somalier
Sample to Sample Relatedness
Scale by shared-sites
X Axis
Shared hets
Shared hom-alts
Homozygous concordance
Relatedness
IBS0
IBS2
Y Axis
Shared hets
Shared hom-alts
Homozygous concordance
Relatedness
IBS0
IBS2
Sample Depth Metrics
X Axis
Mean depth of genotyped sites
Mean depth of all sites
Mean allele balance
% reads with neither REF nor ALT
Number of 0/0 sites
Number of 0/1 sites
Number of 1/1 sites
Number of unknown sites
Number of known sites
Proportion sites with AB < 0.1 or AB > 0.9
Scaled mean depth on X
Number of 0/0 sites on X
Number of 0/1 sites on X
Number of 1/1 sites on X
Scaled mean depth on Y
Y Axis
Mean depth of genotyped sites
Mean depth of all sites
Mean allele balance
% reads with neither REF nor ALT
Number of 0/0 sites
Number of 0/1 sites
Number of 1/1 sites
Number of unknown sites
Number of known sites
Proportion sites with AB < 0.1 or AB > 0.9
Scaled mean depth on X
Number of 0/0 sites on X
Number of 0/1 sites on X
Number of 1/1 sites on X
Scaled mean depth on Y
Choose pre-set selection for sample plot:
Sex QC: Number of 0/1 sites on X vs scaled mean depth on chrX
Sex ploidy QC: Scaled mean depth on chrX vs. chrY
General QC: number of sites with unknown genotype vs. proportion of hets with allele balance outside of 0.1 - 0.9
Depth and allele QC: mean depth vs. mean het allele-balance