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Table 2 Quality scores of the imputed (I) and study (S) SNPs for each MAF category

From: GACT: a Genome build and Allele definition Conversion Tool for SNP imputation and meta-analysis in genetic association studies

Datasets

.001-.005

.005-.01

.01-.05

.05-.1

.1-.3

.3-.5

GWAS

1KG

I

S

I

S

I

S

I

S

I

S

I

S

All

All

.520 (.222)

.854 (.249)

.727 (.222)

.902 (.184)

.853 (.173)

.945 (.131)

.939 (.118)

.971 (.089)

.965 (.086)

.981 (.060)

.975 (.071)

.981 (.063)

All

NoSin

.584 (.289)

.854 (.239)

.738 (.227)

.906 (.181)

.855 (.174)

.945 (.132)

.939 (.118)

.970 (.092)

.966 (.086)

.982 (.060)

.975 (.071)

.981 (.064)

All

NoSM

.571 (.275)

.859 (.245)

.730 (.222)

.901 (.186)

.854 (.172)

.945 (.131)

.939 (.118)

.971 (.089)

.965 (.086)

.981 (.060)

.975 (.071)

.981 (.063)

NoSin

NoSM

.571 (.275)

.858 (.245)

.730 (.222)

.903 (.184)

.854 (.172)

.945 (.131)

.939 (.118)

.971 (.089)

.965 (.086)

.981 (.060)

.975 (.071)

.981 (.063)

NoAm

NoSM

.572 (.274)

.855 (.245)

.731 (.222)

.900 (.185)

.854 (.172)

.944 (.131)

.940 (.117)

.971 (.091)

.966 (.085)

.981 (.060)

.975 (.071)

.981 (.064)

3per

NoSM

.570 (.274)

.859 (.245)

.730 (.222)

.901 (.187)

.853 (.173)

.944 (.131)

.939 (.118)

.970 (.091)

.965 (.086)

.981 (.061)

.974 (.073)

.981 (.064)

1per

NoSM

.568 (.274)

.851 (.251)

.726 (.223)

.899 (.186)

.851 (.174)

.942 (.134)

.937 (.120)

.969 (.094)

.964 (.088)

.980 (.064)

.973 (.074)

.979 (.067)

0.4per

NoSM

.563 (.273)

.841 (.258)

.722 (.223)

.897 (.190)

.848 (.175)

.938 (.140)

.934 (.121)

.966 (.099)

.962 (.090)

.978 (.067)

.971 (.076)

.977 (.067)

0.2per

NoSM

.557 (.272)

.830 (.263)

.715 (.224)

.884 (.197)

.843 (.177)

.933 (.144)

.930 (.126)

.962 (.104)

.958 (.092)

.975 (.070)

.968 (.079)

.974 (.073)

0.1per

NoSM

.542 (.269)

.810 (.270)

.700 (.225)

.872 (.207)

.830 (.180)

.922 (.152)

.921 (.129)

.954 (.110)

.949 (.100)

.967 (.080)

.960 (.087)

.966 (.080)

0.05per

NoSM

.507 (.258)

.756 (.293)

.662 (.222)

.824 (.231)

.793 (.189)

.891 (.169)

.893 (.138)

.930 (.130)

.923 (.114)

.941 (.102)

.934 (.100)

.943 (.095)

  1. MAF: minor allele frequency.
  2. NoSin: no singletons.
  3. NoAm: no ambiguous.
  4. NoSM: no singletons or monomorphs.
  5. 0.05-3per: after removing SNPs with genotype missing rate higher than 0.05-3%.
  6. The quality (information) scores were generated using IMPUTE2. The mean/average and standard deviation are shown outside and inside the brackets, respectively. We observed a high correlation between the imputed and study (true) genotypes, which incremented from low to high MAF ranges.
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BMC Genomics

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