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Table 1 Filtering and QC procedures in Stage 1: identifying unequivocal segregating sites. Stage 1 started with 13,550,322 sites and after QC ended with 4,235,761 sites

From: Sequencing strategies and characterization of 721 vervet monkey genomes for future genetic analyses of medically relevant traits

QC filtering procedure

Number of variants removed

Multi-allelic or multi-nucleotide

1,110,071

Cumulative coverage outside of twofold range of global median coverage

1,158,822

MAF in 17 monkeys <25 %

6,859,481

>0 % missing data

164,781

Within 5 bp of another site

21,406

TOTAL

9,314,561