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      "isPartOf": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ],
      "command": "samtools index results/sorted/C.bam",
      "startTime": "2026-09-11T13:13:21.911116-04:00",
      "endTime": "2026-09-11T13:13:22.527135-04:00"
    },
    {
      "@id": "ark:59853/computation-samtools-sort-sample-a-3bd01fd",
      "@type": [
        "prov:Activity",
        "https://w3id.org/EVI#Computation"
      ],
      "name": "samtools_sort (sample=A)",
      "description": "Snakemake job for rule 'samtools_sort' with wildcards {'sample': 'A'}",
      "runBy": "Example Researcher",
      "dateCreated": "2026-09-11T13:13:20.095059-04:00",
      "usedSoftware": [
        {
          "@id": "ark:59853/software-samtools-sort-65f7fb4"
        }
      ],
      "usedDataset": [
        {
          "@id": "ark:59853/dataset-a-bam-016e31c"
        }
      ],
      "generated": [
        {
          "@id": "ark:59853/dataset-a-bam-c0907f3"
        }
      ],
      "isPartOf": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ],
      "command": "samtools sort -T results/sorted/A -O bam results/mapped/A.bam > results/sorted/A.bam 2> logs/samtools_sort/A.log",
      "startTime": "2026-09-11T13:13:20.095059-04:00",
      "endTime": "2026-09-11T13:13:20.875083-04:00"
    },
    {
      "@id": "ark:59853/computation-samtools-sort-sample-b-74d837f",
      "@type": [
        "prov:Activity",
        "https://w3id.org/EVI#Computation"
      ],
      "name": "samtools_sort (sample=B)",
      "description": "Snakemake job for rule 'samtools_sort' with wildcards {'sample': 'B'}",
      "runBy": "Example Researcher",
      "dateCreated": "2026-09-11T13:13:20.099059-04:00",
      "usedSoftware": [
        {
          "@id": "ark:59853/software-samtools-sort-65f7fb4"
        }
      ],
      "usedDataset": [
        {
          "@id": "ark:59853/dataset-b-bam-6b7c70e"
        }
      ],
      "generated": [
        {
          "@id": "ark:59853/dataset-b-bam-cbee9ae"
        }
      ],
      "isPartOf": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ],
      "command": "samtools sort -T results/sorted/B -O bam results/mapped/B.bam > results/sorted/B.bam 2> logs/samtools_sort/B.log",
      "startTime": "2026-09-11T13:13:20.099059-04:00",
      "endTime": "2026-09-11T13:13:20.895084-04:00"
    },
    {
      "@id": "ark:59853/computation-samtools-sort-sample-c-1828156",
      "@type": [
        "prov:Activity",
        "https://w3id.org/EVI#Computation"
      ],
      "name": "samtools_sort (sample=C)",
      "description": "Snakemake job for rule 'samtools_sort' with wildcards {'sample': 'C'}",
      "runBy": "Example Researcher",
      "dateCreated": "2026-09-11T13:13:21.155092-04:00",
      "usedSoftware": [
        {
          "@id": "ark:59853/software-samtools-sort-65f7fb4"
        }
      ],
      "usedDataset": [
        {
          "@id": "ark:59853/dataset-c-bam-3e0f2ac"
        }
      ],
      "generated": [
        {
          "@id": "ark:59853/dataset-c-bam-7ccb833"
        }
      ],
      "isPartOf": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ],
      "command": "samtools sort -T results/sorted/C -O bam results/mapped/C.bam > results/sorted/C.bam 2> logs/samtools_sort/C.log",
      "startTime": "2026-09-11T13:13:21.155092-04:00",
      "endTime": "2026-09-11T13:13:21.887115-04:00"
    },
    {
      "@id": "ark:59853/computation-variant-summary-d29c059",
      "@type": [
        "prov:Activity",
        "https://w3id.org/EVI#Computation"
      ],
      "name": "variant_summary",
      "description": "Snakemake job for rule 'variant_summary'",
      "runBy": "Example Researcher",
      "dateCreated": "2026-09-11T13:13:23.355160-04:00",
      "usedSoftware": [
        {
          "@id": "ark:59853/software-variant-summary-aea5e1b"
        }
      ],
      "usedDataset": [
        {
          "@id": "ark:59853/dataset-all-vcf-637cf3e"
        }
      ],
      "generated": [
        {
          "@id": "ark:59853/dataset-variant-summary-tsv-71310c4"
        }
      ],
      "isPartOf": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ],
      "command": "(printf 'chrom\\tpos\\tref\\talt\\tquality\\tdepth\\n'; bcftools query -f '%CHROM\\t%POS\\t%REF\\t%ALT\\t%QUAL\\t%INFO/DP\\n' results/calls/all.vcf) > results/calls/variant_summary.tsv",
      "startTime": "2026-09-11T13:13:23.355160-04:00",
      "endTime": "2026-09-11T13:13:23.999181-04:00"
    },
    {
      "@id": "ark:59853/software-snakefile-68f3c95",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "Snakefile",
