## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-222-TP4.bam --OUTPUT POC-222-TP4.md.bam --METRICS_FILE POC-222-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 02:39:57 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	328	11912446	2526273	0	227	6366731	3141007	0.534463	8775633

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.175234	2675318	0	3494559
2.0	1.477642	1382114	863890	1368277
3.0	1.555456	692295	336701	451722
4.0	1.575479	350406	165441	141022
5.0	1.580632	183973	89032	46569
6.0	1.581958	102386	50090	18144
7.0	1.582299	59178	28085	8506
8.0	1.582386	35494	16404	4672
9.0	1.582409	21889	9287	3009
10.0	1.582415	13723	5516	1940
11.0	1.582416	8878	3263	1430
12.0	1.582417	5608	1873	1088
13.0	1.582417	3954	1113	787
14.0	1.582417	2501	692	570
15.0	1.582417	1759	406	458
16.0	1.582417	1274	261	424
17.0	1.582417	921	166	307
18.0	1.582417	690	87	266
19.0	1.582417	519	65	220
20.0	1.582417	395	42	195
21.0	1.582417	316	33	160
22.0	1.582417	238	19	102
23.0	1.582417	213	14	122
24.0	1.582417	171	8	100
25.0	1.582417	141	6	94
26.0	1.582417	117	6	72
27.0	1.582417	101	5	79
28.0	1.582417	102	3	78
29.0	1.582417	107	1	52
30.0	1.582417	60	3	39
31.0	1.582417	67	0	39
32.0	1.582417	61	0	48
33.0	1.582417	47	0	31
34.0	1.582417	40	0	34
35.0	1.582417	35	0	26
36.0	1.582417	48	1	24
37.0	1.582417	34	0	38
38.0	1.582417	35	0	23
39.0	1.582417	30	0	24
40.0	1.582417	24	0	9
41.0	1.582417	26	0	19
42.0	1.582417	23	0	13
43.0	1.582417	21	0	17
44.0	1.582417	21	1	14
45.0	1.582417	19	0	11
46.0	1.582417	16	0	13
47.0	1.582417	13	0	11
48.0	1.582417	16	0	13
49.0	1.582417	12	0	13
50.0	1.582417	12	0	6
51.0	1.582417	11	0	8
52.0	1.582417	7	0	11
53.0	1.582417	9	0	5
54.0	1.582417	11	0	7
55.0	1.582417	11	0	8
56.0	1.582417	9	0	7
57.0	1.582417	9	0	10
58.0	1.582417	8	0	7
59.0	1.582417	3	0	5
60.0	1.582417	7	0	11
61.0	1.582417	7	0	3
62.0	1.582417	5	0	6
63.0	1.582417	12	0	5
64.0	1.582417	6	0	3
65.0	1.582417	9	0	5
66.0	1.582417	5	0	6
67.0	1.582417	5	0	2
68.0	1.582417	3	0	1
69.0	1.582417	7	0	8
70.0	1.582417	4	0	4
71.0	1.582417	4	0	1
72.0	1.582417	1	0	3
73.0	1.582417	3	0	6
74.0	1.582417	4	0	4
75.0	1.582417	5	0	6
76.0	1.582417	2	0	0
77.0	1.582417	3	0	1
78.0	1.582417	2	0	3
79.0	1.582417	6	0	2
80.0	1.582417	5	0	3
81.0	1.582417	7	0	2
82.0	1.582417	1	0	1
83.0	1.582417	6	0	3
84.0	1.582417	0	0	3
85.0	1.582417	0	0	1
86.0	1.582417	1	0	3
87.0	1.582417	2	0	1
88.0	1.582417	3	0	0
89.0	1.582417	1	0	1
90.0	1.582417	1	0	1
91.0	1.582417	2	0	1
92.0	1.582417	4	0	2
93.0	1.582417	1	0	2
94.0	1.582417	2	0	2
95.0	1.582417	2	0	2
96.0	1.582417	0	0	1
97.0	1.582417	1	0	1
98.0	1.582417	0	0	1
99.0	1.582417	2	0	2
100.0	1.582417	3	0	0
101.0	0	1	0	1
102.0	0	1	0	0
104.0	0	0	0	2
105.0	0	2	0	1
106.0	0	1	0	1
107.0	0	0	0	1
108.0	0	1	0	1
109.0	0	2	0	2
110.0	0	2	0	0
111.0	0	1	0	0
112.0	0	1	0	0
113.0	0	0	0	1
114.0	0	0	0	1
115.0	0	1	0	2
116.0	0	1	0	1
117.0	0	0	0	2
118.0	0	1	0	2
119.0	0	1	0	1
120.0	0	2	0	0
125.0	0	2	0	1
126.0	0	2	0	0
127.0	0	0	0	1
129.0	0	1	0	0
130.0	0	1	0	0
132.0	0	1	0	0
133.0	0	1	0	0
134.0	0	1	0	0
135.0	0	0	0	1
138.0	0	0	0	1
139.0	0	1	0	0
141.0	0	0	0	1
143.0	0	0	0	1
144.0	0	0	0	2
146.0	0	1	0	0
147.0	0	0	0	1
155.0	0	1	0	0
157.0	0	2	0	0
158.0	0	0	0	1
159.0	0	1	0	1
160.0	0	1	0	0
161.0	0	1	0	0
162.0	0	0	0	1
167.0	0	1	0	0
169.0	0	0	0	2
176.0	0	0	0	1
178.0	0	1	0	0
179.0	0	1	0	1
181.0	0	1	0	0
188.0	0	1	0	0
190.0	0	1	0	0
191.0	0	1	0	0
192.0	0	0	0	2
196.0	0	1	0	0
204.0	0	0	0	1
210.0	0	1	0	0
215.0	0	1	0	0
219.0	0	0	0	1
229.0	0	0	0	1
230.0	0	0	0	1
241.0	0	1	0	0
244.0	0	0	0	1
245.0	0	1	0	0
247.0	0	1	0	0
270.0	0	1	0	0
277.0	0	0	0	1
297.0	0	0	0	1
305.0	0	1	0	0
320.0	0	1	0	0
402.0	0	0	0	1
437.0	0	1	0	0