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Geno Summary

Dialog

GenoSummaryDialog.png

Overall Summary

  • Number of Taxa - Number of Taxa in data set.
  • Number of Sites - Number of Sites in data set.
  • Sites x Taxa - Number of sites multiplied by number of taxa.
  • Number Not Missing - Number allele values not unknown (NN)
  • Proportion Not Missing - Number Not Missing / Sites x Taxa
  • Number Missing - Number unknown (NN) values
  • Proportion Missing - Number Missing / Sites x Taxa
  • Number Gametes - Number of Sites x Number Taxa x 2
  • Gametes Not Missing - Number of gametes not unknown
  • Proportion Gametes Not Missing - Gametes Not Missing / Number Gametes
  • Gametes Missing - Number unknown (N) gametes
  • Proportion Gametes Missing - Gametes Missing / Number Gametes
  • Number Heterozygous - Number of heterozygous values
  • Proportion Heterozygous - Number Heterozygous / Sites x Taxa

OverallSummary.png

Allele Summary

  • Alleles - Allele values present in data set. Single letter values are diploid where some letter represent heterozygous. Two letter values are major / minor combinations with count of sites.
  • Number - Number of occurrences
  • Proportion - Percentage the value occurs in data set.
  • Frequency - Percentage the value occurs in data set not counting unknown (N) values.

AlleleSummary.png

Site Summary

  • Site Number - Index of site
  • Site Name - Name of site
  • Chromosome - Chromosome
  • Physical Position - Physical Position on Chromosome
  • Number of Taxa - Number of taxa for site (same of all)
  • Major Allele - The major allele of site
  • Major Allele Gametes - Number of times major allele occurs for site (up to twice number of taxa)
  • Major Allele Proportion - Major Allele Gametes / (Number of Taxa * 2). Number of Taxa * 2 is the Number of Gametes for a Site.
  • Major Allele Frequency - Major Allele Gametes / ((Number of Taxa * 2) - Gametes Missing)
  • Minor Allele - The minor allele of site
  • Minor Allele Gametes - Number of times minor allele occurs for site
  • Minor Allele Proportion - Minor Allele Gametes / (Number of Taxa * 2). Number of Taxa * 2 is the Number of Gametes for a Site.
  • Minor Allele Frequency - Minor Allele Gametes / ((Number of Taxa * 2) - Gametes Missing)
  • Gametes Missing - Number of gametes with unknown (N) value
  • Proportion Missing - Gametes Missing / (Number of Taxa * 2)
  • Number Heterozygous - Number of taxa that are heterozygous for site.
  • Proportion Heterozygous - Number Heterozygous / Number of Taxa (not counting taxa that are unknown (NN))
  • Inbreeding Coefficient -
  • Inbreeding Coefficient Scaled by Missing -

SiteSummary.png

Taxa Summary

  • Taxa - Index of taxa.
  • Taxa Name - Name of taxa
  • Number of Sites - Number of sites for taxon (same for all).
  • Gametes Missing - Number of gametes with unknown (N) value. Every taxa / site combination has two gametes.
  • Proportion Missing - Gametes Missing / (Number of Sites * 2)
  • Number Heterozygous - Number of sites that are heterozygous for taxon
  • Proportion Heterozygous - Number Heterozygous / Number of Sites (not counting sites that are unknown (NN))
  • Inbreeding Coefficient -
  • Inbreeding Coefficient Scaled by Missing -

TaxaSummary.png

Genotype Summary Command Line

#!bash

./run_pipeline.pl -importGuess mdp_genotype.hmp.txt -GenotypeSummaryPlugin -endPlugin -export summary

#!bash

GenotypeSummaryPlugin <options>
-overview <true | false> : Get Overview Report (Default: true)
-siteSummary <true | false> : Get Site Summary (Default: true)
-taxaSummary <true | false> : Get Taxa Summary (Default: true)