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. 2019 Mar 29;123(7):1231–1251. doi: 10.1093/aob/mcz029

Fig. 2.

Fig. 2.

Example of local ancestor allele dose estimation for a triploid accession. (A) Definition of non-overlapping windows of ten DNSPs for each ancestral taxon: w, window of ten DSNPs. (B) Number of reads of the considered ancestor allele/number of reads of the alternative allele. (C) Estimation of allelic dosage of each ancestor per window of ten DSNPs [each pair of dose hypotheses are compared by maximum likelihood (LOD) test; if, for a pair including the more probable hypothesis, –3 < LOD < 3 → indeterminacy]. (D) Division of the chromosome into non-overlapping windows of 100 kb; the allelic dosage of this window is deduced from that of the ten DSNPs window that include the 100 kb window. (E) If the sum of allelic dosage of the four classes of DSNPs is different from the expected ploidy (here 3) → indeterminacy (grey). (F) Unphased karyotype automatic drawings. Blue, C. maxima; yellow, C. medica; green, C. micrantha; red, C. reticulata; grey, indeterminacy.