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_3_hpm_Hi-C_all-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Cell_3_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:  103,848,140
 Normal Paired: 38,918,985 (37.48%)
 Chimeric Paired: 55,227,403 (53.18%)
 Chimeric Ambiguous: 6,364,153 (6.13%)
 Unmapped: 3,337,599 (3.21%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 94,146,388 (90.66%)
WARN [2024-02-27T12:57:33,006]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 78,374,110 (75.47%)
PCR Duplicates: 15,772,278 (15.19%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 248,638,204
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 3,856,514 (3.71% / 4.92%)
Hi-C Contacts: 74,517,596 (71.76% / 95.08%)
 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: 17,030,834  (16.40% / 21.73%)
Intra-chromosomal: 57,486,762  (55.36% / 73.35%)
Short Range (<20Kb): 18,545,916  (17.86% / 23.66%)
Long Range (>20Kb): 38,904,793  (37.46% / 49.64%)