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/2026_Chromera_Hi-C/2026-01-16-Ultima-run-Chromera/juicer-L1273+L4897-Chromera_velia-Hi-C -y none -s none -p /oak/stanford/groups/akundaje/marinovg/genomes/Chromerida/Chromera_velia_CCMP2878-CDMZ01/CDMZ01.chrom.sizes -y none -s none -z /oak/stanford/groups/akundaje/marinovg/genomes/Chromerida/Chromera_velia_CCMP2878-CDMZ01/bwa-indexes/CDMZ01.fa                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
Sequenced Read Pairs:  2,725,434,802
 Normal Paired: 1,281,845,624 (47.03%)
 Chimeric Paired: 1,215,837,552 (44.61%)
 Chimeric Ambiguous: 140,281,534 (5.15%)
 Unmapped: 87,470,092 (3.21%)
 Ligation Motif Present: 0 (0.00%)
Alignable (Normal+Chimeric Paired): 2,497,683,176 (91.64%)
WARN [2026-02-04T09:14:00,610]  [Globals.java:138] [main]  Development mode is enabled
Unique Reads: 428,338,280 (15.72%)
PCR Duplicates: 2,069,300,563 (75.93%)
Optical Duplicates: 44,333 (0.00%)
Library Complexity Estimate: 429,621,437
Intra-fragment Reads: 0 (0.00% / 0.00%)
Below MAPQ Threshold: 75,581,051 (2.77% / 17.65%)
Hi-C Contacts: 352,757,229 (12.94% / 82.35%)
 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: 87,311,678  (3.20% / 20.38%)
Intra-chromosomal: 265,445,551  (9.74% / 61.97%)
Short Range (<20Kb): 262,117,189  (9.62% / 61.19%)
Long Range (>20Kb): 3,310,870  (0.12% / 0.77%)