Table 2 Overall alignment rate and total number of markers obtained after Tassel-GBS pipeline, allele dosage in SuperMASSA software, and selection of up to 5% of missing data (Filter NA), for each reference genome
Reference GenomeOverall alignment rateTassel-GBSSuperMASSAFilter NA
Panicum hallii19.05%77,10512,8356,945
Panicum virgatum22.66%84,11911,2305,598
Setaria italica22.04%92,49415,0478,066
Setaria viridis22.07%92,59115,2718,118
Transcriptome (EMBRAPA)20.11%74,04914,1297,665
Transcriptome (UNICAMP)24.24%56,5469,7775,032
Total476,90478,28941,424