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-Smc1-HA_3_hpm_HiChIP_all-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Smc1-HA_3_hpm_HiChIP_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:  311,645,575
 Normal Paired: 146,612,775 (47.04%)
 Chimeric Paired: 104,104,428 (33.40%)
 Chimeric Ambiguous: 24,774,081 (7.95%)
 Unmapped: 36,154,291 (11.60%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 250,717,203 (80.45%)
WARN [2024-02-27T16:01:29,716]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 41,779,695 (13.41%)
PCR Duplicates: 208,937,508 (67.04%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 41,884,997
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 15,465,215 (4.96% / 37.02%)
Hi-C Contacts: 26,314,480 (8.44% / 62.98%)
 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: 4,701,415  (1.51% / 11.25%)
Intra-chromosomal: 21,613,065  (6.94% / 51.73%)
Short Range (<20Kb): 7,678,398  (2.46% / 18.38%)
Long Range (>20Kb): 13,915,026  (4.47% / 33.31%)