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"skip": false}, "slamdunk/tcperutrpos": {"contents": ["# slamdunk tcperutr"], "num_lines": 1, "shared": false, "skip": false}, "snippy/snippy": {"contents": ["snippy"], "num_lines": 20, "shared": false, "skip": false}, "snippy/snippy-core": {"contents_re": ["re.compile('ID\\\\tLENGTH\\\\tALIGNED\\\\tUNALIGNED\\\\tVARIANT\\\\tHET\\\\tMASKED\\\\tLOWCOV')"], "num_lines": 1, "shared": false, "skip": false}, "snpeff": {"contents": ["SnpEff_version"], "shared": false, "skip": false, "max_filesize": 5000000}, "snpsplit/old": {"contents": ["Writing allele-flagged output file to:"], "num_lines": 2, "shared": false, "skip": false}, "snpsplit/new": {"fn": "*SNPsplit_report.yaml", "shared": false, "skip": false}, "software_versions": {"fn_re": "re.compile('.+_mqc_versions\\\\.(yaml|yml)')", "shared": false, "skip": false}, "sompy": {"fn": "*.stats.csv", "contents": [",sompyversion,sompycmd"], "num_lines": 2, "shared": false, "skip": false}, "sortmerna": {"contents": ["Minimal SW score based on E-value"], "shared": false, "skip": false}, "spaceranger/count_html": [{"fn": "*.html", "contents": ["\"command\":\"Space Ranger\",\"subcommand\":\"count\""], "num_lines": 20, "shared": false, "skip": false}, {"fn": "*.html", "contents": ["\"command\": \"Space Ranger\", \"subcommand\": \"count\""], "num_lines": 20, "shared": false, "skip": false}], "stacks/gstacks": {"fn": "gstacks.log.distribs", "contents": ["BEGIN effective_coverages_per_sample"], "shared": false, "skip": false}, "stacks/populations": {"fn": "populations.log.distribs", "contents": ["BEGIN missing_samples_per_loc_prefilters"], "shared": false, "skip": false}, "stacks/sumstats": {"fn": "*.sumstats_summary.tsv", "contents": ["# Pop ID\tPrivate\tNum_Indv\tVar\tStdErr\tP\tVar"], "shared": false, "skip": false, "max_filesize": 1000000}, "star": {"fn": "*Log.final.out", "shared": false, "skip": false}, "star/genecounts": {"fn": "*ReadsPerGene.out.tab", "shared": false, "skip": false}, "supernova/report": {"fn": 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["re.compile('.*truvari.* bench.*')"], "num_lines": 10, "shared": false, "skip": false}, "umicollapse": {"contents": ["UMI collapsing finished in "], "num_lines": 100, "shared": false, "skip": false}, "umitools/extract": {"contents": ["# output generated by extract"], "num_lines": 100, "shared": false, "skip": false}, "umitools/dedup": {"contents": ["# output generated by dedup"], "num_lines": 100, "shared": false, "skip": false}, "varscan2/mpileup2snp": {"contents": ["Only SNPs will be reported"], "num_lines": 10, "shared": false, "skip": false}, "varscan2/mpileup2indel": {"contents": ["Only indels will be reported"], "num_lines": 10, "shared": false, "skip": false}, "varscan2/mpileup2cns": {"contents": ["Only variants will be reported"], "num_lines": 10, "shared": false, "skip": false}, "vcftools/relatedness2": {"fn": "*.relatedness2", "shared": false, "skip": false}, "vcftools/tstv_by_count": {"fn": "*.TsTv.count", "shared": false, "skip": false}, "vcftools/tstv_by_qual": {"fn": "*.TsTv.qual", "shared": false, "skip": false}, "vcftools/tstv_summary": {"fn": "*.TsTv.summary", "shared": false, "skip": false}, "vep/vep_html": {"fn": "*.html", "contents": ["VEP summary"], "num_lines": 10, "shared": false, "skip": false, "max_filesize": 1000000}, "vep/vep_txt": {"contents": ["[VEP run statistics]"], "num_lines": 1, "shared": false, "skip": false, "max_filesize": 100000}, "verifybamid/selfsm": {"fn": "*.selfSM", "shared": false, "skip": false}, "vg/stats": {"contents": ["Total perfect:", "Total gapless (softclips allowed):", "Speed:", "Total time:"], "num_lines": 30, "shared": false, "skip": false}, "whatshap/stats": {"contents": ["#sample\tchromosome\tfile_name\tvariants\tphased\tunphased\tsingletons"], "num_lines": 1, "shared": false, "skip": false}, "xenome": {"contents": ["B\tG\tH\tM\tcount\tpercent\tclass"], "num_lines": 2, "shared": false, "skip": false}, "xengsort": {"contents": ["# Xengsort classify"], "num_lines": 2, "shared": false, "skip": false}, "ataqv": {"fn": "*.json", "contents": ["ataqv_version"], "num_lines": 10, "shared": false, "skip": false}, "mosaicatcher": {"fn": "*.mosaicatcher_info_raw.txt", "shared": false, "skip": false}}, "parquet_format": "long"}
