DOI: 10.5061/dryad.vg885
title: Data from: Genomic characterization of large heterochromatic gaps in the human genome assembly

description: The largest gaps in the human genome assembly correspond to multi-megabase
 heterochromatic regions composed primarily of two related families of
 tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of
 repetitive DNA in these regions challenges standard mapping and assembly
 algorithms, and as a result, the sequence composition and potential
 biological functions of these regions remain largely unexplored.
 Furthermore, existing genomic tools designed to predict consensus-based
 descriptions of repeat families cannot be readily applied to complex
 satellite repeats such as HSat2,3, which lack a consistent repeat unit
 reference sequence. Here we present an alignment-free method to
 characterize complex satellites using whole-genome shotgun read datasets.
 Utilizing this approach, we classify HSat2,3 sequences into fourteen
 subfamilies and predict their chromosomal distributions, resulting in a
 comprehensive satellite reference database to further enable genomic
 studies of heterochromatic regions. We also identify 1.3 Mb of
 non-repetitive sequence interspersed with HSat2,3 across 17 unmapped
 assembly scaffolds, including eight annotated gene predictions. Finally,
 we apply our satellite reference database to high-throughput sequence data
 from 396 males to estimate array size variation of the predominant HSat3
 array on the Y chromosome, confirming that satellite array sizes can vary
 between individuals over an order of magnitude (7 to 98 Mb) and further
 demonstrating that array sizes are distributed differently within distinct
 Y haplogroups. In summary, we present a novel framework for generating
 initial reference databases for unassembled genomic regions enriched with
 complex satellite DNA, and we further demonstrate the utility of these
 reference databases for studying patterns of sequence variation within
 human populations.
description: SD1_AllUnmappedScaffoldLocalizationsSD1_AllUnmappedScaffoldLocalizations.txt: The first column contains the contig/scaffold ID number from the HuRef Assembly. Columns 2 to 25 contain the marginal probabilities of localization to each of the 24 chromosomes given the available WCS data. That is, a probability of 1 indicates certainty that the scaffold localizes to that particular chromosome according to our model (specified in SOM). The list is limited to the 9950 scaffolds with a marginal localization probability of at least 0.9 on at least 1 chromosome.SD2_SubfamilySpecific24mersSD2_SubfamilySpecific24mers.txt: This file lists all subfamily-specific 24-mers (column 1) along with their subfamily assignments (column 2). A subfamily-specific 24-mer is defined as a 24-mer that occurs on &gt;1% of reads within a given HSat2,3 subfamily and on no more than 0.1% of reads in any other subfamily (and on no non-HSat2,3 reads). Column 3 lists the proportion of reads containing that 24-mer in that subfamily, and column 4 lists the proportion of High Quality (phred&gt;20 for all bases) 24-bp windows matching that 24-mer in that subfamily.SD3_HSat3A6ArraySizeEstimatesSD3_HSat3A6ArraySizeEstimates.txt: This file lists the 396 male samples for whom we estimated HSat3A6 array sizes. The first column lists the Sample ID, the second column lists the sample population (abbreviated according to the conventions used by the 1000 Genomes Project), the third and fourth columns specify the Y haplogroup assignment of each sample (from personal correspondence with Chris Tyler-Smith), and the fifth column lists our HSat3A6 array size estimate in bp.