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-MAC_24_hpm_Hi-C-GSM4161207-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-MAC_24_hpm_Hi-C-GSM4161207-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:  62,437,530
 Normal Paired: 37,452,680 (59.98%)
 Chimeric Paired: 22,873,826 (36.63%)
 Chimeric Ambiguous: 1,355,042 (2.17%)
 Unmapped: 755,982 (1.21%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 60,326,506 (96.62%)
WARN [2024-02-24T09:22:26,723]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 49,304,073 (78.97%)
PCR Duplicates: 11,022,433 (17.65%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 144,296,203
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 4,703,846 (7.53% / 9.54%)
Hi-C Contacts: 44,600,227 (71.43% / 90.46%)
 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: 7,718,779  (12.36% / 15.66%)
Intra-chromosomal: 36,881,448  (59.07% / 74.80%)
Short Range (<20Kb): 17,594,552  (28.18% / 35.69%)
Long Range (>20Kb): 19,286,204  (30.89% / 39.12%)