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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