## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-52-TP2.bam --OUTPUT POC-52-TP2.md.bam --METRICS_FILE POC-52-TP2.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 02:44:31 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	244	15254492	3193349	0	171	9160157	4129358	0.60049	8214922

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.137474	2458408	0	3244584
2.0	1.315092	1529750	987682	1685551
3.0	1.342828	883100	412690	708526
4.0	1.347159	493291	213575	264129
5.0	1.347835	278359	121340	97739
6.0	1.347941	163493	70691	39205
7.0	1.347957	98082	42650	18129
8.0	1.34796	61788	25894	9901
9.0	1.34796	39522	15546	6263
10.0	1.34796	26191	9558	4154
11.0	1.34796	17435	5667	3015
12.0	1.34796	11920	3804	2234
13.0	1.34796	7993	2205	1704
14.0	1.34796	5756	1412	1285
15.0	1.34796	3960	903	1093
16.0	1.34796	2945	597	875
17.0	1.34796	2093	373	678
18.0	1.34796	1686	251	616
19.0	1.34796	1265	171	493
20.0	1.34796	994	117	435
21.0	1.34796	807	79	381
22.0	1.34796	648	56	344
23.0	1.34796	516	39	291
24.0	1.34796	432	46	247
25.0	1.34796	391	26	199
26.0	1.34796	328	24	207
27.0	1.34796	271	12	161
28.0	1.34796	228	11	144
29.0	1.34796	240	7	147
30.0	1.34796	192	10	125
31.0	1.34796	172	2	123
32.0	1.34796	181	8	93
33.0	1.34796	137	5	99
34.0	1.34796	102	3	83
35.0	1.34796	117	7	77
36.0	1.34796	113	4	54
37.0	1.34796	94	2	58
38.0	1.34796	93	0	60
39.0	1.34796	83	1	50
40.0	1.34796	78	0	59
41.0	1.34796	70	2	39
42.0	1.34796	69	1	34
43.0	1.34796	67	0	38
44.0	1.34796	38	4	30
45.0	1.34796	40	2	33
46.0	1.34796	47	2	35
47.0	1.34796	43	0	32
48.0	1.34796	38	0	30
49.0	1.34796	42	1	18
50.0	1.34796	38	0	28
51.0	1.34796	25	1	21
52.0	1.34796	26	0	15
53.0	1.34796	29	0	13
54.0	1.34796	27	0	14
55.0	1.34796	22	0	19
56.0	1.34796	25	0	18
57.0	1.34796	23	1	14
58.0	1.34796	17	0	8
59.0	1.34796	14	0	13
60.0	1.34796	15	0	10
61.0	1.34796	17	0	8
62.0	1.34796	12	0	8
63.0	1.34796	18	0	14
64.0	1.34796	15	0	11
65.0	1.34796	13	0	13
66.0	1.34796	11	0	6
67.0	1.34796	16	0	7
68.0	1.34796	11	0	12
69.0	1.34796	10	0	3
70.0	1.34796	7	0	7
71.0	1.34796	8	0	6
72.0	1.34796	6	0	5
73.0	1.34796	6	0	6
74.0	1.34796	12	0	9
75.0	1.34796	5	1	4
76.0	1.34796	6	0	4
77.0	1.34796	2	0	6
78.0	1.34796	6	0	5
79.0	1.34796	8	0	3
80.0	1.34796	5	0	6
81.0	1.34796	5	0	4
82.0	1.34796	3	0	1
83.0	1.34796	2	0	8
84.0	1.34796	12	0	2
85.0	1.34796	5	0	3
86.0	1.34796	5	0	2
87.0	1.34796	7	0	3
88.0	1.34796	2	0	1
89.0	1.34796	7	0	4
90.0	1.34796	4	0	1
91.0	1.34796	2	0	7
92.0	1.34796	3	0	1
93.0	1.34796	8	0	6
94.0	1.34796	3	0	3
95.0	1.34796	5	0	2
96.0	1.34796	2	0	3
97.0	1.34796	1	0	5
98.0	1.34796	5	0	0
99.0	1.34796	3	0	4
100.0	1.34796	2	0	3
101.0	0	5	0	2
102.0	0	5	0	0
103.0	0	2	0	0
104.0	0	3	0	1
105.0	0	0	0	3
106.0	0	2	0	2
107.0	0	3	0	1
108.0	0	2	0	2
109.0	0	4	0	1
110.0	0	4	0	0
111.0	0	1	0	0
112.0	0	1	0	3
113.0	0	1	0	0
114.0	0	1	0	0
115.0	0	1	0	1
116.0	0	2	0	1
117.0	0	1	0	2
118.0	0	0	0	1
119.0	0	3	0	1
120.0	0	0	0	2
121.0	0	1	0	0
122.0	0	1	0	1
123.0	0	0	0	1
124.0	0	1	0	1
125.0	0	1	0	1
126.0	0	1	0	0
127.0	0	3	0	2
128.0	0	1	0	0
129.0	0	1	0	1
130.0	0	1	0	4
131.0	0	1	0	0
132.0	0	0	0	1
133.0	0	1	0	1
135.0	0	3	0	0
136.0	0	0	0	2
137.0	0	2	0	0
138.0	0	1	0	1
141.0	0	0	0	1
142.0	0	1	0	0
144.0	0	1	0	1
145.0	0	2	0	0
146.0	0	1	0	0
147.0	0	0	0	3
148.0	0	1	0	0
150.0	0	1	0	0
151.0	0	1	0	0
156.0	0	1	0	1
157.0	0	1	0	0
158.0	0	1	0	0
159.0	0	2	0	0
161.0	0	1	0	0
164.0	0	1	0	0
169.0	0	0	0	1
177.0	0	1	0	0
183.0	0	0	0	1
184.0	0	1	0	0
191.0	0	0	0	1
194.0	0	0	0	1
198.0	0	0	0	1
199.0	0	1	0	0
218.0	0	1	0	0
221.0	0	1	0	0
222.0	0	0	0	1
232.0	0	1	0	0
264.0	0	0	0	1
284.0	0	0	0	1
290.0	0	0	0	1
291.0	0	1	0	0
307.0	0	1	0	0
331.0	0	1	0	0
734.0	0	0	0	1
763.0	0	1	0	0
978.0	0	0	0	1
1006.0	0	1	0	0