Fig. 6

Frequency distributions of k-mers as inferred for assemblies of nuclear genomes in S. nebaliae. A) Combined spectra-asm plot for genome assemblies 1 (GA1) and 2 (GA2). The distribution for shared k-mers (green line) peaks at multiplicity values of 72 x and 118 x. The peak at a multiplicity of 8 x gives private k-mers derived from the nuclear genome A of S. nebaliae (red line). In contrast, private k-mers are absent in GA2 (blue curve along the ordinate). B) Spectra-cn plot for GA2. Peaks at multiplicity values of 72 x and 118 x should correspond to heterozygous and homozygous portions in haploid nuclear genome B. A smaller peak at multiplicity of 224 x represents k-mers occurring in duplicates. C) Spectra-cn plot for GA1. The frequency distribution (red line) combines the peak of private GA1 k-mers (genome A) and the peaks corresponding to heterozygous and homozygous k-mers in GA2 (genome B). Numbers in inserts of plots B and C refer to ploidy states. In each plot, the black line gives k-mers lacking matches in the contigs of GA1 and/or GA2. The bar at zero multiplicity gives the fraction of k-mers which is likely due to errors in consensus base calling, each. Colours in each bar refer to the code given in the inserts. As can be seen, the error rate is smallest in GA2. Analyses were carried out with Merqury