Fraction of clones inconsistent with inferred HapMap SNP haplotypes
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Only positions with at least a Q30 sequence quality are considered.
aInformative clones are those clones that intersect with two or more heterozygous SNPs.
bSince each clone was derived from a single DNA molecule, those clones intersecting with SNP alleles assigned to different haplotypes indicate a potential inconsistency in the inferred SNP haplotypes.
cThe data are based only on the analysis of autosomes. We observed a 10-fold increase in inconsistencies with X chromosome inferred haplotypes (based on rel21 HapMap data) for DNA samples from trio pedigrees due to an application error of the phasing algorithm. This error is currently being corrected by the HapMap Consortium.
