The first column (row index) of the mapping summary file is the cell ID. The cell ID pattern for V1 barcoding and V2 barcoding is different.
{Plate1}-{Plate2}-{PCRIndex}-{RandomIndex}, the Plate1 and Plate2 are two plates that multiplexed together by the eight random indexes. The Plate column (see below) is the actual plate that the cell comes from.
{Plate}-{MultiplexGroup}-{PCRIndex}-{RandomIndex}.
The 384-plate ID. Information from the in PlateInfo file.
The PCR index name. Information from the in PlateInfo file.
MultiplexGroup （V2 barcoding only）
The multiplex group number, a int from 1 to 6. Information from the in PlateInfo file.
The random index name. Assigned during yap demultiplex.
The original column in the 384-plate.
The original row in the 384-plate.
Total number of R1 generated from yap demultiplex. This equals to CellInputReadPairs and R2InputReads.
Total number of R1 base pairs generated from yap demultiplex.
Total number of R2 generated from yap demultiplex. This equals to CellInputReadPairs and R1InputReads.
Total number of R2 base pairs generated from yap demultiplex.
Total number of read pairs generated from yap demultiplex. This equals to R1InputReads and R2InputReads.
CellBarcodeRatio
Calculated by CellInputReadPairs / sum(CellInputReadPairs of the same multiplex group) .
Number of R1 trimmed due to having illumina adapter.
Number of R1 base pairs trimmed due to low base quality.
Number of R1 remained after adapter and quality trimming.
R1TrimmedReadsBP
Number of R1 base pairs remained after adapter and quality trimming.
R1TrimmedReadsRate
Calculated by R1TrimmedReads / R1InputReads.
Number of R2 trimmed due to having illumina adapter.
Number of R2 base pairs trimmed due to low base quality.
Number of R2 remained after adapter and quality trimming.
R2TrimmedReadsBP
Number of R2 base pairs remained after adapter and quality trimming.
R2TrimmedReadsRate
Calculated by R2TrimmedReads / R2InputReads.
Bismark Mapped BAM
R1UniqueMappedReads
Number of unique mapped R1 reported by bismark.
R1 mapping rate reported by bismark.
R1UnmappedReads
Number of unmapped R1 reported by bismark.
R1UnuniqueMappedReads
Number of ununique mapped R1 reported by bismark.
R1UnuniqueMappedReads (m3C specific)
Number of R1 that has unique read name (to prevent recount split reads) in MAPQ filtered BAM file.
R1MappingRate (m3C specific)
R1 mapping rate calculated by R1UnuniqueMappedReads / R1TrimmedReads * 100 .
Number of R1 mapped to Original Top strand reported by bismark.
Number of R1 mapped to Original Bottom strand reported by bismark.
Number of R1 that are ComplemenTary to the Original Top strand reported by bismark.
Number of R1 that are ComplemenTary to the Original Bottom strand reported by bismark.
Number of total Cytosine beed covered in R1 reported by bismark.
mCG fraction in R1 reported by bismark.
R1TotalmCHGRate
mCHG fraction in R1 reported by bismark.
R1TotalmCHHRate
mCHH fraction in R1 reported by bismark.
R2UniqueMappedReads
Number of unique mapped R2 reported by bismark.
R2UnuniqueMappedReads (m3C specific)
Number of R2 that has unique read name (to prevent recount split reads) in MAPQ filtered BAM file.
R2MappingRate (m3C specific)
R2 mapping rate calculated by R1UnuniqueMappedReads / R1TrimmedReads * 100 .
R2 mapping rate reported by bismark.
R2UnmappedReads
Number of unmapped R2 reported by bismark.
R2UnuniqueMappedReads
Number of ununique mapped R2 reported by bismark.
Number of R2 mapped to Original Top strand reported by bismark.
Number of R2 mapped to Original Bottom strand reported by bismark.
