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 100% intergenic (‑241/‑98) araB ← / → araC ribulokinase/DNA‑binding transcriptional dual regulator AraC
RA 70,371 T→C 100% intergenic (‑323/‑16) araB ← / → araC ribulokinase/DNA‑binding transcriptional dual regulator AraC
RA 70,434 C→T 100% N16N (AAC→AAT araC → DNA‑binding transcriptional dual regulator AraC
RA 70,581 C→T 100% V65V (GTC→GTT araC → DNA‑binding transcriptional dual regulator AraC
RA 70,740 T→G 100% G118G (GGT→GGG araC → DNA‑binding transcriptional dual regulator AraC
RA 71,079 C→T 100% R231R (CGC→CGT araC → DNA‑binding transcriptional dual regulator AraC
RA 71,082 T→C 100% I232I (ATT→ATC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,085 T→C 100% S233S (AGT→AGC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,109 T→C 100% T241T (ACT→ACC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,175 A→G 100% R263R (CGA→CGG araC → DNA‑binding transcriptional dual regulator AraC
RA 71,214 T→C 100% F276F (TTT→TTC araC → DNA‑binding transcriptional dual regulator AraC
RA 71,272 A→C 100% 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 100% D6N (GAT→AAT)  lacZ ← beta‑galactosidase
RA 366,300 Δ1 bp 100% coding (6/3075 nt) lacZ ← beta‑galactosidase
RA 366,521 C→T 36.8% L330L (CTG→CTA lacI ← DNA‑binding transcriptional repressor LacI
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 3,535,612 A→C 22.5% I86S (ATC→AGC)  envZ ← sensory histidine kinase EnvZ
RA 3,560,455:1 +G 100% pseudogene (151/758 nt) glpR ← DNA‑binding transcriptional repressor GlpR
RA 3,879,686 T→G 65.8% Y145S (TAC→TCC)  gyrB ← DNA gyrase subunit B
RA 4,296,060 C→T 29.2% 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

Unassigned missing coverage evidence
   seq id start end size ←reads reads→ gene description
* * ÷ NC_000913 3423705–3424234 3424594–3424238 5–890 54 [52] [52] 53 [rrfD]–[rrlD] [rrfD],[rrlD]

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 71275122 (1.190)4291 (44.020)
+GCTC
157/168 NT 97.6% intergenic (+10/‑76) araC/yabI DNA‑binding transcriptional dual regulator AraC/DedA family protein YabI
?NC_000913 366286 = 98 (0.960)coding (20/3075 nt) lacZ beta‑galactosidase
* ? NC_000913 1207790 =15 (0.150)85 (1.020) 55/144 NT 88.0% coding (290/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 1209619 = 11 (0.130)pseudogene (37/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 120780515 (0.150)54 (0.650) 41/144 NT 82.3% coding (305/630 nt) ycfK e14 prophage; protein StfP
?NC_000913 = 1209602 11 (0.130)pseudogene (54/537 nt) stfE e14 prophage; putative side tail fiber protein fragment
* ? NC_000913 = 12994980 (0.000)124 (1.270) 79/168 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 =120 (1.170)29 (0.320) 25/158 NT 21.9% intergenic (+49/‑433) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 4542996 = 99 (1.080)intergenic (+363/‑119) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
* ? NC_000913 = 4542690123 (1.200)26 (0.280) 24/158 NT 19.9% intergenic (+57/‑425) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 = 4542986 99 (1.080)intergenic (+353/‑129) fimE/fimA regulator for fimA/type 1 fimbriae major subunit