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-R3-GSM3346692 -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2020-01-22-Trypanosoma-Hi-C-comparison/juicer-Single-marker-R3-GSM3346692 -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:  76,566,936
 Normal Paired: 49,590,759 (64.77%)
 Chimeric Paired: 6,322,457 (8.26%)
 Chimeric Ambiguous: 1,683,063 (2.20%)
 Unmapped: 18,970,657 (24.78%)
 Ligation Motif Present: 42,630,806 (55.68%)
Alignable (Normal+Chimeric Paired): 55,913,216 (73.03%)
Unique Reads: 48,146,498 (62.88%)
PCR Duplicates: 7,766,718 (10.14%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 182,157,338
Intra-fragment Reads: 682,172 (0.89% / 1.42%)
Below MAPQ Threshold: 13,565,700 (17.72% / 28.18%)
Hi-C Contacts: 33,898,626 (44.27% / 70.41%)
 Ligation Motif Present: 16,418,551  (21.44% / 34.10%)
 3' Bias (Long Range): 77% - 23%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 15,128,174  (19.76% / 31.42%)
Intra-chromosomal: 18,770,452  (24.52% / 38.99%)
Short Range (<20Kb): 8,567,884  (11.19% / 17.80%)
Long Range (>20Kb): 10,202,528  (13.32% / 21.19%)