## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-255-TP1.bam --OUTPUT POC-255-TP1.md.bam --METRICS_FILE POC-255-TP1.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 02:42:52 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	231	13461187	2534248	0	155	5452151	3604605	0.40503	22892309

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.270734	5130083	0	6646657
2.0	1.976531	1651755	1132305	1096662
3.0	2.368548	636163	426064	185640
4.0	2.586284	283585	199041	42821
5.0	2.70722	139706	98903	14912
6.0	2.774391	73133	50092	7416
7.0	2.811699	39192	25659	4071
8.0	2.832421	21765	13065	2636
9.0	2.843931	12366	6834	1800
10.0	2.850324	7120	3479	1319
11.0	2.853874	4353	1811	1003
12.0	2.855846	2661	921	673
13.0	2.856942	1667	515	550
14.0	2.85755	1120	269	419
15.0	2.857888	767	184	379
16.0	2.858076	603	76	277
17.0	2.85818	446	41	230
18.0	2.858238	354	43	221
19.0	2.85827	299	22	167
20.0	2.858288	218	18	123
21.0	2.858298	203	13	108
22.0	2.858303	181	7	96
23.0	2.858306	137	9	103
24.0	2.858308	123	6	77
25.0	2.858309	109	9	68
26.0	2.85831	75	1	54
27.0	2.85831	76	5	47
28.0	2.85831	64	1	36
29.0	2.85831	56	5	55
30.0	2.85831	52	0	31
31.0	2.85831	46	1	38
32.0	2.85831	45	2	23
33.0	2.85831	40	2	29
34.0	2.85831	43	0	25
35.0	2.85831	38	0	17
36.0	2.85831	37	2	22
37.0	2.85831	22	0	14
38.0	2.85831	24	1	12
39.0	2.85831	20	0	10
40.0	2.85831	20	1	10
41.0	2.85831	14	0	9
42.0	2.85831	17	0	9
43.0	2.85831	14	0	13
44.0	2.85831	12	0	5
45.0	2.85831	13	0	10
46.0	2.85831	12	2	12
47.0	2.85831	11	1	10
48.0	2.85831	9	0	9
49.0	2.85831	11	0	6
50.0	2.85831	7	0	2
51.0	2.85831	2	0	4
52.0	2.85831	9	1	1
53.0	2.85831	8	0	3
54.0	2.85831	5	0	5
55.0	2.85831	5	0	6
56.0	2.85831	4	0	3
57.0	2.85831	5	1	3
58.0	2.85831	6	0	6
59.0	2.85831	0	0	4
60.0	2.85831	11	0	4
61.0	2.85831	2	0	1
62.0	2.85831	5	0	1
63.0	2.85831	3	0	3
64.0	2.85831	1	0	2
65.0	2.85831	4	0	1
66.0	2.85831	3	0	6
67.0	2.85831	2	0	1
68.0	2.85831	3	0	3
69.0	2.85831	1	0	1
70.0	2.85831	2	0	1
71.0	2.85831	5	0	1
72.0	2.85831	3	0	3
73.0	2.85831	3	0	1
74.0	2.85831	3	0	1
75.0	2.85831	2	0	0
76.0	2.85831	1	0	1
77.0	2.85831	1	0	1
78.0	2.85831	3	0	5
79.0	2.85831	0	0	1
80.0	2.85831	1	0	1
81.0	2.85831	3	0	1
82.0	2.85831	4	0	2
83.0	2.85831	5	0	0
84.0	2.85831	1	0	3
85.0	2.85831	2	0	0
86.0	2.85831	1	0	1
87.0	2.85831	4	0	2
88.0	2.85831	0	0	1
89.0	2.85831	2	0	1
90.0	2.85831	0	0	0
91.0	2.85831	1	0	1
92.0	2.85831	1	0	0
93.0	2.85831	2	0	1
94.0	2.85831	0	0	0
95.0	2.85831	2	0	1
96.0	2.85831	0	0	2
97.0	2.85831	3	0	0
98.0	2.85831	0	0	0
99.0	2.85831	1	0	0
100.0	2.85831	0	0	0
101.0	0	1	0	1
102.0	0	1	0	1
103.0	0	0	0	1
105.0	0	1	0	1
106.0	0	0	0	1
108.0	0	0	0	1
109.0	0	0	0	1
110.0	0	1	0	0
111.0	0	1	0	0
114.0	0	1	0	0
116.0	0	1	0	0
123.0	0	2	0	1
126.0	0	1	0	0
127.0	0	1	0	0
133.0	0	1	0	0
211.0	0	0	0	1
218.0	0	1	0	0
306.0	0	0	0	1
320.0	0	1	0	0