TABLE 3

Frequencies and FST parameters for a comparison of the North Carolina and California populations

NNC to CA contrastbHaplotypesc
 (NC)Haplotypesc
 (CA)
SiteVariantNCaCAaKenyaaWindowFSTP-valueNDiversityNDiversity
35345A7372NA 10.100930.0013 20.2949 20.0526
C16 2NA100.285140.0026 40.6570 40.5833
35697T641025 10.175580.0004 20.4807 20.3945
C4327 3100.074280.0183 60.5754 30.4917
36214G934330 10.136410.0003 20.2817 20.4868
A1931 3100.07650.0001100.4976 50.5889
39010C796730 10.088440.0009 20.4652 20.2722
T4613 5100.038220.0077 80.7818120.8129
40428dG733120 10.075520.0032 20.4806 20.4747
A494916100.065610.0026 60.5875 50.5309
40464dT545120 10.06880.0041 20.4917 20.4622
C702916100.065610.0026 60.5875 50.5309
42023A903623 10.09580.0016 20.4175 20.4986
G384012100.024610.0181100.8110120.7625
  • a Absolute counts of the SNP states at the seven sites in the three populations (NA, site not surveyed in the Kenyan sample).

  • b FST between NC and CA, for individual sites and haplotypes spanning 10 segregating sites with corresponding P-value for each estimate.

  • c Diversity and number (N) of haplotypes (alleles) per population.

  • d Sites 40428 and 40464 are in nearly complete LD (D′ = 1, r2 = 0.9, P < 0.0001 by Fisher's exact test). They are separated by 38 bp and contribute to the same 10-site haplotype.