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 74,220 G→T 14.4% L22F (TTG→TTT yabI → conserved inner membrane protein
RA 166,265 C→A 28.4% A437E (GCA→GAA)  hrpB → predicted ATP‑dependent helicase
RA 380,188 A→C 40.7% F239L (TTT→TTG araJ ← predicted transporter
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 683,496 A→C 100% V65G (GTT→GGT)  nagC ← DNA‑binding transcriptional dual regulator, repressor of N‑acetylglucosamine
RA 980,180 A→G 60.3% D365G (GAC→GGC)  rpsA → 30S ribosomal protein S1
RA 1,329,516 C→T 100% H33Y (CAC→TAC)  topA → DNA topoisomerase I
JC JC 1,733,647 IS150 (–) +3 bp 98.2% coding (683‑685/1413 nt) pykF → pyruvate kinase
JC JC 1,764,698 IS1 (–) +9 bp 52.5% intergenic (‑318/‑7) ppsA ← / → ydiA phosphoenolpyruvate synthase/hypothetical protein
RA 1,976,879 T→G 40.5% intergenic (‑57/‑76) yedW ← / → yedX predicted DNA‑binding response regulator in two‑component system with YedV/hypothetical protein
RA 1,992,583 Δ1 bp 9.1% coding (942/1317 nt) shiA → shikimate transporter
RA 2,082,685 G→A 100% A494V (GCT→GTT)  yegI ← hypothetical protein
RA 2,329,291 A→T 20.6% A22A (GCA→GCT elaD → predicted enzyme
RA 2,336,064 T→G 15.4% I168L (ATC→CTC)  nuoM ← NADH dehydrogenase subunit M
RA 2,342,867 T→G 13.4% Q299P (CAG→CCG)  nuoG ← NADH dehydrogenase subunit G
RA 2,499,315 G→A 36.6% intergenic (‑110/‑179) maeB ← / → talA malic enzyme/transaldolase A
RA 3,045,069 G→T 46.7% T312N (ACC→AAC)  yghJ ← predicted inner membrane lipoprotein
RA 3,248,957 A→T 100% D764E (GAT→GAA infB ← translation initiation factor IF‑2
JC 3,289,962 Δ16 bp 39.4% coding (96‑111/4554 nt) gltB → glutamate synthase, large subunit
RA 3,339,158 A→C 54.9% intergenic (+22/‑4) yhdG → / → fis tRNA‑dihydrouridine synthase B/DNA‑binding protein Fis
RA 3,370,027 T→A 59.4% K117M (AAG→ATG)  rpsM ← 30S ribosomal protein S13
RA 3,483,047 C→A 100% R455S (CGC→AGC)  malT → transcriptional regulator MalT
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
RA 3,893,550 +G 52.5% intergenic (+5/‑51) kup → / → insJ‑5 potassium transporter/IS150 hypothetical protein
RA 3,893,550 +G 13.6% intergenic (+5/‑51) kup → / → insJ‑5 potassium transporter/IS150 hypothetical protein
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 50.0% coding (335/879 nt) pflC → pyruvate formate lyase II activase
RA 4,266,356 G→C 33.3% intergenic (‑52/‑341) acs ← / → nrfA acetyl‑coenzyme A synthetase/nitrite reductase, formate‑dependent, cytochrome
RA 4,366,935 G→T 24.2% A197A (GCC→GCA yjeP ← predicted mechanosensitive channel
JC JC 4,524,522 IS186 (+) +6 bp 68.8% coding (494‑499/549 nt) fimA → major type 1 subunit fimbrin (pilin)
RA 4,560,632 T→C 30.9% Y131C (TAC→TGC)  hsdM ← DNA methylase M
RA 4,616,396 G→A 9.9% G290S (GGC→AGC)  nadR → nicotinamide‑nucleotide adenylyltransferase

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ REL606 240089 240201 113 16 [12] [15] 16 aspV/yafT tRNA‑Asp/predicted aminopeptidase
* * ÷ REL606 558854 558932 79 16 [15] [14] 16 ECB_00517/appY conserved hypothetical protein/DNA‑binding transcriptional activator
* * ÷ REL606 2041399 2041556 158 16 [15] [15] 20 wzx O antigen translocase (Wzx)
* * ÷ REL606 2792257 2792361 105 17 [13] [15] 16 ygcE/ECB_02621 predicted kinase/conserved hypothetical protein
* * ÷ REL606 3022861 3023156 296 17 [14] [15] 18 ECB_02821/ECB_02822 hypothetical protein/bifunctional Ribulose 5‑phosphate reductase/CDP‑ribitol pyrophosphorylase
* * ÷ REL606 3119448 3119564 117 16 [14] [14] 16 yqiC/ygiL hypothetical protein/predicted fimbrial‑like adhesin protein
* * ÷ REL606 3692607 3692700 94 16 [15] [15] 16 yiaY/selB predicted Fe‑containing alcohol dehydrogenase/selenocysteinyl‑tRNA‑specific translation factor

Unassigned new junction evidence...
