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
JC 102,158 +TGGTAATAT 5.1% coding (1394/1476 nt) murC → UDP‑N‑acetylmuramate‑‑L‑alanine ligase
MC JC 257,908 Δ776 bp 100% insB9[crl] insB9, insA9, [crl]
RA 526,792 A→C 6.6% S1178R (AGC→CGC)  rhsD → protein RhsD
RA 526,796 C→G 6.7% A1179G (GCG→GGG)  rhsD → protein RhsD
RA 872,805 C→T 7.6% intergenic (+4/‑174) gsiD → / → pdeI glutathione ABC transporter membrane subunit GsiD/putative c‑di‑GMP phosphodiesterase PdeI
RA 1,529,175 T→C 8.5% pseudogene (1286/2049 nt) rhsE → RhsE protein in rhs element
RA 1,529,180 T→C 8.3% pseudogene (1291/2049 nt) rhsE → RhsE protein in rhs element
RA 1,529,185 C→T 8.6% pseudogene (1296/2049 nt) rhsE → RhsE protein in rhs element
RA 1,529,203 C→A 12.7% pseudogene (1314/2049 nt) rhsE → RhsE protein in rhs element
RA 1,529,218 C→T 16.9% pseudogene (1329/2049 nt) rhsE → RhsE protein in rhs element
RA 1,708,758 G→C 9.7% E614Q (GAA→CAA)  rsxC → SoxR [2Fe‑2S] reducing system protein RsxC
MC JC 1,978,503 Δ776 bp 100% insB‑5insA‑5 insB‑5, insA‑5
RA 2,173,361 Δ2 bp 100% pseudogene (917‑918/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 3,505,145 T→C 5.7% R292R (AGA→AGG yhfS ← putative aminotransferase YhfS
RA 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,815,809 Δ1 bp 6.7% intergenic (‑41/+54) pyrE ← / ← rph orotate phosphoribosyltransferase/truncated RNase PH
RA 3,815,822 T→G 6.7% intergenic (‑54/+41) pyrE ← / ← rph orotate phosphoribosyltransferase/truncated RNase PH
RA 3,815,937 C→A 7.3% E205* (GAA→TAA)  rph ← truncated RNase PH
RA 4,184,809 G→T 64.7% G1189C (GGT→TGT)  rpoB → RNA polymerase subunit beta
RA 4,296,190 A→G 20.6% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,296,191 A→C 23.6% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,296,268 T→C 10.4% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,566,266 T→C 5.3% R327R (CGA→CGG yjiN ← DUF445 domain‑containing protein YjiN

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1207790 =84 (0.740)40 (0.380) 31/462 NT 34.7% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 72 (0.680)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 120780584 (0.740)55 (0.520) 39/462 NT 42.2% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 72 (0.680)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12994980 (0.000)38 (0.340) 34/486 NT 100% intergenic (+253/‑33) ychE/insH21 putative inner membrane protein/IS5 transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 2054966 =113 (1.000)6 (0.060) 5/474 NT 5.5% intergenic (+7/‑95) shiA/amn shikimate:H(+) symporter/AMP nucleosidase
?NC_000913 2054990 = 99 (0.910)intergenic (+31/‑71) shiA/amn shikimate:H(+) symporter/AMP nucleosidase
* ? NC_000913 = 2515616NA (NA)7 (0.060) 7/488 NT 5.4% noncoding (1344/1345 nt) IS186 repeat region
?NC_000913 4543608 = 122 (1.090)coding (494/549 nt) fimA type 1 fimbriae major subunit