Table 3. The number of high-quality variants after each step of filtering.

	III-13		III-4
	SNVs	Indels	SNV	Indels
All high-quality variants	1492	220	35 728	2416
After filtering against public databasesa	50	131	1172	1129
After in-house filtering against in-house exome databaseb	36	22	719	58
After functional effects filteringc	11	1	196	14
Variants disrupting known nonsyndromic hearing loss genes	4	0	4	0
Genes harboring homozygous variants or >=2 heterozygous variants	1		2
Recessive hearing loss genes harboring homozygous variants or >=2 heterozygotes	1		1

Abbreviations: indels, insertions-deletions; SNV, single-nucleotide variants.

^aExcluding variants having alternative allele frequencies >0.01 in any one of the populations in dbSNP and 1000 genomes.

^bExcluding variants having alternative allele frequencies >0.01 in 170 other unrelated in-house exomes.

^cKeeping SNVs that are evolutionarily conserved and cause missense, nonsense changes or potentially disrupt splice sites; and keeping indels that result in inframe or frameshift alternations.