Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; java version "1.8.0_131"; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-L1026-L1027-L1216-L1624-MAC_final_post_review -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-L1026-L1027-L1216-L1624-MAC_final_post_review -p /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1027-Tetrahymena_thermophila_Hi-C_MluCl/juicer-L1027-Tetrahymena_thermophila_Hi-C_MluCl-all-reads-3D_DNA/final-post-review/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.FINAL.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1027-Tetrahymena_thermophila_Hi-C_MluCl/juicer-L1027-Tetrahymena_thermophila_Hi-C_MluCl-all-reads-3D_DNA/final-post-review/bwa-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.FINAL.fasta                                                                           
Sequenced Read Pairs:  722,128,018
 Normal Paired: 557,383,246 (77.19%)
 Chimeric Paired: 18,916,211 (2.62%)
 Chimeric Ambiguous: 502,305 (0.07%)
 Unmapped: 145,326,256 (20.12%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 576,299,457 (79.81%)
WARN [2024-02-27T23:59:53,313]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 303,853,004 (42.08%)
PCR Duplicates: 271,485,678 (37.60%)
Optical Duplicates: 960,775 (0.13%)
Library Complexity Estimate: 397,118,746
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 47,316,336 (6.55% / 15.57%)
Hi-C Contacts: 256,536,668 (35.53% / 84.43%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 65,817,913  (9.11% / 21.66%)
Intra-chromosomal: 190,718,755  (26.41% / 62.77%)
Short Range (<20Kb): 101,674,022  (14.08% / 33.46%)
Long Range (>20Kb): 88,905,280  (12.31% / 29.26%)