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? REL606 308482 =44 (0.720)9 (0.150) 6/70 NT 20.2% coding (554/606 nt) yahD predicted transcriptional regulator with ankyrin domain
?REL606 1580990 = 27 (0.440)coding (757/1389 nt) yneI predicted aldehyde dehydrogenase
* ? REL606 501044 =30 (0.560)3 (0.060) 3/62 NT 9.1% coding (238/261 nt) ybbD hypothetical protein
?REL606 4395045 = 30 (0.490)intergenic (‑120/‑62) yjfO/yjfP hypothetical protein/predicted hydrolase
* ? REL606 = 590471NA (NA)9 (0.160) 9/64 NT 16.7% noncoding (1977/1977 nt) IS150 repeat region
?REL606 = 1821527 45 (0.740)coding (573/1041 nt) ynjI predicted inner membrane protein
* ? REL606 = 592057NA (NA)5 (0.100) 5/60 NT 10.9% noncoding (1343/1343 nt) IS186 repeat region
?REL606 1391825 = 41 (0.680)coding (230/1614 nt) mppA murein tripeptide (L‑ala‑gamma‑D‑glutamyl‑meso‑DAP) transporter subunit
* ? REL606 = 60665122 (0.420)6 (0.120) 3/60 NT 18.8% coding (568/957 nt) fepB iron‑enterobactin transporter subunit
?REL606 3650765 = 30 (0.490)intergenic (+46/+141) cspA/hokA major cold shock protein/toxic polypeptide, small
* ? REL606 640118 =36 (0.670)11 (0.200) 6/62 NT 20.9% intergenic (+36/+19) cspE/ccrB cold shock protein E/camphor resistance protein CrcB
?REL606 3995534 = 47 (0.770)coding (54/768 nt) ECB_03724 putative transcriptional regulator
* ? REL606 1286705 =38 (0.780)7 (0.140) 4/56 NT 17.5% intergenic (+29/‑154) narI/ECB_01206 nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein
?REL606 = 2173876 28 (0.460)coding (454/1716 nt) dld D‑lactate dehydrogenase, FAD‑binding, NADH independent
* ? REL606 1286707 =35 (0.670)6 (0.120) 3/60 NT 16.0% intergenic (+31/‑152) narI/ECB_01206 nitrate reductase 1, gamma (cytochrome b(NR)) subunit/hypothetical protein
?REL606 = 3571661 28 (0.460)coding (110/1470 nt) yhiP predicted transporter
* ? REL606 = 1460974NA (NA)12 (0.200) 7/70 NT NA intergenic (+62/‑37) insB‑12/cybB IS1 protein InsB/cytochrome b561
?REL606 2332094 = NA (NA)intergenic (+34/‑53) yfbM/ECB_02199 hypothetical protein/PROBABLE ISRSO11‑TRANSPOSASE ORFA PROTEIN
* ? REL606 1462251 =34 (0.730)6 (0.130) 6/54 NT 11.4% intergenic (‑13/‑328) mokB/trg regulatory peptide/methyl‑accepting chemotaxis protein III, ribose and galactose sensor receptor
?REL606 = 3413922 59 (0.970)intergenic (‑199/‑103) yhfA/crp hypothetical protein/DNA‑binding transcriptional dual regulator
* ? REL606 1474796 =36 (0.740)9 (0.190) 6/56 NT 25.7% coding (1030/1209 nt) ydcM predicted transposase
