Table 1. Haplotype Caller variant quality metrics and genotype frequencies.

Variant type N	SNPs (biallelic) 1,411,395	SNPs (multi) 43,798	Indels (biallelic) 138,687	Indels (multi) 65,660
Total depth Event length Strand bias* Mapping quality Map qual rank sum Quality-by-depth Quality	6440 (1725) 0 (0) 1.12 (2.25) 62.12 (6.18) 0.25 (1.04) 16.65 (3.51) 34968 (62236)	6316 (2100) 0 (0) 1.34 (3.14) 64.94 (8.57) 0.9 (2.37) 17(3.81) 57028 (67558)	6134 (1836) 2 (5) 1.76 (3.88) 71.17 (12.77) 3.14 (3.21) 18.52 (6.21) 25842 (59889)	5973 (2081) 1 (8) 1.77 (4.45) 69.58 (11.36) 2.68 (2.91) 16.96 (6.39) 40479 (63590)
Genotype counts Reference Heterozygous Homozygous non-ref. No call	151 (120) 70 (118) 0 (0) 0 (1)	102(122) 117(121) 0(0) 1(4)	166(114) 54(114) 0(0) 0(2)	122(123) 95(122) 0(0) 2(5)

Values show the total number of variants, median (and IQR) for each metric. Data generated from vcf file using GATK VariantsToTable, on the quality-filtered data. *Strand bias refers to Phred-scaled p-value from Fisher’s Exact Test. Code and data used to generate this table located at https://doi.org/10.5281/zenodo.159282.