breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Predicted mutations
evidence position mutation freq annotation gene description
MC JC 257,908 Δ776 bp 100% [crl] [crl]
JC JC 458,790 IS186 (–) +6 bp :: Δ1 bp 70.5% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
JC JC 458,790 IS186 (+) +6 bp :: Δ1 bp 13.8% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
RA 1,196,305 C→T 93.9% R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
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 1,619,420 A→G 7.7% T101A (ACC→GCC)  marR → transcriptional repressor of multiple antibiotic resistance
RA 1,708,847 G→A 8.0% E643E (GAG→GAA rsxC → SoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
JC JC 1,710,414 IS5 (–) +4 bp 12.0% coding (211‑214/621 nt) rsxG → SoxR iron‑sulfur cluster reduction factor component; putative membrane protein of electron transport complex
JC JC 1,937,136 IS2 (–) +5 bp 16.1% coding (485‑489/870 nt) yebK → putative DNA‑binding transcriptional regulator
JC JC 1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
RA 2,066,465 T→C 100% K286R (AAG→AGG)  insH1 ← IS5 transposase and trans‑activator
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 2,304,688 A→G 5.7% intergenic (+295/+420) eco → / ← mqo ecotin, a serine protease inhibitor/malate dehydrogenase, FAD/NAD(P)‑binding domain
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 3,560,494 G→A 5.2% pseudogene (112/150 nt) glpR ← pseudogene, DNA‑binding transcriptional repressor;regulator; Energy metabolism, carbon: Anaerobic respiration; repressor of the glp operon
MC JC 3,815,859 Δ82 bp 100% [rph][rph] [rph], [rph]
JC 4,001,645 Δ5 bp 100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
RA 4,070,450 T→C 7.0% intergenic (‑49/+65) yihR ← / ← yihS putative sulphoquinovose mutarotase/sulphoquinovose isomerase
RA 4,118,097 A→C 8.4% intergenic (‑7/‑418) glpF ← / → zapB glycerol facilitator/FtsZ stabilizer, septal ring assembly factor, cell division stimulator
RA 4,184,543 C→A 100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
RA 4,296,060 C→T 13.9% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,190 A→G 18.0% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,191 A→C 23.8% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,268 T→C 18.5% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,286 C→T 10.2% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,303 A→G 6.5% intergenic (+509/+133) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
RA 4,296,304 A→C 6.5% intergenic (+510/+132) 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

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423828–3424235 3424448–3424239 5–621 103 [97] [97] 101 [rrlD] [rrlD]
* * ÷ NC_000913 4233742 4235466 1725 102 [96] [99] 101 pgi pgi

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 224395NA (NA)7 (0.030) 6/428 NT NA noncoding (625/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
?NC_000913 = 224600 NA (NA)noncoding (830/1542 nt) rrsH 16S ribosomal RNA of rrnH operon
* ? NC_000913 458792 =71 (0.290)19 (0.080) 19/432 NT 21.1% intergenic (+92/‑96) clpX/lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
?NC_000913 608007 = NA (NA)noncoding (1/1345 nt) IS186 repeat region
* ? NC_000913 1207790 =76 (0.300)144 (0.620) 76/408 NT 68.5% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 62 (0.270)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 120780572 (0.290)154 (0.660) 87/408 NT 70.5% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 62 (0.270)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 = 12994980 (0.000)123 (0.500) 79/432 NT 100% 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 = 19785020 (0.000)129 (0.530) 77/424 NT 100% intergenic (‑305/+16) flhD/insB1 flagellar class II regulon transcriptional activator, with FlhC/IS1 transposase B
?NC_000913 1979279 = 0 (0.000)intergenic (‑64/‑474) insA/uspC IS1 repressor TnpA/universal stress protein