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/2019-12-14-NextSeq-run-2/juicer-L1273-Chromera_velia-Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-12-14-NextSeq-run-2/juicer-L1273-Chromera_velia-Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Chromerida/Chromera_velia_CCMP2878-CDMZ01/CDMZ01.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Chromerida/Chromera_velia_CCMP2878-CDMZ01/bwa-indexes/CDMZ01_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Chromerida/Chromera_velia_CCMP2878-CDMZ01/bwa-indexes/CDMZ01.fa                                                                                                                                                                                                                                                                                                                
Sequenced Read Pairs:  173,975,683
 Normal Paired: 139,131,930 (79.97%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 34,843,753 (20.03%)
 Ligation Motif Present: 25,684,281 (14.76%)
Alignable (Normal+Chimeric Paired): 139,131,930 (79.97%)
Unique Reads: 78,129,787 (44.91%)
PCR Duplicates: 60,956,259 (35.04%)
Optical Duplicates: 45,884 (0.03%)
Library Complexity Estimate: 107,792,856
Intra-fragment Reads: 1,303,441 (0.75% / 1.67%)
Below MAPQ Threshold: 33,744,665 (19.40% / 43.19%)
Hi-C Contacts: 43,081,681 (24.76% / 55.14%)
 Ligation Motif Present: 1,684,888  (0.97% / 2.16%)
 3' Bias (Long Range): 70% - 30%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 29,392,832  (16.89% / 37.62%)
Intra-chromosomal: 13,688,849  (7.87% / 17.52%)
Short Range (<20Kb): 12,462,063  (7.16% / 15.95%)
Long Range (>20Kb): 1,226,618  (0.71% / 1.57%)