Table 1 Increasing k-mer length decreases the ability of polyCRACKER to assign N. tabacum genome sequences to a subgenome. The threshold for minimum counts for k-mers scales inversely to the k-mer length
Kmer length | Minimum k-mer count threshold | Cohen’s Kappa: unambiguous; all sequences | Amount Sequence Agreement / Total Genome | Number of k-mers used |
|---|---|---|---|---|
15 | 150 | 0.998, 0.991 | 0.868 | 929,119 |
23 | 150 | 0.998, 0.989 | 0.867 | 296,059 |
26 | 150 | 0.998, 0.985 | 0.865 | 195,362 |
33 | 120 | 0.998, 0.986 | 0.866 | 108,370 |
43 | 100 | 0.997, 0.975 | 0.859 | 35,058 |
53 | 80 | 0.993, 0.996 | 0.826 | 13,061 |