breseq  version 0.33.1  revision 8505477f25b3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
RA 2,766 G→A 5.6% L810L (CTG→CTA thrA → Bifunctional aspartokinase/homoserine dehydrogenase 1
RA 83,590 G→T 5.3% intergenic (‑61/+32) leuA ← / ← leuL 2‑isopropylmalate synthase/leu operon leader peptide
MC JC 257,908 Δ776 bp 100% [crl] [crl]
RA 280,618 T→C 5.8% pseudogene (118/309 nt) yagB ← pseudogene, CP4‑6 prophage;Phage or Prophage Related
RA 347,692 C→A 9.5% G251V (GGC→GTC)  prpR ← propionate catabolism operon regulatory protein
RA 755,486 G→T 22.5% E104* (GAA→TAA)  sdhC → succinate dehydrogenase, membrane subunit, binds cytochrome b556
RA 756,061:1 +C 39.2% coding (155/1767 nt) sdhA → succinate dehydrogenase, flavoprotein subunit
JC 756,377 Δ48 bp 6.9% coding (471‑518/1767 nt) sdhA → succinate dehydrogenase, flavoprotein subunit
RA 756,606 C→T 12.1% Q234* (CAG→TAG)  sdhA → succinate dehydrogenase, flavoprotein subunit
JC 757,282 Δ69 bp 10.9% coding (1376‑1444/1767 nt) sdhA → succinate dehydrogenase, flavoprotein subunit
RA 757,972:1 +A 7.2% coding (284/717 nt) sdhB → succinate dehydrogenase, FeS subunit
RA 757,972:2 +G 7.2% coding (284/717 nt) sdhB → succinate dehydrogenase, FeS subunit
RA 812,200 C→G 5.1% Q227E (CAA→GAA)  bioC → malonyl‑ACP O‑methyltransferase, SAM‑dependent
RA 1,057,709 G→A 5.5% R82R (CGC→CGT torR ← response regulator in two‑component regulatory system with TorS
RA 1,240,641 C→T 6.0% P477P (CCG→CCA cvrA ← putative cation/proton antiporter
RA 1,279,940 T→A 8.1% L26H (CTC→CAC)  narG → nitrate reductase 1, alpha subunit
RA 1,287,024 G→A 9.4% intergenic (+498/+42) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
RA 1,287,143 G→A 6.5% noncoding (94/171 nt)
P12S (CCA→TCA) 
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
RA 1,287,152 T→C 8.4% noncoding (85/171 nt)
T9A (ACT→GCT) 
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
RA 1,287,161 G→A 8.3% noncoding (76/171 nt)
Q6* (CAA→TAA) 
rttR ←
tpr ←
rtT sRNA, processed from tyrT transcript
protamine‑like protein
JC JC 1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
RA 1,449,473 C→T 5.6% R626H (CGC→CAC)  tynA ← tyramine oxidase, copper‑requiring
RA 1,466,336 C→G 6.8% pseudogene (945/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,466,345 T→C 6.0% pseudogene (954/2513 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,472,951 C→T 5.0% pseudogene (2435/3497 nt) ydbA → pseudogene, autotransporter homolog; interrupted by IS2 and IS30
RA 1,553,553 T→C 6.1% N96D (AAC→GAC)  adhP ← ethanol‑active dehydrogenase/acetaldehyde‑active reductase
RA 1,560,364 A→G 5.2% L189P (CTG→CCG)  ddpB ← D,D‑dipeptide ABC transporter permease
RA 1,587,836 C→A 15.1% G154V (GGA→GTA)  ydeR ← putative fimbrial‑like adhesin protein
RA 1,852,303 C→A 5.1% R139R (CGC→CGA pncA → nicotinamidase/pyrazinamidase
RA 1,957,069 A→C 5.5% F355C (TTC→TGC)  torY ← TMAO reductase III (TorYZ), cytochrome c‑type subunit
MC JC 1,978,503 Δ776 bp 100% insB1insA insB1, insA
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,030,947 C→T 6.8% A457A (GCG→GCA dcm ← DNA cytosine methyltransferase
RA 2,132,787 A→C 100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
RA 2,173,361 Δ2 bp 100% pseudogene (1‑2/442 nt) gatC ← pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
RA 2,252,476 T→A 5.2% N259K (AAT→AAA yeiI → putative kinase
RA 2,278,883 G→T 5.1% A293E (GCA→GAA)  bcr ← bicyclomycin/cysteine/sulfonamide efflux transporter
RA 2,305,085 A→G 5.6% intergenic (+692/+23) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,086 C→G 5.2% intergenic (+693/+22) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,305,087 C→T 5.4% intergenic (+694/+21) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
RA 2,357,836 G→A 5.5% pseudogene (33/198 nt) ypaA → pseudogene, C‑terminal fragment, Transposase_31 family
RA 2,357,848 A→G 6.1% pseudogene (45/198 nt) ypaA → pseudogene, C‑terminal fragment, Transposase_31 family
RA 2,368,810 A→T 5.2% S258C (AGC→TGC)  arnA → fused UDP‑L‑Ara4N formyltransferase/UDP‑GlcA C‑4'‑decarboxylase
RA 2,378,333 A→G 5.9% V309V (GTT→GTC menD ← 2‑succinyl‑5‑enolpyruvyl‑6‑hydroxy‑3‑ cyclohexene‑1‑carboxylate synthase; SEPHCHC synthase
RA 2,560,996 G→T 16.8% intergenic (+98/‑372) yffL → / → yffM CPZ‑55 prophage; uncharacterized protein/CPZ‑55 prophage; uncharacterized protein
RA 2,695,037 C→A 5.3% Q169H (CAG→CAT purL ← phosphoribosylformyl‑glycineamide synthetase
