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Table 1 Number of REF– and REF+ candidates after different filtering steps

From: AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

REF– filtering steps
 REF– variations detected in 2,241 individuals 572,081
 REF– candidates that can be located in the reference genome 379,523
 REF– candidates that have unique location in the reference genome 298,907
 REF– candidates after removal of duplicate, closely located and GC-rich k-mers 13,128
 REF– elements that generate reliable genotypes 9,712
REF+ filtering steps
 Alu signature sequences detected in the reference genome 267,377
 REF+ candidates with 5 bp TSD sequence within 270–350 bp 110,938
 REF+ candidates with BLAST homology 98,711
 REF+ candidates that are not present in chimpanzee genome 16,434
 REF+ candidates after removal of duplicate k-mers 15,834
 REF+ candidates that generate reliable genotypes 13,396