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_24_hpm_Hi-C-GSM4161210-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-MIC_24_hpm_Hi-C-GSM4161210-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:  98,109,007
 Normal Paired: 72,383,156 (73.78%)
 Chimeric Paired: 20,467,008 (20.86%)
 Chimeric Ambiguous: 3,476,078 (3.54%)
 Unmapped: 1,782,765 (1.82%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 92,850,164 (94.64%)
WARN [2024-02-28T02:02:47,175]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 73,879,231 (75.30%)
PCR Duplicates: 18,970,933 (19.34%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 195,082,760
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 16,868,307 (17.19% / 22.83%)
Hi-C Contacts: 57,010,924 (58.11% / 77.17%)
 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: 7,720,585  (7.87% / 10.45%)
Intra-chromosomal: 49,290,339  (50.24% / 66.72%)
Short Range (<20Kb): 13,678,252  (13.94% / 18.51%)
Long Range (>20Kb): 35,610,615  (36.30% / 48.20%)