Table 4. Explanation for the 14,147 RNA SNPs not found in WGS data.

Reason for absence	Number of SNPs (%)
Position was heterozygous in WGS but filtered because it didn’t meet the default parameters for variant detection.	1225 (8.7)
No reads were mapped to region/position.	1693 (12)
Position was homozygous in WGS	3471 (24.5)
Position was heterozygous in WGS but removed by our custom filtering pipeline	7758 (54.8)