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Sample information : $sampleid



Estimated number of cells
The total number of barcodes identified as cells.
Mean Read Pairs per Cell
The mean number of reads detected per cell.
Number of 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.
Reads Mapped to Any V(D)J Gene
Fraction of reads that partially or wholly map to any germline V(D)J gene segment.
$Estimated_number_of_cells

Estimated number of cell

$Mean_Read_Pairs_per_Cell

Mean Read Pairs per Cell

$Number_of_Cells_With_Productive_V_J_Spanning_Pair

Number of Cells With Productive V-J Spanning Pair

$Reads_Mapped_to_Any_VDJ_Gene

Reads Mapped to Any V(D)J Gene

Summary


Estimated number of cells
The total number of barcodes identified as cells.
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.
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.
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 TRA UMIs per Cell
$Median_TRA_UMIs_per_Cell
Median TRB UMIs per Cell
$Median_TRB_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 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.
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 TRA
$Reads_Mapped_to_TRA
Reads Mapped to TRB
$Reads_Mapped_to_TRB
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 (TRA, TRB) Pair
Fraction of cell-associated barcodes with at least one productive contig for each chain of the (TRA, TRB) 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 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 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 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 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 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.
Cells With Productive V-J Spanning Pair
$Cells_With_Productive_V_J_Spanning_Pair
Cells With Productive V-J Spanning (TRA, TRB) Pair
$Cells_With_Productive_V_J_Spanning_TRA_TRB_Pair
Paired Clonotype Diversity
$Paired_Clonotype_Diversity
Cells With TRA Contig
$Cells_With_TRA_Contig
Cells With TRB Contig
$Cells_With_TRB_Contig
Cells With CDR3-annotated TRA Contig
$Cells_With_CDR3_annotated_TRA_Contig
Cells With CDR3-annotated TRB Contig
$Cells_With_CDR3_annotated_TRB_Contig
Cells With V-J Spanning TRA Contig
$Cells_With_V_J_Spanning_TRA_Contig
Cells With V-J Spanning TRB Contig
$Cells_With_V_J_Spanning_TRB_Contig
Cells With Productive TRA Contig
$Cells_With_Productive_TRA_Contig
Cells With Productive TRB Contig
$Cells_With_Productive_TRB_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.
$plot2



$table