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 26 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AP0123061,091,9920TG35.0% 577.1 / 64.1 286intergenic (+38/‑145)narI/ychSnitrate reductase 1, gamma (cytochrome b(NR)) subunit/predicted protein
*AP012306341,3770TG34.9% 178.6 / 15.7 109G60G (GGT→GGGribDfused diaminohydroxyphosphoribosylaminopyrimidin e deaminase and 5‑amino‑6‑(5‑phosphoribosylamino) uracil reductase
*AP0123061,421,1470TG30.3% 458.7 / 15.2 231T79P (ACC→CCC) ydhBpredicted DNA‑binding transcriptional regulator
*AP012306644,4170GA29.1% 851.4 / inf 516intergenic (+32/‑401)lysQ/nadAtRNA‑Lys/quinolinate synthase, subunit A
*AP0123061,854,8510AC28.7% 543.0 / 71.9 240T25P (ACC→CCC) yejHpredicted ATP‑dependet helicase
*AP012306257,1370TG27.6% 360.4 / 12.8 174L496V (TTG→GTG) betTcholine transporter of high affinity
*AP0123061,944,2880AC27.5% 532.0 / 28.3 222G361G (GGT→GGGmenEo‑succinylbenzoate‑CoA ligase
*AP0123063,938,8870CT25.3% 537.3 / 128.3 249S44F (TCT→TTT) bglJDNA‑binding transcriptional regulator
*AP012306800,6750AC24.6% 643.2 / 26.2 256T192P (ACC→CCC) lolAchaperone for lipoproteins
*AP0123063,527,3680AC24.6% 594.1 / 52.3 242L140F (TTA→TTCrhaSDNA‑binding transcriptional activator, L‑rhamnose‑binding
*AP0123063,182,8610AC24.6% 287.7 / 18.9 114L198F (TTA→TTCyiaNpredicted transporter
*AP0123062,758,9090TG24.0% 648.4 / 17.8 242G33G (GGT→GGGagaDN‑acetylgalactosamine‑specific enzyme IID component of PTS
*AP0123063,903,7910AG23.5% 539.7 / 67.3 230E189G (GAA→GGA) yjgJpredicted transcriptional regulator
*AP0123063,639,0400TG22.9% 130.7 / 17.0 61noncoding (54/76 nt)gltVtRNA‑Glu
*AP012306472,8680TG22.4% 546.4 / 22.6 205D435A (GAC→GCC) cusSsensory histidine kinase in two‑component regulatory system with CusR, senses copper ions
*AP0123062,558,0710AC22.3% 609.1 / 31.9 238V302G (GTA→GGA) visCpredicted oxidoreductase, FAD/NAD(P)‑binding domain
*AP012306202,4170TG21.7% 724.9 / 22.9 269V409G (GTA→GGA) tilStRNA(Ile)‑lysidine synthetase
*AP0123062,499,4140AC21.6% 804.7 / 62.1 301P126P (CCA→CCCyqeIpredicted transcriptional regulator
*AP0123061,226,5570AG21.5% 497.1 / 74.7 200G55G (GGA→GGGydcUpredicted spermidine/putrescine transporter subunit
*AP0123061,128,4120TG20.9% 631.6 / 42.0 235V29G (GTG→GGG) yciOconserved protein

Marginal new junction evidence (lowest skew 10 of 29 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? AP012306 = 997497287 (0.900)14 (0.050) 14/268 17.0 5.3% coding (41/1305 nt) ndh respiratory NADH dehydrogenase 2/cupric reductase
?AP012306 997993 = 241 (0.840)coding (537/1305 nt) ndh respiratory NADH dehydrogenase 2/cupric reductase
* ? AP012306 = 1092512376 (1.180)12 (0.040) 8/258 19.4 4.1% intergenic (+100/+3) ychS/tpr predicted protein/predicted protamine‑like protein
?AP012306 1092985 = 239 (0.870)noncoding (66/85 nt) tyrT tRNA‑Tyr
* ? AP012306 3838276 =450 (1.420)6 (0.020) 6/268 20.9 1.4% intergenic (+79/‑101) rnr/rlmB exoribonuclease R, RNase R/23S rRNA (Gm2251)‑methyltransferase
?AP012306 3838337 = 432 (1.510)intergenic (+140/‑40) rnr/rlmB exoribonuclease R, RNase R/23S rRNA (Gm2251)‑methyltransferase
* ? AP012306 = 2275071209 (0.660)36 (0.130)
+GTATCAGTCTGCTTCGCAAG
5/258 21.2 13.2% noncoding (1/76 nt) gltW tRNA‑Glu
?AP012306 = 3597478 339 (1.070)intergenic (+65/‑107) rrsB/gltT 16S ribosomal RNA (rrnB)/tRNA‑Glu
* ? AP012306 = 1092334315 (0.990)6 (0.020) 5/258 21.2 2.3% coding (198/276 nt) ychS predicted protein
?AP012306 1092985 = 239 (0.870)noncoding (66/85 nt) tyrT tRNA‑Tyr
* ? AP012306 = 2252778404 (1.270)6 (0.020) 6/292 21.6 1.5% intergenic (‑27/+171) lepA/rseC GTP binding membrane protein/RseC protein
?AP012306 = 2252788 410 (1.320)intergenic (‑37/+161) lepA/rseC GTP binding membrane protein/RseC protein
* ? AP012306 = 2382041281 (0.890)6 (0.020) 6/294 21.7 2.1% coding (275/480 nt) ispF 2C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase
?AP012306 = 2382058 290 (0.930)coding (258/480 nt) ispF 2C‑methyl‑D‑erythritol 2,4‑cyclodiphosphate synthase
* ? AP012306 = 215364NA (NA)5 (0.020) 5/288 22.1 NA noncoding (745/2905 nt) rrlH 23S ribosomal RNA (rrlH)
?AP012306 = 215372 NA (NA)noncoding (753/2905 nt) rrlH 23S ribosomal RNA (rrlH)
* ? AP012306 = 3540501281 (0.890)4 (0.010) 4/274 22.4 1.5% coding (220/768 nt) tpiA triosephosphate isomerase
?AP012306 = 3540489 255 (0.870)coding (232/768 nt) tpiA triosephosphate isomerase
* ? AP012306 = 2947811264 (0.830)4 (0.010) 4/274 22.4 1.6% coding (1875/2544 nt) nirB nitrite reductase, large subunit, NAD(P)H‑binding
?AP012306 = 2947799 254 (0.870)coding (1863/2544 nt) nirB nitrite reductase, large subunit, NAD(P)H‑binding