Number of R2 that are ComplemenTary to the Original Top strand reported by bismark.
Number of R2 that are ComplemenTary to the Original Bottom strand reported by bismark.
Number of total Cytosine beed covered in R2 reported by bismark.
mCG fraction in R2 reported by bismark.
R2TotalmCHGRate
mCHG fraction in R2 reported by bismark.
R2TotalmCHHRate
mCHH fraction in R2 reported by bismark.
R1MAPQFilteredReads
Number of R1 after filtering by MAPQ.
R1DuplicatedReads
Number of R1 that are marked as PCR duplicates.
R1DeduppedReads (m3C specific)
Number of R1 remained after removing PCR duplicates. Counted reads that have unique read name (to prevent recount split reads) from dedupplicate BAM file.
R1DuplicationRate
Calculated as R1DuplicatedReads / R1MAPQFilteredReads.
R1DuplicationRate (m3C specific)
Calculated as (1 - R1DeduppedReads(m3c) / R1UniqueMappedReads(m3c)) * 100 .
R1FinalBismarkReads
Final number of R1 used in generating ALLC file in mC mode. Calculated as R2MAPQFilteredReads - R2DuplicatedReads. In mCT mode, reads are further filtered by mC fraction (see FinalDNAReads.)
R2MAPQFilteredReads
Number of R1 after filtering by MAPQ.
R2DuplicatedReads
Number of R1 that are marked as PCR duplicates.
R2DeduppedReads (m3C specific)
Number of R2 remained after removing PCR duplicates. Counted reads that have unique read name (to prevent recount split reads) from dedupplicate BAM file.
R2DuplicationRate
Calculated as R2DuplicatedReads / R2MAPQFilteredReads.
R2DuplicationRate (m3C specific)
Calculated as (1 - R2DeduppedReads(m3c) / R2UniqueMappedReads(m3c)) * 100 .
R2FinalBismarkReads
Final number of R2 used in generate ALLC file in mC mode. Calculated as R2MAPQFilteredReads - R2DuplicatedReads. In mCT mode, reads are further filtered by mC fraction (see FinalDNAReads.)
Final number of total reads (R1 + R2) used in generating ALLC file. Calculated as R1FinalBismarkReads + R2FinalBismarkReads.
FinalmCReads (m3C specific)
Final number of total reads (R1 + R2) that has unique read name (to prevent recount split reads). Counted as R1DeduppedReads (m3c) + R2DeduppedReads (m3c) .
Total methylated cytosine in the CH context.
Total covered cytosine in the CH context.
Calculated as mCHmC / mCHCov
Total methylated cytosine in the CG context.
Total covered cytosine in the CG context.
Calculated as mCGmC / mCGCov
Total methylated cytosine in the CCC context.
Total covered cytosine in the CCC context.
Calculated as mCCCmC / mCCCCov
Percentage of cytosine in the genome that been covered by at least one read.
DNA and RNA Reads Separation (mCT specific)
Number of final DNA reads that passed read-level mC fraction filtering. These reads were used in generating ALLC file.
SelectedDNAReadsRatio
Calculated as FinalDNAReads / FinalmCReads.
RNAUniqueMappedReads
Number of reads uniquely mapped by STAR.
Number of RNA reads (assigned to gene) counted by featureCount
FinalCountedReads
Number of reads counted by featureCount.
SelectedRNAReadsRatio
Calculated as FinalRNAReads / RNAUniqueMappedReads
Number of genes that covered by at least one read.
Number of contact whose two ends are from the same chromosome and closer than min_gap parameter in the MappingConfig.
Number of contact whose two ends are from the same chromosome and further than min_gap parameter in the MappingConfig.
Number of contact whose two ends are from different chromosome.
Calculated as CisShortContact + CisLongContact + TransContact .
Calculated as CisShortContact / TotalContacts .
Calculated as CisLongContact / TotalContacts .
Calculated as TransContact / TotalContacts .