Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data

BMC Bioinformatics

Table 1 Summary of loci genotyped and phasing success with WhatsHap in each test dataset

Dataset	Oyster	Salmon	Lamprey
Mean sequencing depth	18 ± 2	15 ± 3	22 ± 3
Number of SNPs	809,951	139,518	28,257
Number of microhaplotype loci	355,285	25,245	7366
Mean allelic richness	4.7 ± 2.0	3.0 ± 1.2	3.9 ± 4.1
Mean number of phased genotypes	22.10 ± 2.73	47.21 ± 4.06	82.13 ± 7.06
Mean number of unphased genotypes	0.01 ± 0.10	0.03 ± 0.25	0.05 ± 0.77

The number of microhaplotype loci, allelic richness, number of phased genotypes, and number of unphased genotypes only includes microhaplotype loci with expected heterozygosity of 0.1 or greater. Means are given as mean ± SD. Mean sequencing depth was calculated using the number of mapped reads after duplicate removal for the oyster and salmon WGS datasets and using the mean depth of called SNP genotypes for the lamprey RAD-seq dataset

ISSN: 1471-2105