HiCExplorer QC report
Pairs sequenced
Unmappable and non-unique pairs
This figure contains the fraction of reads, with respect to the total number of reads, that did not map, that have a low quality score or that didn't map uniquely to the genome.
Unmappable and non-unique table
%%TABLE_UNMAP%% Download table (tab separated)Pairs discarded
This figure contains the fraction read pairs (with respect to mappable reads) that were discarded when building the Hi-C matrix.
- Dangling ends
- These are reads that start with the restriction site and constitute reads that were digested but no ligated.
- Same fragment
- These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between. These read pairs are not valid Hi-C pairs
- Self circle
- self circles are defined as pairs within 25kb with 'outward' read orientation
- Self ligation
- These are read pairs with a restriction site in between that are within 800 bp.
Discarded pairs table
%%TABLE_DISCARDED%% Download table (tab separated)Contact distance
Contact distance table
%%TABLE_DISTANCE%% Download table (tab separated)Read orientation
