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 66,528 T→C Q8R (CAG→CGG)  araD ← L‑ribulose‑5‑phosphate 4‑epimerase
MC JC 66,533 3540 bp→27 bp [araD]araB [araD], araA, araB
RA 70,289 G→T intergenic (‑241/‑98) araB ← / → araC L‑ribulokinase/DNA‑binding transcriptional dual regulator
JC JC 370,982 IS30 (+) +2 bp coding (520‑521/867 nt) mhpC → 2‑hydroxy‑6‑ketonona‑2,4‑dienedioic acid hydrolase
RA 502,653 C→T intergenic (‑191/+47) ybaL ← / ← fsr putative transporter with NAD(P)‑binding Rossmann‑fold domain/putative fosmidomycin efflux system
RA 547,694 A→G pseudogene (114/252 nt) ylbE → putative protein, C‑ter fragment (pseudogene)
RA 547,835 +G pseudogene (4/1008 nt) ylbE → putative protein, C‑ter fragment (pseudogene)
RA 704,236 T→C L357S (TTG→TCG)  nagE → fused N‑acetyl glucosamine specific PTS enzyme: IIC, IIB, and IIA components
RA 1,301,461 C→A A180E (GCG→GAG)  oppB → oligopeptide transporter subunit
RA 1,335,418 A→G S522G (AGC→GGC)  acnA → aconitate hydratase 1
JC JC 1,434,821 IS5 (+) +4 bp coding (94‑97/1134 nt) ompN ← outer membrane pore protein N, non‑specific
RA 1,634,011 A→G pseudogene (381/528 nt) nohQ ← pseudogene, Qin prophage; predicted packaging protein;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin
RA 1,650,355 T→C pseudogene (781/1158 nt) intQ → pseudogene, Qin prophage; predicted defective integrase;Phage or Prophage Related
MC JC 1,976,527 Δ776 bp insB1insA insB1, insA
RA 2,842,032 G→T R67R (CGC→CGA hycG ← hydrogenase 3 and formate hydrogenase complex, HycG subunit
RA 3,108,443 C→A noncoding (56/76 nt) pheV → tRNA‑Phe
RA 3,957,957 C→T intergenic (‑121/+78) ppiC ← / ← yifN peptidyl‑prolyl cis‑trans isomerase C (rotamase C)/conserved protein (pseudogene)
RA 4,091,793 C→T G168D (GGC→GAC)  rhaD ← rhamnulose‑1‑phosphate aldolase
MC JC 4,092,014 3461 bp→29 bp [rhaD]rhaB [rhaD], rhaA, rhaB
RA 4,159,271 G→T G42V (GGC→GTC)  fabR → DNA‑binding transcriptional repressor
RA 4,162,146 C→G A162G (GCA→GGA)  btuB → vitamin B12/cobalamin outer membrane transporter
RA 4,294,404 +GC intergenic (+587/+55) gltP → / ← yjcO glutamate/aspartate:proton symporter/hypothetical protein
RA 4,472,857 A→G intergenic (+117/‑28) bdcR → / → tabA transcriptional repressor for divergent bdcA/biofilm modulator regulated by toxins
RA 4,583,503 G→A Q428* (CAA→TAA)  hsdR ← endonuclease R Type I restriction enzyme
RA 4,600,532 C→T W117* (TGG→TAG)  yjjP ← inner membrane protein, H‑NS‑repressed, DUF1212 family
RA 4,614,692 G→T L133I (CTA→ATA)  yjjI ← hypothetical protein

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 363567 365526 1960 145 [144] [0] 320 lacZ beta‑D‑galactosidase
* * ÷ NC_000913 2518985–2519021 2519127–2519078 58–143 147 [141] [143] 146 [valU]–[valX] [valU],[valX]
* * ÷ NC_000913 3421725–3422256 3422619–3422260 5–895 146 [144] [142] 146 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 365527 =0 (0.000)295 (1.010) 135/192 0.2 64.8% coding (3/3075 nt) lacZ beta‑D‑galactosidase
?NC_000913 4589683 = 321 (1.100)coding (4/1656 nt) tsr methyl‑accepting chemotaxis protein I, serine sensor receptor
* ? NC_000913 1207013 =78 (0.260)250 (1.000) 113/166 0.3 77.1% coding (290/630 nt) stfP e14 prophage; putative protein
?NC_000913 1208842 = 83 (0.330)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; predicted side tail fiber protein fragment;Phage or Prophage Related
* ? NC_000913 = 120702878 (0.260)193 (0.770) 103/166 0.7 72.2% coding (305/630 nt) stfP e14 prophage; putative protein
?NC_000913 = 1208825 83 (0.330)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; predicted side tail fiber protein fragment;Phage or Prophage Related