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
JC 980,293 3 bp x 2 7.6% duplication rpsA → 30S ribosomal protein S1
RA 1,329,516 C→T 100% H33Y (CAC→TAC)  topA → DNA topoisomerase I
JC 1,733,288 8 bp x 2 17.7% duplication pykF → pyruvate kinase
JC 1,733,579 7 bp x 2 49.5% duplication pykF → pyruvate kinase
JC JC 1,733,647 IS150 (–) +3 bp 18.4% coding (683‑685/1413 nt) pykF → pyruvate kinase
RA 1,806,030 C→A 17.9% E324* (GAA→TAA)  astD ← succinylglutamic semialdehyde dehydrogenase
RA 2,082,685 G→A 16.2% A494V (GCT→GTT)  yegI ← hypothetical protein
RA 3,293,142 G→T 21.1% L1092F (TTG→TTT gltB → glutamate synthase, large subunit
RA 3,750,741 C→A 19.1% L58F (TTG→TTT radC ← DNA repair protein RadC
RA 3,762,741 A→T 100% K662I (AAA→ATA)  spoT → bifunctional (p)ppGpp synthetase II/ guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase
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 16.6% M192I (ATG→ATA hslU ← ATP‑dependent protease ATP‑binding subunit
JC JC 4,524,522 IS186 (+) +6 bp 25.9% coding (494‑499/549 nt) fimA → major type 1 subunit fimbrin (pilin)

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 240075 240181 107 14 [12] [13] 14 aspV/yafT tRNA‑Asp/predicted aminopeptidase
* * ÷ REL606 2041400 2041537 138 14 [13] [13] 15 wzx O antigen translocase (Wzx)
* * ÷ REL606 3119447 3119558 112 14 [13] [13] 14 yqiC/ygiL hypothetical protein/predicted fimbrial‑like adhesin protein

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 = 31070538 (0.930)3 (0.070) 3/50 NT 8.6% coding (1279/1548 nt) yahF predicted acyl‑CoA synthetase with NAD(P)‑binding domain and succinyl‑CoA synthetase domain
?REL606 580473 = 26 (0.450)coding (857/3144 nt) cusA copper/silver efflux system, membrane component
* ? REL606 = 60665120 (0.410)6 (0.120) 5/60 NT 20.7% coding (568/957 nt) fepB iron‑enterobactin transporter subunit
?REL606 3650765 = 26 (0.450)intergenic (+46/+141) cspA/hokA major cold shock protein/toxic polypeptide, small
* ? REL606 640118 =35 (0.690)6 (0.120) 3/62 NT 13.6% intergenic (+36/+19) cspE/ccrB cold shock protein E/camphor resistance protein CrcB
?REL606 = 2825478 41 (0.710)coding (741/1629 nt) ECB_02649 protein similar to L‑ribulokinase AraB
* ? REL606 = 78925746 (1.000)6 (0.130) 4/56 NT 15.2% intergenic (‑235/+241) ECB_00726/ECB_00727 integrase/phage related protein
?REL606 2994085 = 21 (0.370)coding (731/2136 nt) speC ornithine decarboxylase, constitutive
* ? REL606 = 84006430 (0.630)4 (0.080) 3/58 NT 12.9% coding (566/747 nt) glnH glutamine ABC transporter periplasmic protein
?REL606 = 1619524 24 (0.420)intergenic (‑133/+84) rem/hokD predicted protein/small toxic polypeptide
* ? REL606 1109621 =28 (0.490)7 (0.120) 5/70 NT 18.4% coding (461/1359 nt) ycdT predicted diguanylate cyclase
?REL606 = 3061117 34 (0.590)coding (752/1173 nt) ECB_02854 conserved hypothetical protein
* ? REL606 1199793 =68 (1.290)9 (0.170) 8/64 NT 12.6% coding (22/828 nt) potB spermidine/putrescine ABC transporter membrane protein
?REL606 = 1588685 57 (0.990)coding (219/900 nt) eamA cysteine and O‑acetyl‑L‑serine efflux system
* ? REL606 1241529 =31 (0.670)7 (0.150) 4/56 NT 21.5% coding (693/1737 nt) ycgO potassium/proton antiporter
?REL606 = 2574504 20 (0.350)intergenic (+346/+472) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
* ? REL606 = 129226920 (0.470)5 (0.120) 3/52 NT 16.4% intergenic (+110/+34) galU/hns glucose‑1‑phosphate uridylyltransferase/global DNA‑binding transcriptional dual regulator H‑NS
?REL606 = 2173874 31 (0.540)coding (452/1716 nt) dld D‑lactate dehydrogenase, FAD‑binding, NADH independent
* ? REL606 1340206 =27 (0.470)6 (0.100) 3/70 NT 15.6% intergenic (+107/‑86) yciM/pyrF hypothetical protein/orotidine 5'‑phosphate decarboxylase
?REL606 3170213 = 38 (0.660)coding (104/1005 nt) ygjR predicted NAD(P)‑binding dehydrogenase
* ? REL606 = 137072339 (0.880)4 (0.090) 3/54 NT 11.9% coding (447/1293 nt) ycjN predicted sugar transporter subunit: periplasmic‑binding component of ABC superfamily
?REL606 = 2574504 20 (0.350)intergenic (+346/+472) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
* ? REL606 = 140096352 (1.090)13 (0.270) 7/58 NT 22.6% coding (773/1311 nt) abgA predicted peptidase, aminobenzoyl‑glutamate utilization protein
?REL606 = 3875872 37 (0.640)intergenic (‑306/+47) glmU/atpC bifunctional N‑acetylglucosamine‑1‑phosphate uridyltransferase/glucosamine‑1‑phosphate acetyltransferase/F0F1 ATP synthase subunit epsilon
* ? REL606 = 161952929 (0.590)6 (0.120) 4/60 NT 20.0% intergenic (‑138/+79) rem/hokD predicted protein/small toxic polypeptide
?REL606 1946064 = 19 (0.330)coding (144/390 nt) cheY chemotaxis regulator transmitting signal to flagellar motor component
* ? REL606 = 208161438 (0.800)6 (0.130) 4/58 NT 11.5% coding (755/1353 nt) yegD predicted chaperone
?REL606 4281474 = 54 (0.940)coding (427/2052 nt) yjcQ predicted multidrug efflux system component
* ? REL606 = 257451122 (0.480)4 (0.090) 4/56 NT 10.1% intergenic (+353/+465) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
?REL606 3715185 = 49 (0.850)coding (2195/4851 nt) ECB_03460 putative adhesin
* ? REL606 3944628 =35 (0.730)12 (0.250) 6/58 NT 24.5% intergenic (+17/‑130) proM/aslB tRNA‑Pro/predicted regulator of arylsulfatase activity
?REL606 = 4258591 39 (0.680)coding (1180/1350 nt) yjcD predicted permease