haploid vs diploid graph models for unidentified ploidy

[gunjanpandey]

Could you please help in interpretation of these graphs for Illumina reads for a Cladocopium sp where ploidy level is not clear? Genomescope2 was given -p2 and -p1 flags

Is there a homozygous peak identified as error peak with the haploid model?

[mschatz]

The coverage is low so it is always hard to fully determine. Of these two options I prefer the diploid plot as it has a better fit with the data. It also suggests a very low rate of heterozygosity (~0.001%) which will make smudgeplot unreliable. Are you able to generate any more data to get deeper coverage? How does the assembly look so far? Good luck! Mike

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