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: 16,105,303 (17.52% / 28.59%)
Hi-C Contacts: 39,452,624 (42.92% / 70.04%)
 Ligation Motif Present: 19,872,450  (21.62% / 35.28%)
 3' Bias (Long Range): 79% - 21%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 17,941,658  (19.52% / 31.85%)
Intra-chromosomal: 21,510,966  (23.40% / 38.19%)
Short Range (<20Kb): 9,727,880  (10.58% / 17.27%)
Long Range (>20Kb): 11,783,036  (12.82% / 20.92%)