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-L1276-Chlamydomonas_reinhardtii_CC125-Hi-C -d /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2019-12-14-NextSeq-run-2/juicer-L1276-Chlamydomonas_reinhardtii_CC125-Hi-C -p /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC.chrom.sizes -y /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/bwa-indexes/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC_MboI.txt -z /oak/stanford/groups/akundaje/marinovg/genomes/Chlorophyta/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt/bwa-indexes/Chlamydomonas_reinhardtii-v5.5_CC_503_cw92_mt.20+chrM+chrC.fa                                                                  
Sequenced Read Pairs:  31,948,494
 Normal Paired: 29,577,737 (92.58%)
 Chimeric Paired: 0 (0.00%)
 Chimeric Ambiguous: 0 (0.00%)
 Unmapped: 2,370,757 (7.42%)
 Ligation Motif Present: 10,778 (0.03%)
Alignable (Normal+Chimeric Paired): 29,577,737 (92.58%)
Unique Reads: 22,870,310 (71.58%)
PCR Duplicates: 6,699,873 (20.97%)
Optical Duplicates: 7,554 (0.02%)
Library Complexity Estimate: 54,972,551
Intra-fragment Reads: 13,545,489 (42.40% / 59.23%)
Below MAPQ Threshold: 4,743,277 (14.85% / 20.74%)
Hi-C Contacts: 4,581,544 (14.34% / 20.03%)
 Ligation Motif Present: 3,579  (0.01% / 0.02%)
 3' Bias (Long Range): 49% - 51%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 389,406  (1.22% / 1.70%)
Intra-chromosomal: 4,192,138  (13.12% / 18.33%)
Short Range (<20Kb): 3,890,209  (12.18% / 17.01%)
Long Range (>20Kb): 301,885  (0.94% / 1.32%)