Table 3 Discrepancies between cytogenetic and computational karyotypes in Ag1000G mosquitoes analyzed
Specimens with discrepancies
Inversion TagsPartitionCYTSpecimens (N)Mismatch CYT-TAG (%)Match TAG-PCA (%)No. tag SNPs scored (% matching TAG)
2La01175 (4.3)5 (100)200-203 (99.5-100)
1685 (7.4)5 (100)193-203 (100)
21602 (1.3)2 (100)201-203 (99.5-100)
2Rj-gambiaegambiae02360 (0)
140 (0)
2450 (0)
2Rb01272 (1.6)2 (100)348 (85.3-87.6)
11244 (3.2)4 (100)346-349 (86.8-93.7)
21216 (5.0)6 (100)331-348 (88.8-91.6)
2Rc-gambiaegambiaea01847 (3.8)7 (100)48-49 (83.7-98.0)
1323 (9.4)2 (66.7)47-49 (42.9b-91.5)
2242 (8.3)2 (100)48-49 (90.0-91.8)
2Rc-coluzzicoluzzii0131 (7.7)1 (100)56 (87.5)
1250 (0)
2160 (0)
2Rd-gambiaegambiae02349 (3.8)9 (100)143-147 (84.9-96.6)
1284 (14.3)4 (100)146-147 (88.4-93.9)
2223 (13.6)3 (100)146-147 (89.1-91.8)
2Rucol+gam02631 (0.38)1 (100)176 (85.2)
12918 (62.1)18 (100)170-177 (88.7-99.4)
2471 (2.1)1 (100)176 (97.2)
  • CYT, cytogenetic genotype; TAG, computational genotype; PCA, genotype inferred by PCA.

  • a An. gambiae excluding BAMAKO.

  • b This value corresponds to one of three non-BAMAKO An. gambiae carriers of the 2Ru inversion, AZ0267-C. The next highest value is 85.7.