## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-52-TP4.bam --OUTPUT POC-52-TP4.md.bam --METRICS_FILE POC-52-TP4.md.MarkDuplicates.metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Pocillopora_meandrina_HIv1.assembly.fasta --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_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_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 --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 --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Jul 22 02:40:10 GMT 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	201	13430497	2827728	0	123	6127206	4090857	0.456217	18176175

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.300042	4289332	0	5799468
2.0	1.920988	1609338	1148766	1186843
3.0	2.217574	683779	462623	227378
4.0	2.359235	327607	226936	52091
5.0	2.426897	169776	118555	16244
6.0	2.459214	92587	63354	7359
7.0	2.474651	52439	34096	4088
8.0	2.482023	30250	18457	2548
9.0	2.485545	17864	10186	1701
10.0	2.487227	10562	5576	1206
11.0	2.48803	6472	2978	877
12.0	2.488414	3978	1638	671
13.0	2.488597	2581	988	484
14.0	2.488685	1660	535	366
15.0	2.488727	1171	312	306
16.0	2.488747	749	165	229
17.0	2.488756	602	115	189
18.0	2.488761	465	59	169
19.0	2.488763	333	43	142
20.0	2.488764	263	35	125
21.0	2.488765	209	21	103
22.0	2.488765	167	17	88
23.0	2.488765	128	10	79
24.0	2.488765	106	5	64
25.0	2.488765	110	7	52
26.0	2.488765	71	4	45
27.0	2.488765	74	3	32
28.0	2.488765	67	4	28
29.0	2.488765	53	0	23
30.0	2.488765	52	1	23
31.0	2.488765	34	3	30
32.0	2.488765	32	1	24
33.0	2.488765	26	1	23
34.0	2.488765	32	0	18
35.0	2.488765	33	0	9
36.0	2.488765	25	1	11
37.0	2.488765	17	0	8
38.0	2.488765	20	0	6
39.0	2.488765	18	0	9
40.0	2.488765	14	0	7
41.0	2.488765	8	0	5
42.0	2.488765	13	1	8
43.0	2.488765	17	1	7
44.0	2.488765	9	0	2
45.0	2.488765	7	0	7
46.0	2.488765	9	0	3
47.0	2.488765	6	0	8
48.0	2.488765	8	0	7
49.0	2.488765	6	0	7
50.0	2.488765	9	0	6
51.0	2.488765	6	0	4
52.0	2.488765	3	0	3
53.0	2.488765	6	0	3
54.0	2.488765	8	0	2
55.0	2.488765	7	0	6
56.0	2.488765	5	0	4
57.0	2.488765	5	0	2
58.0	2.488765	4	0	3
59.0	2.488765	1	0	2
60.0	2.488765	2	0	0
61.0	2.488765	3	0	1
62.0	2.488765	3	0	1
63.0	2.488765	3	0	1
64.0	2.488765	1	0	1
65.0	2.488765	3	0	2
66.0	2.488765	2	0	3
67.0	2.488765	1	0	2
68.0	2.488765	2	0	0
69.0	2.488765	0	0	1
70.0	2.488765	3	0	0
71.0	2.488765	1	0	4
72.0	2.488765	1	0	0
73.0	2.488765	1	0	1
74.0	2.488765	1	0	0
75.0	2.488765	1	0	2
76.0	2.488765	2	0	0
77.0	2.488765	3	0	2
78.0	2.488765	2	0	1
79.0	2.488765	2	0	0
80.0	2.488765	1	0	1
81.0	2.488765	1	0	2
82.0	2.488765	2	0	1
83.0	2.488765	3	0	1
84.0	2.488765	3	0	0
85.0	2.488765	0	0	1
86.0	2.488765	0	0	0
87.0	2.488765	0	0	2
88.0	2.488765	0	0	0
89.0	2.488765	1	0	0
90.0	2.488765	0	0	0
91.0	2.488765	1	0	0
92.0	2.488765	0	0	0
93.0	2.488765	0	0	0
94.0	2.488765	1	0	0
95.0	2.488765	1	0	0
96.0	2.488765	0	0	1
97.0	2.488765	0	0	0
98.0	2.488765	0	0	0
99.0	2.488765	0	0	0
100.0	2.488765	0	0	0
103.0	0	1	0	0
105.0	0	0	0	1
108.0	0	1	0	1
109.0	0	1	0	0
114.0	0	1	0	0
148.0	0	0	0	1
155.0	0	1	0	0
220.0	0	0	0	1
227.0	0	1	0	0
373.0	0	0	0	1
396.0	0	1	0	0