RA 2,852,543 A→G 5.1% P136P (CCA→CCG hypD → hydrogenase maturation protein
RA 2,863,159 A→G 5.0% P275P (CCA→CCG ygbK → FliA‑regulated DUF1537 family protein
RA 2,947,465 Δ1 bp 10.0% intergenic (+2/‑32) metZ → / → metW tRNA‑Met/tRNA‑Met
RA 3,140,844 G→A 6.2% A148V (GCG→GTG)  hybD ← maturation protease for hydrogenase 2
RA 3,269,967 C→T 5.0% intergenic (+365/+249) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,269,969 A→C 7.0% intergenic (+367/+247) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,269,970 A→G 5.1% intergenic (+368/+246) yhaC → / ← rnpB pentapetide repeats‑related protein/RNase P, M1 RNA component
RA 3,392,260 C→T 5.8% intergenic (‑232/+198) tldD ← / ← yhdP putative peptidase/DUF3971‑AsmA2 domains protein
RA 3,424,661 C→A 5.2% noncoding (2123/2904 nt) rrlD ← 23S ribosomal RNA of rrnD operon
RA 3,472,627 G→A 5.2% N296N (AAC→AAT fusA ← protein chain elongation factor EF‑G, GTP‑binding
RA 3,560,455:1 +G 100% intergenic (‑2/+1) glpR ← / ← glpR pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon/pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
RA 3,683,472 G→A 5.0% intergenic (‑25/+158) dctA ← / ← yhjK C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase
RA 3,683,473 G→A 5.0% intergenic (‑26/+157) dctA ← / ← yhjK C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase
RA 3,683,479 T→C 6.0% intergenic (‑32/+151) dctA ← / ← yhjK C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase
RA 3,683,497 G→A 43.6% intergenic (‑50/+133) dctA ← / ← yhjK C4‑dicarboxylic acid, orotate and citrate transporter/cyclic‑di‑GMP phosphodiesterase
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
RA 3,882,476 A→G 5.7% T418T (ACT→ACC dnaA ← chromosomal replication initiator protein DnaA, DNA‑binding transcriptional dual regulator
RA 3,959,480 A→T 5.9% intergenic (+35/+52) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 3,959,481 C→G 5.9% intergenic (+36/+51) ilvC → / ← ppiC ketol‑acid reductoisomerase, NAD(P)‑binding/peptidyl‑prolyl cis‑trans isomerase C (rotamase C)
RA 3,975,356 Δ1 bp 5.1% coding (211/1131 nt) wecE → TDP‑4‑oxo‑6‑deoxy‑D‑glucose transaminase
MC JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,224,845 T→C 5.2% C340R (TGC→CGC)  metH → homocysteine‑N5‑methyltetrahydrofolate transmethylase, B12‑dependent
RA 4,296,060 C→T 36.7% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,307,038 G→A 5.3% F254F (TTC→TTT alsK ← D‑allose kinase
JC JC 4,504,598 IS5 (–) +4 bp 38.8% coding (541‑544/1218 nt) yjhB → putative MFS transporter, membrane protein
RA 4,549,932 T→A 5.6% intergenic (+222/+21) fimH → / ← gntP minor component of type 1 fimbriae/fructuronate transporter

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 761495 762756 1262 37 [34] [36] 38 [sucA]–sucB [sucA],sucB
* * ÷ NC_000913 3423762–3424234 3424544–3424238 5–783 37 [36] [35] 37 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 274620 =NA (NA)7 (0.070) 6/238 NT NA noncoding (530/1195 nt) IS5 repeat region
?NC_000913 274663 = NA (NA)noncoding (487/1195 nt) IS5 repeat region
* ? NC_000913 = 275149NA (NA)7 (0.070) 6/256 NT 5.7% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 1196386 = 116 (1.150)intergenic (+13/+481) icd/ymfD isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase/e14 prophage; putative SAM‑dependent methyltransferase
* ? NC_000913 1207790 =24 (0.240)63 (0.710) 52/224 NT 67.0% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 41 (0.460)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780526 (0.260)29 (0.330) 28/224 NT 47.6% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 41 (0.460)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994981 (0.010)157 (1.600) 103/248 NT 99.7% intergenic (+253/‑1684) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
?NC_000913 1300698 = 0 (0.000)intergenic (+1453/‑484) ychE/oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 1411899 =111 (1.100)15 (0.190) 13/204 NT 15.6% coding (50/936 nt) ttcA tRNA s(2)C32 thioltransferase, iron sulfur cluster protein
?NC_000913 = 1434958 74 (0.920)pseudogene (51/51 nt) ttcC pseudogene, prophage Rac integration site ttcA duplication;Phage or Prophage Related
* ? NC_000913 = 4542690172 (1.700)10 (0.110) 10/238 NT 5.8% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 163 (1.740)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)