      "author": "Example Researcher",
      "description": "Snakemake workflow definition 'Snakefile' for this run",
      "format": "snakemake",
      "contentUrl": "Snakefile",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ]
    },
    {
      "@id": "ark:59853/software-snakemake-059f146",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "Snakemake",
      "author": "Johannes K\u00f6ster",
      "description": "Snakemake workflow management system (https://snakemake.github.io/)",
      "format": "application/x-python",
      "version": "9.26.1",
      "contentUrl": "https://github.com/snakemake/snakemake",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ]
    },
    {
      "@id": "ark:59853/software-bcftools-call-7c9ed78",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "bcftools_call",
      "author": "Example Researcher",
      "description": "(bcftools mpileup {params.mpileup} -f {input.genome} {input.bam} | bcftools call {params.call} -o {output}) 2> {log}",
      "format": "snakemake",
      "contentUrl": "Snakefile",
      "isPartOf": [
        {
          "@id": "ark:59853/software-snakefile-68f3c95"
        }
      ],
      "condaEnvironment": "{'channels': ['conda-forge', 'bioconda'], 'dependencies': ['bcftools =1.24']}",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        }
      ]
    },
    {
      "@id": "ark:59853/software-bwa-map-0bcb380",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "bwa_map",
      "author": "Example Researcher",
      "description": "bwa mem -t {threads} -R '{params.read_group}' {input.genome} {input.reads} 2> {log} | samtools view -Sb - > {output}",
      "format": "snakemake",
      "contentUrl": "Snakefile",
      "isPartOf": [
        {
          "@id": "ark:59853/software-snakefile-68f3c95"
        }
      ],
      "condaEnvironment": "{'channels': ['conda-forge', 'bioconda'], 'dependencies': ['bwa =0.7.19', 'samtools =1.24']}",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/software-plot-quals-d88cf8f",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "plot_quals",
      "author": "Example Researcher",
      "description": "\"\"\"Plot the quality-score distribution of the called variants.\n\nSnakemake runs this with a ``snakemake`` object in scope carrying the rule's\ninput and output paths \u2014 which is also why the crate records this file as the\nrule's Software rather than a shell command.\n\"\"\"\n\nimport matplotlib\n\nmatplotlib.use(\"Agg\")\n\nimport matplotlib.pyplot as plt\nfrom pysam import VariantFile\n\nquals = [record.qual for record in VariantFile(snakemake.input[0])]\n\nfigure, axes = plt.subplots(figsize=(6, 4))\naxes.hist(quals, bins=30, color=\"#3b6ea5\", edgecolor=\"white\")\naxes.set_xlabel(\"variant quality (Phred)\")\naxes.set_ylabel(\"variants\")\naxes.set_title(f\"{len(quals)} variants called across all samples\")\nfigure.tight_layout()\nfigure.savefig(snakemake.output[0])",
      "format": "python",
      "contentUrl": "scripts/plot_quals.py",
      "isPartOf": [
        {
          "@id": "ark:59853/software-snakefile-68f3c95"
        }
      ],
      "condaEnvironment": "{'channels': ['conda-forge', 'bioconda'], 'dependencies': ['python =3.11', 'pysam =0.24.1', 'matplotlib =3.10']}",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-plot-quals-8e2e10d"
        }
      ]
    },
    {
      "@id": "ark:59853/software-samtools-index-b6cd086",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "samtools_index",
      "author": "Example Researcher",
      "description": "samtools index {input}",
      "format": "snakemake",
      "contentUrl": "Snakefile",
      "isPartOf": [
        {
          "@id": "ark:59853/software-snakefile-68f3c95"
        }
      ],
      "condaEnvironment": "{'channels': ['conda-forge', 'bioconda'], 'dependencies': ['bwa =0.7.19', 'samtools =1.24']}",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-samtools-index-sample-a-13242d2"
        },
        {
          "@id": "ark:59853/computation-samtools-index-sample-b-f89dac4"
        },
        {
          "@id": "ark:59853/computation-samtools-index-sample-c-d37cbd8"
        }
      ]
    },
    {
      "@id": "ark:59853/software-samtools-sort-65f7fb4",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "samtools_sort",
      "author": "Example Researcher",
      "description": "samtools sort -T results/sorted/{wildcards.sample} -O bam {input} > {output} 2> {log}",
      "format": "snakemake",
      "contentUrl": "Snakefile",
      "isPartOf": [
        {
          "@id": "ark:59853/software-snakefile-68f3c95"
        }
      ],
