For the 5441 individuals with alcohol phenotypes, the number of unique autosomal markers per individual ranged from 1 to 1359 (mean = 553.7 ±232.3, median = 394), with 103 individuals having fewer than 300 markers (65 having fewer than 200, 39 having fewer than 100 and 18 having fewer than 50). Intermarker distances for all chromosomes are reported for this sample in Supplementary Table 3 (means range 7.0–8.9cM, standard deviations range 2.7–3.8, and medians range 6.7–10.4cM). The number of unique autosomal markers for the 1642 parents ranged from 3 to 1236 (mean = 490.0 ±213.9, median = 389), with 91 individuals having fewer than 300 markers. These samples were further checked for genotyping errors using MERLIN (1.0.1) and flagged markers were dropped from the dataset (single markers were dropped for each of 104 participants and two markers were dropped for each of 7 participants). Average marker heterozygosity of 75.1% was found using MERLIN (1.0.1) and PEDSTATS (Wigginton and Abecasis, 2005). This cleaned dataset was the one used for analyses.
