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_1.5_hpm_HiChIP_all-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Smc1-HA_1.5_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:  295,646,698
 Normal Paired: 151,267,267 (51.16%)
 Chimeric Paired: 97,008,364 (32.81%)
 Chimeric Ambiguous: 26,300,418 (8.90%)
 Unmapped: 21,070,649 (7.13%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 248,275,631 (83.98%)
WARN [2024-02-27T17:52:24,637]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 44,243,096 (14.96%)
PCR Duplicates: 204,032,535 (69.01%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 44,408,851
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 17,773,317 (6.01% / 40.17%)
Hi-C Contacts: 26,469,779 (8.95% / 59.83%)
 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: 3,873,724  (1.31% / 8.76%)
Intra-chromosomal: 22,596,055  (7.64% / 51.07%)
Short Range (<20Kb): 9,938,208  (3.36% / 22.46%)
Long Range (>20Kb): 12,626,256  (4.27% / 28.54%)