breseq  version 0.24  revision cd15a9d216e1
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 15,395 G→A 6.0% intergenic (+99/‑48) dnaJ → / → insL‑1 chaperone Hsp40, co‑chaperone with DnaK/IS186 hypothetical protein
JC JC 16,972 IS150 (–) +3 bp 100% intergenic (‑14/‑514) mokC ← / → nhaA regulatory protein for HokC, overlaps CDS of hokC/pH‑dependent sodium/proton antiporter
RA 161,041 T→G 100% N302H (AAC→CAC)  pcnB ← poly(A) polymerase I
RA 380,188 A→C 100% F239L (TTT→TTG araJ ← predicted transporter
RA 430,835 C→T 100% intergenic (‑48/‑108) insL‑2 ← / → lon putative transposase insL for insertion sequence IS186/DNA‑binding ATP‑dependent protease La
RA 475,288 +G 100% coding (18/1677 nt) ybaL ← predicted transporter with NAD(P)‑binding Rossmann‑fold domain
MC JC 547,700 Δ8,224 bp 100% IS1‑mediated [nmpC][ECB_00513] [nmpC], ybcR, ybcS, ybcT, ybcU, ECB_00510, nohB, ECB_00512, [ECB_00513]
RA 649,391 T→A 100% I471F (ATC→TTC)  mrdA ← transpeptidase involved in peptidoglycan synthesis (penicillin‑binding protein 2)
RA 668,787 A→C 100% Y65D (TAC→GAC)  gltI ← glutamate and aspartate transporter subunit
RA 683,496 A→C 100% V65G (GTT→GGT)  nagC ← DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine
RA 910,316 T→C 100% intergenic (+176/‑175) ybjN → / → potF predicted oxidoreductase/putrescine transporter subunit: periplasmic‑binding component of ABC superfamily
RA 1,004,251 T→C 100% intergenic (‑177/+425) ompF ← / ← asnS outer membrane porin 1a (Ia;b;F)/asparaginyl‑tRNA synthetase
RA 1,248,380 A→C 100% D295E (GAT→GAG dhaM ← fused predicted dihydroxyacetone‑specific PTS enzymes: HPr component/EI component
RA 1,286,699 C→A 100% intergenic (+23/‑160) narI → / → ECB_01206 nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein
RA 1,329,516 C→T 100% H33Y (CAC→TAC)  topA → DNA topoisomerase I
JC JC 1,733,647 IS150 (–) +3 bp 100% coding (683‑685/1413 nt) pykF → pyruvate kinase
JC JC 1,821,525 IS150 (–) +3 bp 100% coding (573‑575/1041 nt) ynjI ← predicted inner membrane protein
RA 1,976,879 T→G 100% intergenic (‑57/‑76) yedW ← / → yedX predicted DNA‑binding response regulator in two‑component system with YedV/hypothetical protein
RA 2,082,685 G→A 100% A494V (GCT→GTT)  yegI ← hypothetical protein
RA 2,732,014 C→A 34.6% R91L (CGC→CTC)  hypF ← carbamoyl phosphate phosphatase and maturation protein for [NiFe] hydrogenases
JC JC 3,015,771 IS150 (–) +4 bp 98.3% coding (1192‑1195/1677 nt) ECB_02816 → KpsD protein
RA 3,045,069 G→T 100% T312N (ACC→AAC)  yghJ ← predicted inner membrane lipoprotein
RA 3,155,168 G→A 100% G296S (GGC→AGC)  ebgR → DNA‑binding transcriptional repressor
RA 3,248,957 A→T 100% D764E (GAT→GAA infB ← translation initiation factor IF‑2
RA 3,288,092 G→A 100% R57C (CGT→TGT)  arcB ← hybrid sensory histidine kinase in two‑component regulatory system with ArcA
MC JC 3,289,962 Δ16 bp 100% coding (96‑111/4554 nt) gltB → glutamate synthase, large subunit
RA 3,339,158 A→C 100% intergenic (+22/‑4) yhdG → / → fis tRNA‑dihydrouridine synthase B/DNA‑binding protein Fis
RA 3,369,432 T→C 100% D50G (GAC→GGC)  rpsD ← 30S ribosomal protein S4
RA 3,370,027 T→A 100% K117M (AAG→ATG)  rpsM ← 30S ribosomal protein S13
RA 3,483,047 C→A 100% R455S (CGC→AGC)  malT → transcriptional regulator MalT
RA 3,490,112 C→T 100% A105T (GCG→ACG)  glpE ← thiosulfate sulfurtransferase
RA 3,762,741 A→T 100% K662I (AAA→ATA)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
