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-L1026-L1027-L1216-L1624-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-L1026-L1027-L1216-L1624-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:  722,128,018
 Normal Paired: 604,148,947 (83.66%)
 Chimeric Paired: 24,382,378 (3.38%)
 Chimeric Ambiguous: 1,766,389 (0.24%)
 Unmapped: 91,830,304 (12.72%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 628,531,325 (87.04%)
WARN [2024-02-29T18:53:38,825]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 326,824,809 (45.26%)
PCR Duplicates: 300,726,009 (41.64%)
Optical Duplicates: 980,507 (0.14%)
Library Complexity Estimate: 422,478,785
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 47,810,444 (6.62% / 14.63%)
Hi-C Contacts: 279,014,365 (38.64% / 85.37%)
 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: 58,743,276  (8.13% / 17.97%)
Intra-chromosomal: 220,271,089  (30.50% / 67.40%)
Short Range (<20Kb): 105,465,811  (14.60% / 32.27%)
Long Range (>20Kb): 114,656,232  (15.88% / 35.08%)