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.