Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21 Nila Patil, Anthony J. Berno, David A. Hinds, Wade A. Barrett, Jigna M. Doshi, Coleen R. Hacker, Curtis R. Kautzer, Danny H. Lee, Claire Marjoribanks, David P. McDonough, Bich T. N. Nguyen, Michael C. Norris, John B. Sheehan, Naiping Shen, David Stern, Renee P. Stokowski, Daryl J. Thomas, Mark O. Trulson, Kanan R. Vyas, Kelly A. Frazer, Stephen P. A. Fodor, and David R. Cox

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Supplemental Table 2. Properties of SNP blocks versus sample coverage. 80% sample coverage are the SNP blocks in which 80% or more of the chromosomes providing data are defined by haplotypes present more than once in the sample of 20 chromosomes. Common SNPs/block are the common SNPs are the 24,047 SNPs with a minor allele present more than once in our data set which were used to define SNP blocks. Avg. no. common haplotypes/block are the common haplotypes are the haplotypes in each block represented by more than one chromosome. % of all bases are the 32,397,439 bases of finished chromosome 21 genomic DNA sequence which were the basis of this study. Randomized genotypes are the observed alleles for each SNP were randomly permuted among the 20 chromosomes in the sample prior to applying the greedy algorithm.

80% sample coverage

Common SNPs / block	No. of blocks	Avg. size / block (kb)	Avg. no. Common haplotypes / block	% of all blocks	% of all bases
>10	589	23.9	3.7	14.2%	43.5%
3 to 10	1408	8.52	2.9	34.1%	37.0%
<3	2138	2.96	2.3	51.7%	19.5%
TOTAL	4135	7.83	2.7	100.0%	100.0%

Randomized genotypes, 80% sample coverage

Common SNPs / block	No. of blocks	Avg. size / block (kb)	Avg. no. common haplotypes / block	% of all blocks	% of all bases
>10	1	12.91	5	0.0%	0.0%
3 to 10	976	4.73	2.8	6.1%	14.2%
<3	14942	1.86	2.3	93.9%	85.7%
TOTAL	15919	2.04	2.3	100.0%	100.0%

70% sample coverage

Common SNPs / block	No. of blocks	Avg. size / block (kb)	Avg. no. common haplotypes / block	% of all blocks	% of all bases
>10	636	29.85	3.6	23.4%	58.6%
3 to 10	1046	9.75	3.2	38.5%	31.5%
<3	1032	3.11	2.3	38.0%	9.9%
TOTAL	2714	11.94	3.0	100.0%	100.0%

90% SAMPLE COVERAGE

Common SNPs / Block	No. of blocks	Avg. size / block (kb)	Avg. no. common haplotypes / block	% of all blocks	% of all bases
>10	461	19.2	4	6.4%	27.3%
3 to 10	1655	7.5	2.8	22.9%	38.3%
<3	5102	2.18	2	70.7%	34.4%
TOTAL	7218	4.49	2.3	100.0%	100.0%

Supplemental Table 3. Properties of SNP blocks versus snp minor allele frequency. 10% SNPs are the 24,047 SNPs with a minor allele present two or more times in the 20 chromosome sample, which were used to define SNP blocks. Common haplotypes are the haplotypes in each block represented by more than one chromosome. All bases are the 32,397,439 bases of finshed chromosome 21 genomic DNA sequence which were the basis of this study. 20% SNPs are the 16,503 SNPs with a minor allele present four or more times in the 20 chromosome sample, which were used to define SNP blocks.

>10% SNPs, 80% sample coverage

>10% SNPs / block	No. of blocks	size / block (kb)	Avg. no. common haplotypes / block	% of all blocks	% of all bases
>10	589	23.90	3.7	14.2%	43.5%
3 to 10	1408	8.52	2.9	34.1%	37.0%
<3	2138	2.96	2.3	51.7%	19.5%
TOTAL	4135	7.83	2.7	100.0%	100.0%

>20% SNPs, 80% sample coverage

>20% SNPs / block	No. of Blocks	Avg. size / block (kb)	Avg. no. common haplotypes / block	% of all blocks	% of all blocks
>10	400	30.50	3.4	13.3%	37.7%
3 to 10	973	13.40	2.8	32.4%	40.2%
<3	1630	4.39	2.1	54.3%	22.1%
TOTAL	3003	10.79	2.5	100.0%	100.0%

Supplemental Table 4. Properties of SNP blocks versus sample size. For 20 chromosomes: 10% SNPs are SNPs with a minor allele present two or more times in the sample of 20 chromosomes which were used to define SNP blocks; 10% haplotypes are the haplotypes in each block represented by two or more chromosomes. For 38 chromosomes: 10% SNPs are SNPs with a minor allele present four or more times in the sample of 38 chromosomes which were used to define SNP blocks; 10% haplotypes are the haplotypes in each block represented by four or more chromosomes.

20 chromosomes, 80% sample coverage

>10% SNPs / block	Avg. size / block (kb)	Avg. no. of >10% haplotypes / block	% of all blocks	% of all bases
>10	23.90	3.7	14.2%	43.5%
3 to 10	8.52	2.9	34.1%	37.0%
<3	2.96	2.3	51.7%	19.5%
TOTAL	7.83	2.7	100.0%	100.0%

38 CHROMOSOMES, 80% SAMPLE COVERAGE

>10% SNPs / block	Avg. size / block (kb)	Avg. no. of >10% haplotypes / block	% of all blocks	% of all bases
>10	21.99	4.3	11.1%	41.1%
3 to 10	6.8	3.3	34.2%	39.3%
<3	2.12	2.4	54.7%	19.6%
TOTAL	5.92	2.9	100.0%	100.0%