Experiment description: Juicer version 1.5.6; BWA 0.7.12-r1039; 20 threads; java version "1.8.0_40"; scripts/juicer.sh -t 20 -D /srv/scratch/marinovg/juicer-L1193-Euglena_gracilis_Hi-C -d /srv/scratch/marinovg/juicer-L1193-Euglena_gracilis_Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Euglenida/Euglena_gracilis-EugGra_PACBIO_Illumina_merge_V1/GCA_900893395.1_EugGra_PACBIO_Illumina_merge_V1_genomic+chrP+mitochondrial.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Euglenida/Euglena_gracilis-EugGra_PACBIO_Illumina_merge_V1/bwa-indexes/Euglena_gracilis-EugGra_PACBIO_Illumina_merge_V1_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Euglenida/Euglena_gracilis-EugGra_PACBIO_Illumina_merge_V1/bwa-indexes/GCA_900893395.1_EugGra_PACBIO_Illumina_merge_V1_genomic+chrP+mitochondrial.fa                                                                                                                                                                                      
Sequenced Read Pairs:  498,388,775
 Normal Paired: 327,567,835 (65.73%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 170,820,940 (34.27%)
 Ligation Motif Present: 114,021,675 (22.88%)
Alignable (Normal+Chimeric Paired): 327,567,835 (65.73%)
Unique Reads: 318,474,754 (63.90%)
PCR Duplicates: 9,059,770 (1.82%)
Optical Duplicates: 33,311 (0.01%)
Library Complexity Estimate: 5,810,928,373
Intra-fragment Reads: 2,870,455 (0.58% / 0.90%)
Below MAPQ Threshold: 254,442,636 (51.05% / 79.89%)
Hi-C Contacts: 61,161,663 (12.27% / 19.20%)
 Ligation Motif Present: 3,252,097  (0.65% / 1.02%)
 3' Bias (Long Range): 51% - 49%
 Pair Type %(L-I-O-R): 23% - 24% - 28% - 25%
Inter-chromosomal: 54,869,270  (11.01% / 17.23%)
Intra-chromosomal: 6,292,393  (1.26% / 1.98%)
Short Range (<20Kb): 6,292,166  (1.26% / 1.98%)
Long Range (>20Kb): 123  (0.00% / 0.00%)