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10x Genomics
Chromium Genome & Exome

Summary Metrics

The longranger wgs and longranger targeted pipelines output summary_csv.csv which contains a number of key metrics about the barcoding and sequencing process. These metrics are also displayed in the Loupe summary page. Below are the definitions of the reported metrics.

Metrics Definitions

longranger_versionThe version of the Long Ranger software used to generate the results.
instrument_idsThe list of instrument IDs used to generate the input reads.
gems_detectedThe number of Chromium GEMs that were collected and which generated a non-trivial number of read-pairs.
mean_dna_per_gemThe average number of base pairs of genomic DNA loaded into each GEM. This metric is based on the observed extents of read-pairs on each molecule.
bc_on_whitelistThe fraction of reads that carried a valid 10x barcode sequence.
bc_mean_qscoreThe mean base quality value on the barcode bases.
n50_linked_reads_per_moleculeThe N50 number of read-pairs per input DNA molecule. Equivalently, half of read-pairs came from molecules with this many or greater read-pairs, and half came from molecules with fewer read pairs.
loaded_mass_ngDeprecated and unavailable. This metric was found to overestimate the true loading by a factor of 1.6, due primarily to denaturation of the input DNA. It was available in longranger 1.3 and 2.0 but has been removed starting in 2.1 in favor of corrected_loaded_mass_ng, found below.
corrected_loaded_mass_ngThe estimated number of nanograms of DNA loaded into the input well of the Chromium chip. This metric is calculated by measuring the mean amount of DNA covered by input molecules in each GEM, then multiplying by the ratio of the chip input to the sample volume in each GEM. A probabilistic model corrects for biases caused by low Linked-Reads per Molecule. This metric is then corrected by a factor of 1.6 to account for the denaturation of double stranded input material, which can result in opposite strands of an input molecule ending up in different GEMs and being double counted. This metric is only available in Long Ranger 2.1 and above.
snps_phasedFraction of called SNPs that were phased.
genes_phased_lt_100kbFraction of genes shorter than 100kb with >1 heterozygous SNP that are phased into a single phase block.
longest_phase_blockSize of the longest phase block, in base pairs.
n50_phase_blockN50 length of the called phase blocks, in base pairs.
molecule_length_meanThe length-weighted mean input DNA length in base pairs.
molecule_length_stddevThe length-weighted standard deviation of the input DNA length distribution in base pairs.
number_readsTotal number of reads supplied to Long Ranger.
median_insert_sizeMedian insert size of aligned read pairs.
mean_depthMean read depth, including PCR duplicate reads. In WGS mode, this is measured across the genome; in targeted mode, this is the measure inside targeted regions.
zero_coverageFraction of non-N bases in the genome with zero coverage.
mapped_readsPercentage of input reads that were mapped.
pcr_duplicationFraction of reads marked as PCR duplicates. To be marked as PCR duplicates, reads must have the same mapping extents on the genome and the same 10x barcode.
on_target_basesFraction of aligned bases mapped with the target regions in targeted mode. Only bases inside the intervals of target BED file are counted.
r1_q20_bases_fractFraction of bases in R1 with base quality >= 20.
r1_q30_bases_fractFraction of bases in R1 with base quality >= 30.
r2_q20_bases_fractFraction of bases in R2 with base quality >= 20.
r2_q30_bases_fractFraction of bases in R2 with base quality >= 30.
si_q20_bases_fractFraction of bases in the sample index with base quality >= 20.
si_q30_bases_fractFraction of bases in the sample index with base quality >= 30.
bc_q20_bases_fractFraction of bases in the barcode with base quality >= 20.
bc_q30_bases_fractFraction of bases in the barcode with base quality >= 30.