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: 21,726,089 (16.12% / 35.75%)
Hi-C Contacts: 16,739,325 (12.42% / 27.54%)
 Ligation Motif Present: 35,364  (0.03% / 0.06%)
 3' Bias (Long Range): 42% - 58%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 780,701  (0.58% / 1.28%)
Intra-chromosomal: 15,958,624  (11.84% / 26.26%)
Short Range (<20Kb): 15,857,307  (11.76% / 26.09%)
Long Range (>20Kb): 101,255  (0.08% / 0.17%)