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 25 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC1,070,2462.A73.3% 69.5 / 24.5 31intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC697,0940AG57.7% ‑5.3 / 23.9 29intergenic (+21/‑730)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC699,7220AG57.4% 27.7 / 119.1 101intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC1,712,0750GT56.0% ‑5.0 / 17.9 25intergenic (+66/‑192)ppc/adkphosphoenolpyruvate carboxylase/adenylate kinase
*NC_002947_CJ‑RC4,809,8830AC54.5% ‑6.3 / 12.1 11intergenic (‑289/‑266)PP_4234/dsbD‑IIbifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*NC_002947_CJ‑RC1,327,1210CT52.0% 52.0 / 251.7 174intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC4,348,8120AG50.0% 30.3 / 206.0 134intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC697,1140TG43.8% 29.4 / 13.9 35intergenic (+41/‑710)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC6,092,7220GT39.5% 71.0 / 10.5 43R362R (CGG→CGTpotF‑IVputrescine‑binding protein
*NC_002947_CJ‑RC195,6340CT34.9% 134.8 / 116.3 130T380T (ACC→ACTPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC418,2890CA27.4% 178.9 / 12.9 74F24L (TTC→TTAPP_0345heptose kinase WapP
*NC_002947_CJ‑RC196,8790GA27.3% 46.2 / 18.6 33V795V (GTG→GTAPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC5,773,9490TG26.9% 129.3 / 11.2 69E610A (GAG→GCG) betT‑Icholine transporter
*NC_002947_CJ‑RC2,737,1090TG25.4% 139.8 / 10.2 63V1336G (GTG→GGG) PP_2394leucine‑rich repeat‑containing protein
*NC_002947_CJ‑RC1,404,0180AC25.4% 137.9 / 10.1 67V555G (GTG→GGG) PP_1228methyl‑accepting chemotaxis transducer
*NC_002947_CJ‑RC196,3900TC24.8% 181.6 / 67.9 109D632D (GAT→GACPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC2,489,0650TG24.2% 151.7 / 10.1 66V21G (GTG→GGG) PP_2184formate dehydrogenase subunit beta
*NC_002947_CJ‑RC5,211,9310AG24.0% 95.2 / 12.3 51intergenic (‑94/+84)rnd/PP_4592ribonuclease D/metal dependent hydrolase
*NC_002947_CJ‑RC196,3510CG23.4% 248.3 / 103.6 141T619T (ACC→ACGPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC197,5900TC22.9% 197.4 / 69.2 125D1032D (GAT→GACPP_0168putative surface adhesion protein

Marginal new junction evidence (lowest skew 10 of 23 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC = 48098825 (0.060)24 (0.300) 19/268 5.4 42.3% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC 5991580 = 61 (0.770)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 295708047 (0.540)13 (0.160) 13/282 7.9 23.6% intergenic (+35/‑161) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
?NC_002947_CJ‑RC 2957165 = 39 (0.470)intergenic (+120/‑76) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
* ? NC_002947_CJ‑RC = 55584236 (0.070)14 (0.170)
+GCC
13/286 8.0 70.4% intergenic (‑84/+87) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
?NC_002947_CJ‑RC 5558424 = 6 (0.070)intergenic (‑85/+86) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
* ? NC_002947_CJ‑RC = 247211531 (0.360)12 (0.150) 11/278 8.6 19.4% intergenic (+19/+130) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947_CJ‑RC 2472313 = 70 (0.850)coding (1783/1851 nt) PP_2167 PhoD‑like phosphatase
* ? NC_002947_CJ‑RC = 178006616 (0.190)10 (0.120) 10/278 9.0 36.2% intergenic (+25/+81) PP_1587/dapC NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase
?NC_002947_CJ‑RC 1780129 = 20 (0.240)intergenic (+88/+18) PP_1587/dapC NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase
* ? NC_002947_CJ‑RC 1737987 =116 (1.340)7 (0.090) 7/258 9.9 6.8% coding (32/348 nt) yffB glutathione‑dependent thiol reductase
?NC_002947_CJ‑RC = 1777401 89 (1.170)intergenic (+135/+157) PP_5476/PP_1585 hypothetical protein/antidote protein
* ? NC_002947_CJ‑RC 1114870 =36 (0.420)6 (0.080) 6/242 10.0 16.5% intergenic (‑64/+115) rlmF/valS ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase
?NC_002947_CJ‑RC 1114946 = 31 (0.430)intergenic (‑140/+39) rlmF/valS ribosomal RNA large subunit methyltransferase F/valine‑‑tRNA ligase
* ? NC_002947_CJ‑RC = 599158659 (0.680)6 (0.070) 6/276 11.1 9.6% intergenic (+65/‑481) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
?NC_002947_CJ‑RC 5991778 = 57 (0.700)intergenic (+257/‑289) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 599157272 (0.830)6 (0.070) 6/276 11.1 8.2% intergenic (+51/‑495) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
?NC_002947_CJ‑RC 5991794 = 66 (0.810)intergenic (+273/‑273) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 581968620 (0.230)5 (0.070) 5/256 11.1 29.0% intergenic (+57/+72) PP_5092/pilT NLP/P60 protein/twitching motility protein
?NC_002947_CJ‑RC = 5819713 7 (0.090)intergenic (+84/+45) PP_5092/pilT NLP/P60 protein/twitching motility protein