breseq  version 0.24rc1  revision 83e50355436e
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation annotation gene description
JC JC 16,972 IS150 (–) +3 bp intergenic (‑14/‑514) mokC ← / → nhaA regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter
RA 161,041 T→G N302H (AAC→CAC)  pcnB ← poly(A) polymerase I
RA 380,188 A→C F239L (TTT→TTG araJ ← predicted transporter
RA 430,835 C→T intergenic (‑48/‑108) insL‑2 ← / → lon putative transposase insL for insertion sequence IS186/DNA‑binding ATP‑dependent protease La
RA 475,288 +G coding (18/1677 nt) ybaL ← predicted transporter with NAD(P)‑binding Rossmann‑fold domain
RA 649,391 T→A I471F (ATC→TTC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 668,787 A→C Y65D (TAC→GAC)  gltI ← glutamate and aspartate transporter subunit
RA 683,496 A→C V65G (GTT→GGT)  nagC ← DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine
RA 910,316 T→C intergenic (+176/‑175) ybjN → / → potF predicted oxidoreductase/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily
RA 1,004,251 T→C intergenic (‑177/+425) ompF ← / ← asnS outer membrane porin 1a (Ia;b;F)/asparaginyl‑tRNA synthetase
RA 1,248,380 A→C D295E (GAT→GAG dhaM ← fused predicted dihydroxyacetone‑specific PTS enzymes: HPr component/EI component
RA 1,286,699 C→A intergenic (+23/‑160) narI → / → ECB_01206 nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein
RA 1,329,516 C→T H33Y (CAC→TAC)  topA → DNA topoisomerase I
JC JC 1,733,647 IS150 (–) +3 bp coding (683‑685/1413 nt) pykF → pyruvate kinase
JC JC 1,821,525 IS150 (–) +3 bp coding (573‑575/1041 nt) ynjI ← predicted inner membrane protein
RA 1,976,879 T→G intergenic (‑57/‑76) yedW ← / → yedX predicted DNA‑binding response regulator in two‑component system with YedV/hypothetical protein
RA 2,082,685 G→A A494V (GCT→GTT)  yegI ← hypothetical protein
RA 2,732,014 C→A R91L (CGC→CTC)  hypF ← carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
JC JC 3,015,771 IS150 (–) +4 bp coding (1192‑1195/1677 nt) ECB_02816 → KpsD protein
RA 3,045,069 G→T T312N (ACC→AAC)  yghJ ← predicted inner membrane lipoprotein
RA 3,155,168 G→A G296S (GGC→AGC)  ebgR → DNA‑binding transcriptional repressor
RA 3,200,643 C→A intergenic (+11/‑245) tdcR → / → yhaB DNA‑binding transcriptional activator/hypothetical protein
RA 3,248,957 A→T D764E (GAT→GAA infB ← translation initiation factor IF‑2
RA 3,288,092 G→A R57C (CGT→TGT)  arcB ← hybrid sensory histidine kinase in two‑component regulatory system with ArcA
MC JC 3,289,962 Δ16 bp coding (96‑111/4554 nt) gltB → glutamate synthase, large subunit
RA 3,339,158 A→C intergenic (+22/‑4) yhdG → / → fis tRNA‑dihydrouridine synthase B/DNA‑binding protein Fis
RA 3,369,432 T→C D50G (GAC→GGC)  rpsD ← 30S ribosomal protein S4
RA 3,370,027 T→A K117M (AAG→ATG)  rpsM ← 30S ribosomal protein S13
RA 3,483,047 C→A R455S (CGC→AGC)  malT → transcriptional regulator MalT
RA 3,490,112 C→T A105T (GCG→ACG)  glpE ← thiosulfate sulfurtransferase
RA 3,762,741 A→T K662I (AAA→ATA)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,875,625 +T intergenic (‑59/+294) glmU ← / ← atpC bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon
RA 3,893,550 +G intergenic (+5/‑51) kup → / → insJ‑5 potassium transporter/IS150 hypothetical protein
MC JC 3,894,997 Δ6,934 bp IS150‑mediated rbsD[yieO] rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO]
RA 4,100,655 C→T M192I (ATG→ATA hslU ← ATP‑dependent protease ATP‑binding subunit
RA 4,126,699 Δ1 bp coding (335/879 nt) pflC → pyruvate formate lyase II activase
RA 4,201,911 C→T A217T (GCG→ACG)  iclR ← DNA‑binding transcriptional repressor
JC JC 4,524,522 IS186 (+) +6 bp coding (494‑499/549 nt) fimA → major type 1 subunit fimbrin (pilin)
RA 4,616,396 G→A G290S (GGC→AGC)  nadR → nicotinamide‑nucleotide adenylyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 546958–547700 555936–555805 8106–8979 18 [15] [15] 16 [insB‑6]–[ECB_00513] [insB‑6], insA‑6, nmpC, ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513]
* * ÷ REL606 2031674–2031721 2054972–2054943 23223–23299 20 [15] [15] 16 [manB]–[cpsG] 23 genes
[manB], manC, insB‑14, insA‑14, wbbD, wbbC, wzy, wbbB, wbbA, vioB, vioA, wzx, rmlC, rfbA, rfbD, rfbB, galF, wcaM, wcaL, wcaK, wzxC, wcaJ, [cpsG]

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 547699NA (NA)52 (0.940) 27/70 0.7 NA noncoding (1/768 nt) IS1 repeat region
?REL606 555924 = NA (NA)coding (1209/2346 nt) ECB_00513 conserved hypothetical protein
* ? REL606 589886 =NA (NA)37 (0.710) 21/66 1.2 NA noncoding (437/768 nt) IS1 repeat region
?REL606 = 590471 NA (NA)noncoding (1977/1977 nt) IS150 repeat region
* ? REL606 664688 =NA (NA)35 (0.670) 24/66 0.8 100% noncoding (1/1443 nt) IS150 repeat region
?REL606 1270660 = 0 (0.000)intergenic (‑167/+238) ldrC/chaA toxic polypeptide, small/calcium/sodium:proton antiporter
* ? REL606 = 3630716NA (NA)31 (0.560) 22/70 1.2 NA intergenic (‑171/‑305) ldrD/yhjV toxic polypeptide, small/predicted transporter
?REL606 = 3652533 NA (NA)noncoding (1443/1443 nt) IS150 repeat region
* ? REL606 3651091 =NA (NA)68 (1.230) 34/70 0.2 NA noncoding (1/1443 nt) IS150 repeat region
?REL606 = 3741531 NA (NA)noncoding (435/768 nt) IS1 repeat region