breseq  version 0.27.1  revision 87c22d663cc3
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence (highest frequency 20 of 38 shown)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,947,5910A.39.6% 227.2 / 154.5 101intergenic (+18/‑16)metW/metVtRNA‑Met/tRNA‑Met
*NC_0009132,947,4670AC31.3% 207.0 / 122.6 116intergenic (+4/‑30)metZ/metWtRNA‑Met/tRNA‑Met
*NC_000913422,4290TG29.9% 587.3 / 107.1 354intergenic (+70/‑89)proY/malZproline‑specific permease/maltodextrin glucosidase
*NC_0009132,818,1450TC29.6% 259.9 / 141.7 198intergenic (‑10/+53)argZ/argYtRNA‑Arg/tRNA‑Arg
*NC_0009131,708,9010AC28.1% 305.5 / 54.7 261R661R (CGA→CGCrsxCSoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*NC_000913423,5520TG26.5% 584.6 / 84.2 322G345G (GGT→GGGmalZmaltodextrin glucosidase
*NC_0009134,606,1920GC26.4% 116.7 / 14.6 78intergenic (‑27/+8)leuV/leuPtRNA‑Leu/tRNA‑Leu
*NC_0009133,269,9940GT26.3% 209.5 / 21.0 180intergenic (+392/+631)yhaC/garKpentapetide repeats‑related protein/glycerate kinase I
*NC_0009131,708,9300CA25.9% 476.6 / 67.0 252P671Q (CCG→CAG) rsxCSoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*NC_0009131,708,8050TA25.6% 101.3 / 38.3 156R629R (CGT→CGArsxCSoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*NC_0009131,552,1910CA25.4% 924.9 / 86.9 456intergenic (+200/+207)fdnI/yddMformate dehydrogenase‑N, cytochrome B556 (gamma) subunit, nitrate‑inducible/putative DNA‑binding transcriptional regulator
*NC_000913696,5340GT25.4% 255.1 / 49.1 134intergenic (‑30/+8)glnX/glnVtRNA‑Gln/tRNA‑Gln
*NC_000913422,4320TG25.0% 767.2 / 61.3 354intergenic (+73/‑86)proY/malZproline‑specific permease/maltodextrin glucosidase
*NC_0009132,947,4650T.24.8% 382.6 / 132.2 150intergenic (+2/‑32)metZ/metWtRNA‑Met/tRNA‑Met
*NC_0009132,818,1580TA24.3% 286.5 / 85.5 174intergenic (‑23/+40)argZ/argYtRNA‑Arg/tRNA‑Arg
*NC_0009133,270,1630CA23.3% 345.3 / 19.1 234intergenic (+561/+462)yhaC/garKpentapetide repeats‑related protein/glycerate kinase I
*NC_0009133,781,0320TG23.2% 638.9 / 58.5 321intergenic (+15/‑183)lldD/trmLL‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
*NC_0009132,818,1490TC23.0% 301.8 / 105.5 191intergenic (‑14/+49)argZ/argYtRNA‑Arg/tRNA‑Arg
*NC_0009131,708,9100GC22.9% 469.0 / 28.5 246A664A (GCG→GCCrsxCSoxR iron‑sulfur cluster reduction factor component; putative membrane‑associated NADH oxidoreductase of electron transport complex
*NC_0009133,270,1510AC22.3% 220.8 / 21.9 202intergenic (+549/+474)yhaC/garKpentapetide repeats‑related protein/glycerate kinase I

Marginal new junction evidence (lowest skew 10 of 36 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_000913 = 4542690396 (0.940)139 (0.350) 109/282 9.1 27.4% intergenic (+57/‑425) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 = 4542986 365 (0.920)intergenic (+353/‑129) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 4542682 =387 (0.920)136 (0.340) 107/282 9.5 26.7% intergenic (+49/‑433) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
?NC_000913 4542996 = 385 (0.970)intergenic (+363/‑119) fimE/fimA tyrosine recombinase/inversion of on/off regulator of fimA/major type 1 subunit fimbrin (pilin)
* ? NC_000913 = 1207805327 (0.770)59 (0.160) 52/268 24.4 16.8% coding (305/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 = 1209602 294 (0.780)pseudogene (18/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 1207790 =328 (0.780)50 (0.130) 44/268 27.9 14.4% coding (290/630 nt) stfP e14 prophage; uncharacterized protein
?NC_000913 1209619 = 300 (0.790)pseudogene (1/501 nt) stfE pseudogene, e14 prophage; side tail fiber protein fragment family;Phage or Prophage Related
* ? NC_000913 781369 =272 (0.640)138 (0.340)
+GAAG
45/292 30.2 38.6% noncoding (1/76 nt) lysZ tRNA‑Lys
?NC_000913 = 2521006 180 (0.430)noncoding (76/76 nt) valU tRNA‑Val
* ? NC_000913 781577 =314 (0.740)191 (0.460)
+GAAG
43/292 31.1 44.3% noncoding (1/76 nt) lysQ tRNA‑Lys
?NC_000913 = 2521006 180 (0.430)noncoding (76/76 nt) valU tRNA‑Val
* ? NC_000913 780554 =464 (1.100)94 (0.230)
+GAAG
43/292 31.1 23.1% noncoding (1/76 nt) lysT tRNA‑Lys
?NC_000913 = 2521006 180 (0.430)noncoding (76/76 nt) valU tRNA‑Val
* ? NC_000913 696863 =146 (0.350)91 (0.230)
+GAAGAAACAATC
38/276 31.7 26.5% intergenic (‑33/+2) glnW/glnU tRNA‑Gln/tRNA‑Gln
?NC_000913 = 697134 402 (0.950)intergenic (‑1/+379) metT/asnB tRNA‑Met/asparagine synthetase B
* ? NC_000913 = 1287084175 (0.410)82 (0.220) 34/260 31.9 26.2% intergenic (+558/+3) narI/tpr nitrate reductase 1, gamma (cytochrome b(NR)) subunit/protamine‑like protein
?NC_000913 1287557 = 311 (0.850)noncoding (66/85 nt) tyrT tRNA‑Tyr
* ? NC_000913 781369 =272 (0.640)107 (0.250)
+G
37/298 34.7 35.9% noncoding (1/76 nt) lysZ tRNA‑Lys
?NC_000913 = 2521128 113 (0.270)intergenic (+2/‑45) valX/valY tRNA‑Val/tRNA‑Val