Table 1.

Benchmarks for SEQSpark Analysis of UK10K Hip-to-Waist Ratio Data

	Variants: MAF ≥ 0.01a	Rare Variants: MAF < 0.01b
Load datac	21.75 min	16.25 min
Annotation	N/A	1.40 min
Ti/Tv ratio	1.92 min	0.20 min
PCAd	11.65 min	N/A
Single variant	16.03 min	N/A
CMC	N/A	0.22 min
BRV	N/A	0.23 min
VT	N/A	7.90 min
SKAT	N/A	0.18 min
SKAT-O	N/A	0.22 min

Quality control was performed using data from 1,927 individuals with WGS data. PCA was performed using 1,811 individuals who had data on WHRs and association analysis was performed using 1,798 individuals with WHRs data who were not outliers in the PC analysis.

^aA total of 9,332,772 variants with an MAF ≥ 0.01 analyzed.

^bA total of 542,616 rare variants within coding regions were loaded and after annotation, a total of 163,578 missense, splice-site, frameshift, and nonsense variants in 18,011 genes were available for analysis.

^cThe dataset size is 669.4 GB in LZ4 compression format.

^dTen PCs were generated using all variants with an MAF ≥ 0.01.