Table 1.

Feature groups and descriptions for the genome variant refinement model

Feature group	Feature name	explanation
DeepVariant used features	Read base (not used)	Base letters of aligned reads
	Mapping quality	Average Alignment quality of aligned reads
	Strand mapping	Strand orientation of mapped reads
Confidence features	Variant likelihood	Phred-scaled quality score representing the confidence level of DeepVariant’s variant call
	Genotype quality	Probability of the correct genotype assignment
	Phenotype Likelihood	Likelihood estimates for genotype possibilities
Alignment features	Read depth	Number of aligned reads
	Allele depth	Number of reads supporting the reference and variant alleles
	Variant allele fraction	Proportion of reads supporting the variant allele
	Matching base ratio	Proportion of aligned bases that match the reference genome
	Soft clipping read ratio	Ratio of soft-clipped reads, which may indicate misalignment or structural variants
	Low mapping quality read ratio	Proportion of reads with low mapping quality
	Total aligned read count	Total number of reads aligned to variant site