{{ alerts.length}}
SUMMARY      ANALYSIS
The analysis detected some serious issues.   Details »

Estimated Number of Cells

3,077

Mean Read Pairs per Cell

14,172

Number of Cells With Productive V-J Spanning Pair

1,410
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 IGH
Fraction of reads that map partially or wholly to a germline IGH gene segment.
Reads Mapped to IGK
Fraction of reads that map partially or wholly to a germline IGK gene segment.
Reads Mapped to IGL
Fraction of reads that map partially or wholly to a germline IGL gene segment.

Enrichment

Reads Mapped to Any V(D)J Gene 98.1%
Reads Mapped to IGH 31.8%
Reads Mapped to IGK 41.8%
Reads Mapped to IGL 23.0%
Median IGH UMIs per Cell
Median number of UMIs assigned to a IGH contig per cell. For B cells, only the max of {IGK, IGL} are counted.
Median IGK UMIs per Cell
Median number of UMIs assigned to a IGK contig per cell. For B cells, only the max of {IGK, IGL} are counted.
Median IGL UMIs per Cell
Median number of UMIs assigned to a IGL contig per cell. For B cells, only the max of {IGK, IGL} are counted.

V(D)J Expression

Median IGH UMIs per Cell 9.0
Median IGK UMIs per Cell 19.0
Median IGL UMIs per Cell 14.0
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 (IGK, IGH) 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 (IGL, IGH) 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 IGH Contig
Fraction of cell-associated barcodes with at least one IGH contig annotated as a full or partial V(D)J gene.
Cells With IGK Contig
Fraction of cell-associated barcodes with at least one IGK contig annotated as a full or partial V(D)J gene.
Cells With IGL Contig
Fraction of cell-associated barcodes with at least one IGL contig annotated as a full or partial V(D)J gene.
Cells With CDR3-annotated IGH Contig
Fraction of cell-associated barcodes with at least one IGH contig where a CDR3 was detected.
Cells With CDR3-annotated IGK Contig
Fraction of cell-associated barcodes with at least one IGK contig where a CDR3 was detected.
Cells With CDR3-annotated IGL Contig
Fraction of cell-associated barcodes with at least one IGL contig where a CDR3 was detected.
Cells With V-J Spanning IGH 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 IGH.
Cells With V-J Spanning IGK 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 IGK.
Cells With V-J Spanning IGL 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 IGL.
Cells With Productive IGH 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 IGH, 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 IGK 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 IGK, 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 IGL 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 IGL, 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 45.8%
Cells With Productive V-J Spanning (IGK, IGH) Pair 28.1%
Cells With Productive V-J Spanning (IGL, IGH) Pair 18.7%
Paired Clonotype Diversity 475.86
Cells With IGH Contig 81.9%
Cells With IGK Contig 62.7%
Cells With IGL Contig 48.8%
Cells With CDR3-annotated IGH Contig 58.3%
Cells With CDR3-annotated IGK Contig 54.6%
Cells With CDR3-annotated IGL Contig 35.7%
Cells With V-J Spanning IGH Contig 55.2%
Cells With V-J Spanning IGK Contig 52.8%
Cells With V-J Spanning IGL Contig 38.3%
Cells With Productive IGH Contig 52.8%
Cells With Productive IGK Contig 51.0%
Cells With Productive IGL Contig 33.3%
Contigs Unannotated 0.0%
 
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 3,077
Cell Count Confidence 63.4%
Mean Read Pairs per Cell 14,172
Mean Used Read Pairs per Cell 4,111
Fraction Reads in Cells 95.0%
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 43,609,508
Valid Barcodes 97.0%
Q30 Bases in Barcode 95.9%
Q30 Bases in RNA Read 1 93.5%
Q30 Bases in RNA Read 2 92.2%
Q30 Bases in Sample Index 91.4%
Q30 Bases in UMI 95.1%

Sample

Name vdj_v1_nsclc_b
Description Targeted enrichment of B cell Igs from a 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
{{ chart.description }}

{{ chart.title }}

 
{{ chart.description }}

{{ chart.title }}

{{chart.table.cols[0].label}} {{chart.table.cols[1].label}} {{chart.table.cols[2].label}} {{chart.table.cols[3].label}}
{{row[0].f}} {{row[2].f}}