Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1188; 60 threads; java version "1.8.0_131"; scripts/juicer.sh -t 60 -D /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2025-07-26-NextSeq-run/juicer-L4132-K562_Hi-KAS -d /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2025-07-26-NextSeq-run/juicer-L4132-K562_Hi-KAS -p /oak/stanford/groups/akundaje/marinovg/genomes/hg20/hg38-no-haps.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bwa-indexes/hg38-no-haps_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/hg20/bwa-indexes/hg38-no-haps.fa                                                                                                                                                                                                                                                                                                                                                                                                   
Sequenced Read Pairs:  134,816,899
 Normal Paired: 121,215,272 (89.91%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 13,601,627 (10.09%)
 Ligation Motif Present: 306,261 (0.23%)
Alignable (Normal+Chimeric Paired): 121,215,272 (89.91%)
Unique Reads: 60,776,795 (45.08%)
PCR Duplicates: 60,428,946 (44.82%)
Optical Duplicates: 9,531 (0.01%)
Library Complexity Estimate: 76,425,333
Intra-fragment Reads: 22,311,381 (16.55% / 36.71%)
Below MAPQ Threshold: 24,145,407 (17.91% / 39.73%)
Hi-C Contacts: 14,320,007 (10.62% / 23.56%)
 Ligation Motif Present: 29,532  (0.02% / 0.05%)
 3' Bias (Long Range): 38% - 62%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 441,056  (0.33% / 0.73%)
Intra-chromosomal: 13,878,951  (10.29% / 22.84%)
Short Range (<20Kb): 13,815,711  (10.25% / 22.73%)
Long Range (>20Kb): 63,191  (0.05% / 0.10%)