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. Author manuscript; available in PMC: 2023 Jan 4.
Published in final edited form as: Nat Methods. 2022 Mar 31;19(6):687–695. doi: 10.1038/s41592-022-01440-3

Figure 4 |. Examples of the largest CHM13 regions with a copy number in the reference that differs from GRCh38 and most individuals.

Figure 4 |

a, One of the two largest examples of rare collapses in CHM13, where one copy of a common 72 kb tandem duplication is absent in CHM13. b, The largest rare duplication in CHM13, a 142 kb tandem duplication of sequence in GRCh38 that is rare in the population. CHM13 and HG002 PacBio HiFi coverage tracks are displayed for both references, GRCh38 (top) and CHM13v1.0 (bottom), to demonstrate that CHM13 reads support the CHM13 copy-number but HG002 reads are consistent with the GRCh38 copy-number. Read-depth copy-number estimates in CHM13 are shown at the bottom for ‘k-merized’ versions of GRCh38 and CHM13v1.0 references, CHM13 Illumina reads, and Illumina reads from a diverse subset (n=34) of SGDP individuals.