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. 2020 Nov 2;10:369. doi: 10.1038/s41398-020-01060-5

Fig. 6. SV alleles are shorter on GRCh38 reference assembly.

Fig. 6

A Pairwise comparison of all SV alleles. Cells on the left of the diagonal display counts of SV alleles for which the haplotype on the x-axis is at least 50 bp smaller than the haplotype on the y-axis. Cells on the right of the diagonal display counts of SV alleles for which the haplotype on the x-axis is at least 50 bp larger than the haplotype on the y-axis. All PacBio haplotypes contain more expanded alleles than contracted alleles with respect to GRCh38 (red vs green dotted lines). Expansion vs contraction counts are balanced for CHM1 and CHM13 (blue) and the two w115 haplotypes (pink). B Density plots of the difference between SV-lengths to the mean SV-length across all SVs (expressed in standard deviations), per haplotype. Negative values indicate SV alleles with a shorter than average allele (contractions), positive values indicate SV alleles with a longer than average allele (expansions). Red circle: The GRCh38 reference haplotype encodes a disproportionate number of short SV alleles that are ~2 standard deviations smaller than the mean SV allele size. The four PacBio haplotype assemblies show very similar profiles.