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 |