Table 3 Number and percentage of SNP pairs among different genes with r2 > 0.1 for three linkage classes
MAFADEPT2 Unrelated AssociationCCLONES Multiple-Family Pedigree
No. (total)%No. (total)%
Within LGs, <1 cM
Before r2 adjustment0.001110 (2617)4.2210 (2921)7.2
0.181 (1247)6.5134 (1286)10.4
0.263 (501)12.692 (504)18.1
After r2 adjustment0.001103 (2617)3.9186 (2921)6.4
0.179 (1247)6.3115 (1284)9.0
0.258 (501)11.662 (507)12.2
Within LGs, >1 cM
Before r2 adjustment0.001142 (174,032)<0.13498 (198,910)1.8
0.188 (82,576)0.11274 (85,524)1.5
0.273 (32,452)0.2621 (33,007)1.9
After r2 adjustment0.001125 (174,032)<0.11434 (198,910)0.7
0.180 (82,576)0.1412 (85,524)0.5
0.260 (32,452)0.2116 (33,007)0.4
Between LGs
Before r2 adjustment0.001305 (1,933,979)<0.116,999 (2,208,279)0.8
0.18 (922,248)<0.15256 (953,810)0.6
0.20 (360,875)02485 (368,881)0.7
After r2 adjustment0.001229 (1,933,979)<0.13052 (2208,279)0.1
0.10 (922,248)0558 (953,810)0.1
0.20 (360,875)0370 (368,881)0.1
  • Number and percentage of SNP pairs among different genes with r2 > 0.1 for three linkage classes before and after adjusting r2 for subpopulation structure in ADEPT2 (unrelated) and kinship in CCLONES (multiple-family pedigree). MAF, minimum minor allele frequency threshold for SNP pairs; LG, linkage group.