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 34 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC1,070,2461.G66.7% 41.8 / 24.5 25intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC697,1000TG65.0% ‑0.7 / 10.9 22intergenic (+27/‑724)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC1,070,2462.A64.0% 42.6 / 29.2 25intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC699,7220AG60.0% 81.9 / 153.7 141intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC4,338,6080GT54.5% 13.4 / 28.3 22intergenic (+121/+21)PP_3812/PP_5632lipase/allo‑isoleucine metabolism protein
*NC_002947_CJ‑RC1,327,1210CT53.6% 35.7 / 217.1 154intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC697,1140TG52.4% 8.0 / 24.9 22intergenic (+41/‑710)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC697,0940AG47.6% 0.9 / 15.8 23intergenic (+21/‑730)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC4,348,8120AG47.3% 48.6 / 159.4 111intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC195,6340CT43.6% 73.9 / 131.8 111T380T (ACC→ACTPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC5,512,7110AC38.1% 21.7 / 10.7 45Q32P (CAG→CCG) urtBurea ABC transporter permease
*NC_002947_CJ‑RC1,544,3590CG34.2% 61.9 / 14.6 38A388G (GCG→GGG) mdfAmultidrug MFS transporter
*NC_002947_CJ‑RC4,740,9510CG33.3% 13.0 / 11.5 18intergenic (+81/+672)gltA/yeiWcitrate synthase/putative oxidoreductase
*NC_002947_CJ‑RC3,975,9890TG30.4% 120.8 / 11.5 56P293P (CCA→CCCPP_3506magnesium chelatase subunit ChII
*NC_002947_CJ‑RC5,773,9490TG29.1% 95.1 / 10.6 55E610A (GAG→GCG) betT‑Icholine transporter
*NC_002947_CJ‑RC195,5590CA28.6% 151.6 / 58.8 81T355T (ACC→ACAPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC3,578,4330GT28.6% 78.2 / 36.5 57intergenic (+110/‑214)PP_3158/PP_5589hypothetical protein/rhs repeat‑associated core domain‑containing protein
*NC_002947_CJ‑RC196,8790GA28.2% 55.8 / 22.8 39V795V (GTG→GTAPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC4,433,5800GC28.0% 95.2 / 23.4 50intergenic (‑29/‑89)PP_5648/PP_3928hypothetical protein/hypothetical protein
*NC_002947_CJ‑RC196,3510CG27.0% 179.3 / 103.9 115T619T (ACC→ACGPP_0168putative surface adhesion protein

Marginal new junction evidence (lowest skew 10 of 24 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC = 295708041 (0.530)26 (0.350) 23/282 3.9 36.0% intergenic (+35/‑161) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
?NC_002947_CJ‑RC 2957165 = 53 (0.710)intergenic (+120/‑76) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
* ? NC_002947_CJ‑RC = 55584231 (0.010)14 (0.180)
+GCC
14/286 6.4 93.5% intergenic (‑84/+87) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
?NC_002947_CJ‑RC 5558424 = 1 (0.010)intergenic (‑85/+86) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
* ? NC_002947_CJ‑RC = 65278260 (0.780)12 (0.180) 11/252 6.6 31.7% coding (1961/1962 nt) ctpL methyl‑accepting chemotaxis protein CtpL
?NC_002947_CJ‑RC = 4809862 0 (0.000)intergenic (‑268/‑287) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
* ? NC_002947_CJ‑RC = 48098824 (0.050)12 (0.170) 11/268 7.0 37.1% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC 5991580 = 37 (0.520)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC 1737987 =102 (1.320)12 (0.180) 10/258 7.2 12.4% coding (32/348 nt) yffB glutathione‑dependent thiol reductase
?NC_002947_CJ‑RC = 1777401 80 (1.170)intergenic (+135/+157) PP_5476/PP_1585 hypothetical protein/antidote protein
* ? NC_002947_CJ‑RC = 178006617 (0.220)8 (0.110) 8/278 8.6 33.9% intergenic (+25/+81) PP_1587/dapC NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase
?NC_002947_CJ‑RC 1780129 = 15 (0.200)intergenic (+88/+18) PP_1587/dapC NhaP‑type Na+(K+)/H+ antiporter/N‑succinyl‑L,L‑diaminopimelate aminotransferase
* ? NC_002947_CJ‑RC = 56842303 (0.040)8 (0.110)
+CGGG
8/284 8.8 73.3% intergenic (‑133/+71) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
?NC_002947_CJ‑RC 5684231 = 3 (0.040)intergenic (‑134/+70) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
* ? NC_002947_CJ‑RC = 48098824 (0.050)10 (0.150) 6/252 9.0 25.8% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991764 54 (0.810)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 464770219 (0.250)4 (0.070) 4/214 9.0 20.6% intergenic (+48/+83) fusB/PP_4112 elongation factor G 2/sulfate transporter
?NC_002947_CJ‑RC = 4647732 17 (0.300)intergenic (+78/+53) fusB/PP_4112 elongation factor G 2/sulfate transporter
* ? NC_002947_CJ‑RC = 247211514 (0.180)7 (0.100) 7/278 9.2 13.8% intergenic (+19/+130) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947_CJ‑RC 2472313 = 74 (1.010)coding (1783/1851 nt) PP_2167 PhoD‑like phosphatase