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. 2024 Jul 4;25:176. doi: 10.1186/s13059-024-03319-2

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — a Assessing Mendelian consistency of TR calls in an Ashkenazi trio using PacBio HiFi reads. The x-axis gives the LongTR score threshold to include calls, and the y-axis gives the percentage of TRs for which genotypes in the trio follow Mendelian consistency. Trio-TR pairs for which all members were called as homozygous for the reference allele were excluded. Dashed = TRGT; solid = LongTR. Note TRGT does not report a quality score and thus a single horizontal line is shown. Color indicates the size of the repeat unit (in bp) considered. b Concordance of TR genotypes obtained from PacBio HiFi with assembly alleles in HG002. TRs were binned by length of the repeat (in bp, bin size = 250bp) in GRCh38. The x-axis shows the TR length, and the y-axis shows the percent of alleles that match the assembly. Blue lines show when only length is considered. Orange lines show when both length and sequence are considered. Dashed = TRGT; solid = LongTR. The top panel shows the number of repeats in each bin, on a logarithmic scale