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 27 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC697,0940AG55.0% ‑6.4 / 19.5 24intergenic (+21/‑730)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC1,712,0750GT55.0% 3.4 / 24.5 20intergenic (+66/‑192)ppc/adkphosphoenolpyruvate carboxylase/adenylate kinase
*NC_002947_CJ‑RC4,348,8120AG53.1% 7.9 / 168.8 128intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC1,712,0900GC52.2% 21.4 / 35.4 23intergenic (+81/‑177)ppc/adkphosphoenolpyruvate carboxylase/adenylate kinase
*NC_002947_CJ‑RC699,7220AG51.5% ‑0.9 / 134.1 97intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC1,327,1210CT50.7% 57.5 / 213.1 144intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC4,809,8900GT50.0% ‑2.2 / 12.9 10intergenic (‑296/‑259)PP_4234/dsbD‑IIbifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
*NC_002947_CJ‑RC5,455,9110GT41.2% 17.9 / 10.7 18intergenic (+109/‑246)lnt/PP_4791apolipoprotein N‑acyltransferase/transposase
*NC_002947_CJ‑RC5,512,7110AC38.2% 28.1 / 17.0 59Q32P (CAG→CCG) urtBurea ABC transporter permease
*NC_002947_CJ‑RC2,821,3950G.36.8% 38.7 / 22.6 19intergenic (‑64/‑327)PP_2474/PP_2475glutathione S‑transferase family protein/TetR family transcriptional regulator
*NC_002947_CJ‑RC2,737,1090TG36.7% 76.3 / 13.1 49V1336G (GTG→GGG) PP_2394leucine‑rich repeat‑containing protein
*NC_002947_CJ‑RC5,512,7200TG34.5% 55.6 / 15.1 63L35R (CTG→CGG) urtBurea ABC transporter permease
*NC_002947_CJ‑RC5,773,9490TG32.2% 95.6 / 13.6 59E610A (GAG→GCG) betT‑Icholine transporter
*NC_002947_CJ‑RC441,3180TG30.4% 67.6 / 10.2 47W67G (TGG→GGG) bioF8‑amino‑7‑oxononanoate synthase
*NC_002947_CJ‑RC5,743,2820TG30.4% 29.7 / 18.8 23intergenic (+32/+39)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC5,743,2850AT29.2% 28.4 / 16.1 24intergenic (+35/+36)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC5,743,2860AT29.2% 26.0 / 16.1 24intergenic (+36/+35)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC5,743,2890CA29.2% 38.1 / 17.8 24intergenic (+39/+32)hutF/PP_5037formiminoglutamate deiminase/lipocalin family lipoprotein
*NC_002947_CJ‑RC2,737,0810CA25.0% 109.6 / 11.5 49Q1327K (CAA→AAA) PP_2394leucine‑rich repeat‑containing protein
*NC_002947_CJ‑RC1,751,0590AG24.6% 105.8 / 11.9 58T140A (ACC→GCC) PP_1551replication protein O

Marginal new junction evidence (lowest skew 10 of 44 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC = 65278274 (0.940)19 (0.280) 13/250 6.3 37.4% 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 = 295708034 (0.430)16 (0.210) 15/280 6.5 31.7% intergenic (+35/‑161) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
?NC_002947_CJ‑RC 2957165 = 36 (0.480)intergenic (+120/‑76) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
* ? NC_002947_CJ‑RC = 55584231 (0.010)17 (0.220)
+GCC
15/284 6.6 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 4809877 =12 (0.150)10 (0.170) 10/220 6.6 34.4% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991750 29 (0.490)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 48098823 (0.040)17 (0.240) 12/266 7.2 43.2% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC 5991580 = 42 (0.580)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 48098823 (0.040)14 (0.210) 10/250 7.5 37.5% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991764 44 (0.650)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 56842303 (0.040)12 (0.160)
+CGGG
10/282 8.5 80.5% 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 = 599158644 (0.560)10 (0.140) 9/274 8.7 18.6% intergenic (+65/‑481) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
?NC_002947_CJ‑RC 5991778 = 46 (0.620)intergenic (+257/‑289) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC 4809877 =12 (0.150)7 (0.110) 6/238 9.2 26.0% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC 5991594 = 30 (0.470)intergenic (+73/‑473) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 3968879NA (NA)6 (0.080) 6/276 10.4 8.6% coding (1007/1179 nt) PP_3498 transposase
?NC_002947_CJ‑RC 3968942 = 67 (0.860)coding (1070/1179 nt) PP_3498 transposase