Table 1 Distribution of consequences of genetic variants using three different variant callers.
Consequence | GATK HC | Varsha | MuTect2 |
|---|---|---|---|
3_prime_UTR_variant | 58,135 (13.33%) | 52,305 (17.03%) | 4013 (24.00%) |
5_prime_UTR_variant | 12,376 (2.84%) | 9712 (3.16%) | 444 (2.66%) |
Downstream_gene_variant | 42,903 (9.84%) | 32,376 (10.54%) | 1933 (11.56%) |
Intron_variant | 249,984 (57.34%) | 156,050 (50.81%) | 8259 (49.40%) |
Missense_variant | 2310 (0.53%) | 2046 (0.67%) | 35 (0.21%) |
Non_coding_transcript_exon_variant | 6349 (1.46%) | 5702 (1.86%) | 204 (1.22%) |
Regulatory_region_variant | 776 (0.18%) | 681 (0.22%) | 21 (0.13%) |
Splice_acceptor_variant | 12 (0.00%) | 9 (0.00%) | 0 (0.00%) |
Splice_donor_variant | 162 (0.04%) | 63 (0.02%) | 3 (0.02%) |
Splice_region_variant | 5302 (1.22%) | 4350 (1.42%) | 276 (1.65%) |
Start_lost | 0 (0.00%) | 0 (0.00%) | 1 (0.01%) |
Stop_gained | 316 (0.07%) | 254 (0.08%) | 8 (0.05%) |
Stop_lost | 5 (0.00%) | 5 (0.00%) | 1 (0.01%) |
Synonymous_variant | 28,813 (6.61%) | 25,128 (8.18%) | 467 (2.79%) |
Upstream_gene_variant | 28,555 (6.55%) | 18,471 (6.01%) | 1053 (6.30%) |
Sum | 435,998 (100.00%) | 307,152 (100.00%) | 16,718 (100.00%) |
