All Mapping Metrics

All mapping metrics from the mapping pipeline

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 .