## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-53-TP4.bam --OUTPUT POC-53-TP4.md.bam --METRICS_FILE POC-53-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 02:50:57 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	184	11922249	2199841	0	127	5764065	3443871	0.483473	12512552

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.24827	3442609	0	4601228
2.0	1.729666	1408686	977065	1155702
3.0	1.915317	623963	384131	270051
4.0	1.986914	302312	186262	71594
5.0	2.014525	157766	97323	24655
6.0	2.025173	87243	52536	11621
7.0	2.02928	50763	29127	6566
8.0	2.030863	29888	15950	3982
9.0	2.031474	18180	9018	2818
10.0	2.03171	11455	5111	2034
11.0	2.0318	7208	2949	1482
12.0	2.031835	4799	1664	1081
13.0	2.031849	3252	982	786
14.0	2.031854	2108	563	663
15.0	2.031856	1559	350	564
16.0	2.031857	1104	226	436
17.0	2.031857	856	115	344
18.0	2.031857	625	89	307
19.0	2.031857	502	59	232
20.0	2.031857	408	35	206
21.0	2.031857	319	17	165
22.0	2.031857	281	14	179
23.0	2.031857	225	17	136
24.0	2.031857	193	13	119
25.0	2.031857	177	14	116
26.0	2.031857	148	3	93
27.0	2.031857	126	4	54
28.0	2.031857	129	8	72
29.0	2.031857	102	1	55
30.0	2.031857	74	5	50
31.0	2.031857	77	3	50
32.0	2.031857	68	1	51
33.0	2.031857	58	2	37
34.0	2.031857	57	2	43
35.0	2.031857	52	1	30
36.0	2.031857	43	2	30
37.0	2.031857	36	1	35
38.0	2.031857	49	0	33
39.0	2.031857	38	1	27
40.0	2.031857	45	1	25
41.0	2.031857	31	2	22
42.0	2.031857	30	0	15
43.0	2.031857	18	1	24
44.0	2.031857	36	1	14
45.0	2.031857	22	1	15
46.0	2.031857	27	0	17
47.0	2.031857	16	0	14
48.0	2.031857	21	0	12
49.0	2.031857	18	0	14
50.0	2.031857	18	0	12
51.0	2.031857	14	0	11
52.0	2.031857	16	0	8
53.0	2.031857	10	0	16
54.0	2.031857	13	0	10
55.0	2.031857	12	0	10
56.0	2.031857	15	0	5
57.0	2.031857	15	0	6
58.0	2.031857	12	0	13
59.0	2.031857	12	0	7
60.0	2.031857	13	0	1
61.0	2.031857	8	0	5
62.0	2.031857	9	0	8
63.0	2.031857	4	0	9
64.0	2.031857	2	0	3
65.0	2.031857	8	0	4
66.0	2.031857	12	0	2
67.0	2.031857	5	0	9
68.0	2.031857	4	0	8
69.0	2.031857	10	0	6
70.0	2.031857	8	0	6
71.0	2.031857	3	0	2
72.0	2.031857	4	0	6
73.0	2.031857	4	0	3
74.0	2.031857	7	0	4
75.0	2.031857	8	0	2
76.0	2.031857	4	0	3
77.0	2.031857	2	1	4
78.0	2.031857	3	0	2
79.0	2.031857	4	0	2
80.0	2.031857	3	0	3
81.0	2.031857	2	0	2
82.0	2.031857	5	0	3
83.0	2.031857	1	0	1
84.0	2.031857	7	0	1
85.0	2.031857	3	0	4
86.0	2.031857	6	0	3
87.0	2.031857	2	0	7
88.0	2.031857	4	0	2
89.0	2.031857	0	0	1
90.0	2.031857	3	0	4
91.0	2.031857	0	0	1
92.0	2.031857	1	0	2
93.0	2.031857	4	0	2
94.0	2.031857	3	0	2
95.0	2.031857	1	0	2
96.0	2.031857	3	0	0
97.0	2.031857	0	0	0
98.0	2.031857	1	0	0
99.0	2.031857	1	0	1
100.0	2.031857	4	0	2
101.0	0	2	0	3
102.0	0	1	0	0
103.0	0	1	0	3
104.0	0	0	0	1
105.0	0	3	0	2
106.0	0	2	0	1
107.0	0	2	0	0
108.0	0	0	0	2
109.0	0	3	0	0
110.0	0	4	0	1
112.0	0	1	0	0
113.0	0	2	0	1
116.0	0	1	0	0
117.0	0	2	0	0
118.0	0	0	0	1
120.0	0	0	0	1
121.0	0	0	0	1
123.0	0	1	0	1
124.0	0	0	0	1
125.0	0	1	0	1
126.0	0	1	0	2
127.0	0	3	0	0
128.0	0	0	0	1
130.0	0	0	0	1
131.0	0	0	0	2
133.0	0	0	0	4
134.0	0	1	0	0
135.0	0	3	0	0
136.0	0	1	0	0
137.0	0	0	0	1
140.0	0	1	0	0
141.0	0	4	0	0
142.0	0	1	0	1
144.0	0	0	0	2
145.0	0	0	0	2
146.0	0	1	0	0
148.0	0	1	0	0
149.0	0	0	0	1
150.0	0	1	0	0
151.0	0	0	0	1
152.0	0	1	0	1
154.0	0	1	0	0
155.0	0	0	0	1
156.0	0	1	0	0
157.0	0	1	0	1
159.0	0	1	0	0
160.0	0	1	0	0
162.0	0	1	0	0
163.0	0	1	0	0
164.0	0	0	0	1
167.0	0	0	0	2
169.0	0	1	0	1
171.0	0	1	0	1
174.0	0	1	0	0
175.0	0	0	0	1
179.0	0	1	0	0
182.0	0	1	0	0
185.0	0	1	0	0
186.0	0	1	0	0
189.0	0	1	0	0
198.0	0	0	0	1
200.0	0	1	0	0
202.0	0	1	0	0
213.0	0	0	0	1
234.0	0	0	0	1
242.0	0	1	0	0
256.0	0	1	0	0
260.0	0	0	0	1
299.0	0	1	0	0
320.0	0	0	0	1
337.0	0	0	0	1
364.0	0	1	0	0
413.0	0	1	0	0
541.0	0	0	0	1
568.0	0	1	0	0
742.0	0	0	0	1
768.0	0	1	0	0