Experiment description: Juicer version 1.5.6; BWA 0.7.17-r1188; 60 threads; java version "1.8.0_131"; scripts/juicer.sh -t 60 -D /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-11-19-NextSeq-run/juicer-L1108-Tetrahymena_starved_Hi-C-final-post-review -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-11-19-NextSeq-run/juicer-L1108-Tetrahymena_starved_Hi-C-final-post-review -p /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1027-Tetrahymena_thermophila_Hi-C_MluCl/juicer-L1027-Tetrahymena_thermophila_Hi-C_MluCl-all-reads-3D_DNA/final-post-review/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.FINAL.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1027-Tetrahymena_thermophila_Hi-C_MluCl/juicer-L1027-Tetrahymena_thermophila_Hi-C_MluCl-all-reads-3D_DNA/final-post-review/bwa-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.FINAL_MluCl.txt -z /oak/stanford/groups/akundaje/marinovg/ENCODE4/datasets-Hi-C/L1027-Tetrahymena_thermophila_Hi-C_MluCl/juicer-L1027-Tetrahymena_thermophila_Hi-C_MluCl-all-reads-3D_DNA/final-post-review/bwa-indexes/Tetrahymena_thermophila.JCVI-TTA1-2.2.20.FINAL.fasta
Sequenced Read Pairs:  220,558,086
 Normal Paired: 176,253,019 (79.91%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 44,305,067 (20.09%)
 Ligation Motif Present: 50,893 (0.02%)
Alignable (Normal+Chimeric Paired): 176,253,019 (79.91%)
Unique Reads: 137,449,259 (62.32%)
PCR Duplicates: 38,675,537 (17.54%)
Optical Duplicates: 128,223 (0.06%)
Library Complexity Estimate: 339,875,364
Intra-fragment Reads: 1,623,089 (0.74% / 1.18%)
Below MAPQ Threshold: 22,708,179 (10.30% / 16.52%)
Hi-C Contacts: 113,117,991 (51.29% / 82.30%)
 Ligation Motif Present: 28,072  (0.01% / 0.02%)
 3' Bias (Long Range): 48% - 52%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 68,881,749  (31.23% / 50.11%)
Intra-chromosomal: 44,236,242  (20.06% / 32.18%)
Short Range (<20Kb): 26,386,667  (11.96% / 19.20%)
Long Range (>20Kb): 17,847,217  (8.09% / 12.98%)