Additional file 2 of Systematically identifying genetic signatures including novel SNP-clusters, nonsense variants, frame-shift INDELs, and long STR expansions that potentially link to unknown phenotypes existing in dog breeds

Additional file 2: Table S1. Breed-specific SNP distribution by breed and by variant category. Table S2. Genomic regions with at least 40 breed-specific SNP signature from the single breed. Table S3. Detailed information of SNPs exclusively shared by breed-pairs. Table S4. Breed-specific INDEL distribution by breed and by variant category. Table S5. Breeds with breed-specific large STR expansions. Table S6. SNP based genetic signatures distribution across 76 breeds. Table S7. Breed similarity matrix based on shared SNP signatures. Table S8. Breed-pair list sorted by SNP signature similarity score. Table S9. Number of SNP signature within X chromosome pseudo autosomal region. Table S10. Breed history information of the 76 breeds. Table S11. GS-based similarity analysis of the 23 dogs. Table S12. Information of four nonsense BSGS loci for validation. Table S13. Sanger sequencing results for five additionally collected samples. Table S14. Correlation between SNP, INDEL and STR based GS similarity scores. Table S15. Top five breeds similar to French Bulldog according to SNP based GS similarity score. Table S16. Biological pathway annotations of highlighted breed-specific functional structures.