QC metrics

snipe writes 32 metrics to every QC report — two of them expand at runtime into one column per chromosome and per contamination source. A further 51 are available with --advanced (collapsed at the end of this page). For the reasoning behind the numbers, see How QC works.

Note

Metric values are the science — snipe’s QC output is fixed and reproducible. This page documents what each metric means; it never changes a value.

Basic Metadata Metrics

experiment_id

Unique identifier for the experiment, extracted from the signature file name or metadata. Used to track and distinguish between different sequencing runs or samples.

k-size

The length of k-mers (short DNA sequences) used for analysis. For example, k=21 means the analysis uses 21-base sequences as the fundamental unit for comparison.

edgemer_extension_length

Number of bases extended from K1 to K2 edgemer. This extension length is critical for calculating per-base error and mutation rates. Typically 2 bases (e.g., K1=51, K2=53).

sketching_scale

The downsampling factor used during signature creation. A scale of 1000 means approximately 1 in 1000 k-mers are retained, reducing computational requirements while maintaining statistical accuracy.

sketch_file_path

Full file system path to the signature file being analyzed. Useful for tracking data provenance and debugging.

Sequencing Statistics

no_of_input_sequences

Total number of DNA sequences (reads) processed from the input file. This represents the raw sequencing depth before any filtering.

avg_sequence_length

$$\frac{\text{total\_bases\_processed}}{\text{sequences\_processed}}$$

Mean length of all processed sequences in base pairs. Important for understanding sequencing technology characteristics (e.g., short reads vs long reads).

GC%

$$\frac{\text{gc\_bases}}{\text{total\_bases\_processed}} \times 100$$

Percentage of guanine (G) and cytosine (C) bases in the sequenced data. GC content affects sequencing efficiency and can indicate contamination or bias.

no_of_input_bases

Total number of DNA bases (A, T, G, C) processed from all sequences. Represents the total sequencing yield in base pairs.

no_of_input_kmers

Number of valid k-mer positions examined in the sequences. Some positions may be invalid due to ambiguous bases (N) or sequence boundaries.

Processing Efficiency Metrics

kmer_yield

$$\frac{\text{no\_of\_input\_kmers}}{\text{no\_of\_input\_bases}}$$

Ratio of valid k-mers to total bases. Values close to 1 indicate high-quality sequences with few ambiguous bases or edge effects.

fracminhash_precision

$$\frac{\text{kmer\_total\_abundance} \times \text{sketching\_scale}}{\text{no\_of\_input\_kmers}}$$

Measure of sketch precision. Higher values indicate better representation of the original data in the downsampled sketch.

Sequence Change and Error Metrics

basepair_change_rate

$$1 - \left(\frac{\text{match\_total}}{\text{match\_total} + \text{unmatched\_extension\_total}}\right)^{\frac{1}{\text{k2\_length} - \text{k1\_length}}}$$

Exact rate of sequence changes detected between sample and reference. Accounts for the extension length between K1 and K2 to estimate per-base error rate.

sequencing_error_rate

$$\frac{\text{reference\_unmatched\_edgemer\_extension\_singletons}}{(\text{match\_total} + \text{unmatched\_extension\_total}) \times (\text{k2\_length} - \text{k1\_length})}$$

Estimated rate of sequencing errors based on singleton mismatches. Single-occurrence changes are likely errors rather than true variants.

mutation_rate

$$\frac{\text{reference\_unmatched\_edgemer\_extension\_nonsingletons}}{(\text{match\_total} + \text{unmatched\_extension\_total}) \times (\text{k2\_length} - \text{k1\_length})}$$

Estimated rate of true mutations (non-error changes). Multi-occurrence changes are likely real variants rather than sequencing errors.

Corrected Coverage Metrics

total_reference-mapped_bases

$$\frac{\text{reference\_matched\_kmers\_total\_abundance}}{(1 - \text{seq\_change\_rate})^{\text{k1\_size}} \times \text{kmers\_to\_bases}}$$

Estimated total bases mapped to reference after correcting for sequencing errors and k-mer to base conversion.

mean_depth_of_reference_coverage

$$\frac{\text{reference\_kmers\_mean\_depth\_of\_coverage}}{(1 - \text{seq\_change\_rate})^{\text{k1\_size}} \times \text{kmers\_to\_bases}}$$

Corrected mean sequencing depth across the reference genome accounting for errors and sketching.

reference_mapping_rate

$$\frac{\text{reference\_matched\_kmers\_total\_abundance}}{(1 - \text{seq\_change\_rate})^{\text{k1\_size}} \times \text{sample\_total\_abundance}}$$

Corrected fraction of sample that maps to reference, accounting for sequencing errors.

