Table 2.

Distribution of derived alleles by functional class

Derived alleles, n (%)
Polymorphic positions (SNPs)Homozygous positions (“fixed”)
CategoryNeandertals*AfricansEuropeansAsiansNeandertals*AfricansEuropeansAsians
Coding
 Synonymous2,501 (48.9)8,250 (54.3)5,571 (53.6)5,518 (53.3)1,273 (56.1)383 (59.3)624 (57.2)603 (57.8)
 Nonsynonymous2,611 (51.1)6,947 (45.7)4,820 (46.4)4,839 (46.7)996 (43.9)263 (40.7)467 (42.8)441 (42.2)
PP-2
 Benign1,354 (54.6)3,596 (63.6)2,266 (62.1)2,292 (61.9)600 (63.8)16 (55.2)53 (66.3)59 (64.1)
 Deleterious1,128 (45.4)2,057 (36.4)1,385 (37.9)1,409 (38.1)340 (36.2)13 (44.8)31 (36.9)33 (35.9)
PC
 Benign1,296 (49.9)4,280 (61.9)2,872 (59.8)2,903 (60.3)601 (60.4)185 (70.6)335 (72.2)321 (73.1)
 Deleterious1,303 (50.1)2,635 (38.1)1,931 (40.2)1,913 (39.7)394 (39.6)77 (29.4)129 (27.8)118 (26.9)
GS
 Benign2,112 (80.9)5,673 (81.7)3,936 (81.7)3,954 (81.7)833 (83.6)231 (87.8)413 (88.4)374 (84.8)
 Deleterious499 (19.1)1,274 (18.3)884 (18.3)885 (18.3)163 (16.4)32 (12.2)54 (11.6)67 (15.2)
  • For the coding category, the number and proportion of coding alleles that are either synonymous or nonsynonymous are shown. For the PolyPhen-2 (PP-2), PhastCons (PC) and Grantham score (GS) categories, the number and proportion of nonsynonymous alleles that are predicted to be either benign or deleterious are shown.

  • * Derived in Neandertals and homozygous ancestral in Africans. See Table S18 for additional details.

  • Derived in Africans, Europeans, or Asians and homozygous ancestral in Neandertals.