[{"name": "NanoStat", "anchor": "nanostat", "info": "<p>Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).</p>", "intro": "<p>Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).<a href=\"https://github.com/wdecoster/nanostat/\" class=\"text-muted ms-2 small\" target=\"_blank\">https://github.com/wdecoster/nanostat</a>; <a href=\"https://github.com/wdecoster/nanoplot/\" class=\"text-muted ms-2 small\" target=\"_blank\">https://github.com/wdecoster/nanoplot</a><span class=\"text-muted small ms-2\">DOI:  <a class=\"module-doi text-muted\" data-doi=\"10.1093/bioinformatics/bty149\" data-bs-toggle=\"popover\" href=\"https://doi.org/10.1093/bioinformatics/bty149\" target=\"_blank\">10.1093/bioinformatics/bty149</a></span></p>Programs are part of the NanoPack family for summarising results of sequencing on Oxford Nanopore methods (MinION, PromethION etc.)", "comment": "", "sections": [{"name": "Summary Statistics (FASTQ)", "anchor": "nanostat_fastq_stats", "id": "nanostat_fastq_stats", "description": "", "module": "NanoStat", "module_anchor": "nanostat", "module_info": "<p>Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).</p>", "comment": "", "helptext": "", "content_before_plot": "", "content": "", "plot": "<div id='mqc_violintable_wrapper_nanostat_fastq_stats_table' style='display: none;'><div class=\"mqc_hcplot_plotgroup\"><div class='row' style='align-items: center;'>\n<div class='col-12'>\n<button  class=\"btn btn-outline-secondary btn-sm mqc-violin-to-table \" data-table-anchor=\"nanostat_fastq_stats_table_table\" data-violin-anchor=\"nanostat_fastq_stats_table\" data-plot-anchor=\"nanostat_fastq_stats_table\" ><svg xmlns=\"http://www.w3.org/2000/svg\" width=\"16\" height=\"16\" viewBox=\"0 0 24 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data-bs-toggle=\"tooltip\"\n                    title=\"Copy table data for use with AI tools like ChatGPT\"\n                >\n                    <svg width=\"11\" height=\"10\" viewBox=\"0 0 17 15\" fill=\"currentColor\" xmlns=\"http://www.w3.org/2000/svg\">\n  <path\n    d=\"M6.4375 7L7.9375 1.5L9.4375 7L14.9375 8.5L9.4375 10.5L7.9375 15.5L6.4375 10.5L0.9375 8.5L6.4375 7Z\"\n    stroke=\"currentColor\"\n    stroke-width=\"0.75\"\n    stroke-linejoin=\"round\"\n  ></path>\n  <path\n    d=\"M13.1786 2.82143L13.5 4L13.8214 2.82143L15 2.5L13.8214 2.07143L13.5 1L13.1786 2.07143L12 2.5L13.1786 2.82143Z\"\n    stroke=\"var(--bs-text-emphasis)\"\n    stroke-width=\"0.5\"\n    stroke-linejoin=\"round\"\n  ></path>\n</svg>\n\n                    <span class=\"button-text\">Copy Prompt</span>\n                </button>\n                <button\n                    class=\"btn btn-outline-secondary btn-sm ai-generate-button ai-generate-button-table ai-generate-button-wrapper\"\n                    data-response-div=\"nanostat_fastq_stats_ai_summary_response\"\n                    data-error-div=\"nanostat_fastq_stats_ai_summary_error\"\n                    data-disclaimer-div=\"nanostat_fastq_stats_ai_summary_disclaimer\"\n                    data-continue-in-chat-button=\"nanostat_fastq_stats_ai_summary_continue_in_chat\"\n                    data-detailed-analysis-div=\"nanostat_fastq_stats_ai_summary_detailed_analysis_response\"\n                    data-wrapper-div=\"nanostat_fastq_stats_ai_summary_wrapper\"\n                    data-section-anchor=\"nanostat_fastq_stats\"\n                    data-plot-anchor=\"nanostat_fastq_stats_table\"\n                    data-module-anchor=\"nanostat\"\n                    data-plot-view=\"table\"\n                    data-action=\"generate\"\n                    data-clear-text=\"Clear summary\"\n                    type=\"button\"\n                    data-bs-toggle=\"tooltip\"\n                    aria-controls=\"nanostat_fastq_stats_table_table_ai_summary_wrapper\"\n                    title=\"Dynamically generate AI summary for this table\"\n                >\n                    <svg width=\"11\" height=\"10\" viewBox=\"0 0 17 15\" fill=\"currentColor\" xmlns=\"http://www.w3.org/2000/svg\">\n  <path\n    d=\"M6.4375 7L7.9375 1.5L9.4375 7L14.9375 8.5L9.4375 10.5L7.9375 15.5L6.4375 10.5L0.9375 8.5L6.4375 7Z\"\n    stroke=\"currentColor\"\n    stroke-width=\"0.75\"\n    stroke-linejoin=\"round\"\n  ></path>\n  <path\n    d=\"M13.1786 2.82143L13.5 4L13.8214 2.82143L15 2.5L13.8214 2.07143L13.5 1L13.1786 2.07143L12 2.5L13.1786 2.82143Z\"\n    stroke=\"var(--bs-text-emphasis)\"\n    stroke-width=\"0.5\"\n    stroke-linejoin=\"round\"\n  ></path>\n</svg>\n\n                    <span class=\"button-text\">Summarize table</span>\n                </button>\n            </div>\n            \n</div>\n</div>\n        \n        <div id=\"nanostat_fastq_stats_table_table_container\" class=\"mqc_table_container\">\n            <div class=\"table-responsive mqc-table-responsive \" data-collapsed=\"false\">\n                <table id=\"nanostat_fastq_stats_table_table\" class=\"table table-sm mqc_table mqc_per_sample_table\" data-title=\"NanoStat fastq\" data-sortlist=\"\">\n        <thead><tr><th class=\"rowheader\">Sample Name</th><th id=\"header_nanostat-Median_read_length_fastq\" class=\"nanostat-Median_read_length_fastq\" data-dmax=\"7634.1\" data-dmin=\"0\" data-namespace=\"\"  data-shared-key=nucleotides><span