## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-57-TP4.bam --OUTPUT POC-57-TP4.md.bam --METRICS_FILE POC-57-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 02:41:01 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	235	16312856	3124577	0	164	7732805	4376558	0.474033	17025551

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.223122	4793014	0	6253275
2.0	1.692319	2002509	1273799	1720887
3.0	1.872306	879563	499950	422284
4.0	1.941349	415372	242311	109221
5.0	1.967835	212286	125119	34864
6.0	1.977995	114433	65300	14587
7.0	1.981893	64590	34809	7625
8.0	1.983388	36640	18679	4498
9.0	1.983961	21841	10162	3029
10.0	1.984181	13330	5503	2063
11.0	1.984266	8199	3030	1454
12.0	1.984298	5217	1617	1097
13.0	1.98431	3325	963	886
14.0	1.984315	2249	494	722
15.0	1.984317	1630	319	529
16.0	1.984318	1091	174	425
17.0	1.984318	853	110	355
18.0	1.984318	618	59	276
19.0	1.984318	492	33	234
20.0	1.984318	390	29	205
21.0	1.984318	305	15	142
22.0	1.984318	240	14	127
23.0	1.984318	193	8	128
24.0	1.984318	176	6	129
25.0	1.984318	155	8	87
26.0	1.984318	123	1	69
27.0	1.984318	107	4	70
28.0	1.984318	101	1	68
29.0	1.984318	85	0	57
30.0	1.984318	77	1	58
31.0	1.984318	67	0	47
32.0	1.984318	47	1	42
33.0	1.984318	77	0	34
34.0	1.984318	44	0	36
35.0	1.984318	54	1	29
36.0	1.984318	36	1	26
37.0	1.984318	27	0	25
38.0	1.984318	32	0	18
39.0	1.984318	34	0	20
40.0	1.984318	25	0	22
41.0	1.984318	23	0	16
42.0	1.984318	20	1	10
43.0	1.984318	27	0	20
44.0	1.984318	15	0	10
45.0	1.984318	15	0	11
46.0	1.984318	10	1	14
47.0	1.984318	15	0	10
48.0	1.984318	32	0	11
49.0	1.984318	11	0	8
50.0	1.984318	9	0	8
51.0	1.984318	9	0	10
52.0	1.984318	13	0	9
53.0	1.984318	16	0	10
54.0	1.984318	6	0	5
55.0	1.984318	7	0	3
56.0	1.984318	7	0	6
57.0	1.984318	2	0	3
58.0	1.984318	9	0	6
59.0	1.984318	8	0	10
60.0	1.984318	4	0	2
61.0	1.984318	7	0	11
62.0	1.984318	10	0	5
63.0	1.984318	5	0	8
64.0	1.984318	7	0	4
65.0	1.984318	9	0	3
66.0	1.984318	7	0	2
67.0	1.984318	8	0	5
68.0	1.984318	1	0	0
69.0	1.984318	1	0	4
70.0	1.984318	5	0	2
71.0	1.984318	3	0	3
72.0	1.984318	2	0	3
73.0	1.984318	2	0	4
74.0	1.984318	1	0	0
75.0	1.984318	2	0	3
76.0	1.984318	0	0	4
77.0	1.984318	2	0	3
78.0	1.984318	6	0	4
79.0	1.984318	1	0	1
80.0	1.984318	6	0	1
81.0	1.984318	4	0	1
82.0	1.984318	2	0	2
83.0	1.984318	1	0	4
84.0	1.984318	3	0	0
85.0	1.984318	1	0	1
86.0	1.984318	0	0	0
87.0	1.984318	2	0	0
88.0	1.984318	0	0	2
89.0	1.984318	1	0	2
90.0	1.984318	0	0	1
91.0	1.984318	1	0	1
92.0	1.984318	3	0	0
93.0	1.984318	2	0	0
94.0	1.984318	2	0	1
95.0	1.984318	0	0	1
96.0	1.984318	1	0	1
97.0	1.984318	1	0	1
98.0	1.984318	0	0	0
99.0	1.984318	2	0	1
100.0	1.984318	2	0	1
101.0	0	0	0	1
102.0	0	1	0	0
104.0	0	1	0	1
106.0	0	0	0	1
107.0	0	1	0	0
108.0	0	2	0	0
109.0	0	1	0	0
111.0	0	0	0	1
112.0	0	0	0	1
113.0	0	1	0	0
114.0	0	0	0	1
115.0	0	1	0	0
116.0	0	1	0	0
117.0	0	0	0	1
118.0	0	0	0	1
119.0	0	1	0	0
122.0	0	1	0	0
124.0	0	1	0	0
125.0	0	0	0	1
126.0	0	0	0	2
127.0	0	0	0	1
129.0	0	1	0	0
130.0	0	2	0	0
131.0	0	0	0	1
134.0	0	1	0	0
135.0	0	0	0	1
139.0	0	1	0	0
141.0	0	0	0	1
144.0	0	0	0	2
146.0	0	1	0	0
148.0	0	1	0	1
149.0	0	1	0	1
154.0	0	1	0	0
156.0	0	1	0	0
159.0	0	1	0	0
165.0	0	0	0	1
168.0	0	0	0	1
170.0	0	0	0	1
171.0	0	0	0	1
175.0	0	1	0	0
181.0	0	0	0	1
183.0	0	1	0	0
190.0	0	1	0	0
191.0	0	1	0	0
194.0	0	1	0	0
196.0	0	0	0	1
203.0	0	1	0	0
233.0	0	0	0	1
255.0	0	1	0	0
306.0	0	0	0	1
313.0	0	0	0	1
326.0	0	1	0	0
351.0	0	1	0	0
370.0	0	0	0	1
378.0	0	1	0	0