      "condaEnvironment": "{'channels': ['conda-forge', 'bioconda'], 'dependencies': ['bwa =0.7.19', 'samtools =1.24']}",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-samtools-sort-sample-a-3bd01fd"
        },
        {
          "@id": "ark:59853/computation-samtools-sort-sample-b-74d837f"
        },
        {
          "@id": "ark:59853/computation-samtools-sort-sample-c-1828156"
        }
      ]
    },
    {
      "@id": "ark:59853/software-variant-summary-aea5e1b",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Software"
      ],
      "name": "variant_summary",
      "author": "Example Researcher",
      "description": "(printf 'chrom\\tpos\\tref\\talt\\tquality\\tdepth\\n'; bcftools query -f '%CHROM\\t%POS\\t%REF\\t%ALT\\t%QUAL\\t%INFO/DP\\n' {input}) > {output}",
      "format": "snakemake",
      "contentUrl": "Snakefile",
      "isPartOf": [
        {
          "@id": "ark:59853/software-snakefile-68f3c95"
        }
      ],
      "condaEnvironment": "{'channels': ['conda-forge', 'bioconda'], 'dependencies': ['bcftools =1.24']}",
      "softwareUsedBy": [
        {
          "@id": "ark:59853/computation-variant-summary-d29c059"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-config-yaml-b5106b5",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "config.yaml",
      "author": "Example Researcher",
      "description": "Snakemake configuration file 'config.yaml' for this run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/yaml",
      "generatedBy": [],
      "isPartOf": [
        {
          "@id": "ark:59853/software-snakefile-68f3c95"
        }
      ],
      "contentUrl": "config.yaml",
      "contentSize": "375"
    },
    {
      "@id": "ark:59853/dataset-genome-fa-f891ca0",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "genome.fa",
      "author": "Example Researcher",
      "description": "Input file 'data/genome.fa' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "text/x-fasta",
      "generatedBy": [],
      "contentUrl": "data/genome.fa",
      "contentSize": "234112",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-genome-fa-amb-c2df282",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "genome.fa.amb",
      "author": "Example Researcher",
      "description": "Input file 'data/genome.fa.amb' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "amb",
      "generatedBy": [],
      "contentUrl": "data/genome.fa.amb",
      "contentSize": "2598",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-genome-fa-ann-936b248",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "genome.fa.ann",
      "author": "Example Researcher",
      "description": "Input file 'data/genome.fa.ann' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "ann",
      "generatedBy": [],
      "contentUrl": "data/genome.fa.ann",
      "contentSize": "83",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-genome-fa-bwt-0a9c7e3",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "genome.fa.bwt",
      "author": "Example Researcher",
      "description": "Input file 'data/genome.fa.bwt' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "bwt",
      "generatedBy": [],
      "contentUrl": "data/genome.fa.bwt",
      "contentSize": "230320",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-genome-fa-pac-28b255e",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "genome.fa.pac",
      "author": "Example Researcher",
      "description": "Input file 'data/genome.fa.pac' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/x-ns-proxy-autoconfig",
      "generatedBy": [],
      "contentUrl": "data/genome.fa.pac",
      "contentSize": "57556",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-genome-fa-sa-90bdcc1",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "genome.fa.sa",
      "author": "Example Researcher",
      "description": "Input file 'data/genome.fa.sa' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "sa",
      "generatedBy": [],
      "contentUrl": "data/genome.fa.sa",
      "contentSize": "115160",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-a-fastq-d4611b6",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "A.fastq",
      "author": "Example Researcher",
      "description": "Input file 'data/samples/A.fastq' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "text/x-fastq",
      "generatedBy": [],
      "contentUrl": "data/samples/A.fastq",
      "contentSize": "5752788",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-b-fastq-7ed58c5",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "B.fastq",
      "author": "Example Researcher",