class=\"mqc_table_tooltip\" title=\"Median read length (bp)\" data-html=\"true\">Median length</span></th><th id=\"header_nanostat-Mean_read_length_fastq\" class=\"nanostat-Mean_read_length_fastq column-hidden\" data-dmax=\"7634.1\" data-dmin=\"0\" data-namespace=\"\"  data-shared-key=nucleotides><span class=\"mqc_table_tooltip\" title=\"Mean read length (bp)\" data-html=\"true\">Mean length</span></th><th id=\"header_nanostat-Read_length_N50_fastq\" class=\"nanostat-Read_length_N50_fastq\" data-dmax=\"8296.0\" data-dmin=\"0\" data-namespace=\"\" ><span class=\"mqc_table_tooltip\" title=\"Read length N50\" data-html=\"true\">Read N50</span></th><th id=\"header_nanostat-Median_read_quality_fastq\" class=\"nanostat-Median_read_quality_fastq\" data-dmax=\"39.8\" data-dmin=\"0\" data-namespace=\"\"  data-shared-key=phred_score><span class=\"mqc_table_tooltip\" title=\"Median read quality (Phred scale)\" data-html=\"true\">Median Qual</span></th><th id=\"header_nanostat-Mean_read_quality_fastq\" class=\"nanostat-Mean_read_quality_fastq column-hidden\" data-dmax=\"39.8\" data-dmin=\"0\" data-namespace=\"\"  data-shared-key=phred_score><span class=\"mqc_table_tooltip\" title=\"Mean read quality (Phred scale)\" data-html=\"true\">Mean Qual</span></th><th id=\"header_nanostat-Number_of_reads_fastq\" class=\"nanostat-Number_of_reads_fastq\" data-dmax=\"5899.468\" data-dmin=\"0.0\" data-namespace=\"\"  data-shared-key=long_read_count><span class=\"mqc_table_tooltip\" title=\"Number of reads (thousands)\" data-html=\"true\"># Reads (K)</span></th><th id=\"header_nanostat-Total_bases_fastq\" class=\"nanostat-Total_bases_fastq\" data-dmax=\"37377.010531\" data-dmin=\"0.0\" data-namespace=\"\"  data-shared-key=base_count><span class=\"mqc_table_tooltip\" title=\"Total bases (millions)\" data-html=\"true\">Total Bases (Mb)</span></th></tr></thead><tbody><tr data-sample-group=\"bc2041\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2041\"><span class=\"th-sample-name\" data-original-sn=\"bc2041\">bc2041</span></th><td data-sorting-val=\"6516.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:85.35387275513813%; background-color:rgba(130,23,129,0.3) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>516<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"7634.1\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:100.0%; background-color:rgba(63,0,125,0.29999999999999993) !important;\"></span><span class=\"val\">7<span class=\"mqc_small_space\"></span>634<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"8296.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:100.0%; background-color:rgba(73,0,106,0.3) !important;\"></span><span class=\"val\">8<span class=\"mqc_small_space\"></span>296<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"38.8\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:97.48743718592965%; background-color:rgba(6,116,61,0.29999999999999993) !important;\"></span><span class=\"val\">38.8</span></div></td><td data-sorting-val=\"29.0\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:72.8643216080402%; background-color:rgba(167,214,114,0.2999999999999998) !important;\"></span><span class=\"val\">29.0</span></div></td><td data-sorting-val=\"3258.991\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:55.24211674679819%; background-color:rgba(96,186,109,0.29999999999999993) !important;\"></span><span class=\"val\">3<span class=\"mqc_small_space\"></span>259.0<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"24879.406312\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:66.56339273405867%; background-color:rgba(152,214,205,0.2999999999999997) !important;\"></span><span class=\"val\">24<span class=\"mqc_small_space\"></span>879.4<span class='mqc_small_space'></span>Mb</span></div></td></tr><tr data-sample-group=\"bc2068\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2068\"><span class=\"th-sample-name\" data-original-sn=\"bc2068\">bc2068</span></th><td data-sorting-val=\"3778.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:49.488479323037424%; background-color:rgba(140,151,198,0.2999999999999999) !important;\"></span><span class=\"val\">3<span class=\"mqc_small_space\"></span>778<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"4224.0\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:55.33068731088143%; background-color:rgba(145,141,194,0.2999999999999999) !important;\"></span><span class=\"val\">4<span class=\"mqc_small_space\"></span>224<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"4541.