File Sequenced reads Min rest. site distance Max library insert size Pairs mappable, unique and high quality Hi-C contacts One mate unmapped One mate not unique Low mapping quality dangling end GATC self ligation (removed) One mate not close to rest site same fragment self circle duplicated pairs inter chromosomal Intra short range (< 20kb) Intra long range (>= 20kb) Read pair type: inward pairs Read pair type: outward pairs Read pair type: left pairs Read pair type: right pairs GM12878_HiKAS_10M_Merge_HiC_Explorer.h5 513627084 300 1000 391856521 7963164 21158380 59841028 40771155 78175996 75009486 0 170003494 2532589 60704381 2804744 3774177 1384243 507713 3553717 554744 542246