## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-255-TP2.bam --OUTPUT POC-255-TP2.md.bam --METRICS_FILE POC-255-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 02:43:47 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	269	14235834	3226174	0	191	8743679	4075898	0.614203	7317753

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.141958	2105564	0	2840529
2.0	1.305181	1363470	931075	1535459
3.0	1.32851	819244	399506	672693
4.0	1.331845	476161	211189	261684
5.0	1.332322	276505	120918	98425
6.0	1.33239	163605	71607	38585
7.0	1.332399	99070	42986	17056
8.0	1.332401	62581	26292	8685
9.0	1.332401	39942	16418	5029
10.0	1.332401	26473	10267	3135
11.0	1.332401	17435	6335	2207
12.0	1.332401	11901	3849	1565
13.0	1.332401	7992	2420	1175
14.0	1.332401	5593	1650	950
15.0	1.332401	3938	1100	761
16.0	1.332401	2894	657	598
17.0	1.332401	1987	428	456
18.0	1.332401	1528	289	404
19.0	1.332401	1137	167	314
20.0	1.332401	857	109	256
21.0	1.332401	647	71	206
22.0	1.332401	474	61	195
23.0	1.332401	375	27	172
24.0	1.332401	319	26	141
25.0	1.332401	276	23	137
26.0	1.332401	221	13	121
27.0	1.332401	198	11	107
28.0	1.332401	148	9	92
29.0	1.332401	149	7	76
30.0	1.332401	114	5	60
31.0	1.332401	125	8	65
32.0	1.332401	103	9	59
33.0	1.332401	73	1	51
34.0	1.332401	73	0	53
35.0	1.332401	72	3	41
36.0	1.332401	52	3	44
37.0	1.332401	64	1	53
38.0	1.332401	49	0	42
39.0	1.332401	38	1	13
40.0	1.332401	46	0	27
41.0	1.332401	33	0	25
42.0	1.332401	39	0	21
43.0	1.332401	34	0	25
44.0	1.332401	29	2	19
45.0	1.332401	31	0	13
46.0	1.332401	30	0	20
47.0	1.332401	22	0	26
48.0	1.332401	14	0	12
49.0	1.332401	28	0	15
50.0	1.332401	20	0	17
51.0	1.332401	27	0	13
52.0	1.332401	22	0	11
53.0	1.332401	11	0	10
54.0	1.332401	12	0	7
55.0	1.332401	15	0	10
56.0	1.332401	13	0	12
57.0	1.332401	15	0	8
58.0	1.332401	10	0	11
59.0	1.332401	18	0	7
60.0	1.332401	15	0	6
61.0	1.332401	11	0	6
62.0	1.332401	11	0	6
63.0	1.332401	9	0	2
64.0	1.332401	13	0	3
65.0	1.332401	5	0	3
66.0	1.332401	6	0	4
67.0	1.332401	6	0	5
68.0	1.332401	4	0	7
69.0	1.332401	9	0	2
70.0	1.332401	4	0	4
71.0	1.332401	8	0	4
72.0	1.332401	5	0	3
73.0	1.332401	4	0	3
74.0	1.332401	8	0	3
75.0	1.332401	4	0	4
76.0	1.332401	3	0	2
77.0	1.332401	8	0	4
78.0	1.332401	1	0	3
79.0	1.332401	4	0	6
80.0	1.332401	3	0	1
81.0	1.332401	1	0	3
82.0	1.332401	5	0	3
83.0	1.332401	3	0	1
84.0	1.332401	1	0	4
85.0	1.332401	4	0	2
86.0	1.332401	0	0	2
87.0	1.332401	4	0	1
88.0	1.332401	5	0	3
89.0	1.332401	3	0	0
90.0	1.332401	8	0	0
91.0	1.332401	2	0	1
92.0	1.332401	5	0	0
93.0	1.332401	1	0	4
94.0	1.332401	0	0	1
95.0	1.332401	1	0	2
96.0	1.332401	1	0	2
97.0	1.332401	1	0	2
98.0	1.332401	1	0	0
99.0	1.332401	2	0	3
100.0	1.332401	3	0	4
101.0	0	2	0	1
102.0	0	2	0	0
103.0	0	2	0	0
106.0	0	1	0	0
107.0	0	3	0	0
108.0	0	1	0	1
109.0	0	0	0	1
110.0	0	1	0	0
111.0	0	0	0	1
112.0	0	1	0	1
114.0	0	1	0	1
115.0	0	1	0	1
116.0	0	1	0	1
117.0	0	1	0	1
119.0	0	1	0	1
121.0	0	1	0	1
123.0	0	1	0	1
125.0	0	1	0	1
126.0	0	1	0	0
127.0	0	1	0	0
128.0	0	1	0	0
129.0	0	1	0	0
132.0	0	1	0	1
133.0	0	1	0	1
135.0	0	0	0	1
145.0	0	2	0	0
148.0	0	0	0	2
153.0	0	0	0	1
154.0	0	0	0	2
156.0	0	1	0	0
157.0	0	1	0	2
158.0	0	0	0	1
159.0	0	2	0	0
164.0	0	1	0	1
165.0	0	1	0	1
169.0	0	1	0	0
171.0	0	2	0	0
172.0	0	0	0	1
173.0	0	2	0	0
175.0	0	0	0	1
181.0	0	0	0	1
186.0	0	0	0	1
193.0	0	1	0	0
196.0	0	1	0	0
206.0	0	1	0	0
212.0	0	1	0	0
265.0	0	0	0	1
286.0	0	1	0	0
506.0	0	0	0	1
530.0	0	1	0	0
748.0	0	0	0	1
775.0	0	1	0	0