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: 14,637,982 (22.29% / 35.08%)
Hi-C Contacts: 26,465,665 (40.31% / 63.43%)
 Ligation Motif Present: 12,998,053  (19.80% / 31.15%)
 3' Bias (Long Range): 79% - 21%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 10,607,936  (16.16% / 25.42%)
Intra-chromosomal: 15,857,729  (24.15% / 38.01%)
Short Range (<20Kb): 7,538,947  (11.48% / 18.07%)
Long Range (>20Kb): 8,318,746  (12.67% / 19.94%)