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 39 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC699,7220AG57.0% 33.8 / 130.7 107intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC4,353,2990CA55.6% 3.0 / 10.1 9F106L (TTC→TTAyrpB2‑nitropropane dioxygenase
*NC_002947_CJ‑RC4,952,6750TG53.8% ‑3.3 / 10.2 14intergenic (‑122/+35)fliL/fliKflagellar protein FliL/flagellar hook‑length control protein FliK
*NC_002947_CJ‑RC4,348,8120AG51.2% 34.7 / 185.9 129intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC1,327,1210CT41.7% 123.9 / 155.1 132intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC2,101,7510AC40.4% 24.6 / 20.2 55L186R (CTG→CGG) PP_1878hypothetical protein
*NC_002947_CJ‑RC5,743,2820TG37.5% 10.5 / 18.0 16intergenic (+32/+39)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC5,512,7230TG36.5% 44.5 / 13.4 54L36R (CTC→CGC) urtBurea ABC transporter permease
*NC_002947_CJ‑RC856,5980GC34.1% 80.4 / 13.0 44intergenic (+28/+88)pagL‑I/PP_0738lipid A 3‑O‑deacylase/hypothetical protein
*NC_002947_CJ‑RC5,512,7110AC34.0% 40.2 / 12.9 55Q32P (CAG→CCG) urtBurea ABC transporter permease
*NC_002947_CJ‑RC1,703,2500GC33.3% 16.4 / 12.9 15intergenic (+99/‑68)lysS/PP_1497lysine‑‑tRNA ligase/TetR family transcriptional regulator
*NC_002947_CJ‑RC4,648,3410AC32.7% 85.8 / 11.5 52V302G (GTG→GGG) PP_4112sulfate transporter
*NC_002947_CJ‑RC1,625,2080AC32.0% 12.1 / 10.9 25intergenic (+31/+26)PP_1425/nadBhypothetical protein/L‑aspartate oxidase
*NC_002947_CJ‑RC5,743,2850AT31.6% 23.0 / 11.5 19intergenic (+35/+36)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC5,743,2860AT31.6% 19.9 / 13.3 19intergenic (+36/+35)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC5,743,2890CA31.6% 32.1 / 10.2 19intergenic (+39/+32)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC1,130,1990GT31.0% 108.0 / 12.7 58intergenic (‑254/+50)gcvH‑I/PP_0990glycine cleavage system protein H/DoxX family protein
*NC_002947_CJ‑RC5,194,4391.G30.8% 12.1 / 13.9 13intergenic (+117/‑85)PP_4572/PP_4573hypothetical protein/AAA family ATPase
*NC_002947_CJ‑RC1,013,2410GC30.0% 80.3 / 33.0 40intergenic (+69/+62)prfC/potF‑Ipeptide chain release factor 3/putrescine‑binding protein
*NC_002947_CJ‑RC1,013,2420GC30.0% 79.1 / 31.4 40intergenic (+70/+61)prfC/potF‑Ipeptide chain release factor 3/putrescine‑binding protein

Marginal new junction evidence (lowest skew 10 of 42 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC 4809877 =7 (0.090)21 (0.360) 14/220 5.0 49.2% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991750 38 (0.650)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 55584231 (0.010)17 (0.220)
+GCC
14/284 6.9 94.5% 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 = 65278259 (0.760)13 (0.190) 10/250 7.5 33.8% 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)9 (0.130) 7/250 9.0 24.5% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991764 52 (0.780)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC 4895256 =21 (0.270)5 (0.080) 5/236 9.8 22.2% intergenic (+28/‑180) pyk/PP_4302 pyruvate kinase/urea transporter
?NC_002947_CJ‑RC 4895335 = 18 (0.290)intergenic (+107/‑101) pyk/PP_4302 pyruvate kinase/urea transporter
* ? NC_002947_CJ‑RC = 295708038 (0.490)7 (0.090) 7/280 9.9 14.5% intergenic (+35/‑161) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
?NC_002947_CJ‑RC 2957165 = 46 (0.610)intergenic (+120/‑76) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
* ? NC_002947_CJ‑RC = 56842303 (0.040)7 (0.090)
+CGGG
7/282 10.0 70.6% 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 6003718 =37 (0.480)4 (0.070) 4/230 10.2 13.5% intergenic (+10/+99) PP_5256/amaA cyclic nucleotide‑binding protein/L‑pipecolate oxidase
?NC_002947_CJ‑RC 6003812 = 22 (0.360)intergenic (+104/+5) PP_5256/amaA cyclic nucleotide‑binding protein/L‑pipecolate oxidase
* ? NC_002947_CJ‑RC = 394794020 (0.260)5 (0.080) 4/234 10.4 24.3% coding (109/1797 nt) PP_3483 type II secretion system protein
?NC_002947_CJ‑RC = 3947969 15 (0.240)coding (80/1797 nt) PP_3483 type II secretion system protein
* ? NC_002947_CJ‑RC 5384101 =21 (0.270)3 (0.050) 3/220 10.6 20.7% intergenic (+18/+115) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR
?NC_002947_CJ‑RC 5384199 = 7 (0.120)intergenic (+116/+17) smpB/pdhR SsrA‑binding protein/DNA‑binding transcriptional regulator LldR