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:54.73722275795564%; background-color:rgba(237,84,157,0.3) !important;\"></span><span class=\"val\">4<span class=\"mqc_small_space\"></span>541<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"39.8\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:100.0%; background-color:rgba(0,104,55,0.29999999999999993) !important;\"></span><span class=\"val\">39.8</span></div></td><td data-sorting-val=\"30.2\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:75.87939698492463%; background-color:rgba(150,203,93,0.29999999999999993) !important;\"></span><span class=\"val\">30.2</span></div></td><td data-sorting-val=\"3287.622\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:55.72743169384087%; background-color:rgba(94,185,108,0.29999999999999993) !important;\"></span><span class=\"val\">3<span class=\"mqc_small_space\"></span>287.6<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"13887.000171\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:37.15385466550971%; background-color:rgba(239,221,175,0.2999999999999999) !important;\"></span><span class=\"val\">13<span class=\"mqc_small_space\"></span>887.0<span class='mqc_small_space'></span>Mb</span></div></td></tr><tr data-sample-group=\"bc2069\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2069\"><span class=\"th-sample-name\" data-original-sn=\"bc2069\">bc2069</span></th><td data-sorting-val=\"6046.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:79.19728586211865%; background-color:rgba(133,48,145,0.2999999999999999) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>046<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6836.2\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:89.54821131502075%; background-color:rgba(80,32,140,0.29999999999999993) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>836<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"7356.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:88.66923818707811%; background-color:rgba(117,0,117,0.2999999999999999) !important;\"></span><span class=\"val\">7<span class=\"mqc_small_space\"></span>356<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"38.9\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:97.73869346733669%; background-color:rgba(5,114,60,0.2999999999999999) !important;\"></span><span class=\"val\">38.9</span></div></td><td data-sorting-val=\"29.0\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:72.8643216080402%; background-color:rgba(167,214,114,0.2999999999999998) !important;\"></span><span class=\"val\">29.0</span></div></td><td data-sorting-val=\"1348.642\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:22.8604002937214%; background-color:rgba(222,242,166,0.29999999999999977) !important;\"></span><span class=\"val\">1<span class=\"mqc_small_space\"></span>348.6<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"9219.541519999999\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:24.666342730522636%; background-color:rgba(205,159,82,0.3) !important;\"></span><span class=\"val\">9<span class=\"mqc_small_space\"></span>219.5<span class='mqc_small_space'></span>Mb</span></div></td></tr><tr data-sample-group=\"bc2070\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2070\"><span class=\"th-sample-name\" data-original-sn=\"bc2070\">bc2070</span></th><td data-sorting-val=\"5499.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:72.0320666483279%; background-color:rgba(136,74,161,0.30000000000000004) !important;\"></span><span class=\"val\">5<span class=\"mqc_small_space\"></span>499<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6180.7\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:80.96173746741593%; background-color:rgba(95,60,153,0.2999999999999999) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>181<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6549.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:78.94165863066537%; background-color:rgba(157,1,123,0.2999999999999999) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>549<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"39.2\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:98.4924623115578%; background-color:rgba(3,111,58,0.2999999999999999) !important;\"></span><span class=\"val\">39.2</span></div></td><td data-sorting-val=\"29.4\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:73.86934673366834%; background-color:rgba(161,210,107,0.2999999999999999) !important;\"></span><span class=\"val\">29.4</span></div></td><td data-sorting-val=\"3019.621\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:51.18463224141567%; background-color:rgba(114,195,118,0.2999999999999999) !important;\"></span><span class=\"val\">3<span class=\"mqc_small_space\"></span>019.6<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"18663.483819999998\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:49.933056589747196%; background-color:rgba(245,244,244,0.3) !important;\"></span><span class=\"val\">18<span class=\"mqc_small_space\"></span>663.5<span class='mqc_small_space'></span>Mb</span></div></td></tr><tr data-sample-group=\"bc2071\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2071\"><span class=\"th-sample-name\" data-original-sn=\"bc2071\">bc2071</span></th><td data-sorting-val=\"5349.