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Table 6 Genotype accuracy

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

   

Tangram

RetroSeq

  

Genotype from validation

Genotype call

Genotype call

  

Het

Homo

Het

Homo

Alu

NA12878

Het

120

8

119

0

Homo

1

26

37

1

NA12891

Het

95

13

93

0

Homo

0

40

44

0

NA12892

Het

106

11

104

0

Homo

0

32

42

0

L1

NA12878

Het

5

1

4

0

Homo

0

2

1

1

NA12891

Het

4

0

2

0

Homo

0

2

1

0

NA12892

Het

3

1

3

0

Homo

0

3

3

0

  1. A contingency table is shown for MEI genotypes reported by Tangram and RetroSeq on deep coverage sequencing data from a CEU trio (NA12878, NA12891 and NA12892). The “Genotype from validation” column shows the genotype that was validated in Stewart et al. 2011. The “Genotype call” column shows the genotype predicted by Tangram and RetroSeq at the same loci. The “Genotype” column in Table 5 was calculated based on the results in this table.
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BMC Genomics

ISSN: 1471-2164

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