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-Cell_24_hpm_Hi-C_all-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Cell_24_hpm_Hi-C_all-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:  161,804,315
 Normal Paired: 62,756,897 (38.79%)
 Chimeric Paired: 85,721,195 (52.98%)
 Chimeric Ambiguous: 7,712,894 (4.77%)
 Unmapped: 5,613,329 (3.47%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 148,478,092 (91.76%)
WARN [2024-02-27T14:46:51,382]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 120,198,198 (74.29%)
PCR Duplicates: 28,279,894 (17.48%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 338,530,682
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 6,212,787 (3.84% / 5.17%)
Hi-C Contacts: 113,985,411 (70.45% / 94.83%)
 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: 22,595,825  (13.96% / 18.80%)
Intra-chromosomal: 91,389,586  (56.48% / 76.03%)
Short Range (<20Kb): 32,324,955  (19.98% / 26.89%)
Long Range (>20Kb): 59,019,037  (36.48% / 49.10%)