Aligned Reads Summary Metrics

Various summary metrics are added to the aligned reads entity for query by the user. These are generated by such tools as SAMtools, Picard, and GATK4. These may be helpful to determine underlying quality or summary information regarding the submitted data. Examples are included below:

  • average_base_quality
  • average_insert_size
  • average_read_length
  • contamination
  • contamination_error
  • mean_coverage
  • msi_score
  • msi_status
  • pairs_on_diff_chr
  • proportion_base_mismatch
  • proportion_coverage_10x
  • proportion_coverage_30x
  • proportion_reads_duplicated
  • proportion_reads_mapped
  • proportion_targets_no_coverage
  • total_reads

For a complete list of the summary metrics as well as the tools used to generate them please visit the Data Dictionary Viewer.