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.