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

Predicted mutations
evidence position mutation annotation gene description
RA 6,155 T→C D102G (GAT→GGT)  yaaA ← peroxide stress resistance protein YaaA
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 889,923 A→G intergenic (‑104/‑166) ybjL ← / → ybjM putative transport protein YbjL/putative inner membrane protein
RA 1,196,220 C→T H366H (CAC→CAT)  icd → isocitrate dehydrogenase
RA 1,196,232 C→T T370T (ACC→ACT)  icd → isocitrate dehydrogenase
RA 1,196,245 T→C L375M (TTA→CTG)  icd → isocitrate dehydrogenase
RA 1,196,247 A→G L375M (TTA→CTG)  icd → isocitrate dehydrogenase
MC JC 1,299,499 Δ1,199 bp insH21 insH21
JC JC 1,879,829 Δ1 bp :: IS186 (–) +6 bp :: Δ1 bp coding (115‑120/360 nt) yeaR ← DUF1971 domain‑containing protein YeaR
MC JC 1,978,503 Δ776 bp insB‑5–insA‑5 insB‑5, insA‑5
RA 2,173,363 Δ2 bp pseudogene (915‑916/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 3,354,487 C→T intergenic (‑437/‑238) yhcC ← / → gltB radical SAM family oxidoreductase YhcC/glutamate synthase subunit GltB
RA 3,560,455 +G pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH
RA 3,879,830 A→G V97A (GTT→GCT)  gyrB ← DNA gyrase subunit B
RA 4,123,133 T→G K69N (AAA→AAC)  ftsN ← cell division protein FtsN
RA 4,296,381 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 15287 15342 56 2 [1] [1] 2 [dnaJ] [dnaJ]
* * ÷ NC_000913 253838 253873 36 2 [1] [0] 4 prfH putative peptide chain release factor
* * ÷ NC_000913 354215 354307 93 2 [1] [1] 2 prpE propionyl‑CoA synthetase
* * ÷ NC_000913 523791 523894 104 2 [1] [1] 2 rhsD protein RhsD
* * ÷ NC_000913 777117 777132 16 2 [0] [1] 3 tolA Tol‑Pal system protein TolA
* * ÷ NC_000913 861994 862032 39 2 [1] [1] 3 ybiW putative pyruvate formate lyase
* * ÷ NC_000913 1106182 1106313 132 5 [1] [1] 2 ymdB 2'‑O‑acetyl‑ADP‑ribose deacetylase, regulator of RNase III activity
* * ÷ NC_000913 1196280 1199048 2769 2 [1] [0] 2 [icd]–[lit] [icd],ymfD,ymfE,[lit]
* * ÷ NC_000913 1199174 1211428 12255 2 [0] [1] 2 [lit]–[icdC] [lit],intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,ymfN,aaaE,ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
* * ÷ NC_000913 1781555 1781565 11 2 [1] [0] 2 ydiS putative oxidoreductase with FAD/NAD(P)‑binding domain
* * ÷ NC_000913 1842937 1842985 49 2 [1] [1] 2 gdhA glutamate dehydrogenase
* * ÷ NC_000913 1848214 1848227 14 3 [1] [1] 2 ydjA putative oxidoreductase
* * ÷ NC_000913 1971069 1971116 48 3 [1] [1] 2 tar methyl‑accepting chemotaxis protein Tar
* * ÷ NC_000913 2126736 2126751 16 2 [0] [1] 2 fcl GDP‑L‑fucose synthase
* * ÷ NC_000913 2628584 2628629 46 2 [1] [1] 3 pdeF cyclic di‑GMP phosphodiesterase PdeF
* * ÷ NC_000913 2632565 2632573 9 5 [0] [0] 5 guaA/guaB GMP synthetase/inosine 5'‑monophosphate dehydrogenase
* * ÷ NC_000913 2687012 2687030 19 2 [0] [0] 2 [hmp] [hmp]
* * ÷ NC_000913 2890427 2890441 15 4 [1] [0] 4 cysJ sulfite reductase, flavoprotein subunit
* * ÷ NC_000913 3119866 3119893 28 2 [1] [1] 2 glcA glycolate/lactate:H(+) symporter GlcA
* * ÷ NC_000913 3423787–3424233 3424514–3424238 6–728 2 [0] [1] 2 [rrfD]–[rrlD] [rrfD],[rrlD]
* * ÷ NC_000913 3498066 3498088 23 2 [0] [0] 4 cysG siroheme synthase
* * ÷ NC_000913 3537281 3537304 24 2 [0] [1] 3 [greB] [greB]
* * ÷ NC_000913 3539711 3539718 8 3 [1] [0] 3 yhgF/feoA putative RNA‑binding protein YhgF/ferrous iron transport protein A

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 1979418 =12 (0.640)3 (0.160) 3/272 2.0 20.0% intergenic (‑203/‑335) insA‑5/uspC IS1 protein InsA/universal stress protein C
?NC_000913 = 2102943 NA (NA)noncoding (1/1195 nt) IS5 repeat region
* ? NC_000913 3363001 =28 (1.480)27 (1.440) 22/270 0.1 65.2% coding (195/2382 nt) yhcD putative fimbrial usher protein YhcD
?NC_000913 3766087 = 1 (0.050)coding (3905/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 = 3653230NA (NA)26 (1.380) 22/272 0.1 100% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3766089 0 (0.000)coding (3907/4134 nt) rhsA rhs element protein RhsA