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Table 2 Unsupervised separation of subgenomes from polyploid plants using PolyCRACKER’s differential k-mer analysis

From: PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

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