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        Note that additional data was saved in multiqc_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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        About MultiQC

        This report was generated using MultiQC, version 1.11

        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/ewels/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 2022-01-12, 17:07 based on data in: /qi/isp/climb/work/89/755aac638f77a53f6d1c3303617364

        General Statistics

        Showing 3/3 rows and 9/12 columns.
        Sample NameN50 (Kbp)Length (Mbp)OrganismContigsCDS% DuplicationGC content% PF% Adapter
        GCA009944615
        89.2Kbp
        0.1Mbp
        Genus species
        1.0
        102
        0.0%
        58.9%
        100.0%
        0.0%
        SRR12825099
        6.1Kbp
        0.0Mbp
        Genus species
        1.0
        8
        4.7%
        56.8%
        99.8%
        0.1%
        T7
        39.9Kbp
        0.0Mbp
        Genus species
        1.0
        51
        0.4%
        47.5%
        94.6%
        1.3%

        Abricate summary

        Summary of the AMR genes detected by Abricate

        Showing 3/3 rows and 6/6 columns.
        SampleNUM_FOUNDaadA1blaTEM-2dfrA1sat2_gentet(A)
        GCA009944615
        5
        100
        100
        100
        100
        100
        SRR12825099
        0
        .
        .
        .
        .
        .
        T7
        0
        .
        .
        .
        .
        .

        QUAST

        QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

        Assembly Statistics

        Showing 3/3 rows and 6/6 columns.
        Sample NameN50 (Kbp)N75 (Kbp)L50 (K)L75 (K)Largest contig (Kbp)Length (Mbp)
        GCA009944615
        89.2Kbp
        89.2Kbp
        0.0K
        0.0K
        89.2Kbp
        0.1Mbp
        SRR12825099
        6.1Kbp
        6.1Kbp
        0.0K
        0.0K
        6.1Kbp
        0.0Mbp
        T7
        39.9Kbp
        39.9Kbp
        0.0K
        0.0K
        39.9Kbp
        0.0Mbp

        Number of Contigs

        This plot shows the number of contigs found for each assembly, broken down by length.

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        Prokka

        Prokka is a software tool for the rapid annotation of prokaryotic genomes.

        This barplot shows the distribution of different types of features found in each contig.

        Prokka can detect different features:

        • CDS
        • rRNA
        • tmRNA
        • tRNA
        • miscRNA
        • signal peptides
        • CRISPR arrays

        This barplot shows you the distribution of these different types of features found in each contig.

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        fastp

        fastp An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)

        Filtered Reads

        Filtering statistics of sampled reads.

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        Insert Sizes

        Insert size estimation of sampled reads.

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        Sequence Quality

        Average sequencing quality over each base of all reads.

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        GC Content

        Average GC content over each base of all reads.

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        N content

        Average N content over each base of all reads.

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        MultiQC v1.11 - Written by Phil Ewels, available on GitHub.

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