{
  "categories": [
    {
      "name": "Sample QC",
      "key": "sample_summary_stats",
      "additionalAxes": false,
      "defaultFilters": []
    },
    {
      "name": "SampleQC",
      "key": "metrics_cellranger_stats",
      "additionalAxes": false,
      "defaultFilters": [
        {
          "type": "bar",
          "field": "Number_of_reads_in_the_library",
          "label": "Number of reads per library",
          "description": "Sequencing depth per sample. Higher values generally indicate more comprehensive cell profiling.",
          "nBins": 10,
          "groupBy": "sample_id",
          "xAxisType": "linear",
          "yAxisType": "linear"
        },
        {
          "type": "bar",
          "field": "Confidently_mapped_reads_in_cells",
          "label": "Confidently mapped reads in cells",
          "description": "Number of reads that were mapped unambiguously to the reference genome within cell-containing droplets.",
          "groupBy": "sample_id",
          "nBins": 10,
          "yAxisType": "linear"
        },
        {
          "type": "bar",
          "field": "Estimated_number_of_cells",
          "label": "Estimated number of cells",
          "description": "CellRanger's estimate of the number of cells per sample based on the UMI count distribution.",
          "groupBy": "sample_id",
          "nBins": 10,
          "yAxisType": "linear"
        },
        {
          "type": "bar",
          "field": "Sequencing_saturation",
          "label": "Sequencing saturation",
          "description": "Fraction of reads that are duplicates of existing UMIs. Higher values suggest deeper sequencing coverage.",
          "groupBy": "sample_id",
          "nBins": 10,
          "yAxisType": "linear"
        }
      ]
    },
    {
      "name": "Cell RNA QC",
      "key": "cell_rna_stats",
      "additionalAxes": true,
      "defaultFilters": [
        {
          "type": "histogram",
          "field": "total_counts",
          "label": "Total UMI per cell",
          "description": "Total number of RNA molecules detected per cell. Low values typically indicate empty droplets or low-quality cells that should be filtered out.",
          "cutoffMin": null,
          "cutoffMax": null,
          "zoomMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "num_nonzero_vars",
          "label": "Number of non-zero genes per cell",
          "description": "Count of unique genes detected in each cell. Low gene counts often indicate poor-quality cells.",
          "cutoffMin": null,
          "cutoffMax": null,
          "zoomMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "fraction_mitochondrial",
          "label": "Fraction UMI of mitochondrial genes per cell",
          "description": "Proportion of cell's RNA from mitochondrial genes.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "fraction_ribosomal",
          "label": "Fraction UMI of ribosomal genes per cell",
          "description": "Proportion of cell's RNA from ribosomal protein genes. Extreme values may indicate stress responses or cell cycle abnormalities.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "pct_of_counts_in_top_50_vars",
          "label": "Fraction UMI in top 50 genes per cell",
          "description": "Proportion of RNA molecules from the 50 most-expressed genes in each cell.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "cellbender_cell_probability",
          "label": "CellBender cell probability",
          "description": "CellBender's statistical confidence (0-1) that a barcode represents a real cell, with higher values indicating stronger confidence.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "cellbender_background_fraction",
          "label": "CellBender background fraction",
          "description": "Estimated percentage of each cell's RNA that comes from the ambient solution rather than the cell itself.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "cellbender_cell_size",
          "label": "CellBender cell size",
          "description": "CellBender's estimate of the true number of RNA molecules in each cell after removing ambient contamination. Reflects actual cell RNA content rather than raw UMI counts.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        },
        {
          "type": "histogram",
          "field": "cellbender_droplet_efficiency",
          "label": "CellBender droplet efficiency",
          "description": "CellBender's estimate of how efficiently each droplet captured RNA molecules. Higher values indicate more reliable RNA sampling within individual droplets.",
          "cutoffMin": null,
          "cutoffMax": null,
          "nBins": 50,
          "groupBy": "sample_id",
          "yAxisType": "linear"
        }
      ]
    }
  ]
}
