# 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

## Read orientation table

%%TABLE_ORIENTATION%% Download table (tab separated)

## Number of reads table

%%TABLE%% Download table (tab separated)