Fraction of cell-associated barcodes with at least one productive contig for each chain of the receptor pair. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to 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.
Reads Mapped to Any V(D)J Gene
Fraction of reads that partially or wholly map to any germline V(D)J gene segment.
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.
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.
Plot
The plot shows the count of filtered UMIs mapped to each barcode. A barcode must have a contig that aligns to a V segment to be identified as a targeted cell. (In the denovo case, the only requirement is a contig's presence.) There must also be at least three filtered UMIs with at least two read pairs each. It is possible that a barcode with at least as many filtered UMIs as another cell-associated barcode is not identified as a targeted cell. The color of the graph is based on the local density of cell-associated barcodes.
Sample ID
$sampleid
Species
$species
Estimated number of cells
$Estimated_number_of_cells
Mean Read Pairs per Cell
$Mean_Read_Pairs_per_Cell
Mean Used Read Pairs per Cell
$Mean_Used_Read_Pairs_per_Cell
Fraction Reads in Cells
$Fraction_Reads_in_Cells
Median IGH UMIs per Cell
$Median_IGH_UMIs_per_Cell
Median IGK UMIs per Cell
$Median_IGK_UMIs_per_Cell
Median IGL UMIs per Cell
$Median_IGL_UMIs_per_Cell
$plot1
Sequencing
Number of reads
Number of raw off-machine reads obtained by this sequencing program.
Reads pass QC
Number of reads after quality control (QC) that can be used for downstream analysis. QC includes filtering low quality reads and invalid barcodes.
Q30 bases in cell barcode
Fraction of cell barcode bases with Q-score ≥ 30.
Q30 bases in UMI
Fraction of UMI bases with Q-score ≥ 30.
Q30 bases in reads
Fraction of RNA read bases with Q-score ≥ 30.
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.
Number of reads
$Number_of_reads
Reads pass QC
$Reads_pass_QC
Q30 bases in cell barcode
$Q30_Bases_in_Barcode
Q30 bases in UMI
$Q30_Bases_in_UMI
Q30 bases in reads
$Q30_Bases_in_Reads
Reads Mapped to Any V(D)J Gene
$Reads_Mapped_to_Any_VDJ_Gene
Reads Mapped to IGH
$Reads_Mapped_to_IGH
Reads Mapped to IGK
$Reads_Mapped_to_IGK
Reads Mapped to IGL
$Reads_Mapped_to_IGL
Annotation
Cells With Productive V-J Spanning Pair
Fraction of cell-associated barcodes with at least one productive contig for each chain of the receptor pair. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to 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 productive contig for each chain of the (IGK, IGH) receptor pair. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to 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 productive contig for each chain of the (IGL, IGH) receptor pair. A productive contig satisfies the following conditions: the contig annotations span the 5' end of the V region to 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 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 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 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 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 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 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.
Cells With Productive V-J Spanning Pair
$Cells_With_Productive_V_J_Spanning_Pair
Cells With Productive V-J Spanning (IGK, IGH) Pair
$Cells_With_Productive_V_J_Spanning_IGH_IGK_Pair
Cells With Productive V-J Spanning (IGL, IGH) Pair
$Cells_With_Productive_V_J_Spanning_IGH_IGL_Pair
Paired Clonotype Diversity
$Paired_Clonotype_Diversity
Cells With IGH Contig
$Cells_With_IGH_Contig
Cells With IGK Contig
$Cells_With_IGK_Contig
Cells With IGL Contig
$Cells_With_IGL_Contig
Cells With CDR3-annotated IGH Contig
$Cells_With_CDR3_annotated_IGH_Contig
Cells With CDR3-annotated IGK Contig
$Cells_With_CDR3_annotated_IGK_Contig
Cells With CDR3-annotated IGL Contig
$Cells_With_CDR3_annotated_IGL_Contig
Cells With V-J Spanning IGH Contig
$Cells_With_V_J_Spanning_IGH_Contig
Cells With V-J Spanning IGK Contig
$Cells_With_V_J_Spanning_IGK_Contig
Cells With V-J Spanning IGL Contig
$Cells_With_V_J_Spanning_IGL_Contig
Cells With Productive IGH Contig
$Cells_With_Productive_IGH_Contig
Cells With Productive IGK Contig
$Cells_With_Productive_IGK_Contig
Cells With Productive IGL Contig
$Cells_With_Productive_IGL_Contig
Clonotype
Plot
Top 10 clonotypes by frequency in this sample. A clonotype is defined as a unique set of CDR3 nucleotide sequences. For the full table and more details, please refer to the "clonotypes.csv" file produced by the pipeline.
Table
All clonotypes by frequency in this sample. A clonotype is defined as a unique set of CDR3 nucleotide sequences. For the full table and more details, please refer to the "clonotypes.csv" file produced by the pipeline.