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

Marginal read alignment evidence (highest frequency 20 of 31 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,604,3440CT48.3% 82.2 / 111.6 120S62F (TCT→TTT) bglJDNA‑binding transcriptional regulator BglJ
*NC_0009134,296,0600CT33.3% 185.3 / 105.6 117intergenic (+266/+376)gltP/yjcOglutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO
*NC_00091329,4960TA32.5% 138.0 / 50.8 77intergenic (+301/‑155)dapB/carA4‑hydroxy‑tetrahydrodipicolinate reductase/carbamoyl phosphate synthetase subunit alpha
*NC_0009132,001,9180AC31.8% 141.7 / 41.1 88intergenic (‑129/+192)fliA/fliCRNA polymerase, sigma 28 (sigma F) factor/flagellar filament structural protein
*NC_0009133,206,4350CT31.5% 121.0 / 44.2 73intergenic (‑179/‑28)ttdR/ttdADNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*NC_000913650,8090TG30.4% 244.0 / 44.1 139T350P (ACC→CCC) citCcitrate lyase synthetase
*NC_0009131,068,1730TG29.5% 208.9 / 37.1 112G31G (GGT→GGGymdFconserved protein YmdF
*NC_0009134,568,5040TG28.9% 305.3 / 20.2 160T6P (ACC→CCC) mdtMmultidrug efflux pump/bile salt:H(+) antiporter/Na(+):H(+) antiporter/K(+):H(+) antiporter
*NC_0009134,111,7470GT28.6% 158.7 / 38.7 63N156K (AAC→AAAyiiQDUF1454 domain‑containing protein YiiQ
*NC_000913501,5750AC27.4% 162.4 / 33.9 84V555G (GTG→GGG) ybaLputative transporter YbaL
*NC_000913753,1250TA26.1% 258.7 / 39.2 111intergenic (‑330/+60)ybgD/gltAputative fimbrial protein YbgD/citrate synthase
*NC_000913501,5640AC25.8% 177.1 / 38.6 89*559E (TAA→GAA) ybaLputative transporter YbaL
*NC_000913770,8970TG25.0% 174.0 / 18.0 93intergenic (+286/‑561)mngB/cydAalpha‑mannosidase/cytochrome bd‑I ubiquinol oxidase subunit I
*NC_0009132,326,4500TG25.0% 157.1 / 37.9 80G114G (GGT→GGGatoBacetyl‑CoA acetyltransferase
*NC_0009133,943,4880TG25.0% 129.9 / 11.4 68noncoding (54/76 nt)gltUtRNA‑Glu
*NC_0009133,206,4440TA23.9% 157.3 / 26.1 71intergenic (‑188/‑19)ttdR/ttdADNA‑binding transcriptional activator Dan/L(+)‑tartrate dehydratase subunit alpha
*NC_0009133,240,9850TG23.6% 261.5 / 35.8 123S348A (TCT→GCT) sstTserine/threonine:Na(+) symporter
*NC_0009133,404,2150TG23.6% 224.6 / 37.0 106G244G (GGT→GGGyhdHacrylyl‑CoA reductase
*NC_000913646,7470TG23.5% 242.8 / 58.8 119T255P (ACC→CCC) citGtriphosphoribosyl‑dephospho‑CoA synthase
*NC_000913888,0140TG23.1% 202.7 / 15.4 91noncoding (44/81 nt)rybBsmall regulatory RNA RybB

Marginal new junction evidence (lowest skew 10 of 35 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 4542690149 (1.010)22 (0.160) 17/258 5.6 14.0% intergenic (+57/‑425) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 = 4542986 131 (0.950)intergenic (+353/‑129) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
* ? NC_000913 = 375219NA (NA)9 (0.080) 9/216 7.1 NA noncoding (1/36 nt) other REP31f
?NC_000913 = 377333 NA (NA)intergenic (+22/+202) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 374921 =NA (NA)15 (0.150) 7/190 7.2 NA intergenic (+40/‑538) mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
?NC_000913 377531 = NA (NA)intergenic (+220/+4) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 = 375118NA (NA)8 (0.070) 8/216 7.5 NA noncoding (1/36 nt) other REP31d
?NC_000913 = 377333 NA (NA)intergenic (+22/+202) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 = 375320NA (NA)8 (0.060) 8/232 7.9 NA noncoding (1/36 nt) other REP31h
?NC_000913 = 377333 NA (NA)intergenic (+22/+202) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 = 374958NA (NA)6 (0.060) 6/202 8.0 NA noncoding (28/34 nt) other REP31a
?NC_000913 = 377392 NA (NA)noncoding (31/34 nt) other REP32b
* ? NC_000913 4542682 =166 (1.120)9 (0.070) 9/258 8.1 5.9% intergenic (+49/‑433) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
?NC_000913 4542996 = 133 (0.960)intergenic (+363/‑119) fimE/fimA regulator for fimA/type 1 fimbriae major subunit
* ? NC_000913 375023 =NA (NA)12 (0.120) 5/192 8.2 NA intergenic (+142/‑436) mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
?NC_000913 377530 = NA (NA)intergenic (+219/+5) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB
* ? NC_000913 375248 =NA (NA)13 (0.100) 6/238 9.0 NA noncoding (15/34 nt) other REP31g
?NC_000913 377507 = NA (NA)noncoding (16/34 nt) other REP32d
* ? NC_000913 374922 =NA (NA)19 (0.140) 6/260 9.5 NA intergenic (+41/‑537) mhpE/mhpT 4‑hydroxy‑2‑oxovalerate aldolase/3‑hydroxyphenylpropionate/3‑ hydroxycinnamate:H(+) symporter
?NC_000913 377329 = NA (NA)intergenic (+18/+206) yaiL/frmB DUF2058 domain‑containing protein YaiL/S‑formylglutathione hydrolase FrmB