Table 1.

Comparison of Sequence-Based and SNP-Based Coordinates for AMD Samples

Range of Off-Target Coverage	Number of Samples	POPRES Reference Panel	Mean Off-Target Coverage	Average Number of Covered Loci	Procrustes Similarity to SNP-Based Coordinates
					K′ = 2	K′ = 20
0.04–0.17a	225	original	0.14	32,349	0.8680	0.8878
		imputed	0.21	583,105	0.7165	0.9579
0.17–0.21a	224	original	0.19	43,723	0.9326	0.9313
		imputed	0.29	764,267	0.7111	0.9665
0.21–0.26a	224	original	0.24	52,856	0.9147	0.9248
		imputed	0.36	892,775	0.7115	0.9576
0.26–0.71	224	original	0.33	68,994	0.9459	0.9505
		imputed	0.48	1,114,473	0.7705	0.9666
Total	897	original	0.22	49,461	0.9171	0.9244
		imputed	0.33	838,370	0.7230	0.9628

The 897 AMD samples were evenly split into four bins according to their mean off-target sequencing depth across 318,682 loci in the original POPRES reference panel. For each bin, we estimated their ancestry coordinates with both original and imputed POPRES reference panels at K′ = 2 and 20, respectively. We set K = 2 in all the analyses. Note that setting K′ = 2 is equivalent to LASER 1.0. We compared each set of sequence-based coordinates to those based on 47,235 genome-wide SNPs genotyped in both the AMD GWAS data and the original POPRES data (K = K′ = 2).

^aRanges are inclusive of the low number but not the high number.