Table 1 Distribution of alleles associated with malaria disease severity, as well as off-target non-synonymous variants, identified on HBB, G6PD, Dantu, and ACKR1 loci in Northeast Tanzania using amplicon sequencing.
Gene | Chrom | Position | rs IDa | Variant information | Homozygous negative (−/−) | Heterozygous (−/+) | Homozygous positive (+/+) | Mean DP | Concordanceb % | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
G6PD | X | 154532738 | rs2230036 | C>T | CC | 87 | CT | 6 | TT | 6 | 803 | NA |
154533025 | rs76723693 | 968 A>G | AA | 99 | AG | 0 | GG | 0 | 798 | 100 | ||
154533122 | rs137852327 | C>T | CC | 99 | CT | 0 | TT | 0 | 798 | NA | ||
154534125 | rs137852328 | 680 C>A | CC | 99 | CA | 0 | AA | 0 | 629 | 100 | ||
154534177 | rs5986875 | G>A | GG | 98 | GA | 1 | AA | 0 | 629 | NA | ||
154534440 | rs5030872 | 542 T>A | TT | 99 | TA | 0 | AA | 0 | 622 | 100 | ||
154535443 | NA | G>A | GG | 86 | GA | 1 | AA | 0 | 622 | NA | ||
154535468 | NA | G>T | GG | 86 | GT | 1 | TT | 0 | 622 | NA | ||
154534527 | NA | T>C | TT | 86 | TC | 1 | CC | 0 | 622 | NA | ||
154535277 | rs1050829 | 376 T>C | TT | 48 | TC | 16 | CC | 23 | 956 | 96.6 | ||
154536002 | rs1050828 | 202 C>T | CC | 71 | CT | 8 | TT | 8 | 530 | 100 | ||
HBB | 11 | 5226867 | NA | C>G | CC | 98 | CG | 1 | GG | 0 | 1020 | NA |
5226925 | rs33915217 | β + thal | CC | 99 | CA | 0 | AA | 0 | 1020 | NA | ||
5226932 | rs35578002 | G>T | GG | 98 | GT | 1 | TT | 0 | 1020 | NA | ||
5226943 | rs33950507 | HbE | CC | 99 | CT | 0 | TT | 0 | 1020 | 100 | ||
5226963 | rs33972047 | β + thal | TT | 99 | TC | 0 | CC | 0 | 1020 | NA | ||
5226966 | rs35382661 | A>C | AA | 97 | AC | 2 | CC | 0 | 1118 | NA | ||
5227002 | rs334 | HbS | TT | 90 | TA | 4 | AA | 5 | 2003 | 100 | ||
5227003 | rs33930165 | HbC | CC | 99 | CT | 0 | TT | 0 | 2003 | 100 | ||
5227013 | rs713040 | β + thal; HPFHc | AA | 4 | AG | 27 | GG | 65 | 2002 | NA | ||
5227072 | rs386134236 | A>G | AA | 98 | AG | 1 | GG | 0 | 984 | NA | ||
ACKR1 | 1 | 159204646 | NA | A>C | AA | 76 | AC | 19 | CC | 0 | 644 | NA |
159204893 | rs2814778 | Fy(a-b-) T>C | TT | 0 | TC | 0 | CC | 95 | 623 | 100 | ||
Dantu | 4 | 143781321 | rs186873296 | Intergenic A>G | AA | 95 | AG | 3 | GG | 0 | 132 | 99.0 |
143781342 | NA | G>T | GG | 98 | GT | 1 | TT | 0 | 184 | NA | ||
