breseq  version 0.35.4  revision f352f80f4bc9
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 668,742 C→G E99Q (GAA→CAA)  rsfS ← ribosomal silencing factor
RA 1,399,451 T→G S26R (AGC→CGC)  fnr ← oxygen‑sensing anaerobic growth regulon transcriptional regulator FNR; autorepressor
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 2,513,351 C→A L104M (CTG→ATG)  nupC → nucleoside (except guanosine) transporter
RA 2,662,004 T→A E43V (GAA→GTA)  iscR ← isc operon transcriptional repressor; suf operon transcriptional activator; oxidative stress‑ and iron starvation‑inducible; autorepressor
RA 2,664,591 C→A P68T (CCT→ACT)  yfhR → putative S9 family prolyl oligopeptidase
RA 3,486,594 A→C T159P (ACT→CCT)  crp → cAMP‑activated global transcription factor, mediator of catabolite repression
RA 3,552,719 G→T intergenic (‑246/‑366) malP ← / → malT maltodextrin phosphorylase/mal regulon transcriptional activator
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 4,015,910 Δ1 bp coding (260/816 nt) ysgA ← putative carboxymethylenebutenolidase
JC 4,233,757 +46 bp intergenic (‑524/‑583) lysC ← / → yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
JC 4,233,840 +46 bp intergenic (‑607/‑500) lysC ← / → yjbE lysine‑sensitive aspartokinase 3/extracellular polysaccharide production threonine‑rich protein
RA 4,294,815 +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_3_KO_pgi 2101364 2102890–2101747 384–1527 194 [0] [84] 86 wbbL–[insH1] wbbL,[insH1]
* * ÷ NC_000913_3_KO_pgi 3423723–3424234 3424591–3424238 5–869 89 [85] [85] 86 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_KO_pgi = 12994981 (0.010)171 (1.160) 110/266 0.1 99.7% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913_3_KO_pgi 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913_3_KO_pgi = 21013630 (0.000)188 (1.240) 110/274 0.2 100% intergenic (‑95/+33) gnd/wbbL 6‑phosphogluconate dehydrogenase, decarboxylating/pseudogene, lipopolysaccharide biosynthesis protein
?NC_000913_3_KO_pgi 2101749 = NA (NA)intergenic (‑5/+146) wbbL/insH1 pseudogene, lipopolysaccharide biosynthesis protein/IS5 transposase and trans‑activator