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 663,746 C→T S73N (AGC→AAC)  dacA ← D‑alanyl‑D‑alanine carboxypeptidase (penicillin‑binding protein 5)
JC JC 1,293,196 IS5 (+) +4 bp intergenic (‑274/‑328) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,903,497 T→C I139T (ATC→ACC)  manY → mannose‑specific enzyme IIC component of PTS
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
MC JC 2,810,080 Δ1,165 bp [ygaZ]–[mprA] [ygaZ], ygaH, [mprA]
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 3,922,483 G→A intergenic (‑43/+574) atpI ← / ← rsmG ATP synthase, membrane‑bound accessory factor/16S rRNA m(7)G527 methyltransferase, SAM‑dependent; glucose‑inhibited cell‑division protein
RA 3,966,727 C→T P104L (CCG→CTG)  rho → transcription termination factor
RA 4,183,802 A→G D853G (GAC→GGC)  rpoB → RNA polymerase, beta 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 3423714–3424234 3424594–3424238 5–881 41 [38] [39] 40 [rrfD]–[rrlD] [rrfD], [rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =28 (0.370)46 (0.690) 43/266 1.1 62.6% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 30 (0.450)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780528 (0.370)31 (0.460) 30/266 2.8 53.0% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 30 (0.450)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)83 (1.140) 76/290 0.0 100% 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 = 2729953NA (NA)56 (0.750) 51/296 0.9 NA noncoding (1205/1542 nt) rrsG 16S ribosomal RNA of rrnG operon
?NC_000913 2729960 = NA (NA)noncoding (1198/1542 nt) rrsG 16S ribosomal RNA of rrnG operon