## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-53-TP2.bam --OUTPUT POC-53-TP2.md.bam --METRICS_FILE POC-53-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 02:44:25 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	207	13471226	2886130	0	128	6712360	3902975	0.498275	12917787

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.237619	3609548	0	4827939
2.0	1.673819	1602825	1064834	1415402
3.0	1.827558	736521	428829	361160
4.0	1.881743	359798	212392	93998
5.0	1.900841	187899	113062	28568
6.0	1.907572	104380	61798	11610
7.0	1.909945	60137	34473	5849
8.0	1.910781	35327	19402	3581
9.0	1.911075	21826	10727	2407
10.0	1.911179	13424	6280	1657
11.0	1.911216	8371	3419	1181
12.0	1.911229	5441	2060	952
13.0	1.911233	3531	1146	706
14.0	1.911235	2306	673	550
15.0	1.911236	1612	405	450
16.0	1.911236	1172	233	372
17.0	1.911236	836	160	315
18.0	1.911236	604	82	246
19.0	1.911236	476	54	215
20.0	1.911236	366	47	148
21.0	1.911236	287	27	135
22.0	1.911236	234	15	133
23.0	1.911236	210	13	123
24.0	1.911236	165	13	96
25.0	1.911236	128	6	77
26.0	1.911236	126	8	81
27.0	1.911236	111	3	72
28.0	1.911236	111	2	74
29.0	1.911236	85	5	52
30.0	1.911236	60	4	50
31.0	1.911236	80	1	56
32.0	1.911236	68	0	33
33.0	1.911236	51	1	37
34.0	1.911236	55	1	35
35.0	1.911236	45	0	36
36.0	1.911236	37	1	25
37.0	1.911236	29	2	14
38.0	1.911236	27	2	22
39.0	1.911236	30	2	12
40.0	1.911236	31	0	27
41.0	1.911236	28	0	18
42.0	1.911236	28	1	11
43.0	1.911236	20	1	17
44.0	1.911236	22	1	16
45.0	1.911236	17	0	16
46.0	1.911236	20	0	10
47.0	1.911236	15	1	16
48.0	1.911236	15	0	14
49.0	1.911236	15	0	7
50.0	1.911236	17	0	13
51.0	1.911236	11	1	14
52.0	1.911236	14	0	12
53.0	1.911236	10	0	5
54.0	1.911236	12	0	3
55.0	1.911236	14	0	6
56.0	1.911236	8	0	10
57.0	1.911236	6	0	8
58.0	1.911236	5	0	6
59.0	1.911236	5	0	7
60.0	1.911236	11	0	4
61.0	1.911236	6	0	3
62.0	1.911236	5	0	3
63.0	1.911236	10	0	6
64.0	1.911236	5	0	9
65.0	1.911236	9	0	5
66.0	1.911236	6	0	8
67.0	1.911236	7	0	7
68.0	1.911236	11	0	6
69.0	1.911236	6	0	1
70.0	1.911236	5	0	2
71.0	1.911236	6	0	7
72.0	1.911236	1	0	3
73.0	1.911236	4	0	4
74.0	1.911236	2	0	1
75.0	1.911236	4	0	2
76.0	1.911236	0	0	1
77.0	1.911236	5	0	0
78.0	1.911236	3	0	1
79.0	1.911236	1	0	0
80.0	1.911236	5	0	0
81.0	1.911236	4	0	2
82.0	1.911236	1	0	0
83.0	1.911236	0	0	1
84.0	1.911236	4	0	3
85.0	1.911236	1	0	2
86.0	1.911236	2	0	1
87.0	1.911236	2	0	2
88.0	1.911236	3	0	3
89.0	1.911236	0	0	2
90.0	1.911236	4	0	1
91.0	1.911236	0	0	0
92.0	1.911236	1	0	4
93.0	1.911236	1	0	1
94.0	1.911236	1	0	3
95.0	1.911236	1	0	3
96.0	1.911236	1	0	1
97.0	1.911236	2	0	4
98.0	1.911236	3	0	1
99.0	1.911236	0	0	1
100.0	1.911236	1	0	1
101.0	0	2	0	1
102.0	0	2	0	2
103.0	0	1	0	1
104.0	0	2	0	3
105.0	0	2	0	0
106.0	0	3	0	1
107.0	0	6	0	0
109.0	0	1	0	1
110.0	0	0	0	1
111.0	0	1	0	2
112.0	0	1	0	0
113.0	0	3	0	1
114.0	0	2	0	1
115.0	0	1	0	0
117.0	0	3	0	2
118.0	0	0	0	1
119.0	0	1	0	2
120.0	0	2	0	1
122.0	0	1	0	0
126.0	0	1	0	0
128.0	0	0	0	1
129.0	0	1	0	1
131.0	0	0	0	2
132.0	0	1	0	0
133.0	0	1	0	0
134.0	0	1	0	0
135.0	0	1	0	0
136.0	0	1	0	2
143.0	0	1	0	2
144.0	0	1	0	1
145.0	0	1	0	1
147.0	0	0	0	2
149.0	0	1	0	0
151.0	0	1	0	1
152.0	0	0	0	1
153.0	0	1	0	0
155.0	0	0	0	1
159.0	0	1	0	2
160.0	0	1	0	1
161.0	0	1	0	0
165.0	0	1	0	1
166.0	0	1	0	0
167.0	0	1	0	0
168.0	0	1	0	0
172.0	0	1	0	0
183.0	0	1	0	0
188.0	0	1	0	0
191.0	0	0	0	1
194.0	0	0	0	1
195.0	0	1	0	0
196.0	0	0	0	1
198.0	0	1	0	0
203.0	0	0	0	1
205.0	0	0	0	1
222.0	0	1	0	0
223.0	0	0	0	1
224.0	0	0	0	1
225.0	0	1	0	0
231.0	0	1	0	1
242.0	0	1	0	0
244.0	0	1	0	0
248.0	0	1	0	0
254.0	0	0	0	1
287.0	0	1	0	0
317.0	0	0	0	1
333.0	0	0	0	1
348.0	0	1	0	0
360.0	0	1	0	0
391.0	0	0	0	1
441.0	0	1	0	0
491.0	0	0	0	1
502.0	0	1	0	0