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Reference Genome: Heterozygous loci?

asked 2013-04-19 01:52:26 -0600

Christine Baes gravatar image

Hi there, I've got what might be a silly question, but I would appreciate any help. When I look at my BAM files in the Genome Browser, I also see the reference genome. This reference is only one strand of DNA. I am, however, quite sure, that Dominette (I'm looking at bovine BAMS) has two strands of DNA and is heterozygous at some loci. Now my question is, how do I know where the reference is heterozygous if I only see one strand of DNA? Thanks for the help!

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answered 2013-04-19 17:10:09 -0600

Hi Christine,

The reference sequence for any particular genome will only contains one allele at any given position. This single allele is selected from the pool of sample genomes used in creating the assembly for that genome and is generally the allele that either occurs the most for a group of samples or has the most reads associated with that location on the genome depending on sequencing methods used. Each sequencing consortium can have their own guidelines for picking the "reference" allele that is included in a particular genome assembly.

In particular for the Bos taurus BTAU_4.6.1 genome available in GenomeBrowse the reference sequence was assembled from the pooled reads of BACs and whole shotgun sequences from two cattle, one male and one female. You can find specifics on how the assembly was created from the NCBI website.

When viewing BAM files in GenomeBrowse the reads in the coverage plots will be color coded according to whether they match the reference sequence for your species and build. Any reads that support the reference will be gray and the alternate alleles will be blue, green, yellow, or red. So if variant calling was performed on your BAM file any potential heterozygous calls that exist could look similar to the below screenshot.

image description

Please let me know if I can clarify further.

Thanks, Jami...

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Asked: 2013-04-19 01:52:26 -0600

Seen: 2,877 times

Last updated: Apr 19 '13