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_24_hpm_HiChIP_all-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Smc1-HA_24_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:  286,531,306
 Normal Paired: 149,894,958 (52.31%)
 Chimeric Paired: 91,369,896 (31.89%)
 Chimeric Ambiguous: 25,159,386 (8.78%)
 Unmapped: 20,107,066 (7.02%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 241,264,854 (84.20%)
WARN [2024-02-27T15:48:59,758]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 30,688,312 (10.71%)
PCR Duplicates: 210,576,542 (73.49%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 30,700,173
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 15,940,404 (5.56% / 51.94%)
Hi-C Contacts: 14,747,908 (5.15% / 48.06%)
 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: 2,954,843  (1.03% / 9.63%)
Intra-chromosomal: 11,793,065  (4.12% / 38.43%)
Short Range (<20Kb): 4,484,147  (1.56% / 14.61%)
Long Range (>20Kb): 7,267,395  (2.54% / 23.68%)