Table 3.

Functional classification of the identified genetic variants in Baka Pygmies and Bantu subjects

Populations	Baka Pygmies			Bantu
Functional classification	Total	Novel	%	Total	Novel	%
3′UTR variant	10,577	1562	14.77	9405	1381	14.68
5′UTR prem. start codon gain	583	38	6.52	500	30	6.00
5′UTR variant	3499	531	15.18	3138	435	13.86
Disruptive inframe deletion	89	89	100.00	75	74	98.67
Disruptive inframe insertion	40	40	100.00	44	42	95.45
Downstream gene variant	1163	180	15.48	1012	156	15.42
Frameshift variant	347	343	98.85	284	282	99.30
Inframe deletion	164	164	100.00	143	142	99.30
Inframe insertion	80	80	100.00	74	71	95.95
Initiator codon variant	2	0	0.00	2	0	0.00
INTERGENIC region	33	3	9.09	28	3	10.71
Intragenic variant	1	0	0.00	1	0	0.00
Intron variant	474	73	15.40	416	55	13.22
Missense variant	29,836	2464	8.26	23,786	1514	6.37
Non coding exon variant	1064	130	12.22	853	93	10.90
Sequence feature	785	99	12.61	643	77	11.98
Splice acceptor variant	61	33	54.10	53	31	58.49
Splice donor variant	57	17	29.82	54	17	31.48
Splice region variant	1308	147	11.24	1066	120	11.26
Start lost	74	9	12.16	57	8	14.04
stop gained	286	54	18.88	235	48	20.43
Stop lost	45	2	4.44	37	2	5.41
Stop retained variant	22	2	9.09	20	1	5.00
Synonymous variant	31,011	1162	3.75	24,987	580	2.32
Upstream gene variant	1484	212	14.29	1277	179	14.02
Total	83,085	7434	8.95	68,190	5348	7.84

Functional distribution and percentage of WES variants (total and novel) found in Baka Pygmies and Bantu individuals compared with 1000 Genomes and db137 databases. Impact of variants were estimated according the SnpEff predictor