## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1166_20/G1166_20_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1166_20/G1166_20_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1166_20/G1166_20_dedup_metrics.txt CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 29 15:41:05 NOVT 2025

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	27431	43318243	43161963	33181	3321	1833835	0	0.042359	497080933

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	39742703	39742703
2.0	1.916544	1654954	1654954
3.0	2.756597	81832	81832
4.0	3.526542	4550	4550
5.0	4.232231	307	307
6.0	4.879026	44	44
7.0	5.471841	13	13
8.0	6.015183	2	2
9.0	6.51318	1	1
10.0	6.969616	1	1
11.0	7.387959	1	1
12.0	7.771389	0	0
13.0	8.12282	0	0
14.0	8.444921	0	0
15.0	8.740142	0	0
16.0	9.010724	0	0
17.0	9.258725	0	0
18.0	9.486028	0	0
19.0	9.694362	0	0
20.0	9.885309	0	0
21.0	10.06032	0	0
22.0	10.220725	0	0
23.0	10.367744	0	0
24.0	10.502493	0	0
25.0	10.625997	0	0
26.0	10.739193	0	0
27.0	10.842942	0	0
28.0	10.938033	0	0
29.0	11.025188	0	0
30.0	11.10507	0	0
31.0	11.178285	0	0
32.0	11.245389	0	0
33.0	11.306894	0	0
34.0	11.363265	0	0
35.0	11.414932	0	0
36.0	11.462287	0	0
37.0	11.50569	0	0
38.0	11.54547	0	0
39.0	11.581931	0	0
40.0	11.615349	0	0
41.0	11.645978	0	0
42.0	11.674051	0	0
43.0	11.699781	0	0
44.0	11.723363	0	0
45.0	11.744978	0	0
46.0	11.764788	0	0
47.0	11.782946	0	0
48.0	11.799588	0	0
49.0	11.814841	0	0
50.0	11.828821	0	0
51.0	11.841634	0	0
52.0	11.853378	0	0
53.0	11.864142	0	0
54.0	11.874008	0	0
55.0	11.88305	0	0
56.0	11.891338	0	0
57.0	11.898934	0	0
58.0	11.905896	0	0
59.0	11.912277	0	0
60.0	11.918125	0	0
61.0	11.923486	0	0
62.0	11.928399	0	0
63.0	11.932902	0	0
64.0	11.937029	0	0
65.0	11.940812	0	0
66.0	11.944279	0	0
67.0	11.947457	0	0
68.0	11.950369	0	0
69.0	11.953039	0	0
70.0	11.955485	0	0
71.0	11.957728	0	0
72.0	11.959783	0	0
73.0	11.961667	0	0
74.0	11.963394	0	0
75.0	11.964976	0	0
76.0	11.966427	0	0
77.0	11.967756	0	0
78.0	11.968974	0	0
79.0	11.970091	0	0
80.0	11.971115	0	0
81.0	11.972053	0	0
82.0	11.972913	0	0
83.0	11.973701	0	0
84.0	11.974423	0	0
85.0	11.975085	0	0
86.0	11.975692	0	0
87.0	11.976248	0	0
88.0	11.976758	0	0
89.0	11.977225	0	0
90.0	11.977653	0	0
91.0	11.978046	0	0
92.0	11.978405	0	0
93.0	11.978735	0	0
94.0	11.979037	0	0
95.0	11.979314	0	0
96.0	11.979568	0	0
97.0	11.979801	0	0
98.0	11.980014	0	0
99.0	11.980209	0	0
100.0	11.980388	0	0