# 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](/mc/tech-background/barcoding.md#version-1-v-1-before-spring-2020) and [V2 barcoding](/mc/tech-background/barcoding.md#version-2-v-2-spring-2020-to-now) 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](/mc/mapping-metrics/all-mapping-metrics.md#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](/mc/mapping-metrics/all-mapping-metrics.md#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` . --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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