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.

国际绵羊基因组联盟（ISGC，https://sheephapmap.org/）开发的绵羊单核苷酸多态性（SNP）芯片数据已映射至参考基因组。报告结果按芯片划分，包括SNP名称、染色体位置、位点、参考/替代碱基、标志位和rsID。探针序列源自Illumina的清单（ISGC_SheepLD2015_15K_20003262_A1、OvineSNP50_B、SheepHD_AgResearch_Cons_15041608_A），并使用bwa mem v0.7.17-r1188默认设置映射至Oarv3.1（GCF_000298735.1）、拉姆布伊耶特版本1（GCF_002742125.1）和拉姆布伊耶特版本2（GCA_016772045.1）参考基因组。请注意，拉姆布伊耶特版本3（GCA_016772045.2）与拉姆布伊耶特版本2相同，唯一的区别是从一只丘拉罗动物中增加了Y染色体。仅映射SNP，忽略插入/缺失（indels）。对于每个SNP，通过使用等位基因A探针序列并附加参考或替代碱基构建探针对。仅接受通过以下过滤器的探针对：-两个探针均无其他映射-两个探针均已映射-一个探针映射时无0个错配-两个探针均非多重映射-不允许插入/缺失-两个探针必须以相同方向映射-两个探针必须映射到相同位置-映射探针之间恰好有1个错配，即SNP。通过Oarv3.1位置的rsID分配映射的SNP（ftp://ftp.ensembl.org/pub/release-100/variation/vcf/ovis_aries/ovis_aries.vcf.gz）。在此共享的任何数据均不提供任何形式的保证，且在任何情况下，作者或版权所有者均不对任何主张、损害或任何责任承担责任。