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# Aggregated Metrics

The spaceranger aggr pipeline outputs summary.json that contains metrics relating to the aggregated datasets. Note: Square brackets denote a variable that depends on the pipeline input, such as, [library_id]_frac_reads_kept means that if your aggregation contains two libraries with IDs sample123 and sample456, there are two output metrics sample123_frac_reads_kept and sample456_frac_reads_kept.

MetricDescription
filtered_bcs_transcriptome_unionThe estimated number of barcodes associated with a spot under tissue, summed across all input libraries.
[pre/post]_total_readsTotal number of sequenced reads, summed across all input libraries.
[pre/post]_multi_transcriptome_total_raw_reads_per_filtered_bctotal_reads divided by filtered_bcs_transcriptome_union.
[library_id]_pre_normalization_raw_reads_per_filtered_bcThe mean total reads per spot prior to depth normalization, for the library denoted by library_id.
[library_id]_pre_normalization_cmb_reads_per_filtered_bcThe mean confidently mapped and barcoded (CMB) reads per spot prior to depth normalization, for the library denoted by library_id.
[library_id]_frac_reads_keptThe fraction of reads that were retained after depth normalization for the library denoted by library_id.
lowest_frac_reads_keptThe lowest fraction of reads retained, corresponding to the library which lost the most reads during normalization. A low value may indicate a large disparity in the initial depth of the input libraries.

If one or more of the aggregated samples was a Targeted Gene Expression sample, these additional metrics will also appear:

MetricDescription
[library_id]_pre_normalization_targeted_reads_per_filtered_bcThe mean targeted reads per spot prior to depth normalization, for the library denoted by library_id.
[library_id]_frac_targeted_reads_keptThe fraction of reads mapped uniquely and confidently to targeted genes that were retained after depth normalization for the library denoted by library_id. This field will be shown instead of the metric [library_id]_frac_reads_kept above.