Repetitive-Free Reference Metrics

fraction_of_reference_covered_by_sample_(%)

$$1 - (1 - \text{repfree\_coverage})^{\frac{1}{\text{correction\_factor}}}$$

Corrected extent of non-repetitive reference coverage. Most accurate measure of genome coverage completeness.

mean_depth_at_1x_covered_reference_bases

$$\frac{\text{corrected\_repfree\_total\_bases}}{\text{fraction\_of\_reference\_covered\_by\_sample} \times \text{reference\_size}}$$

Mean depth at positions with at least 1x coverage after error correction. True sequencing depth where data exists.

ROI/Amplicon Metrics

total_ROI-mapped_bases

$$\frac{\text{ROI-matched\_total\_kmers\_count}}{\text{correction\_factor}}$$

Estimated total bases mapped to ROI after error correction.

mean_depth_of_ROI_coverage

$$\frac{\text{ROI\_kmers\_mean\_depth\_of\_coverage}}{\text{correction\_factor}}$$

Corrected mean sequencing depth in the ROI after accounting for errors.

ROI_mapping_rate

$$\frac{\text{ROI-matched\_total\_kmers\_count}}{(1 - \text{seq\_change\_rate})^{\text{k1\_size}} \times \text{sample\_total}}$$

Corrected fraction of sample mapping to ROI. Efficiency of targeted enrichment.

Non-Repetitive ROI Metrics

fraction_of_ROI_covered_by_sample_(%)

$$1 - (1 - \text{repfree\_ROI\_coverage})^{\frac{1}{\text{correction\_factor}}}$$

Corrected coverage extent of non-repetitive ROI.

mean_depth_at_1x_covered_ROI_bases

$$\frac{\text{corrected\_repfree\_ROI\_total}}{\text{fraction\_of\_ROI\_covered\_by\_sample} \times \text{amplicon\_size}}$$

Mean depth at ROI positions with at least 1x coverage after error correction.

ROI_enrichment_score

$$\frac{\text{ROI\_matched\_kmers\_total\_abundance}}{\text{reference\_matched\_kmers\_total\_abundance}}$$

Enrichment of ROI relative to whole genome. Values >1 indicate successful targeted enrichment.

Chromosome-Specific Metrics

mean_depth_of_chr-{N}

This placeholder is replaced at runtime with specific chromosome metrics (mean_depth_of_chr-{N}) for each chromosome in the reference (1-22, X, Y, MT).

chromosomal_mean_abundance_CV

$$\frac{\sigma_{\text{autosomal}}}{\mu_{\text{autosomal}}}$$

Coefficient of variation in autosomal chromosome coverage. High values indicate uneven coverage or aneuploidy.

chrX_ploidy

$$\frac{\text{chrX\_mean\_abundance}}{\text{autosomal\_mean\_abundance}}$$

X chromosome ploidy relative to autosomes. ~1.0 for XX (female), ~0.5 for XY (male).

chrY_coverage

$$\frac{\text{Y\_specific\_covered}/\text{Y\_specific\_total}}{\text{autosomal\_covered}/\text{autosomal\_total}}$$

Y chromosome coverage relative to autosomes. >0 indicates male sample, ~0 for female.

Contamination and Error Detection

predicted_contamination_index

$$\frac{\text{nonref\_polytons\_abundance}}{\text{sample\_total\_abundance}}$$

Fraction of sample that appears to be contamination based on non-reference multi-occurrence k-mers.

Variance Source Metrics

per-source variance metrics

This placeholder is replaced at runtime with variance source metrics for each provided contamination source or off-target organism.

Advanced metrics

These appear only when you pass --advanced to snipe qc.

Show 51 advanced metrics

Processing Efficiency Metrics

upscaled_kmers_to_bases_ratio

$$\frac{\text{kmer\_total\_abundance} \times \text{sketching\_scale}}{\text{no\_of\_input\_bases}}$$

Estimated ratio of total k-mers to total bases after upscaling from the sketch. Used for coverage corrections.

