## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-219-TP3.bam --OUTPUT POC-219-TP3.md.bam --METRICS_FILE POC-219-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 03:11:19 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	121	3792951	717306	0	87	2521629	833142	0.664821	1465992

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.066382	381404	0	479583
2.0	1.146599	302773	210157	358508
3.0	1.152633	215697	82959	217768
4.0	1.153087	140761	41426	111946
5.0	1.153121	87065	23210	53073
6.0	1.153124	52765	13584	24482
7.0	1.153124	32359	8322	11416
8.0	1.153124	20101	5155	5666
9.0	1.153124	12520	3345	2931
10.0	1.153124	8083	2043	1668
11.0	1.153124	5313	1314	983
12.0	1.153124	3569	817	644
13.0	1.153124	2451	484	460
14.0	1.153124	1660	315	335
15.0	1.153124	1130	194	274
16.0	1.153124	820	123	198
17.0	1.153124	572	74	165
18.0	1.153124	390	52	143
19.0	1.153124	342	28	117
20.0	1.153124	227	25	89
21.0	1.153124	182	14	92
22.0	1.153124	127	11	68
23.0	1.153124	126	15	73
24.0	1.153124	94	2	47
25.0	1.153124	71	2	45
26.0	1.153124	56	3	28
27.0	1.153124	53	0	31
28.0	1.153124	47	2	26
29.0	1.153124	42	1	26
30.0	1.153124	29	0	26
31.0	1.153124	27	1	23
32.0	1.153124	28	1	19
33.0	1.153124	28	0	12
34.0	1.153124	21	1	21
35.0	1.153124	13	0	15
36.0	1.153124	29	0	22
37.0	1.153124	22	0	14
38.0	1.153124	11	0	14
39.0	1.153124	15	0	10
40.0	1.153124	8	0	12
41.0	1.153124	9	0	10
42.0	1.153124	21	1	7
43.0	1.153124	9	0	12
44.0	1.153124	8	0	9
45.0	1.153124	8	0	3
46.0	1.153124	11	0	12
47.0	1.153124	7	0	7
48.0	1.153124	7	0	7
49.0	1.153124	4	0	8
50.0	1.153124	13	0	7
51.0	1.153124	6	0	5
52.0	1.153124	14	0	8
53.0	1.153124	4	0	9
54.0	1.153124	10	0	8
55.0	1.153124	7	0	4
56.0	1.153124	4	0	2
57.0	1.153124	4	0	4
58.0	1.153124	3	0	4
59.0	1.153124	9	0	5
60.0	1.153124	1	0	5
61.0	1.153124	3	0	3
62.0	1.153124	6	0	3
63.0	1.153124	6	0	5
64.0	1.153124	5	0	4
65.0	1.153124	4	0	3
66.0	1.153124	2	0	1
67.0	1.153124	4	0	3
68.0	1.153124	2	0	0
69.0	1.153124	4	0	2
70.0	1.153124	1	0	1
71.0	1.153124	1	0	1
72.0	1.153124	2	0	0
73.0	1.153124	1	0	2
74.0	1.153124	1	0	4
75.0	1.153124	1	0	1
76.0	1.153124	0	0	3
77.0	1.153124	0	0	1
78.0	1.153124	3	0	3
79.0	1.153124	0	0	2
80.0	1.153124	5	0	1
81.0	1.153124	2	0	1
82.0	1.153124	3	0	1
83.0	1.153124	0	0	3
84.0	1.153124	2	0	1
85.0	1.153124	0	0	1
86.0	1.153124	2	0	2
87.0	1.153124	3	0	3
88.0	1.153124	1	0	2
89.0	1.153124	2	0	0
90.0	1.153124	2	0	1
91.0	1.153124	4	0	0
92.0	1.153124	1	0	3
93.0	1.153124	1	0	1
94.0	1.153124	0	0	1
95.0	1.153124	1	0	0
96.0	1.153124	1	0	1
97.0	1.153124	1	0	2
98.0	1.153124	2	0	0
99.0	1.153124	1	0	3
100.0	1.153124	1	0	1
101.0	0	1	0	0
103.0	0	1	0	1
104.0	0	1	0	2
105.0	0	1	0	0
107.0	0	0	0	2
108.0	0	1	0	2
109.0	0	3	0	0
110.0	0	1	0	1
111.0	0	1	0	0
112.0	0	2	0	3
113.0	0	1	0	0
114.0	0	1	0	2
116.0	0	0	0	1
119.0	0	1	0	1
120.0	0	1	0	0
122.0	0	1	0	0
123.0	0	0	0	2
124.0	0	0	0	1
125.0	0	2	0	0
126.0	0	2	0	1
127.0	0	1	0	0
129.0	0	3	0	1
130.0	0	1	0	2
135.0	0	1	0	0
136.0	0	1	0	1
137.0	0	0	0	2
139.0	0	1	0	1
140.0	0	1	0	1
142.0	0	2	0	0
144.0	0	1	0	0
149.0	0	0	0	1
151.0	0	1	0	0
153.0	0	1	0	0
157.0	0	0	0	1
158.0	0	1	0	0
160.0	0	1	0	0
162.0	0	0	0	1
164.0	0	0	0	1
168.0	0	0	0	1
170.0	0	0	0	1
179.0	0	0	0	1
180.0	0	0	0	2
182.0	0	1	0	0
186.0	0	1	0	0
187.0	0	1	0	0
188.0	0	1	0	0
189.0	0	1	0	0
199.0	0	1	0	0
204.0	0	1	0	0
237.0	0	0	0	1
238.0	0	0	0	1
250.0	0	1	0	0
257.0	0	0	0	1
265.0	0	1	0	0
268.0	0	0	0	1
270.0	0	1	0	0
272.0	0	0	0	1
285.0	0	1	0	0
305.0	0	1	0	0
342.0	0	0	0	1
354.0	0	1	0	0
411.0	0	0	0	1
452.0	0	1	0	0