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Table 1 Rate of discordant subfamily annotation in human segmental duplications

From: Transposable element subfamily annotation has a reproducibility problem

Family

# Subfamilies

# in genome

# pairs in filtered seg. duplications

# discordant

% discordant

Alu

47

1196725

10347

1290

12.4

L1

131

951429

6615

933

14.1

  1. TE pairs within segmental duplications were identified as described in the text (hg19 segmental duplicates from [8], TEs based on RepearMasker+Repbase annotation on hg19, filtered for length and quality of overlap between segmental duplicates). Among these, TEs belonging to the Alu and L1 families were considered, because these subfamilies are intended to represent biological history. Discordant annotations are those in which one element in a TE pair is assigned to one subfamily in Repeatmasker, while the other element in the pair is assigned to a different subfamily
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Mobile DNA

ISSN: 1759-8753