Edgemer Analysis Metrics

no_of_distinct_edgemers

Number of unique edgemers in the sample. Edgemers are overlapping k-mer pairs that capture local sequence context for error detection.

edgemers_total_abundance

Total count of all edgemers including duplicates. Represents the total amount of sequence information analyzed at the edgemer level.

reference_matched_distinct_edgemers

$$|\text{sample\_edgemers} \cap \text{reference\_edgemers}|$$

Number of unique edgemers shared between sample and reference. Indicates the overlap between sample and reference at the edgemer level.

reference_matched_edgemers_total_abundance

Total abundance of edgemers that perfectly match the reference genome. Higher values indicate better alignment with the reference.

reference_matched_singleton_edgemers

Number of edgemers seen exactly once that match the reference. Often indicates sequencing errors or low coverage regions.

reference_unmatched_edgemer_extension_total_abundance

Total abundance of edgemers where K1 matches reference but K2 extension doesn’t match. Represents sequence changes (mutations or errors) detected at the extension positions.

reference_unmatched_edgemer_extension_singletons

Single-occurrence unmatched extensions, typically sequencing errors rather than true mutations.

Sequence Change and Error Metrics

beta_sequencing_error_rate

Experimental beta-calibrated sequencing error rate. Uses statistical modeling to provide more accurate error estimates than the basic singleton-based rate.

beta_mutation_rate

Experimental beta-calibrated mutation rate. Uses statistical modeling for more accurate mutation estimates compared to the basic polyton-based rate.

K-mer Statistics

no_of_distinct_kmers

Number of unique k-mers in the sample. Indicates sequence diversity and complexity.

kmer_total_abundance

Total count of all k-mers including duplicates. Represents the total sequence information at k-mer resolution.

kmer_median_abundance

Median occurrence of k-mers. More robust than mean for datasets with outliers or uneven coverage.

kmer_mean_abundance

$$\frac{\text{kmer\_total\_abundance}}{\text{no\_of\_distinct\_kmers}}$$

Average number of times each unique k-mer appears. Indicates sequencing depth and coverage uniformity.

total_singletons

Number of k-mers seen exactly once. High singleton counts may indicate errors or low coverage.

Reference Genome Intersection Metrics

reference_matched_distinct_kmers

$$|\text{sample\_kmers} \cap \text{reference\_kmers}|$$

Number of unique k-mers shared between sample and reference genome. Measures the genomic content captured in the sample.

reference_matched_kmers_total_abundance

Total abundance of k-mers matching the reference. Higher values indicate better coverage of the reference genome.

reference_kmers_median_depth_of_coverage

Median coverage across all reference k-mers including uncovered regions. More robust measure of typical coverage.

reference_kmers_mean_depth_of_coverage

$$\frac{\text{reference\_matched\_kmers\_total\_abundance}}{\text{reference\_total\_kmers}}$$

Mean coverage depth across all reference k-mers including zeros. Indicates overall sequencing depth relative to genome size.

reference_matched_kmers_variance

Variance in coverage across reference k-mers. High variance indicates uneven coverage or amplification bias.

reference_matched_singleton_kmers

Singleton k-mers in the sample-reference intersection. May indicate low coverage of reference regions.

matching_rate_of_kmers_to_reference_(%)

$$\frac{\text{reference\_matched\_kmers\_total\_abundance}}{\text{kmer\_total\_abundance}}$$

Fraction of sample k-mers that map to the reference genome. Low values may indicate contamination.

fraction_of_reference_kmers_covered_by_sample_(%)

$$\frac{\text{reference\_matched\_distinct\_kmers}}{\text{reference\_total\_kmers}}$$

Fraction of reference k-mers covered by the sample. Indicates completeness of genome coverage.

fraction_of_sample_kmers_covered_by_reference_(%)

$$\frac{\text{reference\_matched\_distinct\_kmers}}{\text{no\_of\_distinct\_kmers}} \times 100$$

Percentage of sample k-mers found in the reference. Indicates sample purity and reference completeness.

Repetitive-Free Reference Metrics

nonrepetitive_reference_matched_distinct_kmers

$$|\text{sample\_genome} \cap \text{reference\_without\_repeats}|$$

Unique k-mers in sample matching non-repetitive reference regions. Excludes repetitive elements for cleaner analysis.

nonrepetitive_reference_matched_kmers_total_abundance

Total abundance in non-repetitive regions. Provides cleaner coverage estimates by excluding repeats.

nonrepetitive_reference_kmers_median_depth_of_coverage

Median coverage of non-repetitive regions including uncovered positions.

nonrepetitive_reference_kmers_mean_depth_of_coverage

$$\frac{\text{repfree\_total\_abundance}}{\text{reference\_repfree\_size}}$$

Mean coverage of non-repetitive reference regions including zeros. More accurate for unique genomic regions.

