Table 2. Number of effects by type according to SnpEff classification.

Effect type	Count	Percentage (%)
3_prime_UTR_variant	26,765	14.48%
5_prime_UTR_premature_start_codon_gain_variant	1074	0.58%
5_prime_UTR_variant	9,041	4.89%
disruptive_inframe_deletion	317	0.17%
disruptive_inframe_insertion	223	0.12%
frameshift_variant	2,831	1.53%
inframe_deletion	166	0.09%
inframe_insertion	203	0.11%
initiator_condon_variant	8	0.01%
intergenic_region	17,465	9.46%
intron_variant	38,910	21.04%
missense_variant	34,257	18.53%
non_conding_transcript_variant	10	0.01%
splice_acceptor_variant	10	0.01%
splice_donor_variant	83	0.05%
splice_region_variant	1,815	0.98%
start_lost	66	0.04%
stop_gained	432	0.23%
stop_lost	83	0.05%
stop_retained_variant	82	0.04%
synonymous_variant	50,951	27.56%