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.
| 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 |