nonrepetitive_reference_matched_kmers_variance

Coverage variance in non-repetitive regions. Lower variance indicates more uniform coverage.

nonrepetitive_reference_kmers_mean_depth_at_1x_covered_bases

$$\frac{\text{repfree\_total\_abundance}}{\text{repfree\_unique\_kmers}}$$

Mean coverage of covered non-repetitive regions only, excluding zeros. True depth where coverage exists.

fraction_of_nonrepetitive_reference_kmers_covered_by_sample_(%)

$$\frac{\text{repfree\_unique\_kmers}}{\text{reference\_repfree\_size}}$$

Fraction of non-repetitive reference covered by sample. Better indicator of unique sequence coverage.

ROI/Amplicon Metrics

ROI_matched_distinct_kmers

$$|\text{sample\_kmers} \cap \text{amplicon\_kmers}|$$

Unique k-mers shared between sample and region of interest (ROI/amplicon). Measures targeted region coverage.

ROI_matched_kmers_total_abundance

Total k-mer abundance in the targeted region. Indicates depth of coverage for the ROI.

ROI_kmers_mean_depth_of_coverage

$$\frac{\text{ROI-matched\_total\_kmers\_count}}{\text{amplicon\_total\_kmers}}$$

Mean coverage across all ROI k-mers including zeros. Overall depth in targeted region.

ROI_kmers_median_depth_of_coverage

Median coverage of ROI including uncovered positions. Robust measure of typical ROI coverage.

ROI_matched_kmers_variance

Coverage variance across the ROI. High variance may indicate uneven amplification.

ROI_matched_singleton_kmers

Single-occurrence k-mers in the sample-ROI intersection.

matching_rate_of_kmers_to_ROI_(%)

$$\frac{\text{ROI\_matched\_kmers\_total\_abundance}}{\text{kmer\_total\_abundance}}$$

Fraction of sample k-mers mapping to ROI. Indicates targeting efficiency.

fraction_of_ROI_kmers_covered_by_sample_(%)

$$\frac{\text{ROI\_matched\_distinct\_kmers}}{\text{amplicon\_size}}$$

Fraction of ROI k-mers covered by sample. Completeness of targeted sequencing.

fraction_of_sample_kmers_covered_by_ROI_(%)

$$\frac{\text{ROI\_matched\_distinct\_kmers}}{\text{no\_of\_distinct\_kmers}} \times 100$$

Percentage of sample k-mers found in the ROI. Specificity of targeted sequencing.

Non-Repetitive ROI Metrics

nonrepetitive_ROI_matched_distinct_kmers

$$|\text{sample\_amplicon} \cap \text{amplicon\_without\_repeats}|$$

Unique k-mers in non-repetitive ROI regions. Cleaner measure excluding repeats.

nonrepetitive_ROI_matched_kmers_total_abundance

Total abundance in non-repetitive ROI regions.

nonrepetitive_ROI_kmers_mean_depth_of_coverage

$$\frac{\text{repfree\_ROI\_total}}{\text{amplicon\_repfree\_size}}$$

Mean coverage of non-repetitive ROI including zeros.

nonrepetitive_ROI_kmers_median_depth_of_coverage

Median coverage of non-repetitive ROI regions.

nonrepetitive_ROI_matched_kmers_variance

Coverage variance in non-repetitive ROI regions.

nonrepetitive_ROI_kmers_mean_depth_at_1x_covered_bases

$$\frac{\text{repfree\_ROI\_total}}{\text{repfree\_ROI\_unique}}$$

Mean depth of covered non-repetitive ROI positions only.

fraction_of_nonrepetitive_ROI_kmers_covered_by_sample_(%)

$$\frac{\text{repfree\_ROI\_unique}}{\text{amplicon\_repfree\_size}}$$

Fraction of non-repetitive ROI covered.

nonrepetitive_ROI_enrichment_score

$$\frac{\text{nonrepetitive\_ROI\_total}}{\text{nonrepetitive\_reference\_total}}$$

Enrichment in non-repetitive regions only.

Non-Reference K-mer Analysis

sample_nonref_unique_kmers

$$|\text{sample\_kmers} - \text{reference\_kmers}|$$

K-mers in sample not found in reference. May indicate contamination, errors, or novel sequences.

sample_nonref_total_abundance

Total abundance of non-reference k-mers.

sample_nonref_singletons

Single-occurrence non-reference k-mers, likely sequencing errors.