Table 1 Number of markers generated after GBS-Tassel pipeline analyses to map the GBS sugarcane population data
GBS-Tassel pipeline pseudo-references | SNPs | Indels | Total | Excluded data | Filtered polymorphic sites | |
|---|---|---|---|---|---|---|
Missing dataa | Low coverage locib | |||||
Methyl-filtered sugarcane genome | 110,261 | 41,494 | 151,755 | 16,815 (11.1%) | 96,562 (63.6%) | 38,378 (25.3%) |
Sorghum bicolor genome (v. 2.1) | 84,757 | 35,447 | 120,204 | 13,773 (11.5%) | 78,914 (65.6%) | 27,517 (22.9%) |
RNA-seq sugarcane transcriptome | 73,275 | 26,778 | 100,053 | 11,809 (11.8%) | 63,658 (63.6%) | 24,586 (24.6%) |
SUCEST project sequences | 29,238 | 9,820 | 39,058 | 4,878 (12.5%) | 25,295 (64.8%) | 8,885 (22.7%) |