Hi, My question relates to the linked image. It is kmer spectrum plot from sequencing data of an outbreeding autotetraploid. Anyone good ideas on how best to interpret this in terms of the level of heterozygosity?
Cheers,
Stephen
When looking at whole-genome kmer frequecy specra like this, you are mainly looking at the nature of repeats in the genome. In this case, you would be seeing the impact of not only transposons and simple repeats but also polyploidy. It may be helpful to take a closely related diploid species and compare that data to what you have generated for this autotetraploid.
To answer your question directly, I don't think there is any way to make inference about allelic differences by looking at the frequency spectrum of kmers, especially in this complex case. How would you know the differences in two curves were due to heterozygosity? For that level of resolution, I believe you would need to map your reads directly to the genes in question, or at least compare a subset of just those reads mapping to genes. Also complicating matters are sources of noise, like adapter contamination or sequencing errors, that may influence your interpretation of these results.
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