snm3C Mapping Summary Metrics Overview

The snm3C pipeline outputs a summary CSV file containing trimming, mapping, deduplication, chromatin contact, and ALLC site statistics.

The summary file is generated using the smn3c_summary() function of a custom python3 script.

The snm3C pipeline was adapted from YAP (Yet Another Pipeline) in collaboration with Hanqing Liu, Wei Tian, Wubin Ding, Huaming Chen, Chongyuan Luo, Jingtian Zhou, and the entire laboratory of Joseph Ecker. For more information about the snm3C metrics, please see the YAP documentation created by Hanqing Liu.

Metric	Details
cell	The unique identifier for each cell.
InputReadPairs	Total number of read pairs.
InputReadPairsBP	Total number of base pairs.
TrimmedReadPairs	Total number of trimmed read pairs.
R1WithAdapters	Number of R1 reads trimmed to remove Illumina adapter.
R1QualTrimBP	Number of R1 base pairs trimmed due to low base quality.
R1TrimmedReadsBP	Number of R1 base pairs remaining after adapter and quality trimming.
R2WithAdapters	Number of R2 reads trimmed to remove Illumina adapter.
R2QualTrimBP	Number of R2 base pairs trimmed due to low base quality.
R2TrimmedReadsBP	Number of R2 base pairs remaining after adapter and quality trimming.
UniqueMappedReads	Number of uniquely mapped reads.
UniqueMappingRate	Rate of unique read mapping.
MultiMappedReads	Number of multimapped reads.
MultiMappingRate	Rate of multimapping.
OverallMappingRate	Rate of mapping for all reads.
R1UniqueMappedReads	Number of uniquely mapped R1 reads.
R1MultiMappedReads	Number of multimapped R1 reads.
R1UniqueMappingRate	Rate of unique R1 read mapping.
R1MultiMappingRate	Rate of R1 read multimapping.
R1OverallMappingRate	Rate of mapping for all R1 reads.
R2UniqueMappedReads	Number of uniquely mapped R2 reads.
R2MultiMappedReads	Number of multimapped R2 reads.
R2UniqueMappingRate	Rate of unique R2 read mapping.
R2MultiMappingRate	Rate of R2 read multimapping.
R2OverallMappingRate	Rate of mapping for all R2 reads.
UniqueAlignFinalReads	Final unique mapped total reads after picard deduplication.
UniqueAlignDuplicatedReads	Paired and unpaired duplicated reads.
UniqueAlignPCRDuplicationRate	FinalReads /(FinalReads and DuplicatedReads).
CisContacts	Number of chromatin contacts where the two loci are on the same chromosome.
CisCutContacts	Number of read pairs that are split from the same read at the cut site, and map to the same chromosome.
CisMultiContacts	CisContacts read pair contains multiple read contacts.
CisCutMultiContacts	CisCutContacts read pair contains multiple read contacts.
TransContacts	Number of chromatin contacts where the two loci are on different chromosome.
TransCutContacts	Number of read pairs that are split from the same read at the cut site, and map to different chromosomes.
TransMultiContacts	TransContacts read pair contains multiple read contacts.
TransCutMultiContacts	TransCutContacts read pair contains multiple read contacts.
ChimericContacts	Two reads that are split from the same read, but not at the cut site; may be due to artificial chimeric synthesis events.
NoContacts	Not a contact.
MappedFragments	Total number of mapped fragments.
DeduppedContacts	Total number of deduplicated contacts.
ContactsDeduplicationRate	(Input_contacts - dedup_contacts) / (input_contacts + 0.00001)
TotalCisContacts	Total number of cis contacts.
TotalTransContacts	Total number of trans contacts.
TotalMultiContacts	Total number of multi contacts (read pair contains multiple read contacts).
CisContactsRatio	TotalCisContacts / number of mapped fragments.
TransContactsRatio	TotalTransContacts / number of mapped fragments.
MultiContactsRatio	TotalMultiContacts / number of mapped fragments.
mCCCmC	Total methylated cytosine in the CCC context.
mCGmC	Total methylated cytosine in the CG context.
mCHmC	Total methylated cytosine in the CH context.
mCCCCov	Total covered cytosine in the CCC context.
mCGCov	Total covered cytosine in the CG context.
mCHCov	Total covered cytosine in the CH context.
mCCCFrac	Fraction of methylated cytosine (mCCCmC) divided by covered cytosine (mCCCCov) in the CCC context.
mCGFrac	Fraction of methylated cytosine (mCGmC) divided by covered cytosine (mCGCov) in the CG context.
mCHFrac	Fraction of methylated cytosine (mCHmC) divided by covered cytosine (mCHCov) in the CH context.