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Reference bias at heterozygous indel sites. The plot shows the cumulative distribution of the proportion of reads supporting the non-reference allele in an individual (NA12878) sequenced to high coverage in the 1000 Genomes Project (The 1000 Genomes Project Consortium 2010), and mapped using MAQ, BWA, and Stampy, across high-confidence heterozygous indel sites (see Supplemental material). A left shift of the curve indicates a bias toward the reference allele.