      "description": "Input file 'data/samples/B.fastq' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "text/x-fastq",
      "generatedBy": [],
      "contentUrl": "data/samples/B.fastq",
      "contentSize": "5775000",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-c-fastq-bef0063",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "C.fastq",
      "author": "Example Researcher",
      "description": "Input file 'data/samples/C.fastq' used by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "text/x-fastq",
      "generatedBy": [],
      "contentUrl": "data/samples/C.fastq",
      "contentSize": "5775000",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        },
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-all-vcf-637cf3e",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "all.vcf",
      "author": "Example Researcher",
      "description": "File 'results/calls/all.vcf' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "text/x-vcf",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        }
      ],
      "contentUrl": "results/calls/all.vcf",
      "contentSize": "111627",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-plot-quals-8e2e10d"
        },
        {
          "@id": "ark:59853/computation-variant-summary-d29c059"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-variant-summary-tsv-71310c4",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "variant_summary.tsv",
      "author": "Example Researcher",
      "description": "File 'results/calls/variant_summary.tsv' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "text/tab-separated-values",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-variant-summary-d29c059"
        },
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ],
      "evi:Schema": {
        "@id": "ark:59853/schema-variant-summary-tsv-ec080af"
      },
      "contentUrl": "results/calls/variant_summary.tsv",
      "contentSize": "14609"
    },
    {
      "@id": "ark:59853/dataset-a-bam-016e31c",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "A.bam",
      "author": "Example Researcher",
      "description": "File 'results/mapped/A.bam' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/x-bam",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-bwa-map-sample-a-9183688"
        }
      ],
      "localPath": "results/mapped/A.bam",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-samtools-sort-sample-a-3bd01fd"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-b-bam-6b7c70e",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "B.bam",
      "author": "Example Researcher",
      "description": "File 'results/mapped/B.bam' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/x-bam",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-bwa-map-sample-b-5025f30"
        }
      ],
      "localPath": "results/mapped/B.bam",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-samtools-sort-sample-b-74d837f"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-c-bam-3e0f2ac",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "C.bam",
      "author": "Example Researcher",
      "description": "File 'results/mapped/C.bam' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/x-bam",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-bwa-map-sample-c-c80046e"
        }
      ],
      "localPath": "results/mapped/C.bam",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-samtools-sort-sample-c-1828156"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-quals-svg-81b3cdb",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "quals.svg",
      "author": "Example Researcher",
      "description": "File 'results/plots/quals.svg' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "image/svg+xml",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-plot-quals-8e2e10d"
        },
        {
          "@id": "ark:59853/computation-variant-calling-on-three-sequenced-sampl-f05a611"
        }
      ],
      "contentUrl": "results/plots/quals.svg",
      "contentSize": "32379"
    },
    {
      "@id": "ark:59853/dataset-a-bam-c0907f3",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "A.bam",
      "author": "Example Researcher",
      "description": "File 'results/sorted/A.bam' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/x-bam",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-samtools-sort-sample-a-3bd01fd"
        }
      ],
      "contentUrl": "results/sorted/A.bam",
      "contentSize": "2186140",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        },
        {
