Mapping of ISGC SNP chip probes

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.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.For each SNP a probe pair was constructed by using AlleleA_ProbeSeq and appending either the reference or the alternative allele.Only probe pairs where accepted that passed following filters.-both probes have no alternative mappings-both probes are mapped-one probe is mapped with 0 mismatches-both probes are not multi-mapped-no indels were allowed-both probes had to map in the same orientation-both probes had to map to the same position-mapped probes had between them exactly 1 mismatch, the SNP.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).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.