ConsensusMetrics
Consensus calling metrics with rejection tracking.
These metrics track the consensus calling process, including how many reads were accepted, filtered, and the reasons for rejection.
Fields
| Column | Type | Description |
|---|---|---|
total_input_reads | u64 | Total input reads processed |
consensus_reads | u64 | Number of consensus reads generated |
filtered_reads | u64 | Number of input reads filtered out |
total_umi_groups | u64 | Total number of UMI groups processed |
umi_groups_with_consensus | u64 | UMI groups that generated consensus |
umi_groups_failed | u64 | UMI groups that failed to generate consensus |
avg_input_reads_per_consensus | f64 | Average input reads per consensus read |
avg_raw_read_depth | f64 | Average raw read depth per consensus read |
min_raw_read_depth | u64 | Minimum raw read depth |
max_raw_read_depth | u64 | Maximum raw read depth |
rejected_insufficient_support | u64 | Reads rejected due to insufficient support |
rejected_minority_alignment | u64 | Reads rejected due to minority alignment |
rejected_insufficient_strand_support | u64 | Reads rejected due to insufficient strand support |
rejected_low_base_quality | u64 | Reads rejected due to low base quality |
rejected_excessive_n_bases | u64 | Reads rejected due to excessive N bases |
rejected_no_valid_alignment | u64 | Reads rejected due to no valid alignment |
rejected_low_mapping_quality | u64 | Reads rejected due to low mapping quality |
rejected_n_bases_in_umi | u64 | Reads rejected due to N bases in UMI |
rejected_missing_umi | u64 | Reads rejected due to missing UMI tag |
rejected_not_passing_filter | u64 | Reads rejected due to not passing filter |
rejected_low_mean_quality | u64 | Reads rejected due to low mean quality |
rejected_insufficient_min_depth | u64 | Reads rejected due to insufficient min depth |
rejected_excessive_error_rate | u64 | Reads rejected due to excessive error rate |
rejected_umi_too_short | u64 | Reads rejected due to UMI too short |
rejected_same_strand_only | u64 | Reads rejected due to same strand only |
rejected_duplicate_umi | u64 | Reads rejected due to duplicate UMI |
rejected_orphan_consensus | u64 | Reads rejected due to orphan consensus (only R1 or R2 had consensus) |
rejected_zero_bases_post_trimming | u64 | Reads rejected due to zero bases after trimming |