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Table 1 MEI detection sensitivity for Alu elements

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

    Tangram RetroSeq
Ploidy Read length Coverage Sen (RP) Sen (SR) Sen (RP\SR) Sen (SR\RP) Sen (Union) Sensitivity
Het 76 bp 67.6% 60.0% 25.4% 17.8% 85.4% 43.7%
10× 83.4% 88.9% 8.8% 14.3% 97.7% 93.6%
20× 84.2% 97.8% 1.2% 14.8% 99.0% 98.9%
106 bp 45.1% 67.3% 13.9% 36.1% 81.2% 12.0%
10× 77.0% 93.0% 4.5% 20.5% 97.5% 68.9%
20× 83.4% 98.9% 0.4% 15.9% 99.3% 97.7%
Homo 76 bp 83.4% 88.9% 8.8% 14.3% 97.7% 95.2%
10× 84.2% 97.8% 1.2% 14.8% 99.0% 98.8%
20× 84.6% 99.1% 0.4% 14.9% 99.5% 99.2%
106 bp 77.0% 93.0% 4.5% 20.5% 97.5% 68.9%
10× 83.4% 98.9% 0.4% 15.9% 99.3% 97.7%
20× 83.8% 99.3% 0.4% 15.9% 99.7% 98.9%
  1. Results are shown for the Tangram and RetroSeq programs applied to simulated data (1,000 AluY insertions introduced at random positions on human chromosome 20). Simulated reads were generated under different ploidy values (homozygous or heterozygous), read length (76 bp and 106 bp) and read coverage (5X, 10X, 20X). Columns “Sen (RP)” and “Sen (SR)” indicate the sensitivity of the RP and SR methods respectively. The two columns “Sen (RP\SR)” and “Sen (SR\RP)” indicate the sensitivity of the RP and SR signal in isolation respectively. “Sen (Union)” indicates the overall sensitivity of Tangram when calling MEI with both RP and SR modules. The best result in each row is indicated in boldface text.