breseq  version 0.35.4  revision f352f80f4bc9
mutation predictions | marginal predictions | summary statistics | genome diff | command line log

Marginal read alignment evidence
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_002947_CJ‑RC1,070,2461.G67.7% 59.4 / 29.0 32intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC1,070,2462.A67.7% 57.0 / 30.1 32intergenic (+46/+96)aroP‑I/PP_0928aromatic amino acid transport protein/K+‑dependent Na+/Ca+ exchanger‑like protein
*NC_002947_CJ‑RC697,0940AG55.6% ‑4.9 / 15.9 22intergenic (+21/‑730)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC697,1070TG53.8% 5.1 / 17.1 22intergenic (+34/‑717)mmsA‑I/PP_16SDmethylmalonate‑semialdehyde dehydrogenase/16S ribosomal RNA
*NC_002947_CJ‑RC1,327,1210CT53.6% 23.6 / 134.2 100intergenic (+97/‑196)PP_16SE/PP_23SE16S ribosomal RNA/23S ribosomal RNA
*NC_002947_CJ‑RC1,666,7870GC46.4% 24.4 / 10.6 28intergenic (‑59/‑212)PP_1460/ffhmembrane protein/signal recognition particle GTPase subunit
*NC_002947_CJ‑RC4,348,8120AG45.2% 42.7 / 113.3 84intergenic (‑70/+404)PP_3820/galUgroup II intron‑encoding maturase/UTP‑glucose‑1‑phosphate uridylyltransferase
*NC_002947_CJ‑RC699,7220AG42.7% 40.3 / 89.8 75intergenic (+115/‑129)PP_t06/PP_23SDtRNA‑Ala/23S ribosomal RNA
*NC_002947_CJ‑RC1,130,1990GT41.9% 20.9 / 10.8 31intergenic (‑254/+50)gcvH‑I/PP_0990glycine cleavage system protein H/DoxX family protein
*NC_002947_CJ‑RC5,512,7200TG30.2% 74.4 / 11.4 73L35R (CTG→CGG) urtBurea ABC transporter permease
*NC_002947_CJ‑RC5,512,7110AC29.3% 74.8 / 15.8 76Q32P (CAG→CCG) urtBurea ABC transporter permease
*NC_002947_CJ‑RC661,6660AC25.0% 72.6 / 10.2 40L430W (TTG→TGG) PP_0569MATE efflux family protein
*NC_002947_CJ‑RC5,541,3800AC23.5% 86.7 / 15.3 51intergenic (+55/+66)PP_4871/PP_4872lysine decarboxylase family protein/hypothetical protein
*NC_002947_CJ‑RC2,178,2140GC20.5% 214.4 / 10.4 93V150V (GTG→GTCPP_1931hypothetical protein
*NC_002947_CJ‑RC5,230,8940GC20.2% 248.2 / 11.9 100intergenic (‑133/+43)PP_4606/PP_4607ferric siderophore receptor/transmembrane sensor

Marginal new junction evidence (lowest skew 10 of 39 shown)
  seq id position reads (cov) reads (cov) score skew freq annotation gene product
* ? NC_002947_CJ‑RC 4809877 =5 (0.080)14 (0.290) 12/220 3.9 34.2% intergenic (‑283/‑272) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991750 50 (1.040)intergenic (+229/‑317) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 65278244 (0.690)12 (0.220) 10/250 5.2 38.8% 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 = 55584232 (0.030)13 (0.210)
+GCC
12/284 5.3 86.9% intergenic (‑84/+87) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
?NC_002947_CJ‑RC 5558424 = 2 (0.030)intergenic (‑85/+86) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
* ? NC_002947_CJ‑RC = 48098826 (0.090)11 (0.190) 10/266 5.6 31.6% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC 5991580 = 42 (0.720)intergenic (+59/‑487) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 48098826 (0.090)8 (0.150) 7/250 6.4 19.5% intergenic (‑288/‑267) PP_4234/dsbD‑II bifunctional aldehyde oxidase/xanthine dehydrogenase/thiol/disulfide interchange protein 2
?NC_002947_CJ‑RC = 5991764 61 (1.120)intergenic (+243/‑303) kefB‑III/PP_mr64 glutathione‑regulated potassium/H+ antiporter/C4 ncRNA
* ? NC_002947_CJ‑RC = 247211514 (0.220)7 (0.120) 7/276 7.0 19.6% intergenic (+19/+130) PP_2166/PP_2167 anti‑anti‑sigma factor/PhoD‑like phosphatase
?NC_002947_CJ‑RC 2472313 = 44 (0.730)coding (1783/1851 nt) PP_2167 PhoD‑like phosphatase
* ? NC_002947_CJ‑RC 661513 =40 (0.630)6 (0.110)
+GGGCCGCATAGCGGCC
6/258 7.1 22.3% intergenic (+23/+104) PP_0568/PP_0569 hypothetical protein/MATE efflux family protein
?NC_002947_CJ‑RC 5558424 = 7 (0.110)intergenic (‑85/+86) PP_4887/PP_4888 hypothetical protein/methyl‑accepting chemotaxis transducer
* ? NC_002947_CJ‑RC = 54559536 (0.090)3 (0.070)
+48 bp
3/194 7.2 15.2% intergenic (+151/‑204) lnt/PP_4791 apolipoprotein N‑acyltransferase/transposase
?NC_002947_CJ‑RC 5548441 = 44 (0.690)intergenic (‑766/+111) rpsF/rlmB 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB
* ? NC_002947_CJ‑RC 5226203 =6 (0.090)3 (0.070)
+48 bp
3/194 7.2 15.2% intergenic (‑204/+175) PP_4603/PP_4604 transposase/DMT superfamily permease
?NC_002947_CJ‑RC 5548441 = 44 (0.690)intergenic (‑766/+111) rpsF/rlmB 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB
* ? NC_002947_CJ‑RC 4075618 =1 (0.020)3 (0.070)
+48 bp
3/194 7.2 16.6% intergenic (‑204/+237) PP_3586/tpx transposase/2‑Cys peroxiredoxin
?NC_002947_CJ‑RC 5548441 = 44 (0.690)intergenic (‑766/+111) rpsF/rlmB 30S ribosomal protein S6/23S rRNA (guanosine(2251)‑2'‑O)‑methyltransferase RlmB