Kdr origins and diplotype clustering#
This notebook determines the origin of Kdr for each sample, and performs diplotype clustering.
Unexpected kdr 402 genotype. GH_04 ??
Unexpected kdr 402 genotype. GH_07 ??
Unexpected kdr F genotype. GH_10 ??
Unexpected kdr S genotype. GH_10 ??
Unexpected kdr F genotype. GH_16 ??
Unexpected kdr S genotype. GH_16 ??
Unexpected kdr F genotype. GH_17 ??
Unexpected kdr S genotype. GH_17 ??
Unexpected kdr F genotype. GH_18 ??
Unexpected kdr S genotype. GH_18 ??
Unexpected kdr F genotype. GH_20 ??
Unexpected kdr S genotype. GH_20 ??
Unexpected kdr 402 genotype. GH_20 ??
Unexpected kdr F genotype. GH_22 ??
Unexpected kdr S genotype. GH_22 ??
Unexpected kdr 402 genotype. GH_46 ??
Unexpected kdr F genotype. GH_58 ??
Unexpected kdr S genotype. GH_58 ??
Unexpected kdr F genotype. GH_77 ??
Unexpected kdr S genotype. GH_77 ??
Unexpected kdr F genotype. GH_80_low_vol ??
Unexpected kdr S genotype. GH_80_low_vol ??
Unexpected kdr 402 genotype. GH_80_low_vol ??
Unexpected kdr F genotype. GM_01 ??
Unexpected kdr S genotype. GM_01 ??
Unexpected kdr 402 genotype. GM_01 ??
Unexpected kdr F genotype. GM_06 ??
Unexpected kdr S genotype. GM_06 ??
Unexpected kdr 402 genotype. GM_12 ??
Unexpected kdr F genotype. GM_17 ??
Unexpected kdr S genotype. GM_17 ??
Unexpected kdr F genotype. GM_18 ??
Unexpected kdr S genotype. GM_18 ??
Unexpected kdr F genotype. GM_23 ??
Unexpected kdr S genotype. GM_23 ??
Unexpected kdr 402 genotype. GM_33 ??
Unexpected kdr F genotype. GM_42 ??
Unexpected kdr S genotype. GM_42 ??
Unexpected kdr F genotype. GM_43 ??
Unexpected kdr S genotype. GM_43 ??
Unexpected kdr 402 genotype. GM_44 ??
Unexpected kdr F genotype. GM_54 ??
Unexpected kdr S genotype. GM_54 ??
Unexpected kdr F genotype. GM_56 ??
Unexpected kdr S genotype. GM_56 ??
Unexpected kdr F genotype. GM_59 ??
Unexpected kdr S genotype. GM_59 ??
Unexpected kdr F genotype. GM_60 ??
Unexpected kdr S genotype. GM_60 ??
Unexpected kdr 402 genotype. GM_66 ??
Unexpected kdr F genotype. VK7_alive_01 ??
Unexpected kdr S genotype. VK7_alive_01 ??
Unexpected kdr F genotype. VK7_dead_25 ??
Unexpected kdr S genotype. VK7_dead_25 ??
Unexpected kdr F genotype. VK7_dead_32 ??
Unexpected kdr S genotype. VK7_dead_32 ??
Unexpected kdr 402 genotype. Siaya_Delta_Dead_07 ??
Unexpected kdr 402 genotype. Siaya_Delta_Alive_97 ??
Too many different mutant haplotype backgrounds in sample GH_59
Counts of origins:
| kdr_origin | F | F1 | F2 | S | S1 | S3 | wt | |
|---|---|---|---|---|---|---|---|---|
| location | taxon | |||||||
| Gambia_URR | coluzzii | 1 | 1 | 0 | 0 | 0 | 0 | 24 |
| gambiae | 1 | 5 | 0 | 0 | 0 | 0 | 0 | |
| uncertain | 0 | 0 | 0 | 12 | 0 | 0 | 62 | |
| Obuasi | gambiae | 6 | 122 | 0 | 0 | 0 | 0 | 0 |
| Siaya | gambiae | 4 | 0 | 314 | 8 | 147 | 7 | 0 |
| VK7 | coluzzii | 0 | 142 | 0 | 0 | 0 | 0 | 0 |
Frequencies of known origins:
| kdr_origin | F | F1 | F2 | S | S1 | S3 | wt | |
|---|---|---|---|---|---|---|---|---|
| location | taxon | |||||||
| Gambia_URR | coluzzii | 0.0380 | 0.038 | 0.00 | 0.000 | 0.00 | 0.000 | 0.92 |
| gambiae | 0.1700 | 0.830 | 0.00 | 0.000 | 0.00 | 0.000 | 0.00 | |
| uncertain | 0.0000 | 0.000 | 0.00 | 0.160 | 0.00 | 0.000 | 0.84 | |
| Obuasi | gambiae | 0.0470 | 0.950 | 0.00 | 0.000 | 0.00 | 0.000 | 0.00 |
| Siaya | gambiae | 0.0083 | 0.000 | 0.65 | 0.017 | 0.31 | 0.015 | 0.00 |
| VK7 | coluzzii | 0.0000 | 1.000 | 0.00 | 0.000 | 0.00 | 0.000 | 0.00 |