Characterisation of the genomic architecture of human chromosome 17q and evaluation of different methods for haplotype block definition

Table 2 Haplotype block characteristics according to different definition methods, applied to the subset of 100 common SNPs (minor allele frequency >0.2).

Definition^a	n blocks	Average block length (kb)	Average n SNPs/block	% of sequence covered	n SNPs in blocks
Definition 1	17	31.1	2.6	8.7	44
Definition 2a	14	10.9	2.6	2.4	32
Definition 2b	21	10.8	2.5	3.3	53
Definition 3	19	18.4	2	5.7	33
Definition 4	39	107.0	3.8	55.4	85
Definition 5	27	41.1	2.7	18.2	73

^aDefinition 1 [16], Definitions 2a and 2b (modifications of [16]), Definition 3 [24] and Definition 5 (D' high threshold method) were based on measures of LD, whereas Definition 4 (n+1 method) was based on haplotype diversity.

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