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 29 shown, sorted by frequency from high to low)
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC697,1070TG53.3% 7.0 / 19.3 19intergenic (+34/‑717)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC699,7220AG53.2% 2.1 / 121.1 94intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC4,348,8120AG51.2% 22.1 / 173.7 125intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC1,327,1210CT48.0% 88.3 / 212.8 155intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC5,923,0260AC43.2% 39.8 / 12.9 38K266T (AAG→ACG) PP_5190type II secretion system protein
*NC_002947_CJ‑RC697,1380CG39.1% 22.3 / 11.5 23intergenic (+65/‑686)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC5,442,1280GC36.7% 40.4 / 15.4 30R15G (CGG→GGG) rluE23S rRNA pseudouridine(2457) synthase
*NC_002947_CJ‑RC2,282,7700TG33.3% 11.8 / 18.3 21intergenic (‑162/+67)PP_2010/PP_2011cytochrome b561/hypothetical protein
*NC_002947_CJ‑RC1,615,7160GC31.4% 56.5 / 10.7 35T12T (ACC→ACGPP_1415membrane protein
*NC_002947_CJ‑RC3,597,5260CG30.5% 109.8 / 10.9 59A196P (GCC→CCC) PP_3174oxidoreductase
*NC_002947_CJ‑RC2,282,7790CA30.0% 29.4 / 12.4 20intergenic (‑171/+58)PP_2010/PP_2011cytochrome b561/hypothetical protein
*NC_002947_CJ‑RC1,403,5910TC28.6% 27.8 / 17.9 32intergenic (‑57/+24)PP_1227/PP_1228membrane protein/methyl‑accepting chemotaxis transducer
*NC_002947_CJ‑RC4,140,1430GC27.5% 153.3 / 13.8 69intergenic (+35/‑230)PP_3644/PP_5609monooxygenase subunit/hypothetical protein
*NC_002947_CJ‑RC1,403,5900GA26.7% 36.9 / 14.3 30intergenic (‑56/+25)PP_1227/PP_1228membrane protein/methyl‑accepting chemotaxis transducer
*NC_002947_CJ‑RC3,975,9890TG25.0% 103.3 / 13.4 48P293P (CCA→CCCPP_3506magnesium chelatase subunit ChII
*NC_002947_CJ‑RC1,497,8310TG23.6% 145.5 / 11.5 72V140G (GTC→GGC) PP_1310hypothetical protein
*NC_002947_CJ‑RC4,029,5400AC23.5% 180.5 / 13.9 81A306A (GCA→GCCPP_3553AMP‑binding domain‑containing protein
*NC_002947_CJ‑RC197,6320TC23.2% 117.2 / 38.2 69T1046T (ACT→ACCPP_0168putative surface adhesion protein
*NC_002947_CJ‑RC955,1530TC22.9% 64.2 / 13.1 35intergenic (+107/‑206)cyoE/alaCprotoheme IX farnesyltransferase/aminotransferase
*NC_002947_CJ‑RC2,192,4770GT22.8% 141.6 / 12.5 57intergenic (+86/‑118)PP_1937/PP_1938helicase/hypothetical protein

Marginal new junction evidence (lowest skew 10 of 47 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC 4809877 =5 (0.070)23 (0.410) 15/222 4.3 54.9% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991750 34 (0.600)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 599158656 (0.750)14 (0.200) 14/276 6.0 21.2% intergenic (+65/‑481) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
?NC_002947_CJ‑RC 5991778 = 51 (0.720)intergenic (+257/‑289) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 55584231 (0.010)18 (0.250)
+GCC
14/286 6.3 94.8% 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 = 56842301 (0.010)11 (0.150)
+CGGG
11/284 7.3 91.9% intergenic (‑133/+71) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
?NC_002947_CJ‑RC 5684231 = 1 (0.010)intergenic (‑134/+70) PP_4986/PP_4987 hemolysin III family channel protein/putative Chemotaxis protein
* ? NC_002947_CJ‑RC = 295708040 (0.530)10 (0.140) 10/282 7.7 19.5% intergenic (+35/‑161) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
?NC_002947_CJ‑RC 2957165 = 44 (0.610)intergenic (+120/‑76) PP_2588/PP_2589 class III aminotransferase/aldehyde dehydrogenase family protein
* ? NC_002947_CJ‑RC = 65278263 (0.840)7 (0.110) 6/252 8.9 20.5% 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)6 (0.090) 6/268 9.3 18.0% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC 5991580 = 51 (0.740)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 247214021 (0.280)3 (0.050) 3/214 9.6 13.2% intergenic (+44/+105) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947_CJ‑RC = 2472186 24 (0.440)intergenic (+90/+59) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
* ? NC_002947_CJ‑RC = 48098824 (0.050)4 (0.060) 4/252 10.1 13.5% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991764 48 (0.740)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 600374720 (0.270)3 (0.050) 3/232 10.2 14.0% intergenic (+39/+70) PP_5256/amaA cyclic nucleotide‑binding protein/L‑pipecolate oxidase
?NC_002947_CJ‑RC = 6003781 21 (0.350)intergenic (+73/+36) PP_5256/amaA cyclic nucleotide‑binding protein/L‑pipecolate oxidase