: Data-Field 22051

Data-Field 22051

Description:	UKBiLEVE genotype quality control for samples
Category:	Genomics ⏵ Genotypes ⏵ Interim genotype release
	Genomics

Participants

49,962

Categorical (single)

Both sexes

Mar 2015

49,962

Data

Singular

Mar 2015

Complete

Primary

Notes

sex mismatch (remove sample if submitted gender is different to gender inferred from sex chromosomes);

final call rate (<95%), heterozygosity outliers (outlier if > 3sd from mean heterozygosity);

unintended duplicate (> 98% of alleles shared identical by descent);

ancestry principal components outlier (outlier if >10sd from mean on first 10 principal components).

This derived data field has come from Professor Martin Tobin at the University of Leicester.

Preview	Name	Res ID
	Affymetrix genotype data generation - interim release	155582
	Affymetrix genotype sample processing - interim release	155583
	Analysis workflow for UKB Axiom Array - interim release	157002
	Axiom genotyping solution data analysis guide - interim release	157021
	Example Calls file in Basic format	149842
	Example Calls file in UKB format	149841
	Example Calls mapfile in Ped format	149844
	Example Calls pedfile in Ped format	149843
	Genotype data mapping	149660
	Genotype imputation and genetic association studies using UK Biobank data	157020
	Genotyping and quality control for UK Biobank - interim release	155580
	Probeset usage	149640
	SNPs recommended for exclusion from analyses	976
	UK Biobank / UK BiLEVE low concordance SNPs	483
	UK Biobank sample processing workflow and preparation of DNA for genotyping - interim release	155581
	Imputed minor allele frequencies for Chromosome 1	1201
	Imputed minor allele frequencies for Chromosome 2	1202
	Imputed minor allele frequencies for Chromosome 3	1203
	Imputed minor allele frequencies for Chromosome 4	1204
	Imputed minor allele frequencies for Chromosome 5	1205
	Imputed minor allele frequencies for Chromosome 6	1206
	Imputed minor allele frequencies for Chromosome 7	1207
	Imputed minor allele frequencies for Chromosome 8	1208
	Imputed minor allele frequencies for Chromosome 9	1209
	Imputed minor allele frequencies for Chromosome 10	1210
	Imputed minor allele frequencies for Chromosome 11	1211
	Imputed minor allele frequencies for Chromosome 12	1212
	Imputed minor allele frequencies for Chromosome 13	1213
	Imputed minor allele frequencies for Chromosome 14	1214
	Imputed minor allele frequencies for Chromosome 15	1215
	Imputed minor allele frequencies for Chromosome 16	1216
	Imputed minor allele frequencies for Chromosome 17	1217
	Imputed minor allele frequencies for Chromosome 18	1218
	Imputed minor allele frequencies for Chromosome 19	1219
	Imputed minor allele frequencies for Chromosome 20	1220
	Imputed minor allele frequencies for Chromosome 21	1221
	Imputed minor allele frequencies for Chromosome 22	1222

Preview

Name

Res ID