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-L4133-RAW264-7_Hi-KAS -d /oak/stanford/groups/akundaje/marinovg/ENCODE4/Chromatin-nanopores/2025-07-26-NextSeq-run/juicer-L4133-RAW264-7_Hi-KAS -p /oak/stanford/groups/akundaje/marinovg/genomes/mm10/mm10.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bwa-indexes/mm10_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/mm10/bwa-indexes/mm10.fa                                                                                                                                                                                                                                                                                                                                                                                                                   
Sequenced Read Pairs:  232,454,351
 Normal Paired: 199,893,687 (85.99%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 32,560,664 (14.01%)
 Ligation Motif Present: 128,941 (0.06%)
Alignable (Normal+Chimeric Paired): 199,893,687 (85.99%)
Unique Reads: 124,593,744 (53.60%)
PCR Duplicates: 75,282,410 (32.39%)
Optical Duplicates: 17,533 (0.01%)
Library Complexity Estimate: 193,395,051
Intra-fragment Reads: 63,297,101 (27.23% / 50.80%)
Below MAPQ Threshold: 29,161,186 (12.54% / 23.41%)
Hi-C Contacts: 32,135,457 (13.82% / 25.79%)
 Ligation Motif Present: 25,405  (0.01% / 0.02%)
 3' Bias (Long Range): 47% - 53%
 Pair Type %(L-I-O-R): 21% - 28% - 29% - 22%
Inter-chromosomal: 403,094  (0.17% / 0.32%)
Intra-chromosomal: 31,732,363  (13.65% / 25.47%)
Short Range (<20Kb): 31,646,726  (13.61% / 25.40%)
Long Range (>20Kb): 85,622  (0.04% / 0.07%)