          "@id": "ark:59853/computation-samtools-index-sample-a-13242d2"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-a-bam-bai-9ebeb4d",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "A.bam.bai",
      "author": "Example Researcher",
      "description": "File 'results/sorted/A.bam.bai' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/octet-stream",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-samtools-index-sample-a-13242d2"
        }
      ],
      "contentUrl": "results/sorted/A.bam.bai",
      "contentSize": "344",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-b-bam-cbee9ae",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "B.bam",
      "author": "Example Researcher",
      "description": "File 'results/sorted/B.bam' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/x-bam",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-samtools-sort-sample-b-74d837f"
        }
      ],
      "contentUrl": "results/sorted/B.bam",
      "contentSize": "2189285",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        },
        {
          "@id": "ark:59853/computation-samtools-index-sample-b-f89dac4"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-b-bam-bai-6a20e1e",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "B.bam.bai",
      "author": "Example Researcher",
      "description": "File 'results/sorted/B.bam.bai' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/octet-stream",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-samtools-index-sample-b-f89dac4"
        }
      ],
      "contentUrl": "results/sorted/B.bam.bai",
      "contentSize": "344",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-c-bam-7ccb833",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "C.bam",
      "author": "Example Researcher",
      "description": "File 'results/sorted/C.bam' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/x-bam",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-samtools-sort-sample-c-1828156"
        }
      ],
      "contentUrl": "results/sorted/C.bam",
      "contentSize": "2189379",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        },
        {
          "@id": "ark:59853/computation-samtools-index-sample-c-d37cbd8"
        }
      ]
    },
    {
      "@id": "ark:59853/dataset-c-bam-bai-39648ed",
      "@type": [
        "prov:Entity",
        "https://w3id.org/EVI#Dataset"
      ],
      "name": "C.bam.bai",
      "author": "Example Researcher",
      "description": "File 'results/sorted/C.bam.bai' produced by the Snakemake workflow run",
      "datePublished": "2026-09-11T13:35:02.543766-04:00",
      "keywords": [
        "snakemake",
        "variant calling",
        "bwa",
        "bcftools",
        "genomics"
      ],
      "format": "application/octet-stream",
      "generatedBy": [
        {
          "@id": "ark:59853/computation-samtools-index-sample-c-d37cbd8"
        }
      ],
      "contentUrl": "results/sorted/C.bam.bai",
      "contentSize": "344",
      "datasetUsedBy": [
        {
          "@id": "ark:59853/computation-bcftools-call-c76dde6"
        }
      ]
    },
    {
      "@id": "ark:59853/schema-variant-summary-tsv-ec080af",
      "@type": "EVI:Schema",
      "name": "Schema for variant_summary.tsv",
      "isPartOf": [],
      "@context": {
        "@vocab": "https://schema.org/",
        "evi": "https://w3id.org/EVI#"
      },
      "conformsTo": {
        "@id": "https://json-schema.org/draft/2020-12/schema"
      },
      "properties": {
        "chrom": {
          "description": "Column chrom",
          "index": 0,
          "type": "string"
        },
        "pos": {
          "description": "Column pos",
          "index": 1,
          "type": "integer"
        },
        "ref": {
          "description": "Column ref",
          "index": 2,
          "type": "string"
        },
        "alt": {
          "description": "Column alt",
          "index": 3,
          "type": "string"
        },
        "quality": {
          "description": "Column quality",
          "index": 4,
          "type": "number"
        },
        "depth": {
          "description": "Column depth",
          "index": 5,
          "type": "integer"
        }
      },
      "type": "object",
      "additionalProperties": true,
      "required": [
        "chrom",
        "pos",
        "ref",
        "alt",
        "quality",
        "depth"
      ],
      "separator": "\t",
      "header": true,
      "examples": [],
      "fairscapeVersion": "1.2.2",
      "EVI:schemaType": "tabular",
      "description": "Schema inferred from the tsv file 'results/calls/variant_summary.tsv' by snakemake-report-plugin-fairscape"
    }
  ]
}