Reference based mapping |
|---|
| |
T. cacao
|
T. grandiflorum
|
H. balanensis
|
LTR/Gypsy | 9% | 2% | 0.6% |
LTR/Copia | 7% | 2% | 0.5% |
Graph based clustering |
| |
T. cacao
|
T. grandiflorum
|
H. balanensis
|
LTR/Gypsy | 10% | 10% | 4% |
LTR/Copia | 5% | 9% | 7% |
- Comparison of estimated LTR retrotransposon frequencies as percentages of the genome, calculated with reference based mapping (upper half) and graph based clustering (lower half). Within T. cacao there is little discrepancy between the methods. Heterologous mapping between species produces different results suggesting that graph-based clustering may be more appropriate for inter-species comparisons (see Discussion).
