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Table 5 Sensitivity and genotype accuracy in deep coverage sequencing data from the 1000 Genomes Project

From: Tangram: a comprehensive toolbox for mobile element insertion detection

   Stewart et al. 2011 Tangram RetroSeq TEA
  Sample MEI loci Sensitivity Genotype Sensitivity Genotype Sensitivity Genotype
   Validated Reported Validated Reported   Validated Reported   Validated Reported  
Alu NA12878 408 965 98.8% 93.0% 95.0% 94.1% 87.7% 76.4% 89.5% 82.2% N/A
NA12891 309 675 98.1% 96.3% 91.2% 98.4% 96.4% 67.9% 96.1% 93.8% N/A
NA12892 312 650 98.1% 96.9% 92.6% 99.0% 97.4% 71.2% 94.2% 92.5% N/A
L1 NA12878 38 157 86.8% 52.2% 87.5% 78.9% 45.8% 83.3% 84.2% 49.7% N/A
NA12891 26 64 92.3% 75.0% 100.0% 76.9% 64.1% 66.7% 84.6% 70.3% N/A
NA12892 34 76 94.1% 76.3% 85.7% 79.4% 65.8% 50.0% 76.5% 64.5% N/A
  1. Comparisons are shown for a CEU trio (NA12878, NA12891 and NA12892) processed with Tangram, RetroSeq and TEA. Sensitivity and genotype accuracy was measured by comparing the reported events with those in Stewart et al., 2011. The total number of validated and reported MEI loci are shown under the “Stewart et al. 2011” column. The two sub columns under each detector, “Validated” and “Reported”, show the sensitivity to PCR validated loci and all reported loci in Stewart et al. 2011, respectively. The TEA program does not provide genotype calls, and therefore could not be used for genotype accuracy comparisons. The best result in each row is indicated in boldface text.