Allelotyping of pooled DNA with 250 K SNP microarrays

BMC Genomics

Table 2 Estimation accuracy in the Nsp 250 K array

no. of pool replicates*	mean error	SNPs	correlation	mean SD
1	0.056	91647	0.971	0.000
2	0.051	93654	0.976	0.041
3	0.047	99922	0.980	0.044
4	0.046	102687	0.983	0.046
no. of "AB" references	mean error	SNPs	correlation	mean SD
1	0.095	4790	0.980	0.041
2	0.079	3544	0.987	0.041
3	0.070	3479	0.989	0.041
4	0.064	3523	0.989	0.042
5	0.061	3364	0.986	0.043
6	0.057	3623	0.989	0.043
7	0.054	3543	0.988	0.043
8	0.052	3356	0.987	0.045
9	0.049	3419	0.988	0.045
10	0.048	3524	0.987	0.046
15	0.042	3545	0.980	0.048
20	0.035	3701	0.976	0.048
25	0.030	3208	0.959	0.046
30	0.027	1329	0.941	0.043
35	0.024	141	0.954	0.041
minor allele frequency	mean error	SNPs	correlation	mean SD
0.0 – 0.1	0.096	27688	0.915	0.037
0.1 – 0.2	0.045	23875	0.983	0.043
0.2 – 0.3	0.038	18843	0.977	0.048
0.3 – 0.4	0.033	17339	0.953	0.051
0.4 – 0.5	0.030	15783	0.778	0.053
SNP type	mean error	SNPs	correlation	mean SD
A/T, T/A	0.052	6799	0.979	0.050
A/C, T/G	0.048	16056	0.982	0.046
A/G, T/C	0.045	69445	0.983	0.045
C/G, G/C	0.043	10387	0.981	0.045

*To get the error for different numbers of repeats, we took the mean of all possible combination of the four replicates. For 3 replicates for example we took the mean values of pool combinations 123, 124, 134, 234.

ISSN: 1471-2164