## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G903_22/G903_22_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G903_22/G903_22_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G903_22/G903_22_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	35820	54163398	55334986	47190	3827	1339013	0	0.024749	1077331387

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	51523308	51523308
2.0	1.950967	1264478	1264478
3.0	2.855306	35346	35346
4.0	3.715303	1180	1180
5.0	4.533132	66	66
6.0	5.310861	4	4
7.0	6.050455	2	2
8.0	6.753786	1	1
9.0	7.42263	0	0
10.0	8.058679	0	0
11.0	8.663541	0	0
12.0	9.238744	0	0
13.0	9.785745	0	0
14.0	10.305924	0	0
15.0	10.800597	0	0
16.0	11.271016	0	0
17.0	11.718368	0	0
18.0	12.143786	0	0
19.0	12.548344	0	0
20.0	12.933066	0	0
21.0	13.298924	0	0
22.0	13.646843	0	0
23.0	13.977702	0	0
24.0	14.292339	0	0
25.0	14.591548	0	0
26.0	14.876086	0	0
27.0	15.146672	0	0
28.0	15.403991	0	0
29.0	15.648693	0	0
30.0	15.881397	0	0
31.0	16.10269	0	0
32.0	16.313133	0	0
33.0	16.513257	0	0
34.0	16.703569	0	0
35.0	16.884549	0	0
36.0	17.056655	0	0
37.0	17.220323	0	0
38.0	17.375965	0	0
39.0	17.523976	0	0
40.0	17.66473	0	0
41.0	17.798581	0	0
42.0	17.92587	0	0
43.0	18.046918	0	0
44.0	18.16203	0	0
45.0	18.271498	0	0
46.0	18.375599	0	0
47.0	18.474595	0	0
48.0	18.568737	0	0
49.0	18.658263	0	0
50.0	18.743399	0	0
51.0	18.824361	0	0
52.0	18.901354	0	0
53.0	18.974571	0	0
54.0	19.044198	0	0
55.0	19.110411	0	0
56.0	19.173377	0	0
57.0	19.233256	0	0
58.0	19.290199	0	0
59.0	19.34435	0	0
60.0	19.395846	0	0
61.0	19.444816	0	0
62.0	19.491386	0	0
63.0	19.535672	0	0
64.0	19.577787	0	0
65.0	19.617837	0	0
66.0	19.655923	0	0
67.0	19.692141	0	0
68.0	19.726584	0	0
69.0	19.759338	0	0
70.0	19.790486	0	0
71.0	19.820106	0	0
72.0	19.848274	0	0
73.0	19.875061	0	0
74.0	19.900535	0	0
75.0	19.924759	0	0
76.0	19.947796	0	0
77.0	19.969703	0	0
78.0	19.990536	0	0
79.0	20.010348	0	0
80.0	20.029188	0	0
81.0	20.047104	0	0
82.0	20.064142	0	0
83.0	20.080345	0	0
84.0	20.095753	0	0
85.0	20.110405	0	0
86.0	20.124339	0	0
87.0	20.13759	0	0
88.0	20.150191	0	0
89.0	20.162175	0	0
90.0	20.17357	0	0
91.0	20.184407	0	0
92.0	20.194713	0	0
93.0	20.204513	0	0
94.0	20.213833	0	0
95.0	20.222695	0	0
96.0	20.231124	0	0
97.0	20.239138	0	0
98.0	20.24676	0	0
99.0	20.254009	0	0
100.0	20.260901	0	0