Table 1.

The comparison of properties of haplotype blocks defined by the dynamic programming algorithm and the greedy algorithm of Patil et al. (6) with 80% coverage

Method	Common SNPs/block	No. of blocks	No. of blocks requiring ≥1 SNPs	Average size/block, kb	Average no. common haplotypes/block	All blocks, %	Common SNPs, %
Dynamic programming	>10	742	738	24.27	4.23	28.8	75.5
	3–10	909	842	7.30	3.03	35.3	19.5
	<3	924	274	0.73	2.12	35.9	5.0
	Total	2,575	1,854	12.58	3.05	100.0	100.0
Greedy	>10	589	589	23.90	3.75	14.2	56.8
	3–10	1,408	1,396	8.52	2.92	34.1	30.7
	<3	2,138	1,776	2.96	2.30	51.7	12.4
	Total	4,135	3,761	7.83	2.72	100.0	100.0

Common SNPs are the 24,047 SNPs with minor allele frequency ≥0.1. Common haplotypes are the haplotypes in each block present more than once in the sample of 20 chromosomes.