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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.