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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in XhetRel_interactive_multiqc_report_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

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        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.21

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-05-24, 12:30 UTC based on data in: /content/XhetRel

        General Statistics

        Showing 13/13 rows and 4/5 columns.
        Sample NameVarsSNPIndelTs/Tv
        XhetRel | filter | A_f.vcf.gz
        4076592
        3327013
        749579
        2.09
        XhetRel | filter | A_i.vcf.gz
        4094533
        3339075
        755458
        2.09
        XhetRel | filter | A_m.vcf.gz
        4132104
        3367769
        764335
        2.09
        XhetRel | filter | C_f.vcf.gz
        3596733
        3596733
        0
        2.07
        XhetRel | filter | C_i.vcf.gz
        3298126
        3298126
        0
        2.07
        XhetRel | filter | C_m.vcf.gz
        3641478
        3641478
        0
        2.06
        XhetRel | merge | merged.vcf.gz
        5858370
        5088896
        769474
        2.07
        XhetRel | process | A_f.vcf.vcf.gz
        5598533
        4760985
        837548
        1.80
        XhetRel | process | A_i.vcf.vcf.gz
        5618495
        4775763
        842732
        1.80
        XhetRel | process | A_m.vcf.vcf.gz
        5690410
        4844605
        845805
        1.80
        XhetRel | process | C_f.vcf.vcf.gz
        4634060
        3837687
        781476
        2.02
        XhetRel | process | C_i.vcf.vcf.gz
        4617562
        3929594
        676021
        2.00
        XhetRel | process | C_m.vcf.vcf.gz
        4696072
        3889662
        791484
        2.01

        X heterozygosity

        This plot shows the fraction of heterozygous variants to total variants in X chromosome.

        Created with MultiQC

        Bcftools

        Version: 1.20

        Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.DOI: 10.1093/gigascience/giab008.

        Variant Substitution Types

        Created with MultiQC

        Variant Quality

        Created with MultiQC

        Indel Distribution

        Created with MultiQC

        Variant depths

        Read depth support distribution for called variants

        Created with MultiQC

        VCFTools

        VCFTools is a program for working with and reporting on VCF files.DOI: 10.1093/bioinformatics/btr330.

        Relatedness2

        Input: XhetRel | merge | merged.relatedness2.

        Heatmap of RELATEDNESS_PHI values from the output of vcftools relatedness2.

        RELATEDNESS_PHI gives a relatedness score between two samples. A higher score indicates a higher degree of relatedness, up to a maximum of 0.5. Samples are sorted alphabetically on each axis, and specific IDs can be found in the graph with the Highlight tab.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Bcftools1.20

        MultiQC v1.21 - Written by Phil Ewels, available on GitHub.

        This report uses HighCharts, jQuery, jQuery UI, Bootstrap, FileSaver.js and clipboard.js.