References Management Guide

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Torrent Suite Software space on Ion Community

References Management Guide TOC

Details about the Ion hg19 Reference

This human reference is based on the GRCh37.p5 version of the human genome assembly. The GRCh37.p5 version is described at this web site: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/human/data/index.shtml .

The remainder of this section lists differences between GRCh37.p5 and the Ion Reference hg19 versions of the human genome.

3 positions with ambiguity codes

Three positions on chromosome 3 are marked with 'N' in the UCSC version of the genome. These positions have IUPAC ambiguity codes inour version:

Hard masked PAR regions in chromosome Y

The chromosome Y sequence has the Pseudo Autosomal Regions (PAR) hard masked. This practice is consistent with t he 1000 Genome Consortium's decision to hard mask these regions in chromosome Y in order to prevent mis-mapping of reads and issues in variant calling on the gender chromosomes.

The masked Y pseudoautosomal regions are chrY:10001-2649520 and chrY:59034050-59363566. (A related file can be downloaded from ftp://ftp.ensembl.org/pub/release-56/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.56.dna.chromosome.Y.fa.gz .)

The following background information is from the UCSC site http://genome.ucsc.edu/cgi-bin/hgGateway?org=human&db=hg19

"The Y chromosome in this assembly contains two pseudoautosomal regions (PARs) that were taken from the corresponding regions in the X chromosome and are exact duplicates:

chrY:10001-2649520 and chrY:59034050-59363566

chrX:60001-2699520 and chrX:154931044-155260560"

Chromosome M

We use the Cambridge Reference Sequence (rCRS) for chromosome M with the GenBank accession number NC_012920. UCSC has announced that they also are using this version in the next human assembly release.

The following background information is from the UCSC site http://genome.ucsc.edu/cgi-bin/hgGateway?org=human&db=hg19

"Note on chrM

Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as 'chrM' in the Genome Browser) has been replaced in GenBank with the record NC_012920 . We have not replaced the original sequence, NC_001807 , in the hg19 Genome Browser. We plan to use the Revised Cambridge Reference Sequence (rCRS) in the next human assembly release."

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