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-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-L1026-L1027-L1216-L1624-L1108-MIC -p /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3/bwa-indexes/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3.fa                                                                                                                                                                                                                                                                  
Sequenced Read Pairs:  942,686,104
 Normal Paired: 790,528,794 (83.86%)
 Chimeric Paired: 24,382,378 (2.59%)
 Chimeric Ambiguous: 1,766,389 (0.19%)
 Unmapped: 126,008,543 (13.37%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 814,911,172 (86.45%)
WARN [2024-03-01T03:22:30,853]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 458,274,778 (48.61%)
PCR Duplicates: 355,543,245 (37.72%)
Optical Duplicates: 1,093,149 (0.12%)
Library Complexity Estimate: 633,762,272
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 94,471,462 (10.02% / 20.61%)
Hi-C Contacts: 363,803,316 (38.59% / 79.39%)
 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: 109,601,448  (11.63% / 23.92%)
Intra-chromosomal: 254,201,868  (26.97% / 55.47%)
Short Range (<20Kb): 116,501,691  (12.36% / 25.42%)
Long Range (>20Kb): 137,536,061  (14.59% / 30.01%)