Mapping of ISGC SNP chip probes

<p dir="ltr">Ovine SNP chips created by the International Sheep Genomics Consortium (ISGC, https://sheephapmap.org/) were mapped onto reference genomes. Results are reported per chip and include SNP_name, chrom, pos, ref_alt, flag, rsID.</p><p dir="ltr">Probe sequences were taken from the Illumina manifests (ISGC_SheepLD2015_15K_20003262_A1, OvineSNP50_B, SheepHD_AgResearch_Cons_15041608_A) and mapped onto the Oarv3.1 (GCF_000298735.1) and the Rambouillet version 1 (GCF_002742125.1) and Rambouillet version 2 (GCA_016772045.1) reference genomes using bwa mem v0.7.17-r1188 with default settings. Please note that Rambouillet version 3 (GCA_016772045.2) is identical to Rambouillet version 2, with exception of a Y chromosome being added from a Churro animal. Only SNPs were mapped, indels were ignored.</p><p dir="ltr">For each SNP a probe pair was constructed by using AlleleA_ProbeSeq and appending either the reference or the alternative allele.</p><p dir="ltr">Only probe pairs where accepted that passed following filters.</p><p dir="ltr">-both probes have no alternative mappings</p><p dir="ltr">-both probes are mapped</p><p dir="ltr">-one probe is mapped with 0 mismatches</p><p dir="ltr">-both probes are not multi-mapped</p><p dir="ltr">-no indels were allowed</p><p dir="ltr">-both probes had to map in the same orientation</p><p dir="ltr">-both probes had to map to the same position</p><p dir="ltr">-mapped probes had between them exactly 1 mismatch, the SNP.</p><p dir="ltr">Mapped SNPs got assigned to rsIDs via their Oarv3.1 position (ftp://ftp.ensembl.org/pub/release-100/variation/vcf/ovis_aries/ovis_aries.vcf.gz).</p><p dir="ltr">Any data shared here is without warranty of any kind and in no event shall the authors or copyright holders be liable for any claim, damages or any liability.</p>