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_1.5_hpm_Hi-C-GSM4161205-MIC -d /oak/stanford/groups/akundaje/marinovg/papers/2022_Tetrahymena-Hi-C/2022-05-24-figures/juicer-MAC_1.5_hpm_Hi-C-GSM4161205-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:  60,598,516
 Normal Paired: 36,674,837 (60.52%)
 Chimeric Paired: 21,650,091 (35.73%)
 Chimeric Ambiguous: 1,209,436 (2.00%)
 Unmapped: 1,064,152 (1.76%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 58,324,928 (96.25%)
WARN [2024-02-27T20:45:59,591]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 49,470,029 (81.64%)
PCR Duplicates: 8,854,899 (14.61%)
Optical Duplicates: 0 (0.00%)
Library Complexity Estimate: 172,107,644
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 4,238,695 (6.99% / 8.57%)
Hi-C Contacts: 45,231,334 (74.64% / 91.43%)
 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: 6,765,132  (11.16% / 13.68%)
Intra-chromosomal: 38,466,202  (63.48% / 77.76%)
Short Range (<20Kb): 18,172,167  (29.99% / 36.73%)
Long Range (>20Kb): 20,292,832  (33.49% / 41.02%)