## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-worknov/Alignment/2024-08-28_Rogachev/G1884_20/G1884_20_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-worknov/Alignment/2024-08-28_Rogachev/G1884_20/G1884_20_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-worknov/Alignment/2024-08-28_Rogachev/G1884_20/G1884_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: Wed Nov 26 15:24:08 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	15424	51134568	42939090	33816	2543	3092225	0	0.060488	405570882

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	45166082	45166082
2.0	1.881544	2682281	2682281
3.0	2.658664	177763	177763
4.0	3.343729	13668	13668
5.0	3.947644	1597	1597
6.0	4.480021	392	392
7.0	4.949335	186	186
8.0	5.363056	109	109
9.0	5.72777	53	53
10.0	6.04928	47	47
11.0	6.332706	36	36
12.0	6.582559	26	26
13.0	6.802814	20	20
14.0	6.99698	17	17
15.0	7.168145	11	11
16.0	7.319034	11	11
17.0	7.45205	13	13
18.0	7.569309	7	7
19.0	7.672679	5	5
20.0	7.763803	5	5
21.0	7.844133	1	1
22.0	7.914948	3	3
23.0	7.977374	3	3
24.0	8.032405	1	1
25.0	8.080918	1	1
26.0	8.123684	0	0
27.0	8.161384	0	0
28.0	8.194618	0	0
29.0	8.223916	0	0
30.0	8.249743	0	0
31.0	8.272511	0	0
32.0	8.292581	0	0
33.0	8.310275	0	0
34.0	8.325872	1	1
35.0	8.339622	0	0
36.0	8.351743	1	1
37.0	8.362428	0	0
38.0	8.371847	1	1
39.0	8.380151	0	0
40.0	8.387471	0	0
41.0	8.393924	0	0
42.0	8.399612	0	0
43.0	8.404627	0	0
44.0	8.409048	0	0
45.0	8.412945	0	0
46.0	8.41638	1	1
47.0	8.419409	0	0
48.0	8.422078	0	0
49.0	8.424432	0	0
50.0	8.426507	0	0
51.0	8.428336	0	0
52.0	8.429948	0	0
53.0	8.431369	0	0
54.0	8.432622	0	0
55.0	8.433727	0	0
56.0	8.4347	0	0
57.0	8.435559	1	1
58.0	8.436315	0	0
59.0	8.436982	0	0
60.0	8.43757	0	0
61.0	8.438089	0	0
62.0	8.438546	0	0
63.0	8.438948	0	0
64.0	8.439304	0	0
65.0	8.439617	0	0
66.0	8.439893	0	0
67.0	8.440136	0	0
68.0	8.44035	0	0
69.0	8.440539	0	0
70.0	8.440706	0	0
71.0	8.440853	0	0
72.0	8.440983	0	0
73.0	8.441097	0	0
74.0	8.441197	0	0
75.0	8.441286	0	0
76.0	8.441364	0	0
77.0	8.441433	0	0
78.0	8.441494	0	0
79.0	8.441548	0	0
80.0	8.441595	0	0
81.0	8.441636	0	0
82.0	8.441673	0	0
83.0	8.441706	0	0
84.0	8.441734	0	0
85.0	8.441759	0	0
86.0	8.441781	0	0
87.0	8.441801	0	0
88.0	8.441818	0	0
89.0	8.441833	0	0
90.0	8.441847	0	0
91.0	8.441859	0	0
92.0	8.441869	0	0
93.0	8.441878	0	0
94.0	8.441886	0	0
95.0	8.441893	0	0
96.0	8.4419	0	0
97.0	8.441905	0	0
98.0	8.44191	0	0
99.0	8.441914	0	0
100.0	8.441918	0	0