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_rep2-GSM4161198-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Cell_24_hpm_Hi-C_rep2-GSM4161198-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:  117,173,562
 Normal Paired: 42,984,182 (36.68%)
 Chimeric Paired: 66,346,517 (56.62%)
 Chimeric Ambiguous: 3,998,652 (3.41%)
 Unmapped: 3,844,211 (3.28%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 109,330,699 (93.31%)
WARN [2024-02-24T04:00:57,437]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 87,385,376 (74.58%)
PCR Duplicates: 21,945,323 (18.73%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 234,526,723
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 3,861,683 (3.30% / 4.42%)
Hi-C Contacts: 83,523,693 (71.28% / 95.58%)
 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: 15,293,436  (13.05% / 17.50%)
Intra-chromosomal: 68,230,257  (58.23% / 78.08%)
Short Range (<20Kb): 25,499,179  (21.76% / 29.18%)
Long Range (>20Kb): 42,723,834  (36.46% / 48.89%)