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
MC JC 257,908 Δ776 bp insB9–[crl] insB9, insA9, [crl]
RA 632,233 C→A L18M (CTG→ATG)  ybdD → conserved protein YbdD
RA 697,054 (A)7→8 intergenic (‑7/+3) leuW ← / ← metT tRNA‑Leu/tRNA‑Met
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 1,531,801 IS1 (+) +9 bp intergenic (+162/‑7) yncI → / → ydcC putative transposase YncI/H repeat‑associated putative transposase YdcC
RA 1,566,867 G→T H92N (CAT→AAT)  dosC ← diguanylate cyclase DosC
RA 1,615,629 G→T E276* (GAG→TAG)  yneJ → putative LysR‑type DNA‑binding transcriptional regulator YneJ
RA 1,678,604 G→T A60S (GCA→TCA)  ydgH → DUF1471 domain‑containing protein YdgH
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 2,083,362 C→A R203S (CGC→AGC)  sbcB → exodeoxyribonuclease I
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 4,166,342 G→T intergenic (+57/‑317) murI → / → rrsB glutamate racemase/16S ribosomal RNA
RA 4,261,710 C→A S14R (AGC→AGA)  dusA → tRNA‑dihydrouridine synthase A
RA 4,291,502 C→A intergenic (+70/‑10) nrfD → / → nrfE putative menaquinol‑cytochrome c reductase subunit NrfD/putative cytochrome c‑type biogenesis protein NrfE
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 136268 136288 21 2 [1] [1] 2 speE spermidine synthase
* * ÷ NC_000913 915142 915159 18 2 [0] [0] 2 lysO/aqpZ L‑lysine exporter/water channel AqpZ
* * ÷ NC_000913 1196292 1205283 8992 2 [1] [1] 2 [icd]–[aaaE] [icd],ymfD,ymfE,lit,intE,xisE,ymfH,ymfI,ymfJ,ymfK,ymfT,ymfL,ymfM,oweE,[ymfN],[aaaE]
* * ÷ NC_000913 1205380 1211428 6049 2 [1] [1] 2 [ymfN]–[icdC] [ymfN],[aaaE],ymfR,beeE,jayE,ymfQ,ycfK,tfaP,tfaE,stfE,pinE,mcrA,[icdC]
* * ÷ NC_000913 1640990 1641029 40 2 [1] [1] 3 essQ/cspB Qin prophage; putative S lysis protein/Qin prophage; cold shock‑like protein CspB
* * ÷ NC_000913 1836486 1836596 111 2 [1] [1] 2 ynjB putative ABC transporter periplasmic binding protein YnjB
* * ÷ NC_000913 1841193 1841210 18 2 [1] [1] 2 ynjF putative phosphatidyl transferase, inner membrane protein
* * ÷ NC_000913 1893859 1893873 15 2 [0] [1] 2 yoaB/yoaC RutC family protein YoaB/DUF1889 domain‑containing protein YoaC
* * ÷ NC_000913 2033827 2033873 47 3 [1] [1] 2 rseX/yedS small regulatory RNA RseX/putative outer membrane protein YedS, N‑terminal fragment
* * ÷ NC_000913 2249619 2249693 75 2 [1] [0] 2 yeiE/yeiH putative LysR‑type transcriptional regulator YeiE/conserved inner membrane protein YeiH
* * ÷ NC_000913 2629644 2629655 12 2 [1] [0] 2 yfgG/yfgH protein YfgG/lipoprotein YfgH
* * ÷ NC_000913 3080645 3080745 101 2 [0] [1] 2 tktA transketolase 1
* * ÷ NC_000913 3103015 3104047 1033 4 [1] [1] 2 mutY adenine DNA glycosylase
* * ÷ NC_000913 3131425 3131437 13 2 [1] [0] 2 yghQ putative transport protein YghQ
* * ÷ NC_000913 3285818 3285857 40 2 [1] [1] 3 agaD galactosamine‑specific PTS enzyme IID component
* * ÷ NC_000913 3423792–3424234 3424530–3424238 5–739 2 [1] [1] 2 [rrlD] [rrlD]
* * ÷ NC_000913 3455440 3455508 69 2 [1] [1] 2 gspA/gspC Type II secretion system protein GspA/Type II secretion system protein GspC
* * ÷ NC_000913 3751954 3751986 33 2 [1] [1] 2 yiaT/yiaU outer membrane protein YiaT/putative LysR‑type DNA‑binding transcriptional regulator YiaU

Unassigned new junction evidence
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 374963NA (NA)8 (0.600) 8/190 0.5 NA noncoding (33/34 nt) other REP31a
?NC_000913 = 377487 NA (NA)intergenic (+176/+48) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 3363001 =41 (2.120)33 (1.720) 28/274 0.0 61.9% coding (195/2382 nt) yhcD putative fimbrial usher protein YhcD
?NC_000913 3766087 = 0 (0.000)coding (3905/4134 nt) rhsA rhs element protein RhsA
* ? NC_000913 = 3653230NA (NA)19 (0.980) 15/276 0.3 90.5% noncoding (1/1195 nt) IS5 repeat region
?NC_000913 = 3766089 2 (0.100)coding (3907/4134 nt) rhsA rhs element protein RhsA