Table 2. Array summaries.

Company	Array	Product Informationa	No. Assays	No. Positions	Percent Overlap with 1000 Genomes	Percent Overlap with 1000 Genomes, MAF Filtered
Illumina	HumanCore	12v1-0, A	296,720	296,677	88.2	87.8
Illumina	HumanCore+Exome	12v1-0, B	535,743	528,484	76.3	69.3
Affymetrix	Axiom Biobank	na33	716,836	645,209	73.6	67.7
Illumina	OmniExpress	12v1, H	727,413	727,410	98.8	98.8
Affymetrix	Axiom World Array 4	na32	841,602	814,831	98.6	98.5
Illumina	Omni2.5M	8v1, A	2,368,218	2,362,580	93.2	93.0
Illumina	Omni2.5M+Exome	8v1, A	2,556,812	2,513,578	91.5	89.9
Illumina	Omni5M	4v1, C	4,285,657	4,279,793	94.4	93.2

Summaries of each array included in these genomic coverage analyses, restricted to assays mapped to chromosomes 1 through 22 and the non-pseudoautosomal portion of the X chromosome. For each array, the columns give (1) the company manufacturing the array; (2) the array name; (3) additional product information; (4) the total number of assays; (5) the total number of unique map locations represented by those assays; (6) the percent overlap with 1000 Genomes phase 1 integrated variant set, at any frequency; and (7) the percent overlap with 1000 Genomes phase 1 integrated variant set, with a minimum of two copies of the minor allele seen in at least one of the four ancestry groups. The counts in (5) are less than (4) when there is more than one assay/feature for a given genomic position. The percentages given in (6) and (7) are with a denominator of unique positions, rather than unique assays. MAF, minor allele frequency.

^aProduct information. For Illumina arrays, number of samples (e.g., 4, 8, or 12), version of the array (e.g., “v1”), and version of the array manifest file (.bpm, e.g., “A” or “B”). For Affymetrix arrays, the NetAffx release number.