3K RG SNPs Datasets
32 million full 3K RG SNPs Dataset biallelic & multiallelic SNP set v.5
Total SNPs: 32,064,217
Samples : 3024
A Base SNP set of ~18 million SNPs was created from the ~29 million biallelic SNPs by removing SNPs with excess of heterozygous calls.
18,128,777 SNPs (the Base SNP set)
404k CoreSNP dataset
The Core SNP set (v0.7) was obtained from the filtered SNP set (v0.7) by applying two-step LD pruning procedure as follows:
1) LD pruning with window size 10kb, step 1 SNP, R2 threshold 0.8
2) LD pruning with window size 50 SNPs, step 1 SNP, R2 threshold 0.8
4.8million filtered SNP dataset
The filtered SNP set was obtained from the Base SNP set by applying the following filtering criteria:
1K-Rice Custom Amplicon, or 1k-RiCA, a robust custom sequencing-based amplicon panel of ~1000-SNPs (version 3 = xxxx SNPs) that are uniformly distributed across the rice genome, designed to be highly informative within indica rice breeding pools, and tailored for genomic prediction in elite indica rice breeding programs.
The Cornell_6K_Array_Infinium_Rice panel includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups.