Table 4. Time used by a bit-block based algorithm and the conventional algorithm for computing Pearson correlation of genotypes.

Number of variants	Bit-block	Conventional	Ratio
4000	0:0:2.59	50:01.36	1:1159
7000	0:0:7.59	2:31:56.48	1:1201
10 000	0:0:14.99	5:08:54.14	1:1236
13 000	0:0:23.60	8:43:17.78	1:1330
16 000	0:0:35.18	13:18:33.96	1:1362

Note: The variants were randomly drawn from chromosome 22 and genotypes of 2504 subjects were used to calculate the correlation. The time format a:b:c.d stands for a hour(s), b minute(s) and c.d second(s), respectively. The version of Java running environment was 1.7. CPU frequency was 3.457 GHz. a: For the conventional approach, the genotypes were encoded according to the number of alternative alleles, i.e. 0, 1 and 2 first. The Pearson correlation coefficients were calculated for each pair of variants by a fast Java package Colt (https://dst.lbl.gov/ACSSoftware/colt/).