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Table 2 Reclassification of SNP allele calls by use of polar transformation compared to conventional methods

From: Differentiating Plasmodium falciparum alleles by transforming Cartesian X,Y data to polar coordinates

Genotype Dhfr Locus 59 Chr1SNP Chr7SNP Chr8SNP Chr9SNP Chr13SNP
Status XYa Polarb XYa Polarb XYa Polarb XYa Polarb XYa Polarb XYa Polarb
Not Infected 127 137 77 104 92 92 70 28 66 95 92 93
Inf. w/Allele 1 25c 63 19 28 48 60 141 147 4 127 47 108
Inf. w/Allele 2 25d 37 46 166 102 152 42 27 44 71 77 83
Mixed Infection 87 17 215 24 115 28 41 34 243 36 141 41
Uncertain e - 10 - 35 - 25 - 58 - 28 - 32
Total Samples f 264 357 357 294 357 357
Reclassified g 86 226 96 76 237 126
  1. aCounts determined based on the conventional threshold of 3× standard deviations above the mean - see Figure 4A.
  2. bCounts determined after applying polar transformation method - see Figure 4C.
  3. cFor Dhfr locus 59, allele 1 is associated with drug sensitivity.
  4. dFor Dhfr locus 59, allele 2 is associated with drug resistance.
  5. eNo samples are considered uncertain by conventional (XY) methods, as confidence intervals are not considered.
  6. fThe total number of samples genotyped at each locus.
  7. gThe number of samples whose allele calls differed between the XY and polar transformation methods.