4.3 Running kin example and sample output

Under the subdirectory `IBD/', run the example above using the command below. To send the output to a file instead of the screen, include `> filename' (without quotes) after the parameter file name on the command line.

./kin jv_rep_kin.par

Below is the relevant part of the kin output.

Component 1: Kinship coefficients: 531 431 .32031 431 432 .10938 Inbreeding coefficients: 332 .00000 531 .10938 2-locus inbreeding coefficients: (g4link is probability of IBD at both of 2 linked loci) proband recomb g4link freq prob 531 .000 .10938 .010 .10234 .040 .08386 .050 .07849 .100 .05660 .180 .03455 .300 .01910 .500 .01196 Component 2: Kinship coefficients: 341 442 .15625 Inbreeding coefficients: 441 .06250 541 .10938 2-locus inbreeding coefficients: (g4link is probability of IBD at both of 2 linked loci) proband recomb g4link freq prob 441 .000 .06250 .010 .05885 .040 .04905 .050 .04614 .100 .03388 .180 .02060 .300 .01008 .500 .00391

Note that when the recombination frequency is 0.0, the two-locus inbreeding coefficient is the same as the one-locus inbreeding coefficient, as there is no recombination between the loci, thus they act as a single locus. When the recombination frequency is 0.5, the two loci are independent and the two-locus inbreeding coefficient is the squared one-locus inbreeding coefficient.