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-L1108-MAC_final_post_review -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-L1026-L1027-L1216-L1624-L1108-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:  942,686,104
 Normal Paired: 733,636,265 (77.82%)
 Chimeric Paired: 18,916,211 (2.01%)
 Chimeric Ambiguous: 502,305 (0.05%)
 Unmapped: 189,631,323 (20.12%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 752,552,476 (79.83%)
WARN [2024-02-28T04:45:23,109]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 427,004,812 (45.30%)
PCR Duplicates: 324,477,700 (34.42%)
Optical Duplicates: 1,069,964 (0.11%)
Library Complexity Estimate: 595,761,967
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 68,623,990 (7.28% / 16.07%)
Hi-C Contacts: 358,380,822 (38.02% / 83.93%)
 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: 134,691,182  (14.29% / 31.54%)
Intra-chromosomal: 223,689,640  (23.73% / 52.39%)
Short Range (<20Kb): 116,795,231  (12.39% / 27.35%)
Long Range (>20Kb): 106,732,119  (11.32% / 25.00%)