Data from: Genomic characterization of large heterochromatic gaps in the human genome assembly

Altemose N, Miga KH, Maggioni M, Willard HF

Date Published: June 10, 2014

DOI: http://dx.doi.org/10.5061/dryad.vg885

 

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Title SD1_AllUnmappedScaffoldLocalizations
Downloaded 14 times
Description SD1_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.
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Title SD2_SubfamilySpecific24mers
Downloaded 5 times
Description SD2_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 >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>20 for all bases) 24-bp windows matching that 24-mer in that subfamily.
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Title SD3_HSat3A6ArraySizeEstimates
Downloaded 17 times
Description SD3_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.
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When using this data, please cite the original publication:

Altemose N, Miga KH, Maggioni M, Willard HF (2014) Genomic characterization of large heterochromatic gaps in the human genome assembly. PLoS Computational Biology 10(5): e1003628. http://dx.doi.org/10.1371/journal.pcbi.1003628

Additionally, please cite the Dryad data package:

Altemose N, Miga KH, Maggioni M, Willard HF (2014) Data from: Genomic characterization of large heterochromatic gaps in the human genome assembly. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.vg885
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