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
RA 111,726 C→T A41T (GCT→ACT)  yacG ← DNA gyrase inhibitor
MC JC 257,908 Δ776 bp [crl] [crl]
RA 264,098 G→T L50L (CTC→CTA ykfH ← uncharacterized protein
RA 275,065 G→A T18I (ACC→ATC)  insH1 ← IS5 transposase and trans‑activator
RA 482,230 G→A P725L (CCG→CTG)  acrB ← multidrug efflux system protein
RA 977,557 C→T T411M (ACG→ATG)  mukB → chromosome condensin MukBEF, ATPase and DNA‑binding subunit
RA 1,197,502 C→T G11R (GGA→AGA)  ymfD ← e14 prophage; putative SAM‑dependent methyltransferase
MC JC 1,299,499 Δ1,199 bp intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
RA 1,544,022 1 bp→AA coding (39/1389 nt) narU ← nitrate/nitrite transporter
RA 1,774,576 G→A G263E (GGG→GAG)  ydiB → quinate/shikimate 5‑dehydrogenase, NAD(P)‑binding
MC JC 1,978,503 Δ776 bp insB1insA insB1, insA
RA 2,106,741 A→T S162S (TCT→TCA wbbH ← O‑antigen polymerase
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 2,679,525 G→T A1074D (GCT→GAT)  yphG ← DUF4380 domain‑containing TPR repeat protein
RA 2,795,396 C→A Q382K (CAG→AAG)  gabP → gamma‑aminobutyrate transporter
RA 2,817,170 C→A E112* (GAA→TAA)  yqaB ← fructose‑1‑P and 6‑phosphogluconate phosphatase
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 4,111,482 G→T intergenic (+797/+115) cdh → / ← yiiQ CDP‑diacylglycerol phosphotidylhydrolase/DUF1454 family putative periplasmic protein
RA 4,111,662 G→A L179L (CTG→TTG)  yiiQ ← DUF1454 family putative periplasmic protein
RA 4,183,186 G→C D654H (GAC→CAC)  rpoB → RNA polymerase, beta subunit
RA 4,296,363 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,392,466 C→G noncoding (13/76 nt) glyX → tRNA‑Gly
RA 4,604,698 C→A A186E (GCA→GAA)  bglJ → bgl operon transcriptional activator

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913_3_hsa_tpiA 366186 366398 213 27 [24] [23] 26 [lacZ] [lacZ]
* * ÷ NC_000913_3_hsa_tpiA 3423758–3424234 3424556–3424238 5–799 25 [23] [24] 26 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913_3_hsa_tpiA 1207790 =8 (0.130)45 (0.840) 38/250 0.5 88.2% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_hsa_tpiA 1209619 = 5 (0.090)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913_3_hsa_tpiA = 12078058 (0.130)56 (1.050) 48/250 0.1 90.3% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913_3_hsa_tpiA = 1209602 5 (0.090)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related