Result Summary Table

This table summurized information available from output files produced by pyGenClean during the data clean up procedure. Numbers correspond to number of lines in output files see Proposed Protocol for details. Only removed SNPs and IDs are indicated in the column SNPs and IDs, flagged SNPs or IDs are present in the \(n\) column.

Summary information of the data clean up procedure.
Description \(n\) SNPs IDs
Total number of SNPs in file received 2,379,855    
Total number of samples 494    
Number of duplicate samples 0    
Number of individuals with no genotype (failed) 0    
Number of SNPs with no physical position (chromosome and physical position = 0) 7,239 -7,239  
Number of INDEL 43 -43  
Number of replicate controls 5    
Number of replicate samples 0    
Number of duplicate SNPs (by chromosome and physical position) 5,643    
Duplicated SNPs by chromosome and physical position with the same allele (merge) 5,417 -5,147  
Number of duplicated SNP with <98% concordance 22 -22  
Completely failed SNPs 1 -1  
All heterozogous SNPs 0    
Number of individuals removed because they have more than 10% missing genotypes 5   -5
Number of SNPs removed because they have more than 2% missing value 128,562 -128,562  
Number of individuals removed because they have more than 2% missing genotypes 7   -7
Number of individuals with gender problem 1    
Number of SNPs with plate bias test P value below threshold of \(1\times10^{-7}\) 19    
Number of SNPs used for IBS analysis 73,651    
Number of duplicates pairs or twin 1    
Number of related pairs (including twins) 2    
Number of SNPs used for MDS analysis 80,262    
Number of individuals with ethnicity other than Caucasian as detected by MDS analysis 20    
Number of gender problems 1   -1
Number of related pairs 2   -2
Number of caucasian outliers 20   -20
Number of controls 5   -5
Number of heterozygote haploid genotypes set to missing (after correction of gender problems) 277,206    
Number of SNPs with MAF=0 602,480 -602,480  
Number of SNPS with HWE test P Value below threshold of \(1\times10^{-4}\) and higher than Bonferroni threshold 603    
Number of SNPS with HWE test below Bonferroni threshold 162 -162  
Total number of SNPs 1,635,931    
Total number of samples 454