Table 2 Unsupervised separation of subgenomes from polyploid plants using PolyCRACKER’s differential k-mer analysis
Species | Fragment length | k-mer length | Genome Size | Cohen’s Kappa (only unambiguous) | Cohen’s Kappa (including ambiguous) | Sequence in agreement / total sequence |
|---|---|---|---|---|---|---|
N. tabacum (including unanchored sequences) | 100 kb | 26 | 3.8 Gb | 0.999 | 0.984 | 0.992 |
N. tabacum (only anchored sequences) | 250 kb | 26 | 2.9 Gb | 0.998 | 0.985 | 0.865 |
N. tabacum (only anchored sequences), repeat elements | 250 kb | n/a | 2.9 Gb | 0.995 | 0.87 | 0.795 |
Triticum aestivum | 250 kb | 26 | 15.3 Gb | 0.993 | 0.993 | 0.997 |