## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-222-TP1.bam --OUTPUT POC-222-TP1.md.bam --METRICS_FILE POC-222-TP1.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 02:41:06 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	14867231	3101993	0	118	6483862	4121875	0.436119	20710765

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.26537	5086666	0	6654927
2.0	1.882616	1824488	1229419	1364818
3.0	2.183709	741321	476022	260448
4.0	2.330582	341217	227980	58406
5.0	2.402227	171644	116039	18679
6.0	2.437175	92066	60719	8482
7.0	2.454223	50535	31755	4849
8.0	2.462539	29003	16739	3071
9.0	2.466595	16746	8889	2101
10.0	2.468574	9931	4711	1530
11.0	2.469539	6105	2585	1070
12.0	2.47001	3723	1437	857
13.0	2.47024	2451	770	647
14.0	2.470352	1671	434	509
15.0	2.470406	1157	247	443
16.0	2.470433	819	148	347
17.0	2.470446	623	91	296
18.0	2.470452	499	46	237
19.0	2.470456	325	41	191
20.0	2.470457	304	25	160
21.0	2.470458	265	24	148
22.0	2.470458	218	7	118
23.0	2.470458	163	8	113
24.0	2.470458	141	6	96
25.0	2.470458	117	7	83
26.0	2.470458	122	4	63
27.0	2.470458	86	1	46
28.0	2.470458	80	1	61
29.0	2.470458	85	1	52
30.0	2.470458	71	0	45
31.0	2.470458	65	2	33
32.0	2.470458	46	1	28
33.0	2.470458	42	4	18
34.0	2.470458	43	2	37
35.0	2.470458	28	0	23
36.0	2.470458	33	0	21
37.0	2.470458	32	0	25
38.0	2.470458	34	0	25
39.0	2.470458	29	0	16
40.0	2.470458	33	0	23
41.0	2.470458	22	2	13
42.0	2.470458	12	2	14
43.0	2.470458	19	0	12
44.0	2.470458	23	0	11
45.0	2.470458	18	0	10
46.0	2.470458	12	0	8
47.0	2.470458	6	0	7
48.0	2.470458	18	0	5
49.0	2.470458	9	0	8
50.0	2.470458	10	0	9
51.0	2.470458	12	0	4
52.0	2.470458	4	2	7
53.0	2.470458	13	0	7
54.0	2.470458	6	0	5
55.0	2.470458	10	0	4
56.0	2.470458	9	0	7
57.0	2.470458	9	0	7
58.0	2.470458	4	0	6
59.0	2.470458	8	0	3
60.0	2.470458	5	0	5
61.0	2.470458	5	0	3
62.0	2.470458	5	0	3
63.0	2.470458	1	0	4
64.0	2.470458	6	0	6
65.0	2.470458	7	0	0
66.0	2.470458	5	0	3
67.0	2.470458	3	0	3
68.0	2.470458	4	0	7
69.0	2.470458	4	0	3
70.0	2.470458	2	0	2
71.0	2.470458	8	0	2
72.0	2.470458	3	0	1
73.0	2.470458	5	0	4
74.0	2.470458	7	0	0
75.0	2.470458	1	0	1
76.0	2.470458	1	0	0
77.0	2.470458	1	0	1
78.0	2.470458	0	0	2
79.0	2.470458	4	0	2
80.0	2.470458	2	0	2
81.0	2.470458	2	0	1
82.0	2.470458	2	0	1
83.0	2.470458	2	0	0
84.0	2.470458	1	0	1
85.0	2.470458	2	0	0
86.0	2.470458	2	0	2
87.0	2.470458	0	0	1
88.0	2.470458	2	0	0
89.0	2.470458	1	0	4
90.0	2.470458	2	0	0
91.0	2.470458	0	0	0
92.0	2.470458	0	0	0
93.0	2.470458	3	0	0
94.0	2.470458	1	0	0
95.0	2.470458	0	0	1
96.0	2.470458	1	0	0
97.0	2.470458	0	0	0
98.0	2.470458	0	0	1
99.0	2.470458	1	0	0
100.0	2.470458	1	0	0
105.0	0	0	0	1
107.0	0	0	0	2
108.0	0	1	0	0
109.0	0	1	0	0
110.0	0	0	0	1
111.0	0	1	0	0
114.0	0	1	0	0
116.0	0	0	0	1
118.0	0	1	0	0
119.0	0	1	0	0
122.0	0	0	0	1
123.0	0	1	0	0
130.0	0	0	0	1
131.0	0	0	0	1
136.0	0	1	0	2
137.0	0	1	0	0
138.0	0	1	0	0
140.0	0	1	0	1
148.0	0	1	0	0
150.0	0	1	0	0
232.0	0	0	0	1
256.0	0	1	0	0
258.0	0	0	0	1
269.0	0	1	0	0
385.0	0	0	0	1
394.0	0	1	0	0