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:70.06719849098126%; background-color:rgba(137,81,164,0.2999999999999999) !important;\"></span><span class=\"val\">5<span class=\"mqc_small_space\"></span>349<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6036.4\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:79.07153430004847%; background-color:rgba(98,67,156,0.3) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>036<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6439.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:77.61571841851494%; background-color:rgba(163,1,124,0.29999999999999993) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>439<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"39.3\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:98.74371859296483%; background-color:rgba(3,110,58,0.29999999999999993) !important;\"></span><span class=\"val\">39.3</span></div></td><td data-sorting-val=\"29.4\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:73.86934673366834%; background-color:rgba(161,210,107,0.2999999999999999) !important;\"></span><span class=\"val\">29.4</span></div></td><td data-sorting-val=\"3405.966\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:57.73344308334243%; background-color:rgba(85,181,103,0.29999999999999993) !important;\"></span><span class=\"val\">3<span class=\"mqc_small_space\"></span>406.0<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"20559.935456\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:55.00690173963447%; background-color:rgba(221,239,236,0.2999999999999994) !important;\"></span><span class=\"val\">20<span class=\"mqc_small_space\"></span>559.9<span class='mqc_small_space'></span>Mb</span></div></td></tr><tr data-sample-group=\"bc2072\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2072\"><span class=\"th-sample-name\" data-original-sn=\"bc2072\">bc2072</span></th><td data-sorting-val=\"5599.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:73.34197875322566%; background-color:rgba(136,70,159,0.2999999999999999) !important;\"></span><span class=\"val\">5<span class=\"mqc_small_space\"></span>599<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6332.9\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:82.95542369107032%; background-color:rgba(91,54,150,0.3) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>333<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6759.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:81.47299903567985%; background-color:rgba(147,1,122,0.29999999999999993) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>759<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"39.2\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:98.4924623115578%; background-color:rgba(3,111,58,0.2999999999999999) !important;\"></span><span class=\"val\">39.2</span></div></td><td data-sorting-val=\"29.3\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:73.61809045226131%; background-color:rgba(163,211,109,0.29999999999999966) !important;\"></span><span class=\"val\">29.3</span></div></td><td data-sorting-val=\"2312.2870000000003\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:39.19483926347257%; background-color:rgba(165,217,139,0.2999999999999998) !important;\"></span><span class=\"val\">2<span class=\"mqc_small_space\"></span>312.3<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"14643.512853999999\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:39.17785998924355%; background-color:rgba(244,228,189,0.2999999999999987) !important;\"></span><span class=\"val\">14<span class=\"mqc_small_space\"></span>643.5<span class='mqc_small_space'></span>Mb</span></div></td></tr><tr data-sample-group=\"bc2073\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2073\"><span class=\"th-sample-name\" data-original-sn=\"bc2073\">bc2073</span></th><td data-sorting-val=\"5693.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:74.57329613182955%; background-color:rgba(136,66,157,0.29999999999999993) !important;\"></span><span class=\"val\">5<span class=\"mqc_small_space\"></span>693<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6487.9\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:84.98578745366186%; background-color:rgba(88,47,147,0.29999999999999993) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>488<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6960.