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GAINQC Graphical Output Files
In addition to the text information files that are output after each of the 2 runs of GAINQC, the QC program also
creates 3 pdf files to summarize the information in a graphical manner. The three files are:
- PDF file with histogram of sample statistics
- PDF file with histogram of snp statistics
- PDF file with histogram of kinship coefficients of pairs in the same relation group
Sample Histograms
The sample histograms are written to a pdf file. The statistics whose histograms are drawn include:
- Genotyping completeness
- Heterozygosity
- Number of mendelian inconsistencies
- Log sex odds (male vs female)
- Log likelihood
- Average quality score
If the samples have labels on them then the histograms have different colors representing different labels. In case
the samples do not have any labels, then the samples that passed QC are shown in greed and the ones that fail QC are shown
in red. An example sample histogram pdf is given here.
SNP Histograms
Similar to the sample histograms file, the program creates a file with all the histograms for the snp statistics. The
statistics with histograms in the snp histogram file include:
- Minor allele frequency
- Genotyping completeness
- Hardy-Weinberg Equillibrium p-values
- Number of mendelian inconsistencies
- Rate of mendelian errors
- Number of duplicate mismatches
- Log odds of being X-linked
- Average quality score
- Number of 1 and 2 alleles transmitted (only if TDT performed)
- Number of trios used for TDT (only if TDT performed)
- TDT chi-squared statistic and p-value (only if TDT performed)
- Association test chi-suqared statistic and p-value (only if association test performed)
In these histograms, the SNPs that failed QC are shown in red, whereas the SNPs that passed QC are shown in green. A toy snp histogram
pdf file is given here.
Kinship Histograms
The kinship coefficients that are estimated for each pair of samples are summarized using a histogram of
estimated kinships for all pairs of samples that are in the same putative relation group. Therefore there are 5
histograms of kinships of 5 types of relationships in this file, viz. unrelated pairs, parent-offspring pairs,
siblings, half-siblings and duplicates/mz twins. An example relationship information pdf is given
here.
 Adobe Acrobat
reader to read pdf files can be obtained here.
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