?REL606 = 2574503 16 (0.260)intergenic (+345/+473) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
* ? REL606 1732688 =44 (0.940)5 (0.110) 3/54 NT 14.5% intergenic (‑280/‑277) ydhZ/pykF hypothetical protein/pyruvate kinase
?REL606 2148171 = 15 (0.250)coding (501/3795 nt) molR molybdate metabolism regulator
* ? REL606 = 192267245 (0.860)4 (0.080) 4/60 NT 10.7% coding (683/786 nt) znuB high‑affinity zinc transporter membrane component
?REL606 = 1983317 22 (0.360)coding (456/7152 nt) yeeJ adhesin
* ? REL606 1946057 =48 (0.990)8 (0.160) 3/56 NT 20.0% coding (151/390 nt) cheY chemotaxis regulator transmitting signal to flagellar motor component
?REL606 = 2574503 16 (0.260)intergenic (+345/+473) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
* ? REL606 = 230571851 (0.840)9 (0.150) 4/70 NT 19.6% coding (948/1290 nt) yfaV predicted transporter
?REL606 3065531 = 23 (0.380)coding (965/1350 nt) yghQ predicted inner membrane protein
* ? REL606 = 230935240 (0.770)5 (0.100) 3/60 NT 13.7% coding (795/1203 nt) yfaY competence damage‑inducible protein A
?REL606 3944634 = 23 (0.380)intergenic (+23/‑124) proM/aslB tRNA‑Pro/predicted regulator of arylsulfatase activity
* ? REL606 = 2333536NA (NA)45 (0.740) 30/70 NT 54.9% noncoding (1441/1441 nt) ISRSO11 repeat region
?REL606 4415710 = 37 (0.610)coding (848/1413 nt) cycA D‑alanine/D‑serine/glycine transporter
* ? REL606 = 2408209NA (NA)5 (0.090) 5/64 NT 6.9% noncoding (1/768 nt) IS1 repeat region
?REL606 = 4621899 68 (1.120)coding (7/522 nt) yjjX NTPase
* ? REL606 = 257451122 (0.470)8 (0.170) 5/54 NT 27.1% intergenic (+353/+465) sseA/sseB 3‑mercaptopyruvate sulfurtransferase/rhodanase‑like enzyme, sulfur transfer from thiosulfate
?REL606 4356096 = 21 (0.350)coding (338/537 nt) blc outer membrane lipoprotein (lipocalin)
* ? REL606 3434228 =46 (1.020)6 (0.130) 4/52 NT 13.8% noncoding (2/768 nt) IS1 repeat region
?REL606 = 4568881 29 (0.480)coding (374/2151 nt) yjiY predicted inner membrane protein
* ? REL606 = 353057743 (0.800)11 (0.200) 5/62 NT 22.0% intergenic (‑234/+37) livJ/rpoH leucine/isoleucine/valine transporter subunit/RNA polymerase sigma factor
?REL606 4043869 = 35 (0.580)coding (155/1404 nt) yihO predited transporter
* ? REL606 = 420234937 (0.630)38 (0.640) 29/68 NT 51.7% coding (211/825 nt) iclR DNA‑binding transcriptional repressor
?REL606 4202661 = 34 (0.560)intergenic (‑102/‑98) iclR/metH DNA‑binding transcriptional repressor/B12‑dependent methionine synthase