# Number of pedigrees: 2 # Total number of individuals: 22 # Number of chromosomes: 1 # Total number of markers: 22 # Number of markers on each chromosome ex_chr01.idx: 22 # Number of genotyped pairs found in each of the # relationship categories analyzed by PREST: # (Note that unrelated pairs are checked within each pedigree.) Total: 49 10 full-sib pairs 0 half-sib pairs 3 grandparent-grandchild pairs 12 avuncular pairs 2 first-cousin pairs 8 unrelated pairs 0 half-avuncular pairs 0 half-first-cousin pairs 0 half-sib-plus-first-cousin pairs 14 parent-offspring pairs # Summary of genotyped pairs found in each pedigree pedid size f.sib h.sib g.p.c avun. f.cous. unrel. h.avun h.f.cous. h.sib+f.cous. p.o. Total 227 9 6 0 3 6 0 4 0 0 0 9 28 301 13 4 0 0 6 2 4 0 0 0 5 21 # Number of pairs that have p-value of either EIBD or AIBS less than 0.2 # (for unrelated, p-value of IBS less than 0.2). # This is the number of pairs for which PREST would perform the MLRT. # (The MLRT will actually be performed only if option 2 is chosen.) # For each pair, performance of the MLRT, including 100,000 # simulated realizations takes approximately 5 minutes on # a Sun Ultra II with 360-MHz processor. 10 # Assuming that there are not many misclassified relative pairs in the # data set and assuming that all the pairs are typed on roughly the # same markers (because which markers are typed affects the null means # of the AIBS and IBS statistics and affects the null variances of the # EIBD, AIBS and IBS statistics), then the sample averaged observed # statistics for each relationship type should not be significantly # different from what is expected. If they are significantly # different, if may indicate that the allele frequencies are not # accurately estimated, or that the assumptions of population # homogeneity and Hardy-Weinberg equilibrium are not appropriate. # It could also indicate a problem with the way the data are coded # (see item #7 in 'Tips' file). The following output contains # the information of sample summary of the statistics # obs = sample averaged observed statistic # mu(std) = sample averaged null mean (sample std. dev. of null mean) # (Note that the null mean of EIBD depends only on the null relationship, not on the data, so for EIBD # we give the null mean in place of the sample averaged null mean # std(std) = sample averaged standard deviation # (sample std. dev. of null standard deviation) # no.mark = sample averaged number of typed markers for a pair # (sample std. dev.) no.pairs no.mark(std) full-sib 10 17.1( 1.1) half-sib 0 NA( NA) grandp-c 3 16.0( 1.7) avuncular 12 16.7( 1.4) f-cousin 2 19.0( 0.0) unrelated 8 17.2( 0.5) h-avuncular 0 NA( NA) h-f-cousin 0 NA( NA) h-sib+f-cous 0 NA( NA) pa-offspring 14 17.4( 1.4) # Sample summary of EIBD obs mu std( std) full-sib 0.9780 1.0000 0.1984(0.006952) half-sib NA NA NA( NA) grandp-c 0.5160 0.5000 0.1019(0.004238) avuncular 0.5231 0.5000 0.0837(0.002658) f-cousin 0.2699 0.2500 0.0542( nan) unrelated NA NA NA( NA) h-avuncular NA NA NA( NA) h-f-cousin NA NA NA( NA) h-sib+f-cousin NA NA NA( NA) pa-offspring NA NA NA( NA) # Sample summary of AIBS obs mu( std) std( std) full-sib 0.7687 0.7751(0.001291) 0.1534(0.004792) half-sib NA NA( NA) NA( NA) grandp-c 0.4333 0.3790(0.001036) 0.0930(0.003764) avuncular 0.4117 0.3797(0.001007) 0.0783(0.002459) f-cousin 0.2056 0.1938(0.000000) 0.0476(0.000000) unrelated NA NA( NA) NA( NA) h-avuncular NA NA( NA) NA( NA) h-f-cousin NA NA( NA) NA( NA) h-sib+f-cousin NA NA( NA) NA( NA) pa-offspring 0.7398 0.7415(0.001984) 0.0647(0.002904) # Sample summary of IBS obs mu( std) std( std) full-sib 1.2450 1.2997(0.002314) 0.2375(0.007404) half-sib NA NA( NA) NA( NA) grandp-c 0.9762 0.9826(0.006137) 0.2036(0.008798) avuncular 1.0044 0.9789(0.005320) 0.1727(0.006094) f-cousin 1.0000 0.8433(0.000000) 0.1634(0.000000) unrelated 0.8448 0.7120(0.006001) 0.1477(0.002149) h-avuncular NA NA( NA) NA( NA) h-f-cousin NA NA( NA) NA( NA) h-sib+f-cousin NA NA( NA) NA( NA) pa-offspring 1.2165 1.2404(0.003288) 0.1014(0.004774)