. 2010 Jun 29;11:57. doi: 10.1186/1471-2156-11-57

Table 2.

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

Genotype	Dhfr Locus 59		Chr1SNP		Chr7SNP		Chr8SNP		Chr9SNP		Chr13SNP
Status	XY^a	Polar^b	XY^a	Polar^b	XY^a	Polar^b	XY^a	Polar^b	XY^a	Polar^b	XY^a	Polar^b
Not Infected	127	137	77	104	92	92	70	28	66	95	92	93
Inf. w/Allele 1	25^c	63	19	28	48	60	141	147	4	127	47	108
Inf. w/Allele 2	25^d	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

^aCounts determined based on the conventional threshold of 3× standard deviations above the mean - see Figure 4A.

^bCounts determined after applying polar transformation method - see Figure 4C.

^cFor Dhfr locus 59, allele 1 is associated with drug sensitivity.

^dFor Dhfr locus 59, allele 2 is associated with drug resistance.

^eNo samples are considered uncertain by conventional (XY) methods, as confidence intervals are not considered.

^fThe total number of samples genotyped at each locus.

^gThe number of samples whose allele calls differed between the XY and polar transformation methods.