Comparison of genetic diversity estimated with NGS and 60K-SNP data. (A) Heterozygosity (Het) with NGS Vs. Observed heterozygosity (Ho) using 60K data at population level in local breeds. Each dot represents the average value in the populations. The size of the dots are proportional to the inbreeding coefficient (F) observed in the population. (B) Heterozygosity (Het) with NGS Vs. Inbreeding coefficient (F) using 60K data at individual level. Each dot represents a single pig. The size of the dots is proportional to the Ho using 60K at population level. The line that best fit the estimates in European pigs is displayed. The lack of correlation observed in Asian pigs indicates high ascertainment bias.