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-Single-marker-R2-GSM3346691 -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-22-Trypanosoma-Hi-C-comparison/juicer-Single-marker-R2-GSM3346691 -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:  65,660,269
 Normal Paired: 42,391,189 (64.56%)
 Chimeric Paired: 5,425,804 (8.26%)
 Chimeric Ambiguous: 1,461,467 (2.23%)
 Unmapped: 16,381,809 (24.95%)
 Ligation Motif Present: 36,125,002 (55.02%)
Alignable (Normal+Chimeric Paired): 47,816,993 (72.82%)
Unique Reads: 41,724,938 (63.55%)
PCR Duplicates: 6,092,055 (9.28%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 171,356,968
Intra-fragment Reads: 621,291 (0.95% / 1.49%)
Below MAPQ Threshold: 11,858,279 (18.06% / 28.42%)
Hi-C Contacts: 29,245,368 (44.54% / 70.09%)
 Ligation Motif Present: 14,130,254  (21.52% / 33.87%)
 3' Bias (Long Range): 78% - 22%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 12,629,757  (19.24% / 30.27%)
Intra-chromosomal: 16,615,611  (25.31% / 39.82%)
Short Range (<20Kb): 7,757,504  (11.81% / 18.59%)
Long Range (>20Kb): 8,858,065  (13.49% / 21.23%)