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 311,500 G→A G176D (GGC→GAC)  yahG → hypothetical protein
RA 473,924 A→C V461G (GTC→GGC)  ybaL ← predicted transporter with NAD(P)‑binding Rossmann‑fold domain
RA 649,079 T→C T575A (ACC→GCC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 1,329,516 C→T H33Y (CAC→TAC)  topA → DNA topoisomerase I
JC 1,733,297 (CGTATGAA)1→2 coding (333/1413 nt) pykF → pyruvate kinase
RA 1,886,608 G→A intergenic (‑438/+231) yobF ← / ← yebO hypothetical protein/hypothetical protein
RA 2,165,180 C→T G221D (GGC→GAC)  yehU ← predicted sensory kinase in two‑component system with YehT
RA 2,193,779 G→T L143I (CTT→ATT)  yeiB ← conserved inner membrane protein
JC 3,014,099 (ACAGGC)3→4 coding (680/1137 nt) ECB_02815 → Capsule polysaccharide export inner‑membrane protein kpsE
RA 3,762,741 A→T K662I (AAA→ATA)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,875,632 (T)7→8 intergenic (‑66/+287) glmU ← / ← atpC bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon
RA 4,155,456 C→T intergenic (+16/‑99) thrT → / → tuf tRNA‑Thr/protein chain elongation factor EF‑Tu (duplicate of tufA)
RA 4,163,752 T→G I966S (ATC→AGC)  rpoB → DNA‑directed RNA polymerase subunit beta
MC 4,506,110 Δ16,229 bp between IS1 sgcR–insA‑27 18 genes
JC JC 4,524,522 IS186 (+) +6 bp coding (494‑499/549 nt) fimA → major type 1 subunit fimbrin (pilin)
RA 4,593,944 T→A I166N (ATC→AAC)  bglJ → DNA‑binding transcriptional activator

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 546980–547700 593356 45657–46377 87 [78] [83] 88 [insB‑6]–[fepA] [insB‑6],insA‑6,nmpC,ybcR,ybcS,ybcT,ybcU,ECB_00510,nohB,ECB_00512,ECB_00513,ECB_00514,ECB_00515,ECB_00516,ECB_00517,appY,ompT,envY,ybcH,nfrA,nfrB,nfrB,ECB_00524,yhhI,ECB_00526,ECB_00527,ECB_00528,ECB_00529,ECB_00530,cusS,cusR,cusC,ylcC,cusB,cusA,pheP,ybdG,nfnB,ybdF,ybdJ,ybdK,insJ‑1,insK‑1,insB‑7,insA‑7,insK‑1,hokE,insL‑3,entD,[fepA]
* * ÷ REL606 593585 619833–619116 25532–26249 87 [83] [84] 94 [fepA]–insA‑8 [fepA],fes,ybdZ,entF,fepE,fepC,fepG,fepD,ybdA,fepB,entC,entE,entB,entA,ybdB,cstA,cstA,ybdD,ybdH,ybdL,ybdM,ybdN,insB‑8,insA‑8
* * ÷ REL606 2031770–2031796 2052603 20808–20834 85 [72] [81] 85 [manB]–[wzxC] [manB],manC,insB‑14,insA‑14,wbbD,wbbC,wzy,wbbB,wbbA,vioB,vioA,wzx,rmlC,rfbA,rfbD,rfbB,galF,wcaM,wcaL,wcaK,[wzxC]
* * ÷ REL606 2052821 2055064–2055014 2194–2244 86 [84] [84] 97 [wzxC]–[cpsG] [wzxC],wcaJ,[cpsG]
* * ÷ REL606 3895000 3901930 6931 122 [0] [0] 321 rbsD–[yieO] rbsD,rbsA,rbsC,rbsB,rbsK,rbsR,[yieO]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 6646873 (0.010)205 (0.750) 68/144 0.8 99.1% intergenic (‑78/‑48) gltL/insJ‑2 ATP‑binding protein of glutamate/aspartate transport system; b0652_1/IS150 hypothetical protein
?REL606 666134 = 1 (0.000)pseudogene (354/387 nt) gltL ATP‑binding protein of glutamate/aspartate transport system; b0652_1
* ? REL606 = 3652533NA (NA)298 (1.080) 96/146 0.1 100% noncoding (1443/1443 nt) IS150 repeat region
?REL606 3901931 = 0 (0.000)coding (489/1428 nt) yieO predicted multidrug or homocysteine efflux system
* ? REL606 4097453 =87 (0.310)250 (0.890) 85/148 0.3 70.4% coding (120/846 nt) glpF glycerol facilitator
?REL606 = 4097477 124 (0.440)coding (96/846 nt) glpF glycerol facilitator