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-R1-GSM3346688 -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-22-Trypanosoma-Hi-C-comparison/juicer-dH3.V-dH4.V-R1-GSM3346688 -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:  107,282,821
 Normal Paired: 67,221,403 (62.66%)
 Chimeric Paired: 9,408,007 (8.77%)
 Chimeric Ambiguous: 2,140,066 (1.99%)
 Unmapped: 28,513,345 (26.58%)
 Ligation Motif Present: 54,424,626 (50.73%)
Alignable (Normal+Chimeric Paired): 76,629,410 (71.43%)
Unique Reads: 34,426,184 (32.09%)
PCR Duplicates: 42,203,226 (39.34%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 40,556,515
Intra-fragment Reads: 707,378 (0.66% / 2.05%)
Below MAPQ Threshold: 14,950,665 (13.94% / 43.43%)
Hi-C Contacts: 18,768,141 (17.49% / 54.52%)
 Ligation Motif Present: 8,429,080  (7.86% / 24.48%)
 3' Bias (Long Range): 85% - 15%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 7,214,000  (6.72% / 20.95%)
Intra-chromosomal: 11,554,141  (10.77% / 33.56%)
Short Range (<20Kb): 5,024,567  (4.68% / 14.60%)
Long Range (>20Kb): 6,529,566  (6.09% / 18.97%)