1.

Original sequences (FASTQ) and aligned sequences (BAM) quality parameters

Parameter	Description
Median base quality for each cycle	Base quality dropped at the end of reads. The average “median base quality” for a batch sequence should not be <20 (Phred quality score)
Duplication rate	Duplication rate reflects the library complexity
Adaptor removal ratio (if applicable)	The ratio of removed adaptor to the reads is an index of sequence quality
Mapping rate	The ratio of reads that are successfully mapped to reference genome
On target rate	The ratio of reads that are mapped to targeted regions
Average sequencing depth on target region	The average sequencing depth for the target regions meeting the clinical needs
Distribution of sequencing depth on target region	Either a distribution plot or a table to indicate the sequencing depth across the target regions meeting the clinical needs
Variants detecting quality parameters
Parameter	Description
Total variant count	Total variant count in target regions meeting the clinical needs should be similar to the same patient population by using the same gene test with the same target regions
Known SNP ratio	In general, the ratio of known SNPs to the total variant count should be >90%
Insertion/deletion (Indel) ratio	The ratio of insertion/deletion to the total variant count
Homozygous variant ratio	The ratio of homozygous variants to the total variant count
Nonsense mutation ratio	The ratio of nonsense mutations to the total variant count
Transition to transversion ratio	The ratio of transition to transversion