12711_2017_345_MOESM14_ESM.tif (4.52 MB)
MOESM14 of Genome-wide SNP data unveils the globalization of domesticated pigs
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posted on 2017-09-21, 05:00 authored by Bin Yang, Leilei Cui, Miguel Perez-Enciso, Aleksei Traspov, Richard Crooijmans, Natalia Zinovieva, Lawrence Schook, Alan Archibald, Kesinee Gatphayak, Christophe Knorr, Alex Triantafyllidis, Panoraia Alexandri, Gono Semiadi, Olivier Hanotte, DeodĂĄlia Dias, Peter DovÄ, Pekka Uimari, Laura Iacolina, Massimo Scandura, Martien Groenen, Lusheng Huang, Hendrik-Jan MegensAdditional file 14: Figure S12. Results of admixture analysis using 30.4 million SNPs called from whole-genome sequence data (A) were similar to those results obtained using 60K SNP data (B). Whole-genome sequence raw data from 188 individuals mainly obtained from [4, 18, 70], were used in the analysis. The whole-genome SNPs were called using GATK best practice workflow ( www.broadinstitute.org/gatk ). A total of 30.4 million SNP with a MAF >0.02 and a call rate >70% were kept for admixture analysis (A). A total of 44,988 SNPs with genome positions that were concordant with those of the Illumina 60K SNPs were extracted from the 30.4 million SNP data to represent the results of 60K SNPs (B).
