Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1188; 20 threads; java version "1.8.0_131"; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-22-Trypanosoma-Hi-C-comparison/juicer-dH3.V-dH4.V-R2-GSM3346689 -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-22-Trypanosoma-Hi-C-comparison/juicer-dH3.V-dH4.V-R2-GSM3346689 -p /oak/stanford/groups/akundaje/marinovg/genomes/Kinetoplastida/Trypanosoma_brucei/Trypanosoma_brucei.TryBru_Apr2005_chr11.20.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Kinetoplastida/Trypanosoma_brucei/bwa-indexes/Trypanosoma_brucei.TryBru_Apr2005_chr11.20_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Kinetoplastida/Trypanosoma_brucei/bwa-indexes/Trypanosoma_brucei.TryBru_Apr2005_chr11.20.fa                                                                                                                                                                                                
Sequenced Read Pairs:  74,697,499
 Normal Paired: 46,894,184 (62.78%)
 Chimeric Paired: 6,002,392 (8.04%)
 Chimeric Ambiguous: 1,395,177 (1.87%)
 Unmapped: 20,405,746 (27.32%)
 Ligation Motif Present: 36,365,198 (48.68%)
Alignable (Normal+Chimeric Paired): 52,896,576 (70.81%)
Unique Reads: 23,014,466 (30.81%)
PCR Duplicates: 29,882,110 (40.00%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 26,694,388
Intra-fragment Reads: 489,602 (0.66% / 2.13%)
Below MAPQ Threshold: 10,141,453 (13.58% / 44.07%)
Hi-C Contacts: 12,383,411 (16.58% / 53.81%)
 Ligation Motif Present: 5,417,169  (7.25% / 23.54%)
 3' Bias (Long Range): 84% - 16%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 4,364,100  (5.84% / 18.96%)
Intra-chromosomal: 8,019,311  (10.74% / 34.84%)
Short Range (<20Kb): 3,428,612  (4.59% / 14.90%)
Long Range (>20Kb): 4,590,696  (6.15% / 19.95%)