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. 2020 Jul 8;10:11227. doi: 10.1038/s41598-020-67373-z

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© The Author(s) 2020

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Location at the contig level of various genomic features on the Dsuz-WT3_v2.0 assembly. Regions assembled as distinct haplotypes, regions of higher nucleotide diversity, regions with structural variants, regions with higher one-nucleotide assembly errors (in the form of indels) are highlighted. The criteria for defining the boundaries of “high indel rate” and “high nucleotide diversity” regions were as follows: a region is initialized if the rate is above 0.005 on at least 5 consecutive windows of 10 kb; the region is closed if the rate drops below 0.001 on at least 5 consecutive 10 kb windows. Using this rule, 64 regions with high indel rates (median length 140 kb) and 27 regions with high nucleotide diversity (median length 420 kb) were identified. Contigs are ordered according to their chromosomal assignment. Only the longest 100 contigs are shown, representing 79% of the total length of the assembly.