Predicted mutations
position mutation breseq GATK_CNVnator annotation gene description
257,908 Δ776 bp 100% [crl] [crl]
348,458 IS5 (+) +4 bp 12.2% intergenic (‑15/‑221) prpR ← / → prpB propionate catabolism operon regulatory protein/2‑methylisocitrate lyase
458,790 IS186 (–) +6 bp :: Δ1 bp 100% intergenic (+90/‑93) clpX → / → lon ATPase and specificity subunit of ClpX‑ClpP ATP‑dependent serine protease/DNA‑binding ATP‑dependent protease La
1,196,305 C→T 100%100% R395C (CGT→TGT)  icd → isocitrate dehydrogenase; e14 prophage attachment site; tellurite reductase
1,269,231 T→C 5.3% A15A (GCA→GCG ldrA ← toxic polypeptide, small
1,269,856 G→T 8.3% intergenic (‑46/‑2) ldrB ← / → rdlB toxic polypeptide, small/sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB
1,269,858:1 +T 5.3% noncoding (1/66 nt) rdlB → sRNA antisense regulator affects LdrB translation; proposed addiction module in LDR‑B repeat, with toxic peptide LdrB
1,286,793 A→G 6.1% intergenic (+267/+273) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
1,293,032 IS1 (–) +8 bp 100% intergenic (‑110/‑488) hns ← / → tdk global DNA‑binding transcriptional dual regulator H‑NS/thymidine kinase/deoxyuridine kinase
1,299,499 Δ1,199 bp 100% intergenic (+254/‑485) ychE → / → oppA UPF0056 family inner membrane protein/oligopeptide ABC transporter periplasmic binding protein
1,978,503 Δ776 bp 100% insB1insA insB1, insA
1,979,486 IS5 (+) +4 bp 100% intergenic (‑271/‑264) insA ← / → uspC IS1 repressor TnpA/universal stress protein
1,988,454 A→G 5.8% N78S (AAC→AGC)  yecR → lipoprotein, function unknown
2,132,787 A→C 100%100% I204S (ATC→AGC)  wcaA ← putative glycosyl transferase
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
2,173,363 Δ2 bp 100% intergenic (‑1/+1) gatC ← / ← gatC pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC/pseudogene, galactitol‑specific enzyme IIC component of PTS;transport; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system galactitol‑specific enzyme IIC
2,490,736 Δ1 bp 6.9% coding (1215/1695 nt) oxc ← oxalyl CoA decarboxylase, ThDP‑dependent
2,600,619 Δ1 bp 13.4% coding (142/471 nt) bcp → peroxiredoxin; thiol peroxidase, thioredoxin‑dependent
3,213,426 T→G 7.3% I127S (ATC→AGC)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
3,213,792 T→G 14.1% I249S (ATC→AGC)  rpoD → RNA polymerase, sigma 70 (sigma D) factor
3,486,714 G→A 16.1% A199T (GCA→ACA)  crp → cAMP‑activated global transcription factor, mediator of catabolite repression
3,560,455:1 +G 100%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
3,769,857 T→A 33.3% intergenic (+74/‑91) yibV → / → yibU pseudogene, putative cryptic Rhs immunity protein/pseudogene, H repeat‑associated protein
3,796,101 Δ12,500 bp 100% [waaC][waaA] [waaC], waaL, waaU, waaZ, waaY, waaR, waaO, waaB, waaS, waaP, waaG, waaQ, [waaA]
3,815,859 Δ82 bp 100%96.2% [rph][rph] [rph], [rph]
4,001,645 Δ5 bp 100%100% coding (220‑224/951 nt) corA → magnesium/nickel/cobalt transporter
4,049,912 IS2 (+) +5 bp 100% noncoding (14‑18/109 nt) spf → Spot 42 sRNA antisense regulator of galK translation, Hfq‑dependent
4,184,543 C→A 100%100% P1100Q (CCG→CAG)  rpoB → RNA polymerase, beta subunit
4,233,801 Δ1,600 bp 100% coding (44‑1643/1650 nt) pgi → glucosephosphate isomerase
4,277,820 G→T 100%100% G118* (GGA→TGA)  soxR → redox‑sensitive transcriptional activator of soxS; autorepressor
4,296,060 C→T 10.3% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,190 A→G 22.0% intergenic (+396/+246) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,191 A→C 22.4% intergenic (+397/+245) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,268 T→C 28.6% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,286 C→T 14.4% intergenic (+492/+150) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,303 A→G 10.4% intergenic (+509/+133) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,304 A→C 10.5% intergenic (+510/+132) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,296,381 +GC 100% intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
4,326,041 C→T 5.5% intergenic (‑300/+358) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
4,326,047 C→T 8.4% intergenic (‑306/+352) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
4,326,088 T→G 8.4% intergenic (‑347/+311) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
4,326,141 T→C 9.7% intergenic (‑400/+258) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein
4,326,147 T→C 7.9% intergenic (‑406/+252) yjdN ← / ← yjdM metalloprotein superfamily protein/zinc‑ribbon family protein