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 Genome | Overall alignment rate | Tassel-GBS | SuperMASSA | Filter NA |
|---|---|---|---|---|
| Panicum hallii | 19.05% | 77,105 | 12,835 | 6,945 |
| Panicum virgatum | 22.66% | 84,119 | 11,230 | 5,598 |
| Setaria italica | 22.04% | 92,494 | 15,047 | 8,066 |
| Setaria viridis | 22.07% | 92,591 | 15,271 | 8,118 |
| Transcriptome (EMBRAPA) | 20.11% | 74,049 | 14,129 | 7,665 |
| Transcriptome (UNICAMP) | 24.24% | 56,546 | 9,777 | 5,032 |
| Total | – | 476,904 | 78,289 | 41,424 |