All Mapping Metrics

Cell ID
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.
V1 cell ID 
{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.
V2 cell ID 
{Plate}-{MultiplexGroup}-{PCRIndex}-{RandomIndex}. 
Plate and Barcode Information
Plate
The 384-plate ID. Information from the in PlateInfo file.
PCRIndex
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.
RandomIndex
The random index name. Assigned during yap demultiplex.
Col384
The original column in the 384-plate.
Row384
The original row in the 384-plate.
FASTQ Metrics
Raw FASTQ
R1InputReads
Total number of R1 generated from yap demultiplex. This equals to CellInputReadPairs and R2InputReads.
R1InputReadsBP
Total number of R1 base pairs generated from yap demultiplex.
R2InputReads
Total number of R2 generated from yap demultiplex. This equals to CellInputReadPairs and R1InputReads.
R2InputReadsBP
Total number of R2 base pairs generated from yap demultiplex.
CellInputReadPairs
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) .
Trimmed FASTQ
R1WithAdapters
Number of R1 trimmed due to having illumina adapter.
R1QualTrimBP
Number of R1 base pairs trimmed due to low base quality.
R1TrimmedReads
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.
R2WithAdapters
Number of R2 trimmed due to having illumina adapter. 
R2QualTrimBP
Number of R2 base pairs trimmed due to low base quality.
R2TrimmedReads
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.
BAM Metrics
Bismark Mapped BAM
R1UniqueMappedReads
Number of unique mapped R1 reported by bismark.
R1MappingRate
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 .
R1OT
Number of R1 mapped to Original Top strand reported by bismark.
R1OB
Number of R1 mapped to Original Bottom strand reported by bismark.
R1CTOT
Number of R1 that are ComplemenTary to the Original Top strand reported by bismark.
R1CTOB
Number of R1 that are ComplemenTary to the Original Bottom strand reported by bismark.
R1TotalC
Number of total Cytosine beed covered in R1 reported by bismark.
R1TotalmCGRate
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 .
R2MappingRate
R2 mapping rate reported by bismark.
R2UnmappedReads
Number of unmapped R2 reported by bismark.
R2UnuniqueMappedReads
Number of ununique mapped R2 reported by bismark.
R2OT
Number of R2 mapped to Original Top strand reported by bismark.
R2OB
Number of R2 mapped to Original Bottom strand reported by bismark.
R2CTOT
Number of R2 that are ComplemenTary to the Original Top strand reported by bismark.
R2CTOB
Number of R2 that are ComplemenTary to the Original Bottom strand reported by bismark.
R2TotalC
Number of total Cytosine beed covered in R2 reported by bismark.
R2TotalmCGRate
mCG fraction in R2 reported by bismark.
R2TotalmCHGRate
mCHG fraction in R2 reported by bismark.
R2TotalmCHHRate
mCHH fraction in R2 reported by bismark.
Filtered BAM
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.)
FinalmCReads
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) .
ALLC Metrics
mCHmC
Total methylated cytosine in the CH context.
mCHCov
Total covered cytosine in the CH context.
mCHFrac
Calculated as mCHmC / mCHCov
mCGmC
Total methylated cytosine in the CG context.
mCGCov
Total covered cytosine in the CG context.
mCGFrac
Calculated as mCGmC / mCGCov
mCCCmC
Total methylated cytosine in the CCC context.
mCCCCov
Total covered cytosine in the CCC context.
mCCCFrac
Calculated as mCCCmC / mCCCCov
GenomeCov
Percentage of cytosine in the genome that been covered by at least one read.
DNA and RNA Reads Separation (mCT specific)
FinalDNAReads
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.
FinalRNAReads
Number of RNA reads (assigned to gene) counted by featureCount
FinalCountedReads
Number of reads counted by featureCount.
SelectedRNAReadsRatio
Calculated as FinalRNAReads / RNAUniqueMappedReads
GenesDetected
Number of genes that covered by at least one read.
Chromatin Contact (m3C specific)
CisShortContact 
Number of contact whose two ends are from the same chromosome and closer than min_gap parameter in the MappingConfig.
CisLongContact
Number of contact whose two ends are from the same chromosome and further than min_gap parameter in the MappingConfig.
TransContact
Number of contact whose two ends are from different chromosome.
TotalContacts
Calculated as CisShortContact + CisLongContact + TransContact .
CisShortRatio
Calculated as CisShortContact / TotalContacts .
CisLongRatio
Calculated as CisLongContact / TotalContacts .
TransRatio
Calculated as TransContact / TotalContacts .
​
Key Mapping Metrics
Generate MCDS
Last modified 1yr ago
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Outline
Cell ID
Plate and Barcode Information
DNA and RNA Reads Separation (mCT specific)
Chromatin Contact (m3C specific)