QC Report for: GI25009_10483403

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        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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        This report was generated using MultiQC, version 1.31

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        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

        QC Report for: GI25009_10483403

        This is a MultiQC report generated from samples in the project GI25009_10483403.

        Report AI Summary
        • All 6 samples show consistent and high-quality metrics with no major QC issues.
        • 31_Anolis334_M2A_10483403_22YNTGLT4_L8 and 33_Anolis334_M2JR_10483403_22YNTGLT4_L8 exhibit moderately elevated duplication rates (54.89% and 55.76%, respectively), but remain within acceptable ranges for typical sequencing data.

        Analysis

        • All samples demonstrate excellent sequencing quality:

          • High Q30 scores across all samples (92.01-92.97%)
          • Consistent GC content (45.72-46.29%)
          • Uniform read lengths (150 bp for both R1 and R2)
          • High percentage of reads passing filter (93.54-94.75%)
          • Low adapter contamination (4.31-5.68%)

        • Duplication rates vary across samples:

          • 31_Anolis334_M2A_10483403_22YNTGLT4_L8 (54.89%) and 33_Anolis334_M2JR_10483403_22YNTGLT4_L8 (55.76%) show moderately elevated duplication
          • 32_Anolis334_M2J_10483403_22YNTGLT4_L8 (49.11%), 34_Anolis2_M2A_10483403_22YNTGLT4_L8 (48.76%), and 36_Anolis2_M2JR_10483403_22YNTGLT4_L8 (45.53%) show acceptable duplication levels
          • 35_Anolis2_M2J_10483403_22YNTGLT4_L8 shows the lowest duplication rate (39.58%)

        • Sequencing depth varies significantly across samples:

          • 32_Anolis334_M2J_10483403_22YNTGLT4_L8 has the highest coverage (942.4M reads)
          • 34_Anolis2_M2A_10483403_22YNTGLT4_L8 has the lowest coverage (295.9M reads)
          • This variation appears intentional based on sample naming (M2A vs M2J vs M2JR tissue types)

        Recommendations

        • Proceed with downstream analysis for all samples - no samples need to be excluded.
        • The moderately elevated duplication rates in 31_Anolis334_M2A_10483403_22YNTGLT4_L8 and 33_Anolis334_M2JR_10483403_22YNTGLT4_L8 are likely due to library complexity or input material limitations rather than technical failures, and should not significantly impact analysis.
        • Consider the variation in sequencing depth when performing comparative analyses between samples.
        • No adapter trimming is urgently needed given the low contamination levels, though it may be performed as part of standard preprocessing if desired.
        • The data quality is suitable for downstream genomic analyses including variant calling, RNA-seq, or other applications.
        Provider: Seqera AI, model: claude-sonnet-4-0 Chat with Seqera AI

        General Statistics

        Showing 6/6 rows and 5/9 columns.
        Sample Name% Duplication% > Q30Mb Q30 bases# ReadsGC content% PF% AdapterMean R1 LengthMean R2 Length
        31_Anolis334_M2A_10483403_22YNTGLT4_L8
        54.9%
        92.7%
        48,218.2Mb
        347,657,542M
        46.2%
        93.5%
        5.7%
        150.0bp
        150.0bp
        32_Anolis334_M2J_10483403_22YNTGLT4_L8
        49.1%
        92.6%
        130,711.4Mb
        942,435,918M
        45.8%
        94.4%
        4.3%
        150.0bp
        150.0bp
        33_Anolis334_M2JR_10483403_22YNTGLT4_L8
        55.8%
        93.0%
        76,567.5Mb
        550,040,834M
        45.7%
        94.4%
        4.4%
        150.0bp
        150.0bp
        34_Anolis2_M2A_10483403_22YNTGLT4_L8
        48.8%
        92.3%
        40,885.3Mb
        295,864,144M
        46.2%
        94.7%
        4.5%
        150.0bp
        150.0bp
        35_Anolis2_M2J_10483403_22YNTGLT4_L8
        39.6%
        92.0%
        93,039.0Mb
        675,485,694M
        46.1%
        94.2%
        4.9%
        150.0bp
        150.0bp
        36_Anolis2_M2JR_10483403_22YNTGLT4_L8
        45.5%
        92.3%
        57,597.7Mb
        416,866,270M
        46.3%
        94.3%
        4.8%
        150.0bp
        150.0bp

        Insert Length Distribution

        Insert Length Distribution

        36-Anolis2-M2JR-10483403-22YNTGLT4-L8_insert_length_distribution.png

        Selected Image

        fastp

        Version: 0.23.2

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Software Versions

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

        SoftwareVersion
        fastp0.23.2

        Raw Read 1 Base Content Summary

        Summary of base contents for all samples (each bold line is the mean for that base, and the shaded region is the standard deviation).

        Raw Read 1 Base Contents

        Base contents for individual samples.

        Read 1: base contents

        35-Anolis2-M2J-10483403-22YNTGLT4-L8.read_1_combined_content_plot.png

        Selected Image

        Raw Read 1 Quality Summary

        Summary of quality for all samples (each bold line is the mean for that base, and the shaded region is the standard deviation).

        Raw Read 1 Quality

        Quality for individual samples.

        Read 1: quality

        34-Anolis2-M2A-10483403-22YNTGLT4-L8.read_1_combined_quality_plot.png

        Selected Image

        Raw Read 2 Base Content Summary

        Summary of base contents for all samples (each bold line is the mean for that base, and the shaded region is the standard deviation).

        Raw Read 2 Base Contents

        Base contents for individual samples.

        Read 2: base contents

        31-Anolis334-M2A-10483403-22YNTGLT4-L8.read_2_combined_content_plot.png

        Selected Image

        Raw Read 2 Quality Summary

        Summary of quality for all samples (each bold line is the mean for that base, and the shaded region is the standard deviation).

        Raw Read 2 Quality

        Quality for individual samples.

        Read 2: quality

        32-Anolis334-M2J-10483403-22YNTGLT4-L8.read_2_combined_quality_plot.png

        Selected Image

        MultiQC v1.31 - Written by Phil Ewels, available on GitHub.

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