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_3_hpm_Hi-C-GSM4161206-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-MAC_3_hpm_Hi-C-GSM4161206-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:  66,538,803
 Normal Paired: 39,089,428 (58.75%)
 Chimeric Paired: 25,128,661 (37.77%)
 Chimeric Ambiguous: 1,471,530 (2.21%)
 Unmapped: 849,184 (1.28%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 64,218,089 (96.51%)
WARN [2024-02-24T09:28:18,949]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 51,661,898 (77.64%)
PCR Duplicates: 12,556,191 (18.87%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 142,032,865
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 2,347,086 (3.53% / 4.54%)
Hi-C Contacts: 49,314,812 (74.11% / 95.46%)
 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: 7,508,296  (11.28% / 14.53%)
Intra-chromosomal: 41,806,516  (62.83% / 80.92%)
Short Range (<20Kb): 18,337,311  (27.56% / 35.49%)
Long Range (>20Kb): 23,468,408  (35.27% / 45.43%)