SNPs mapped to chromosome 0 in bovineHD chip.

Question

[artolkamp]

I've noticed that there are lots of SNPs with chromosome set to 0 in my bovineHD snp data. I downloaded some supporting materials from illumina

(http://support.illumina.com/array/array_kits/bovinehd_dna_analysis_kit/downloads.html)

and downloaded the file BovineHD mapping comment which shows the same! 68240 SNPs with chromosome zero.

For the time being I'm excluding these SNPs from analysis, however am curious where they come from? Are they artifacts from older genome assemblies? There for internal QA or validation?

Thank you for your time.

[GenoMax]

Here is what previous biostars threads have said about similar observations:

Custom exome array chip with 527 SNPs have chromosome information with 0
PLINK .bim file shows chromosome 0 on Affymetrix chip
GenomeStudio genotype format to VCF?

Answer 1

[mastal511]

They might be from contigs that are not yet located on a particular chromosome in the latest genome assembly.