## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G382_21/G382_21_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G382_21/G382_21_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G382_21/G382_21_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 15:41:01 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	47601	66463044	66552490	58173	5099	1385493	0	0.020877	1571906583

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	63728402	63728402
2.0	1.9586	1314740	1314740
3.0	2.877513	32799	32799
4.0	3.758383	1381	1381
5.0	4.602784	163	163
6.0	5.412227	48	48
7.0	6.188159	10	10
8.0	6.931967	5	5
9.0	7.64498	2	2
10.0	8.328475	1	1
11.0	8.983673	0	0
12.0	9.611745	0	0
13.0	10.213815	0	0
14.0	10.790959	0	0
15.0	11.344209	0	0
16.0	11.874555	0	0
17.0	12.382943	0	0
18.0	12.870285	0	0
19.0	13.33745	0	0
20.0	13.785274	0	0
21.0	14.214558	0	0
22.0	14.62607	0	0
23.0	15.020545	0	0
24.0	15.398689	0	0
25.0	15.761177	0	0
26.0	16.108658	0	0
27.0	16.441753	0	0
28.0	16.761058	0	0
29.0	17.067144	0	0
30.0	17.360557	0	0
31.0	17.641823	0	0
32.0	17.911445	0	0
33.0	18.169904	0	0
34.0	18.417663	0	0
35.0	18.655164	0	0
36.0	18.882833	0	0
37.0	19.101076	0	0
38.0	19.310284	0	0
39.0	19.510831	0	0
40.0	19.703075	0	0
41.0	19.88736	0	0
42.0	20.064015	0	0
43.0	20.233357	0	0
44.0	20.395688	0	0
45.0	20.551299	0	0
46.0	20.700467	0	0
47.0	20.843459	0	0
48.0	20.980532	0	0
49.0	21.11193	0	0
50.0	21.237888	0	0
51.0	21.358631	0	0
52.0	21.474375	0	0
53.0	21.585327	0	0
54.0	21.691686	0	0
55.0	21.793642	0	0
56.0	21.891377	0	0
57.0	21.985065	0	0
58.0	22.074875	0	0
59.0	22.160966	0	0
60.0	22.243493	0	0
61.0	22.322604	0	0
62.0	22.398439	0	0
63.0	22.471135	0	0
64.0	22.540821	0	0
65.0	22.607623	0	0
66.0	22.671658	0	0
67.0	22.733043	0	0
68.0	22.791886	0	0
69.0	22.848293	0	0
70.0	22.902364	0	0
71.0	22.954197	0	0
72.0	23.003885	0	0
73.0	23.051515	0	0
74.0	23.097173	0	0
75.0	23.140941	0	0
76.0	23.182897	0	0
77.0	23.223116	0	0
78.0	23.26167	0	0
79.0	23.298627	0	0
80.0	23.334055	0	0
81.0	23.368016	0	0
82.0	23.400571	0	0
83.0	23.431778	0	0
84.0	23.461693	0	0
85.0	23.49037	0	0
86.0	23.517859	0	0
87.0	23.544211	0	0
88.0	23.569471	0	0
89.0	23.593686	0	0
90.0	23.616898	0	0
91.0	23.639149	0	0
92.0	23.660479	0	0
93.0	23.680926	0	0
94.0	23.700526	0	0
95.0	23.719315	0	0
96.0	23.737326	0	0
97.0	23.754591	0	0
98.0	23.771142	0	0
99.0	23.787007	0	0
100.0	23.802216	0	0