The Cyberlindnera fabianii figure illustrated in issue #38 revealed an issue in analysis and/or visualization.
Chromosomes [7, 11, 16, 17] are, by a reasonable approximation, entirely homozygous. They have so little SNP data that the minimal heterozygous signal which is present is overwhelmed by the peculiar error in sequencing data that makes it appear that there is a 1:2 ratio of SNP alleles in low-information regions, even in this diploid case where a 1:2 ratio is inconsistent.
In cases like this, the SNP-ratio histogram should probably be scaled down to avoid misrepresenting the error signal as an informative heterozygosity signal. A difficulty here is in determining the appropriate heuristic to separate chromosomes that are entirely homozygous like these from others that are just mostly homozygous.
The Cyberlindnera fabianii figure illustrated in issue #38 revealed an issue in analysis and/or visualization.
Chromosomes [7, 11, 16, 17] are, by a reasonable approximation, entirely homozygous. They have so little SNP data that the minimal heterozygous signal which is present is overwhelmed by the peculiar error in sequencing data that makes it appear that there is a 1:2 ratio of SNP alleles in low-information regions, even in this diploid case where a 1:2 ratio is inconsistent.
In cases like this, the SNP-ratio histogram should probably be scaled down to avoid misrepresenting the error signal as an informative heterozygosity signal. A difficulty here is in determining the appropriate heuristic to separate chromosomes that are entirely homozygous like these from others that are just mostly homozygous.