Long Ranger2.1, printed on 11/14/2024
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.
| Metric | Description |
|---|---|
longranger_version | The version of the Long Ranger software used to generate the results. |
instrument_ids | The list of instrument IDs used to generate the input reads. |
gems_detected | The number of Chromium GEMs that were collected and which generated a non-trivial number of read-pairs. |
mean_dna_per_gem | The 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_whitelist | The fraction of reads that carried a valid 10x barcode sequence. |
bc_mean_qscore | The mean base quality value on the barcode bases. |
n50_linked_reads_per_molecule | The 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_ng | Deprecated 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_ng | The 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_phased | Fraction of called SNPs that were phased. |
genes_phased_lt_100kb | Fraction of genes shorter than 100kb with >1 heterozygous SNP that are phased into a single phase block. |
longest_phase_block | Size of the longest phase block, in base pairs. |
n50_phase_block | N50 length of the called phase blocks, in base pairs. |
molecule_length_mean | The length-weighted mean input DNA length in base pairs. |
molecule_length_stddev | The length-weighted standard deviation of the input DNA length distribution in base pairs. |
number_reads | Total number of reads supplied to Long Ranger. |
median_insert_size | Median insert size of aligned read pairs. |
mean_depth | Mean 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_coverage | Fraction of non-N bases in the genome with zero coverage. |
mapped_reads | Number of input reads that were mapped. |
pcr_duplication | Fraction 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_bases | Fraction 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_fract | Fraction of bases in R1 with base quality >= 20. |
r1_q30_bases_fract | Fraction of bases in R1 with base quality >= 30. |
r2_q20_bases_fract | Fraction of bases in R2 with base quality >= 20. |
r2_q30_bases_fract | Fraction of bases in R2 with base quality >= 30. |
si_q20_bases_fract | Fraction of bases in the sample index with base quality >= 20. |
si_q30_bases_fract | Fraction of bases in the sample index with base quality >= 30. |
bc_q20_bases_fract | Fraction of bases in the barcode with base quality >= 20. |
bc_q30_bases_fract | Fraction of bases in the barcode with base quality >= 30. |