breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 701,374 C→T 7.4% R74H (CGC→CAC)  nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA 701,554 A→G 5.3% L14P (CTC→CCC)  nagC ← N‑acetylglucosamine‑inducible nag divergent operon transcriptional repressor
RA 702,330 Δ1 bp 6.7% coding (422/1149 nt) nagA ← N‑acetylglucosamine‑6‑phosphate deacetylase
RA 1,158,171 Δ1 bp 6.0% coding (303/1434 nt) ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
JC 1,159,282 +AGT 21.6% coding (1414/1434 nt) ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
JC JC 1,159,287 IS2 (–) +5 bp 7.3% coding (1419‑1423/1434 nt) ptsG → fused glucose‑specific PTS enzymes: IIB component/IIC component
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
MC JC 1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
JC 1,326,599 Δ36 bp 9.4% coding (1854‑1889/1896 nt) yciQ → enhancer of membrane protein expression; putative inner membrane protein
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,304,522 G→T 6.5% intergenic (+129/+586) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,537 A→G 6.5% intergenic (+144/+571) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,567 C→T 6.1% intergenic (+174/+541) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,304,798 T→C 12.3% intergenic (+405/+310) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,314,716 C→A 9.0% A410E (GCG→GAG)  rcsD → phosphotransfer intermediate protein in two‑component regulatory system with RcsBC
JC 2,765,412 Δ8 bp 6.9% intergenic (‑259/+94) yfjL ← / ← yfjM CP4‑57 putative defective prophage, DUF4297/DUF1837 polymorphic toxin family protein/CP4‑57 prophage; uncharacterized protein
RA 3,560,455:1 +G 100% 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 100% [rph][rph] [rph], [rph]
MC JC 3,909,312 Δ774 bp 100% [pstA][pstC] [pstA], [pstC]
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,171,648 A→C 100% noncoding (12/120 nt) rrfB → 5S ribosomal RNA of rrnB operon
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 14.5% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→G 29.4% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 30.9% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 12.4% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,325,948 A→G 6.3% intergenic (‑207/+451) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423882–3424232 3424404–3424238 7–523 52 [51] [49] 53 rrlD 23S ribosomal RNA of rrnD operon
* * ÷ NC_000913 4110665 4111532 868 55 [50] [50] 57 [cdh]–tpiA [cdh],tpiA

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 273955 =NA (NA)5 (0.040) 5/510 NT 6.2% noncoding (1195/1195 nt) IS5 repeat region
?NC_000913 = 702474 75 (0.600)coding (278/1149 nt) nagA N‑acetylglucosamine‑6‑phosphate deacetylase
* ? NC_000913 391708 =NA (NA)3 (0.020)
+GTGCC
3/500 NT NA pseudogene (1458/1458 nt) yaiT pseudogene, autotransporter family;putative structure; Not classified; interrupted by IS3; putative flagellin structural protein
?NC_000913 = 392963 NA (NA)noncoding (4/1258 nt) IS3 repeat region
* ? NC_000913 1207790 =79 (0.630)35 (0.300) 32/478 NT 30.7% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 84 (0.710)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780581 (0.640)32 (0.270) 26/478 NT 28.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 84 (0.710)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 4325842 =NA (NA)12 (0.100)
+AAC
4/504 NT NA noncoding (41/583 nt) REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences
?NC_000913 = 4326338 NA (NA)noncoding (537/583 nt) REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences REP325 (repetitive extragenic palindromic) element; contains 12 REP sequences