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User Guide for ShiNyP: SNP Analysis and Visualization Platform

2 Data QC

➡️ This section includes three subpages: Sample QC, SNP QC, and SNP Density, allowing you to assess the quality of samples and SNPs in data.frame, as well as visualize SNP density across the genome.

2.1 Sample QC

Required File:

  • data.frame file from the Data Input page or
  • SNP post-QC data.frame file from the Data QC/SNP QC subpage .

Step 1: Get Summary

First, obtain the sample summary statistics (missing rate and heterozygosity rate) by clicking both Summary buttons and you will see the results.

Step 2: Sample QC

Adjust the thresholds and click Sample QC by Thresholds. This will generate the Post-QC data.frame file.

Note: If you prefer not to perform sample QC by sample missing rate or heterozygosity rate, please set the threshold to 1.

Outputs:

  • data.frame (RDS): Updated data.frame file — required for downstream analysis.
  • Site Info. (RDS): Updated SNP site information file — required for downstream analysis.


2.2 SNP QC

Required File:

  • data.frame file from the Data Input page or
  • Sample post-QC data.frame file from the Data QC/Sample QC subpage.

Step 1: Get Summary

First, obtain the SNP summary statistics [missing rate, minor allele frequency (MAF), heterozygosity rate, and Hardy-Weinberg equilibrium (HWE)] by clicking all Summary buttons and you will see the results.

Step 2: Sample QC

Adjust the thresholds and click SNP QC by Thresholds. This will generate the Post-QC data.frame file.

Note: If you prefer not to perform QC based on SNP missing rate or heterozygosity rate, set the missing rate threshold to 1, the MAF to 0, and the heterozygosity rate to 0 and 1. Also, leave the ‘Do SNP QC by HWE’ checkbox unticked to skip QC based on SNP HWE.

Outputs:

  • data.frame (RDS): Updated data.frame file — required for downstream analysis.
  • Site Info. (RDS): Updated SNP site information file — required for downstream analysis.

2.3 SNP Density

Required Files:

  • Site Info. (RDS) of the current data.frame, downloadable from Data Input or Data QC pages.

  • Chromosome Info. (CSV): Reference genome information of the current study.

    Download an example of Chromosome Info. (CSV).

    This file should contain three columns: “Chr”, “Start”, and “End”.

    • “Chr” column should specify the chromosome names (as characters, e.g., “Chr01”, “Chr11”)
    • “End” column should indicate the length of each chromosome (numeric)
    • “Start” column can be set to 0 or 1 for each chromosome.

Steps:

  1. Upload Site Info. (RDS) and Chromosome Info. (CSV).
  2. Choose a window size in kilobases (kb).
  3. Click Summary.

Outputs:

  • SNP Density Plot (PDF): An ideogram visualizing SNP density across the genome within a defined window size. A gradient color palette is used to represent varying SNP densities: green for lower densities, yellow for medium densities, and red for higher densities, with grey indicating regions with zero SNP.
  • SNP Density (CSV): A table detailing SNP density across each chromosome. bp_over_SNPs: The total base pairs (bp) per SNP in each window, representing the average spacing between SNPs. SNPs_over_1000bp: The number of SNPs per 1,000 base pairs, providing a normalized measure of SNP density across the genome.