Tangram: a comprehensive toolbox for mobile element insertion detection

BMC Genomics

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

		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

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.

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