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
RA 61,461 G→A Q602* (CAG→TAG)  rapA ← RNA polymerase remodeling/recycling factor ATPase; RNA polymerase‑associated, ATP‑dependent RNA translocase
MC JC 257,908 Δ776 bp [crl] [crl]
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA 1,196,305 C→T R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
MC JC 1,978,503 Δ776 bp insB1–insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,132,787 A→C I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
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 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
MC JC 3,815,859 Δ82 bp [rph]–[rph] [rph], [rph]
MC JC 4,001,645 Δ5 bp coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
JC JC 4,049,912 IS2 (+) +5 bp noncoding (14‑18/109 nt) spf → Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
RA 4,184,543 C→A P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,277,820 G→T G118* (GGA→TGA)  soxR → redox‑sensitive transcriptional activator of soxS; autorepressor
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 1293040 1309434 16395 22 [0] [0] 29 tdk–[kch] tdk,insZ,insZ,insZ,adhE,ychE,oppA,oppB,oppC,oppD,oppF,yciU,clsA,yciY,[kch]
* * ÷ NC_000913 3423756–3424234 3424525–3424238 5–770 8 [7] [7] 9 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 4233770 4235411 1642 8 [7] [7] 8 [pgi] [pgi]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 257908 =NA (NA)22 (0.820) 22/284 0.2 100% noncoding (768/768 nt) IS1 repeat region
?NC_000913 = 1293039 0 (0.000)intergenic (‑117/‑488) hns/tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
* ? NC_000913 = 258675NA (NA)28 (1.040) 25/284 0.1 100% noncoding (1/768 nt) IS1 repeat region
?NC_000913 1309435 = 0 (0.000)coding (835/1254 nt) kch voltage‑gated potassium channel
* ? NC_000913 1207790 =12 (0.450)12 (0.500) 12/252 0.9 48.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 15 (0.630)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780511 (0.410)14 (0.590) 13/252 0.8 53.1% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 15 (0.630)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related