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SUMMARY      ANALYSIS
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Estimated Number of Cells

1,993

Mean Read Pairs per Cell

21,438

Number of Cells With Productive V-J Spanning Pair

1,476
Reads Mapped to Any V(D)J Gene
Fraction of reads that partially or wholly map to any germline V(D)J gene segment.
Reads Mapped to TRA
Fraction of reads that map partially or wholly to a germline TRA gene segment.
Reads Mapped to TRB
Fraction of reads that map partially or wholly to a germline TRB gene segment.

Enrichment

Reads Mapped to Any V(D)J Gene 80.0%
Reads Mapped to TRA 21.5%
Reads Mapped to TRB 46.4%
Median TRA UMIs per Cell
Median number of UMIs assigned to a TRA contig per cell. For B cells, only the max of {IGK, IGL} are counted.
Median TRB UMIs per Cell
Median number of UMIs assigned to a TRB contig per cell. For B cells, only the max of {IGK, IGL} are counted.

V(D)J Expression

Median TRA UMIs per Cell 4.0
Median TRB UMIs per Cell 12.0
Cells With Productive V-J Spanning Pair
Fraction of cell-associated barcodes with at least one contig for each chain of the receptor pair satisfying the following: the contig annotations span the 5' end of the V region to at least 2 bp from the 3' end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the aligned V-J region.
Cells With Productive V-J Spanning (TRA, TRB) Pair
Fraction of cell-associated barcodes with at least one contig for each chain of the receptor pair satisfying the following: the contig annotations span the 5' end of the V region to at least 2 bp from the 3' end of the J region of the chain, a start codon was found in the expected part of the V sequence, an in-frame CDR3 amino acid motif was found, and no stop codons were found in the aligned V-J region.
Paired Clonotype Diversity
Effective diversity of the paired clonotypes, computed as the Inverse Simpson Index of the clonotype frequencies. A value of 1 indicates a minimally diverse sample - only one distinct clonotype was detected. A value equal to the estimated number of cells indicates a maximally diverse sample.
Cells With TRA Contig
Fraction of cell-associated barcodes with at least one TRA contig annotated as a full or partial V(D)J gene.
Cells With TRB Contig
Fraction of cell-associated barcodes with at least one TRB contig annotated as a full or partial V(D)J gene.
Cells With CDR3-annotated TRA Contig
Fraction of cell-associated barcodes with at least one TRA contig where a CDR3 was detected.
Cells With CDR3-annotated TRB Contig
Fraction of cell-associated barcodes with at least one TRB contig where a CDR3 was detected.
Cells With V-J Spanning TRA Contig
Fraction of cell-associated barcodes with at least one contig spanning the 5' end of the V region to at least 2bp from the 3' end of the J region for TRA.
Cells With V-J Spanning TRB Contig
Fraction of cell-associated barcodes with at least one contig spanning the 5' end of the V region to at least 2bp from the 3' end of the J region for TRB.
Cells With Productive TRA Contig
Fraction of cell-associated barcodes with at least one contig that spans the 5' end of the V region to at least 2bp from the 3' end of the J region for TRA, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the aligned V-J region.
Cells With Productive TRB Contig
Fraction of cell-associated barcodes with at least one contig that spans the 5' end of the V region to at least 2bp from the 3' end of the J region for TRB, has a start codon in the expected part of the V sequence, has an in-frame CDR3, and has no stop codons in the aligned V-J region.
Contigs Unannotated
Fraction of assembled contigs not annotated with any V(D)J gene.

V(D)J Annotation

Cells With Productive V-J Spanning Pair 74.1%
Cells With Productive V-J Spanning (TRA, TRB) Pair 74.1%
Paired Clonotype Diversity 640.38
Cells With TRA Contig 90.0%
Cells With TRB Contig 98.6%
Cells With CDR3-annotated TRA Contig 82.3%
Cells With CDR3-annotated TRB Contig 88.6%
Cells With V-J Spanning TRA Contig 81.6%
Cells With V-J Spanning TRB Contig 87.5%
Cells With Productive TRA Contig 77.6%
Cells With Productive TRB Contig 85.6%
Contigs Unannotated 0.1%
 
Estimated Number of Cells
The number of barcodes estimated to be associated with cells that express targeted V(D)J transcripts. A barcode is cell-associated if has 2 UMIs with sufficient read support.
Cell Count Confidence
A measure of the goodness-of-fit of the model used to call cell barcodes based on total UMI counts. This is computed as the fraction of cell barcodes whose predicted posterior probability of being a cell exceeds 99%. Low values indicate that Cell Ranger had trouble estimating the number of cells. Note: This is the value for the first gem group only - this only matters if multiple libraries were combined into one vdj run.
Mean Read Pairs per Cell
Number of input read pairs divided by the estimated number of cells.
Mean Used Read Pairs per Cell
Mean number of read pairs used in assembly per cell-associated barcode. These reads must have a cell-associated barcode, map to a V(D)J gene, and have a UMI with sufficient read support.
Fraction Reads in Cells
Number of reads with cell-associated barcodes divided by the number of reads with valid barcodes.

Cells

Estimated Number of Cells 1,993
Cell Count Confidence 87.4%
Mean Read Pairs per Cell 21,438
Mean Used Read Pairs per Cell 12,412
Fraction Reads in Cells 70.9%
Number of Read Pairs
Total number of read pairs that were assigned to this library in demultiplexing.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist after barcode correction.
Q30 Bases in Barcode
Fraction of cell barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in RNA Read 1
Fraction of RNA read 1 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in RNA Read 2
Fraction of RNA read 2 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in Sample Index
Fraction of sample index bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in UMI
Fraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.

Sequencing

Number of Read Pairs 42,727,096
Valid Barcodes 88.1%
Q30 Bases in Barcode 96.1%
Q30 Bases in RNA Read 1 93.0%
Q30 Bases in RNA Read 2 92.0%
Q30 Bases in Sample Index 93.1%
Q30 Bases in UMI 95.4%

Sample

Name vdj_v1_nsclc_t
Description Targeted enrichment of TCRs from fresh surgical resection of a squamous non-small cell lung carcinoma tumor
V(D)J Reference vdj_GRCh38_alts_ensembl
Chemistry Single Cell V(D)J
Cell Ranger Version 2.1.0
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