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:83.89585342333655%; background-color:rgba(136,1,121,0.29999999999999993) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>960<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"39.1\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:98.24120603015076%; background-color:rgba(4,112,59,0.29999999999999993) !important;\"></span><span class=\"val\">39.1</span></div></td><td data-sorting-val=\"29.2\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:73.36683417085428%; background-color:rgba(164,212,110,0.2999999999999997) !important;\"></span><span class=\"val\">29.2</span></div></td><td data-sorting-val=\"3641.315\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:61.72276890051781%; background-color:rgba(68,172,94,0.3) !important;\"></span><span class=\"val\">3<span class=\"mqc_small_space\"></span>641.3<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"23624.544038\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:63.20608230132828%; background-color:rgba(176,224,217,0.2999999999999998) !important;\"></span><span class=\"val\">23<span class=\"mqc_small_space\"></span>624.5<span class='mqc_small_space'></span>Mb</span></div></td></tr><tr data-sample-group=\"bc2096\" data-table-id=\"nanostat_fastq_stats_table\" class=\"\"><th class=\"rowheader\" data-sorting-val=\"bc2096\"><span class=\"th-sample-name\" data-original-sn=\"bc2096\">bc2096</span></th><td data-sorting-val=\"5216.0\" class=\"data-coloured nanostat-Median_read_length_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:68.32501539146722%; background-color:rgba(138,87,167,0.29999999999999993) !important;\"></span><span class=\"val\">5<span class=\"mqc_small_space\"></span>216<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"6335.7\" class=\"data-coloured nanostat-Mean_read_length_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:82.99210123000746%; background-color:rgba(91,54,150,0.30000000000000004) !important;\"></span><span class=\"val\">6<span class=\"mqc_small_space\"></span>336<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"7191.0\" class=\"data-coloured nanostat-Read_length_N50_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:86.68032786885246%; background-color:rgba(125,1,119,0.3) !important;\"></span><span class=\"val\">7<span class=\"mqc_small_space\"></span>191<span class='mqc_small_space'></span>bp</span></div></td><td data-sorting-val=\"38.8\" class=\"data-coloured nanostat-Median_read_quality_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:97.48743718592965%; background-color:rgba(6,116,61,0.29999999999999993) !important;\"></span><span class=\"val\">38.8</span></div></td><td data-sorting-val=\"29.1\" class=\"data-coloured nanostat-Mean_read_quality_fastq  column-hidden\"><div class=\"wrapper\"><span class=\"bar\" style=\"width:73.11557788944725%; background-color:rgba(166,213,112,0.3) !important;\"></span><span class=\"val\">29.1</span></div></td><td data-sorting-val=\"5899.468\" class=\"data-coloured nanostat-Number_of_reads_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:100.0%; background-color:rgba(0,69,41,0.29999999999999993) !important;\"></span><span class=\"val\">5<span class=\"mqc_small_space\"></span>899.5<span class='mqc_small_space'></span>K</span></div></td><td data-sorting-val=\"37377.010531\" class=\"data-coloured nanostat-Total_bases_fastq \"><div class=\"wrapper\"><span class=\"bar\" style=\"width:100.0%; background-color:rgba(0,60,48,0.3) !important;\"></span><span class=\"val\">37<span class=\"mqc_small_space\"></span>377.0<span class='mqc_small_space'></span>Mb</span></div></td></tr></tbody></table></div></div></div>\n    <!-- MultiQC Table Columns Modal -->\n    <div class=\"modal fade mqc_config_modal\" id=\"nanostat_fastq_stats_table_table_config_modal\" tabindex=\"-1\">\n      <div class=\"modal-dialog modal-xl\">\n        <div class=\"modal-content\">\n          <div class=\"modal-header\">\n            <h4 class=\"modal-title\">NanoStat fastq: Columns</h4>\n            <button type=\"button\" class=\"btn-close\" data-bs-dismiss=\"modal\" aria-label=\"Close\"></button>\n          </div>\n          <div class=\"modal-body\">\n            <p>Uncheck the tick box to hide columns. Click and drag the handle on the left to change order. Table ID: <code>nanostat_fastq_stats_table_table</code></p>\n            <p>\n                <button class=\"btn btn-outline-secondary btn-sm mqc_config_modal_bulk_visible\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table' data-action=\"showAll\">Show All</button>\n                <button class=\"btn btn-outline-secondary btn-sm mqc_config_modal_bulk_visible\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table' data-action=\"showNone\">Show None</button>\n            </p>\n            <table class=\"table mqc_table mqc_sortable mqc_config_modal_table\" id=\"nanostat_fastq_stats_table_table_config_modal_table\" data-title=\"NanoStat