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-MIC_3_hpm_Hi-C-GSM4161209-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-MIC_3_hpm_Hi-C-GSM4161209-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:  96,610,730
 Normal Paired: 75,410,486 (78.06%)
 Chimeric Paired: 16,251,354 (16.82%)
 Chimeric Ambiguous: 2,724,992 (2.82%)
 Unmapped: 2,223,898 (2.30%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 91,661,840 (94.88%)
WARN [2024-02-28T00:29:57,287]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 71,166,451 (73.66%)
PCR Duplicates: 20,495,389 (21.21%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 173,117,663
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 14,892,602 (15.42% / 20.93%)
Hi-C Contacts: 56,273,849 (58.25% / 79.07%)
 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: 5,808,137  (6.01% / 8.16%)
Intra-chromosomal: 50,465,712  (52.24% / 70.91%)
Short Range (<20Kb): 16,455,106  (17.03% / 23.12%)
Long Range (>20Kb): 34,008,844  (35.20% / 47.79%)