Genotyping of a core collection of 163 tomato accessions composed of S. lycopersicum, S. lycopersicum var cerasiforme, and Solanum pimpinellifolium.From the initial 8,784 SNPs of the SOLCAP_TOMATO_6K_SL2.50, 7,720 (87.8%) passed the manufacturing quality control and constituted our raw data set.From this raw data set, the quality filtering gave a total of 5,995 reliable SNPs (77.6%).The overall average percentage of missing data per locus was estimated at 3.84% in the whole population while ranging from 2.25% in S.L to 4.07% in S.P. The minor allele frequency (MAF) values were evenly distributed from 0.001% to 0.5% and showed differences in their distribution between groups. The S.L accessions showed an excess of rare variants with a skewed distribution of the MAF values (median MAF = 0.107), while the S.C and S.P accessions showed a broader distribution of the MAF values (median MAF = 0.161 and 0.214, respectively)
The SNP calling rate threshold per locus was set at 90%. A 0.037 <MAF< 0.45 was used to filter the raw data set. The minimal success rate of genotyping per accession was fixed to 90%. The missing data were imputed by the most common allele of the SNP