breseq version 0.29.0 revision 8f9c342918e4
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 | 1,168,895 | C→T | intergenic (‑63/‑178) | ycfQ ← / → bhsA | repressor for bhsA(ycfR)/biofilm, cell surface and signaling protein |
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 | 2,460,805 | G→A | L44L (CTG→TTG) | yfcZ ← | UPF0381 family protein |
RA | 3,399,666 | G→A | R105C (CGC→TGC) | mreC ← | cell wall structural complex MreBCD transmembrane component MreC |
RA | 3,410,240 | Δ1 bp | intergenic (+289/‑40) | prmA → / → dusB | methyltransferase for 50S ribosomal subunit protein L11/tRNA‑dihydrouridine synthase B |
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 | 3,815,808 | (A)8→7 | intergenic (‑40/+26) | pyrE ← / ← rph | orotate phosphoribosyltransferase/ribonuclease PH (defective);enzyme; Degradation of RNA; RNase PH |
RA | 4,186,605 | A→C | H419P (CAC→CCC) | rpoC → | RNA polymerase, beta prime subunit |
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 | 1209603 | 1209618 | 16 | 61 [0] | [0] 66 | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related |
* | * | ÷ | NC_000913 | 3423731–3424233 | 3424587–3424238 | 6–857 | 30 [29] | [29] 30 | [rrfD]–[rrlD] | [rrfD], [rrlD] |
Unassigned new junction evidence | |||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
* | ? | NC_000913 | 1207790 = | 0 (0.000) | 60 (1.090) | 51/266 | 0.2 | 100% | coding (290/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | NC_000913 | 1209619 = | 0 (0.000) | pseudogene (1/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | NC_000913 | = 1207805 | 0 (0.000) | 56 (1.020) | 46/266 | 0.3 | 100% | coding (305/630 nt) | stfP | e14 prophage; uncharacterized protein |
? | NC_000913 | = 1209602 | 0 (0.000) | pseudogene (18/501 nt) | stfE | pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related | |||||
* | ? | NC_000913 | = 1299498 | 0 (0.000) | 61 (1.020) | 57/290 | 0.1 | 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 |