Experiment description: Juicer version 1.6; BWA 0.7.17-r1188; 20 threads; java version "1.8.0_131"; scripts/juicer.sh -t 20 -D /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Cell_1.5_hpm_Hi-C_all-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-Cell_1.5_hpm_Hi-C_all-MIC -p /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/genomes/Ciliates/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3/bwa-indexes/Tetrahymena_thermophila_SB210-E-JCVI_TeTherMIC_3.fa                                                                                                                                                                                                                                                                                  
Sequenced Read Pairs:  114,930,589
 Normal Paired: 43,932,840 (38.23%)
 Chimeric Paired: 60,906,462 (52.99%)
 Chimeric Ambiguous: 7,119,444 (6.19%)
 Unmapped: 2,971,843 (2.59%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 104,839,302 (91.22%)
WARN [2024-02-27T13:33:48,048]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 87,248,659 (75.91%)
PCR Duplicates: 17,590,643 (15.31%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 276,396,027
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 4,103,770 (3.57% / 4.70%)
Hi-C Contacts: 83,144,889 (72.34% / 95.30%)
 Ligation Motif Present: 0  (0.00% / 0.00%)
 3' Bias (Long Range): 0% - 0%
 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%
Inter-chromosomal: 19,662,184  (17.11% / 22.54%)
Intra-chromosomal: 63,482,705  (55.24% / 72.76%)
Short Range (<20Kb): 19,338,876  (16.83% / 22.17%)
Long Range (>20Kb): 44,112,298  (38.38% / 50.56%)