Fig. 3.
Comparison of coverage of 1000 genomes project reference panel between TxArray and other genome-wide genotyping platforms for variants with MAF >0.05 (a) and >0.01 (b). Coverage (ordinate) for the 1000 Genomes Project Phase I integrated reference panel was assessed using maximum r 2 (abscissa), at an MAF cutoff of 0.05 (a) and 0.01 (b). Populations included: (1) African ancestry (AAM): Yoruba in Ibadan, Nigeria (YRI) and Americans of African Ancestry in SouthWest, USA (ASW); (2) Admixed American (AMR): Colombians from Medellin, Colombia (CLM), Mexican Ancestry from Los Angeles USA (MXL), and Puerto Ricans from Puerto Rico (PUR); (3) Asian (ASN): Han Chinese in Beijing (CHB), Southern Han Chinese (CHS), Japanese in Tokyo, Japan (JPT); and (4) European ancestry (CTI): Utah residents with ancestry from Northern Western Europe (CTU), Central and Eastern European (CEU), and Toscani in Italia (TSI), as described in the HapMap and 1KGP. The platforms compared include the TxArray using 767,203 SNPs passing QC. ILMN_1M and ILMN660 refer to Illumina’s Infinium one million and the Illumina 660K genotyping platforms. Affy_6.0 refers to the Affymetrix 6.0 SNP chip containing approximately 906,600 SNPs