fastq\">\n              <thead>\n                <tr>\n                  <th class=\"sorthandle\" style=\"text-align:center;\">Sort</th>\n                  <th style=\"text-align:center;\">Visible</th>\n                  <th>Group</th>\n                  <th>Column</th>\n                  <th>Description</th>\n                  <th>ID</th>\n                  <th>Scale</th>\n                </tr>\n              </thead>\n              <tbody>\n                \n        <tr class=\"nanostat-Median_read_length_fastq\" style=\"background-color: rgba(None, 0.15);\">\n          <td class=\"sorthandle ui-sortable-handle\">||</span></td>\n          <td style=\"text-align:center;\">\n            <input class=\"mqc_table_col_visible\" type=\"checkbox\"  checked=\"checked\" value=\"nanostat-Median_read_length_fastq\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table'>\n          </td>\n          <td></td>\n          <td>Median length</td>\n          <td>Median read length (bp)</td>\n          <td><code>nanostat-Median_read_length_fastq</code></td>\n          <td>nucleotides</td>\n        </tr>\n        <tr class=\"nanostat-Mean_read_length_fastq text-muted\" style=\"background-color: rgba(None, 0.15);\">\n          <td class=\"sorthandle ui-sortable-handle\">||</span></td>\n          <td style=\"text-align:center;\">\n            <input class=\"mqc_table_col_visible\" type=\"checkbox\"  value=\"nanostat-Mean_read_length_fastq\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table'>\n          </td>\n          <td></td>\n          <td>Mean length</td>\n          <td>Mean read length (bp)</td>\n          <td><code>nanostat-Mean_read_length_fastq</code></td>\n          <td>nucleotides</td>\n        </tr>\n        <tr class=\"nanostat-Read_length_N50_fastq\" style=\"background-color: rgba(None, 0.15);\">\n          <td class=\"sorthandle ui-sortable-handle\">||</span></td>\n          <td style=\"text-align:center;\">\n            <input class=\"mqc_table_col_visible\" type=\"checkbox\"  checked=\"checked\" value=\"nanostat-Read_length_N50_fastq\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table'>\n          </td>\n          <td></td>\n          <td>Read N50</td>\n          <td>Read length N50</td>\n          <td><code>nanostat-Read_length_N50_fastq</code></td>\n          <td></td>\n        </tr>\n        <tr class=\"nanostat-Median_read_quality_fastq\" style=\"background-color: rgba(None, 0.15);\">\n          <td class=\"sorthandle ui-sortable-handle\">||</span></td>\n          <td style=\"text-align:center;\">\n            <input class=\"mqc_table_col_visible\" type=\"checkbox\"  checked=\"checked\" value=\"nanostat-Median_read_quality_fastq\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table'>\n          </td>\n          <td></td>\n          <td>Median Qual</td>\n          <td>Median read quality (Phred scale)</td>\n          <td><code>nanostat-Median_read_quality_fastq</code></td>\n          <td>phred_score</td>\n        </tr>\n        <tr class=\"nanostat-Mean_read_quality_fastq text-muted\" style=\"background-color: rgba(None, 0.15);\">\n          <td class=\"sorthandle ui-sortable-handle\">||</span></td>\n          <td style=\"text-align:center;\">\n            <input class=\"mqc_table_col_visible\" type=\"checkbox\"  value=\"nanostat-Mean_read_quality_fastq\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table'>\n          </td>\n          <td></td>\n          <td>Mean Qual</td>\n          <td>Mean read quality (Phred scale)</td>\n          <td><code>nanostat-Mean_read_quality_fastq</code></td>\n          <td>phred_score</td>\n        </tr>\n        <tr class=\"nanostat-Number_of_reads_fastq\" style=\"background-color: rgba(None, 0.15);\">\n          <td class=\"sorthandle ui-sortable-handle\">||</span></td>\n          <td style=\"text-align:center;\">\n            <input class=\"mqc_table_col_visible\" type=\"checkbox\"  checked=\"checked\" value=\"nanostat-Number_of_reads_fastq\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table'>\n          </td>\n          <td></td>\n          <td># Reads (K)</td>\n          <td>Number of reads (thousands)</td>\n          <td><code>nanostat-Number_of_reads_fastq</code></td>\n          <td>long_read_count</td>\n        </tr>\n        <tr class=\"nanostat-Total_bases_fastq\" style=\"background-color: rgba(None, 0.15);\">\n          <td class=\"sorthandle ui-sortable-handle\">||</span></td>\n          <td style=\"text-align:center;\">\n            <input class=\"mqc_table_col_visible\" type=\"checkbox\"  checked=\"checked\" value=\"nanostat-Total_bases_fastq\" data-table-anchor='nanostat_fastq_stats_table_table' data-violin-anchor='nanostat_fastq_stats_table'>\n          </td>\n          <td></td>\n          <td>Total Bases (Mb)</td>\n          <td>Total bases (millions)</td>\n          <td><code>nanostat-Total_bases_fastq</code></td>\n          <td>base_count</td>\n        </tr>\n              </tbody>\n            </table>\n        </div>\n        <div class=\"modal-footer\"> <button type=\"button\" class=\"btn btn-outline-secondary\" data-bs-dismiss=\"modal\">Close</button> </div>\n    </div> </div> </div>", "print_section": true, "plot_anchor": "nanostat_fastq_stats_table", "ai_summary": "", "status_bar_html": ""}, {"name": "Reads by quality", "anchor": "nanostat_read_qualities", "id": "nanostat_read_qualities", "description": "<p>Read counts categorised by read quality (Phred score).