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
RA 70,289 G→T 9.3% intergenic (‑241/‑98) araB ← / → araC ribulokinase/DNA‑binding transcriptional dual regulator AraC
RA 70,371 T→C 11.8% intergenic (‑323/‑16) araB ← / → araC ribulokinase/DNA‑binding transcriptional dual regulator AraC
RA 70,434 C→T 7.9% N16N (AAC→AAT araC → DNA‑binding transcriptional dual regulator AraC
RA 70,581 C→T 10.5% V65V (GTC→GTT araC → DNA‑binding transcriptional dual regulator AraC
RA 70,740 T→G 9.6% G118G (GGT→GGG araC → DNA‑binding transcriptional dual regulator AraC
RA 71,079 C→T 13.3% R231R (CGC→CGT araC → DNA‑binding transcriptional dual regulator AraC
RA 71,082 T→C 13.7% I232I (ATT→ATC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,085 T→C 13.2% S233S (AGT→AGC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,109 T→C 12.3% T241T (ACT→ACC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,175 A→G 13.2% R263R (CGA→CGG araC → DNA‑binding transcriptional dual regulator AraC
RA 71,214 T→C 14.9% F276F (TTT→TTC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,272 A→C 10.6% intergenic (+7/‑79) araC → / → yabI DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI
MC JC 257,908 Δ776 bp 100% insB9[crl] insB9, insA9, [crl]
RA 366,290 C→T 10.6% D6N (GAT→AAT)  lacZ ← beta‑galactosidase
RA 366,300 Δ1 bp 8.6% coding (6/3075 nt) lacZ ← beta‑galactosidase
RA 1,352,926 C→T 8.1% G235S (GGT→AGT)  sapD ← putrescine ABC exporter ATP binding protein SapD
MC JC 1,397,381 Δ13,756 bp 100% [ynaJ][ttcA] 16 genes
MC JC 1,978,503 Δ776 bp 100% insB‑5insA‑5 insB‑5, insA‑5
RA 2,173,361 Δ2 bp 100% pseudogene (917‑918/1358 nt) gatC ← galactitol‑specific PTS enzyme IIC component
RA 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 4,296,060 C→T 30.5% intergenic (+266/+376) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
RA 4,296,380:1 +CG 100% intergenic (+586/+56) gltP → / ← yjcO glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
JC JC 4,542,330 IS1 (–) +9 bp 39.0% coding (294‑302/597 nt) fimE → regulator for fimA

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423698–3424234 3424600–3424238 5–903 69 [67] [68] 70 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 71275132 (1.230)16 (0.160)
+GCTC
15/168 NT 11.5% intergenic (+10/‑76) araC/yabI DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI
?NC_000913 366286 = 127 (1.190)coding (20/3075 nt) lacZ beta‑galactosidase
* ? NC_000913 1207790 =28 (0.260)54 (0.620) 41/144 NT 67.6% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 29 (0.330)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 120780531 (0.290)55 (0.630) 43/144 NT 67.0% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 29 (0.330)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12994980 (0.000)117 (1.140) 81/168 NT 100% intergenic (+253/‑33) ychE/insH21 putative inner membrane protein/IS5 transposase and trans‑activator
?NC_000913 1300698 = 0 (0.000)intergenic (+151/‑484) insH21/oppA IS5 transposase and trans‑activator/oligopeptide ABC transporter periplasmic binding protein
* ? NC_000913 4542682 =93 (0.870)6 (0.060) 6/174 NT 6.5% intergenic (+49/‑433) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 4542995 = 82 (0.770)intergenic (+362/‑120) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
* ? NC_000913 4542682 =93 (0.870)43 (0.450) 37/158 NT 35.0% intergenic (+49/‑433) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 4542996 = 76 (0.790)intergenic (+363/‑119) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
* ? NC_000913 = 454269096 (0.900)51 (0.530) 37/158 NT 38.6% intergenic (+57/‑425) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 = 4542986 76 (0.790)intergenic (+353/‑129) fimE/fimA regulator for fimA/type 1 fimbriae major subunit