183 | 461 | 26 [25] | [25] 27 | yaiS/tauA | putative PIG‑L family deacetylase/taurine ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 583140 | 583747 | 608 | 27 [25] | [24] 26 | [appY] | [appY] |
| * | * | ÷ | NC_000913 | 1299473 | 1300729 | 1257 | 30 [25] | [24] 26 | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| * | * | ÷ | NC_000913 | 1978398 | 1979316 | 919 | 26 [24] | [24] 26 | insB1–insA | insB1,insA |
| * | * | ÷ | NC_000913 | 2103891 | 2104188 | 298 | 26 [25] | [25] 30 | wbbK | lipopolysaccharide biosynthesis protein |
| * | * | ÷ | NC_000913 | 2994985 | 2995464 | 480 | 26 [25] | [25] 26 | [ygeK]–[ygeN] | [ygeK],[ygeN] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 258675 | NA (NA) | 5 (0.070) | 4/432 | NT | 5.1% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 1293022 | 90 (1.240) | intergenic (‑100/‑505) | hns/tdk | global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase | |||||
| * | ? | NC_000913 | 1207790 = | 23 (0.300) | 39 (0.560) | 31/400 | NT | 63.8% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | 1209619 = | 23 (0.330) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1207805 | 23 (0.300) | 45 (0.640) | 34/400 | NT | 67.0% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
| ? | NC_000913 | = 1209602 | 23 (0.330) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
| * | ? | NC_000913 | = 1299498 | 0 (0.000) | 20 (0.270) | 18/424 | NT | 100% | intergenic (+253/‑1684) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein |
| ? | NC_000913 | 1300698 = | 0 (0.000) | intergenic (+1453/‑484) | ychE/oppA | UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein | |||||
| * | ? | NC_000913 | = 1978502 | 0 (0.000) | 17 (0.230) | 17/416 | NT | 100% | intergenic (‑305/+16) | flhD/insB1 | flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B |
| ? | NC_000913 | 1979279 = | 0 (0.000) | intergenic (‑64/‑474) | insA/uspC | IS1 repressor TnpA/universal stress protein | |||||
| * | ? | NC_000913 | 3721045 = | 85 (1.120) | 237 (3.150) | 113/430 | NT | 76.0% | noncoding (413/1443 nt) | IS150 | repeat region |
| ? | NC_000913 | = 3839774 | 65 (0.860) | coding (220/819 nt) | nlpA | cytoplasmic membrane lipoprotein‑28 | |||||