## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-219-TP1.bam --OUTPUT POC-219-TP1.md.bam --METRICS_FILE POC-219-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 02:47:35 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	241	14603788	3129672	0	150	7122880	3969148	0.487743	14175592

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.218549	4099562	0	5348430
2.0	1.653489	1753892	1117216	1556639
3.0	1.808734	785965	439494	398033
4.0	1.864146	377114	214030	105229
5.0	1.883925	194556	113199	33171
6.0	1.890984	106491	60999	13787
7.0	1.893504	61534	34305	7236
8.0	1.894403	36404	18969	4532
9.0	1.894724	22167	10580	2958
10.0	1.894839	13684	5976	2169
11.0	1.89488	8720	3417	1568
12.0	1.894894	5656	1980	1184
13.0	1.8949	3785	1109	880
14.0	1.894902	2538	670	739
15.0	1.894902	1713	431	602
16.0	1.894902	1290	228	462
17.0	1.894903	935	155	395
18.0	1.894903	750	87	321
19.0	1.894903	568	57	288
20.0	1.894903	441	41	229
21.0	1.894903	361	29	204
22.0	1.894903	311	21	180
23.0	1.894903	251	18	162
24.0	1.894903	201	9	129
25.0	1.894903	198	2	87
26.0	1.894903	162	6	90
27.0	1.894903	111	3	74
28.0	1.894903	111	3	77
29.0	1.894903	121	7	80
30.0	1.894903	97	0	67
31.0	1.894903	83	1	46
32.0	1.894903	81	4	49
33.0	1.894903	58	3	60
34.0	1.894903	62	1	44
35.0	1.894903	50	2	27
36.0	1.894903	54	0	44
37.0	1.894903	38	0	33
38.0	1.894903	43	2	27
39.0	1.894903	33	0	23
40.0	1.894903	39	1	26
41.0	1.894903	33	1	22
42.0	1.894903	24	1	20
43.0	1.894903	35	0	22
44.0	1.894903	34	0	27
45.0	1.894903	36	0	19
46.0	1.894903	18	0	20
47.0	1.894903	20	0	24
48.0	1.894903	31	0	17
49.0	1.894903	17	0	14
50.0	1.894903	17	0	17
51.0	1.894903	16	0	14
52.0	1.894903	23	0	8
53.0	1.894903	17	0	9
54.0	1.894903	13	0	12
55.0	1.894903	6	1	8
56.0	1.894903	11	0	14
57.0	1.894903	12	0	6
58.0	1.894903	9	0	7
59.0	1.894903	9	0	9
60.0	1.894903	13	0	6
61.0	1.894903	12	0	6
62.0	1.894903	8	0	5
63.0	1.894903	10	0	1
64.0	1.894903	6	0	6
65.0	1.894903	6	1	5
66.0	1.894903	6	0	3
67.0	1.894903	4	0	2
68.0	1.894903	2	0	4
69.0	1.894903	4	0	7
70.0	1.894903	5	0	5
71.0	1.894903	8	0	3
72.0	1.894903	5	0	2
73.0	1.894903	4	0	5
74.0	1.894903	5	0	3
75.0	1.894903	4	0	6
76.0	1.894903	2	0	2
77.0	1.894903	6	0	3
78.0	1.894903	3	0	4
79.0	1.894903	6	0	7
80.0	1.894903	4	0	6
81.0	1.894903	6	0	5
82.0	1.894903	4	0	5
83.0	1.894903	5	0	1
84.0	1.894903	3	0	4
85.0	1.894903	9	0	2
86.0	1.894903	3	0	2
87.0	1.894903	3	0	1
88.0	1.894903	2	0	3
89.0	1.894903	5	0	5
90.0	1.894903	2	0	2
91.0	1.894903	2	0	3
92.0	1.894903	3	0	0
93.0	1.894903	2	0	4
94.0	1.894903	2	0	2
95.0	1.894903	3	0	3
96.0	1.894903	4	0	5
97.0	1.894903	1	0	2
98.0	1.894903	2	0	3
99.0	1.894903	0	0	0
100.0	1.894903	4	0	5
101.0	0	1	0	1
102.0	0	3	0	3
103.0	0	7	0	0
104.0	0	3	0	0
105.0	0	1	0	2
106.0	0	2	0	1
107.0	0	1	0	1
108.0	0	2	0	0
109.0	0	1	0	4
110.0	0	1	0	2
111.0	0	3	0	1
112.0	0	2	0	0
113.0	0	0	0	3
114.0	0	2	0	1
115.0	0	1	0	1
116.0	0	0	0	2
117.0	0	1	0	3
118.0	0	1	0	2
119.0	0	2	0	0
120.0	0	2	0	2
121.0	0	1	0	1
122.0	0	2	0	0
123.0	0	2	0	2
125.0	0	0	0	2
126.0	0	4	0	1
127.0	0	1	0	1
129.0	0	2	0	1
130.0	0	2	0	1
132.0	0	0	0	1
133.0	0	1	0	2
134.0	0	0	0	1
135.0	0	2	0	0
137.0	0	1	0	1
138.0	0	0	0	1
141.0	0	5	0	0
142.0	0	0	0	1
146.0	0	2	0	1
148.0	0	1	0	0
150.0	0	0	0	2
152.0	0	0	0	1
153.0	0	1	0	1
155.0	0	0	0	1
156.0	0	0	0	1
157.0	0	0	0	1
159.0	0	2	0	1
160.0	0	0	0	3
161.0	0	3	0	1
162.0	0	1	0	1
163.0	0	2	0	0
164.0	0	0	0	1
165.0	0	1	0	0
166.0	0	1	0	1
170.0	0	1	0	0
171.0	0	1	0	0
172.0	0	0	0	1
174.0	0	1	0	0
176.0	0	1	0	1
177.0	0	2	0	0
182.0	0	0	0	1
183.0	0	0	0	1
184.0	0	1	0	1
185.0	0	2	0	0
189.0	0	1	0	1
193.0	0	1	0	1
198.0	0	0	0	1
199.0	0	1	0	0
201.0	0	1	0	1
203.0	0	0	0	1
204.0	0	0	0	1
207.0	0	2	0	0
213.0	0	0	0	1
214.0	0	1	0	1
216.0	0	1	0	0
220.0	0	0	0	1
221.0	0	2	0	0
223.0	0	0	0	1
227.0	0	0	0	1
233.0	0	0	0	1
235.0	0	1	0	0
239.0	0	1	0	0
240.0	0	0	0	1
243.0	0	0	0	1
248.0	0	1	0	0
250.0	0	3	0	0
270.0	0	0	0	1
277.0	0	1	0	0
285.0	0	0	0	1
298.0	0	0	0	1
301.0	0	0	0	1
302.0	0	1	0	0
304.0	0	1	0	0
305.0	0	1	0	0
313.0	0	1	0	0
336.0	0	0	0	1
341.0	0	0	0	1
350.0	0	0	0	1
359.0	0	0	0	1
360.0	0	1	0	0
364.0	0	1	0	0
368.0	0	1	0	0
404.0	0	1	0	0
410.0	0	0	0	1
420.0	0	1	0	0
608.0	0	0	0	1
672.0	0	1	0	0