Quality metrics for selected HostSeq variants.

Variants were selected to include the top three HGI7no loci (first three rows), the top five hits from the primary HostSeq GWAS (next five rows), and the three WDR89 variants driving the SKAT-O results (last three rows). Values have been extracted from the joint-called VCF of N = 10,059 samples before QC removals (these variants passed all filters described in S1 Fig). WDR89 variants have the lowest ‘MAF’ and higher ‘ExcessHet’ but they pass HostSeq thresholds. However, they failed in gnomAD (v4.0) which used a different method, AS_VQSR, for QC protocol. Description of column headers is given below the table. (XLSX)