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-R1-GSM3346690 -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-22-Trypanosoma-Hi-C-comparison/juicer-Single-marker-R1-GSM3346690 -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:  91,912,233
 Normal Paired: 59,609,491 (64.85%)
 Chimeric Paired: 8,567,127 (9.32%)
 Chimeric Ambiguous: 2,215,333 (2.41%)
 Unmapped: 21,520,282 (23.41%)
 Ligation Motif Present: 54,121,148 (58.88%)
Alignable (Normal+Chimeric Paired): 68,176,618 (74.18%)
Unique Reads: 56,327,148 (61.28%)
PCR Duplicates: 11,849,470 (12.89%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 172,676,091
Intra-fragment Reads: 769,221 (0.84% / 1.37%)
Below MAPQ Threshold: 19,739,790 (21.48% / 35.04%)
Hi-C Contacts: 35,818,137 (38.97% / 63.59%)
 Ligation Motif Present: 18,265,186  (19.87% / 32.43%)
 3' Bias (Long Range): 80% - 20%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 15,251,009  (16.59% / 27.08%)
Intra-chromosomal: 20,567,128  (22.38% / 36.51%)
Short Range (<20Kb): 9,468,482  (10.30% / 16.81%)
Long Range (>20Kb): 11,098,603  (12.08% / 19.70%)