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Department of Biotechnology, Government of India BTISnet Sub DIC

Central Sericultural Research and Training Institute, Mysore

Bioinformatics CentreCSRTI, Mysore

Structure Plot / Tutorial

Preparing a Structure Plot input file

A step by step guide to the Q matrix and tab delimited file format used by Structure Plot.

Read this tutorial before preparing an input file. First time users can download the sample file and use it to become familiar with the input format and drawing parameters.

Sample input file, K equals 4

The sample is a tab delimited text file with population identifiers, individual identifiers and four Q columns.

Download the sample

Preparing the input file

  1. Copy the individual Q matrix from STRUCTURE or CLUMPP output and paste it into a spreadsheet application such as Microsoft Excel.
  2. Edit the header and the first two columns according to the rules below.
  3. Save the file as a tab delimited text file. Only the .txt extension is accepted.

Column rules

  1. The first row must contain a valid header in alpha numeric form, such as Pop1, or in letters, such as Pop. Do not use only numbers as a header.
  2. The mandatory first column must be alpha numeric or alphabetic. Do not use only numbers. Use this column to indicate the population identifier for each individual. The same population identifier can be used for more than one individual.
  3. The mandatory second column is the individual identifier. Each individual identifier should be unique and alpha numeric or alphabetic.
  4. Do not keep any extra columns after the first two columns and the individual Q matrix. For K equals 4, the file should have six columns in total. Remove extra columns before saving.
  5. Use the tab delimited text format. Do not submit CSV or other formats.

Example structure

group	geno	P1	P2	P3	P4
A	G958	0.992	0.003	0.002	0.003
A	G681	0.881	0.01	0.071	0.038

Support

If you have questions or suggestions about input file preparation or the application, write to [email protected]. The download page explains the standalone package and its R requirements.