Table 1 Comparison between RAD-seq and tGBS genotyping technologies
RAD-seqtGBS
Total number of samples genotyped372384
Sequencing platformPaired-endSingle-end
Illumina HiSeq 2000Ion Proton
Average (Median) Reads/Sample after QC12,221,976 (12,097,256)1,793,300 (1,365,265)
Average (Median) Sequence/Sample after QC965,295,176 (955,561,340)195,057,311 (146,026,776)
Average (Median) missing rate / SNP41.39% (41.67%)58.65% (63.02%)
Average (Median) Proportion Het Calls / SNP before imputation2.05% (0.42%)4.12% (3.82%)
Average (Median) Proportion Het Calls / SNP after imputation1.63% (0.53%)4.72% (2.86%)
Average (Median) MAF / SNP before imputation1.89% (1.18%)11.69% (5.43%)
Average (Median) MAF / SNP after imputation1.24% (0.67%)10.37% (3.26%)
Total SNPs649,06773,291
SNPs with MAF >0.05 after imputation15,30632,463