</p>", "module": "NanoStat", "module_anchor": "nanostat", "module_info": "<p>Reports various statistics for long read dataset in FASTQ, BAM, or albacore sequencing summary format (supports NanoPack; NanoPlot, NanoComp).</p>", "comment": "", "helptext": "<p>Sequencing machines assign each generated read a quality score using the\n<a href=\"https://en.wikipedia.org/wiki/Phred_quality_score\">Phred scale</a>.\nThe phred score represents the liklelyhood that a given read contains errors.\nHigh quality reads have a high score.</p>", "content_before_plot": "", "content": "", "plot": "<div class=\"mqc_hcplot_plotgroup\"><div class='row' style='align-items: center;'>\n<div class='col-12'>\n<button  class=\"btn btn-outline-secondary btn-sm interactive-switch-group percent-switch \" data-plot-anchor=\"nanostat_quality_dist\" >Percentages</button>\n\n<button title=\"Show export options\" class=\"btn btn-outline-secondary btn-sm export-plot \" data-plot-anchor=\"nanostat_quality_dist\" data-type=\"bar plot\" data-toggle=\"tooltip\" style=\"float: right; margin-left: 5px;\"><svg width=\"11\" height=\"11\" viewBox=\"0 0 24 17\" fill=\"none\" xmlns=\"http://www.w3.org/2000/svg\"><path d=\"M19 9h-4V3H9v6H5l7 7 7-7zM5 18v2h14v-2H5z\" fill=\"currentColor\"/></svg> Export...</button>\n\n\n            <div class=\"ai-plot-buttons-container\" style=\"float: right;\">\n                <button\n                    class=\"btn btn-outline-secondary btn-sm ai-copy-content ai-copy-content-plot ai-copy-button-wrapper\"\n                    style=\"margin-left: 1px;\"\n                    data-section-anchor=\"nanostat_read_qualities\"\n                    data-plot-anchor=\"nanostat_quality_dist\"\n                    data-module-anchor=\"nanostat\"\n                    data-view=\"plot\"\n                    type=\"button\"\n                    data-bs-toggle=\"tooltip\"\n                    title=\"Copy plot data for use with AI tools like ChatGPT\"\n                >\n                    <svg width=\"11\" height=\"10\" viewBox=\"0 0 17 15\" fill=\"currentColor\" xmlns=\"http://www.w3.org/2000/svg\">\n  <path\n    d=\"M6.4375 7L7.9375 1.5L9.4375 7L14.9375 8.5L9.4375 10.5L7.9375 15.5L6.4375 10.5L0.9375 8.5L6.4375 7Z\"\n    stroke=\"currentColor\"\n    stroke-width=\"0.75\"\n    stroke-linejoin=\"round\"\n  ></path>\n  <path\n    d=\"M13.1786 2.82143L13.5 4L13.8214 2.82143L15 2.5L13.8214 2.07143L13.5 1L13.1786 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data-section-anchor=\"nanostat_read_qualities\"\n                    data-view=\"plot\"\n                    data-action=\"generate\"\n                    data-clear-text=\"Clear summary\"\n                    type=\"button\"\n                    data-bs-toggle=\"tooltip\"\n                    aria-controls=\"nanostat_read_qualities_ai_summary_wrapper\"\n                >\n                    <svg width=\"11\" height=\"10\" viewBox=\"0 0 17 15\" fill=\"currentColor\" xmlns=\"http://www.w3.org/2000/svg\">\n  <path\n    d=\"M6.4375 7L7.9375 1.5L9.4375 7L14.9375 8.5L9.4375 10.5L7.9375 15.5L6.4375 10.5L0.9375 8.5L6.4375 7Z\"\n    stroke=\"currentColor\"\n    stroke-width=\"0.75\"\n    stroke-linejoin=\"round\"\n  ></path>\n  <path\n    d=\"M13.1786 2.82143L13.5 4L13.8214 2.82143L15 2.5L13.8214 2.07143L13.5 1L13.1786 2.07143L12 2.5L13.1786 2.82143Z\"\n    stroke=\"var(--bs-text-emphasis)\"\n    stroke-width=\"0.5\"\n    stroke-linejoin=\"round\"\n  ></path>\n</svg>\n\n                    <span class=\"button-text\">Summarize plot</span>\n                </button>\n            </div>\n            \n</div>\n</div>\n\n\n        <div class=\"hc-plot-wrapper hc-bar plot-wrapper\" id=\"nanostat_quality_dist-wrapper\" style=\"height:387px\">\n            <div\n                id=\"nanostat_quality_dist\"\n                class=\"hc-plot hc-bar plot-plot not_loaded not_rendered \">\n            </div>\n            <div class=\"created-with-multiqc\">Created with MultiQC</div>\n        </div></div>", "print_section": true, "plot_anchor": "nanostat_quality_dist", "ai_summary": "", "status_bar_html": ""}], "versions": {}}]