## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-52-TP3.bam --OUTPUT POC-52-TP3.md.bam --METRICS_FILE POC-52-TP3.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 02:42:20 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	181	12622398	2499408	0	116	6665791	3359590	0.528093	9657940

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.182563	2964817	0	3877101
2.0	1.502618	1454057	912189	1405376
3.0	1.58924	711634	363952	439398
4.0	1.612683	359635	181271	135785
5.0	1.619028	190020	96362	46814
6.0	1.620746	106755	53527	19398
7.0	1.62121	61545	29813	9881
8.0	1.621336	37321	16939	5892
9.0	1.62137	22800	9794	3866
10.0	1.621379	14703	5670	2705
11.0	1.621382	9448	3177	1957
12.0	1.621383	6317	1974	1442
13.0	1.621383	4263	1165	1195
14.0	1.621383	2926	712	862
15.0	1.621383	2140	381	718
16.0	1.621383	1499	253	594
17.0	1.621383	1164	154	455
18.0	1.621383	859	108	355
19.0	1.621383	626	75	356
20.0	1.621383	530	54	279
21.0	1.621383	415	33	244
22.0	1.621383	366	18	193
23.0	1.621383	301	17	188
24.0	1.621383	271	7	143
25.0	1.621383	202	7	146
26.0	1.621383	209	15	129
27.0	1.621383	164	7	86
28.0	1.621383	148	5	94
29.0	1.621383	130	5	94
30.0	1.621383	113	2	80
31.0	1.621383	97	2	57
32.0	1.621383	86	4	59
33.0	1.621383	83	1	48
34.0	1.621383	66	1	34
35.0	1.621383	70	4	45
36.0	1.621383	57	2	30
37.0	1.621383	71	1	38
38.0	1.621383	47	1	29
39.0	1.621383	45	0	39
40.0	1.621383	44	0	31
41.0	1.621383	46	0	29
42.0	1.621383	39	1	19
43.0	1.621383	22	0	21
44.0	1.621383	31	1	19
45.0	1.621383	28	0	13
46.0	1.621383	19	0	12
47.0	1.621383	26	0	17
48.0	1.621383	25	0	21
49.0	1.621383	24	0	12
50.0	1.621383	20	0	16
51.0	1.621383	13	0	9
52.0	1.621383	20	0	11
53.0	1.621383	17	0	12
54.0	1.621383	20	0	13
55.0	1.621383	7	0	8
56.0	1.621383	10	0	6
57.0	1.621383	7	0	8
58.0	1.621383	11	0	4
59.0	1.621383	6	0	6
60.0	1.621383	7	0	4
61.0	1.621383	14	0	8
62.0	1.621383	6	0	3
63.0	1.621383	11	0	3
64.0	1.621383	1	0	8
65.0	1.621383	5	0	3
66.0	1.621383	7	0	6
67.0	1.621383	7	0	4
68.0	1.621383	8	0	2
69.0	1.621383	4	0	1
70.0	1.621383	3	0	1
71.0	1.621383	3	0	3
72.0	1.621383	1	0	4
73.0	1.621383	4	0	4
74.0	1.621383	2	0	3
75.0	1.621383	1	0	1
76.0	1.621383	11	0	5
77.0	1.621383	1	0	1
78.0	1.621383	6	0	3
79.0	1.621383	1	0	2
80.0	1.621383	4	0	0
81.0	1.621383	5	0	3
82.0	1.621383	4	0	1
83.0	1.621383	0	0	0
84.0	1.621383	2	0	0
85.0	1.621383	0	0	1
86.0	1.621383	3	0	2
87.0	1.621383	2	0	3
88.0	1.621383	2	0	1
89.0	1.621383	2	0	2
90.0	1.621383	1	0	0
91.0	1.621383	3	0	0
92.0	1.621383	1	0	2
93.0	1.621383	1	0	0
94.0	1.621383	1	0	0
95.0	1.621383	0	0	0
96.0	1.621383	1	0	3
97.0	1.621383	0	0	1
98.0	1.621383	0	0	2
99.0	1.621383	3	0	0
100.0	1.621383	0	0	0
101.0	0	4	0	0
102.0	0	1	0	1
103.0	0	1	0	1
104.0	0	1	0	0
105.0	0	0	0	1
106.0	0	1	0	0
107.0	0	0	0	1
108.0	0	1	0	0
110.0	0	1	0	0
112.0	0	1	0	0
113.0	0	1	0	0
116.0	0	1	0	1
118.0	0	0	0	1
120.0	0	1	0	0
121.0	0	0	0	1
124.0	0	1	0	2
125.0	0	1	0	0
126.0	0	1	0	0
129.0	0	0	0	1
130.0	0	0	0	1
132.0	0	1	0	2
134.0	0	2	0	1
135.0	0	0	0	1
136.0	0	1	0	0
144.0	0	0	0	1
146.0	0	1	0	0
148.0	0	1	0	0
157.0	0	1	0	0
159.0	0	0	0	1
161.0	0	1	0	0
162.0	0	0	0	1
164.0	0	0	0	1
166.0	0	1	0	0
169.0	0	1	0	0
172.0	0	0	0	1
182.0	0	1	0	0
183.0	0	1	0	0
186.0	0	0	0	1
191.0	0	1	0	1
194.0	0	1	0	0
213.0	0	0	0	1
230.0	0	1	0	0
547.0	0	0	0	1
565.0	0	1	0	0
753.0	0	0	0	1
779.0	0	1	0	0