RA 3,875,625 +T 100% intergenic (‑59/+294) glmU ← / ← atpC bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon
MC JC 3,894,997 Δ6,934 bp 100% IS150‑mediated rbsD[yieO] rbsD, rbsA, rbsC, rbsB, rbsK, rbsR, [yieO]
RA 4,100,655 C→T 100% M192I (ATG→ATA hslU ← ATP‑dependent protease ATP‑binding subunit
RA 4,126,699 Δ1 bp 100% coding (335/879 nt) pflC → pyruvate formate lyase II activase
RA 4,201,911 C→T 100% A217T (GCG→ACG)  iclR ← DNA‑binding transcriptional repressor
JC JC 4,524,522 IS186 (+) +6 bp 98.5% coding (494‑499/549 nt) fimA → major type 1 subunit fimbrin (pilin)
RA 4,616,396 G→A 100% G290S (GGC→AGC)  nadR → nicotinamide‑nucleotide adenylyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 558866 558913 48 8 [7] [6] 8 ECB_00517/appY conserved hypothetical protein/DNA‑binding transcriptional activator
* * ÷ REL606 2031681–2031702 2035058–2034324 2623–3378 8 [7] [0] 14 [manB]–insA‑14 [manB], manC, insB‑14, insA‑14
* * ÷ REL606 2035094 2054966–2054946 19853–19873 64 [0] [7] 10 [wbbD]–[cpsG] 19 genes
[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 = 16728NA (NA)26 (0.680) 19/60 NT 78.8% noncoding (1343/1343 nt) IS186 repeat region
?REL606 2713428 = 7 (0.160)noncoding (77/93 nt) serV tRNA‑Ser
* ? REL606 = 16728NA (NA)4 (0.100) 4/60 NT 14.3% noncoding (1343/1343 nt) IS186 repeat region
?REL606 2448493 = 24 (0.530)intergenic (+24/+26) nupC/yfeA nucleoside (except guanosine) transporter/predicted diguanylate cyclase
* ? REL606 = 237270 (0.000)36 (0.880) 24/64 NT 100% noncoding (437/768 nt) IS1 repeat region
?REL606 = 666130 NA (NA)noncoding (1443/1443 nt) IS150 repeat region
* ? REL606 241691 =0 (0.000)46 (1.090) 29/66 NT 100% noncoding (435/768 nt) IS1 repeat region
?REL606 3893554 = NA (NA)noncoding (1/1443 nt) IS150 repeat region
* ? REL606 588495 =NA (NA)40 (0.940) 30/66 NT 100% noncoding (1/1977 nt) IS150 repeat region
?REL606 1270660 = 0 (0.000)intergenic (‑167/+238) ldrC/chaA toxic polypeptide, small/calcium/sodium:proton antiporter
* ? REL606 = 590471NA (NA)26 (0.610) 20/66 NT 81.2% noncoding (1977/1977 nt) IS150 repeat region
?REL606 = 3630716 6 (0.130)intergenic (‑171/‑305) ldrD/yhjV toxic polypeptide, small/predicted transporter
* ? REL606 = 70144739 (1.050)8 (0.220) 4/58 NT 19.3% coding (1109/2199 nt) speF ornithine decarboxylase isozyme, inducible
?REL606 3424883 = 28 (0.620)intergenic (+101/‑25) nirD/nirC nitrite reductase small subunit/nitrite transporter
* ? REL606 1286706 =15 (0.400)9 (0.240) 4/58 NT 32.7% intergenic (+30/‑153) narI/ECB_01206 nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein
?REL606 = 2780684 22 (0.490)intergenic (‑286/‑30) cysJ/ygcM sulfite reductase, alpha subunit, flavoprotein/6‑pyruvoyl tetrahydrobiopterin synthase (PTPS)
* ? REL606 1290519 =16 (0.450)5 (0.140) 3/56 NT 29.4% coding (484/1014 nt) hnr response regulator of RpoS
?REL606 = 1977651 8 (0.180)coding (175/1005 nt) yedY hypothetical protein
* ? REL606 = 19776589 (0.250)6 (0.170) 4/56 NT 24.0% coding (182/1005 nt) yedY hypothetical protein
?REL606 3323381 = 29 (0.650)coding (769/3801 nt) yhdP conserved membrane protein, predicted transporter
* ? REL606 = 357166623 (0.600)4 (0.100) 4/60 NT 16.0% coding (115/1470 nt) yhiP predicted transporter
?REL606 3944634 = 19 (0.420)intergenic (+23/‑124) proM/aslB tRNA‑Pro/predicted regulator of arylsulfatase activity