breseq version 0.33.1 revision 8505477f25b3
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] | |
JC JC | 302,732 | IS2 (–) +5 bp | intergenic (‑159/‑255) | paoA ← / → yagU | PaoABC aldehyde oxidoreductase, 2Fe‑2S subunit/DUF1440 family inner membrane acid resistance 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 | 1,514,951 | G→T | A64S (GCC→TCC) | ydcV → | putative ABC transporter permease |
RA | 1,610,724 | T→C | intergenic (‑44/+183) | uxaB ← / ← yneF | altronate oxidoreductase, NAD‑dependent/putative membrane‑bound diguanylate cyclase |
MC JC | 1,867,235 | Δ4 bp | coding (328‑331/1935 nt) | yeaG → | protein kinase, endogenous substrate unidentified; autokinase |
RA | 1,881,844 | T→G | intergenic (‑35/‑68) | dmlR ← / → dmlA | transcriptional activator of dmlA/D‑malate oxidase, NAD‑dependent; putative tartrate dehydrogenase |
MC JC | 1,978,503 | Δ776 bp | insB1–insA | insB1, insA | |
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 | 2,416,674 | C→A | S643Y (TCT→TAT) | pta → | phosphate acetyltransferase |
JC | 2,860,769 | Δ20 bp | coding (447‑466/768 nt) | ygbI ← | DeoR family putative transcriptional regulator |
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 | G→T | intergenic (‑42/+24) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
RA | 3,951,538 | Δ1 bp | pseudogene (979/984 nt) | ilvG → | pseudogene, acetolactate synthase 2 large subunit, valine‑insensitive; acetolactate synthase II, large subunit, cryptic, interrupted |
RA | 3,991,184 | G→T | R11I (AGA→ATA) | cyaA → | adenylate cyclase |
RA | 4,001,885 | G→T | D154Y (GAC→TAC) | corA → | magnesium/nickel/cobalt transporter |
RA | 4,296,381 | +GC | intergenic (+587/+55) | 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 | 1196256 | 1211579 | 15324 | 62 [58] | [58] 59 | [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 |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 105 (0.810) | 72/540 | 0.4 | 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 |