## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-255-TP3.bam --OUTPUT POC-255-TP3.md.bam --METRICS_FILE POC-255-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 03:00:43 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	230	12350236	3305184	0	164	9005010	2176525	0.729137	3546599

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.027609	694959	0	836520
2.0	1.059195	670007	584509	814490
3.0	1.060166	588095	224980	659565
4.0	1.060196	455126	108658	444283
5.0	1.060197	319166	59409	261688
6.0	1.060197	212749	34147	142260
7.0	1.060197	137433	20511	75502
8.0	1.060197	88591	12489	40683
9.0	1.060197	56806	7608	22833
10.0	1.060197	36891	4519	13442
11.0	1.060197	24345	3068	8318
12.0	1.060197	16197	1760	5524
13.0	1.060197	11082	1134	3822
14.0	1.060197	7621	770	2687
15.0	1.060197	5431	431	2060
16.0	1.060197	3942	293	1577
17.0	1.060197	2920	205	1264
18.0	1.060197	2238	140	1025
19.0	1.060197	1682	87	872
20.0	1.060197	1357	58	726
21.0	1.060197	1059	36	615
22.0	1.060197	832	24	513
23.0	1.060197	691	15	430
24.0	1.060197	564	11	406
25.0	1.060197	541	8	348
26.0	1.060197	443	11	283
27.0	1.060197	366	6	274
28.0	1.060197	349	3	255
29.0	1.060197	299	4	252
30.0	1.060197	269	2	188
31.0	1.060197	239	2	189
32.0	1.060197	189	4	163
33.0	1.060197	180	0	124
34.0	1.060197	185	3	117
35.0	1.060197	142	3	117
36.0	1.060197	134	2	101
37.0	1.060197	114	0	91
38.0	1.060197	108	1	84
39.0	1.060197	100	0	81
40.0	1.060197	94	1	65
41.0	1.060197	94	0	79
42.0	1.060197	93	0	71
43.0	1.060197	74	0	62
44.0	1.060197	61	0	67
45.0	1.060197	65	0	44
46.0	1.060197	63	0	51
47.0	1.060197	61	0	45
48.0	1.060197	54	0	50
49.0	1.060197	58	0	49
50.0	1.060197	53	0	29
51.0	1.060197	46	0	38
52.0	1.060197	41	0	39
53.0	1.060197	30	0	38
54.0	1.060197	33	0	28
55.0	1.060197	30	0	26
56.0	1.060197	45	0	26
57.0	1.060197	33	0	27
58.0	1.060197	33	0	19
59.0	1.060197	25	0	24
60.0	1.060197	34	0	16
61.0	1.060197	21	1	21
62.0	1.060197	21	0	18
63.0	1.060197	28	0	20
64.0	1.060197	25	0	22
65.0	1.060197	19	0	13
66.0	1.060197	23	0	17
67.0	1.060197	14	0	17
68.0	1.060197	17	0	15
69.0	1.060197	26	0	15
70.0	1.060197	15	0	15
71.0	1.060197	9	0	14
72.0	1.060197	17	0	12
73.0	1.060197	16	0	18
74.0	1.060197	8	0	10
75.0	1.060197	14	0	11
76.0	1.060197	9	0	13
77.0	1.060197	16	0	2
78.0	1.060197	9	0	6
79.0	1.060197	9	0	10
80.0	1.060197	8	0	7
81.0	1.060197	10	0	7
82.0	1.060197	8	0	6
83.0	1.060197	9	0	11
84.0	1.060197	16	0	6
85.0	1.060197	9	0	13
86.0	1.060197	6	0	10
87.0	1.060197	7	0	5
88.0	1.060197	7	0	6
89.0	1.060197	12	0	7
90.0	1.060197	5	0	3
91.0	1.060197	7	0	3
92.0	1.060197	7	0	1
93.0	1.060197	5	0	5
94.0	1.060197	7	0	3
95.0	1.060197	4	0	6
96.0	1.060197	7	0	7
97.0	1.060197	6	0	2
98.0	1.060197	1	0	2
99.0	1.060197	3	0	6
100.0	1.060197	4	0	4
101.0	0	4	0	5
102.0	0	5	0	3
103.0	0	5	0	4
104.0	0	6	0	2
105.0	0	4	0	7
106.0	0	2	0	3
107.0	0	1	0	3
108.0	0	3	0	2
109.0	0	5	0	0
110.0	0	7	0	3
111.0	0	3	0	6
112.0	0	1	0	3
113.0	0	5	0	1
114.0	0	2	0	3
115.0	0	3	0	2
116.0	0	4	0	4
117.0	0	4	0	1
118.0	0	2	0	1
119.0	0	2	0	2
120.0	0	0	0	1
121.0	0	3	0	2
122.0	0	3	0	4
123.0	0	3	0	2
124.0	0	3	0	1
125.0	0	0	0	2
126.0	0	3	0	4
127.0	0	1	0	0
128.0	0	1	0	1
129.0	0	2	0	0
130.0	0	1	0	2
131.0	0	1	0	0
132.0	0	2	0	3
133.0	0	1	0	2
134.0	0	2	0	2
135.0	0	1	0	1
136.0	0	2	0	2
137.0	0	0	0	3
138.0	0	2	0	1
139.0	0	4	0	1
140.0	0	2	0	0
141.0	0	4	0	1
142.0	0	2	0	2
143.0	0	1	0	2
144.0	0	1	0	2
146.0	0	2	0	0
147.0	0	1	0	1
148.0	0	0	0	1
149.0	0	0	0	1
151.0	0	2	0	1
152.0	0	1	0	3
153.0	0	1	0	0
154.0	0	0	0	2
155.0	0	2	0	0
156.0	0	1	0	1
157.0	0	1	0	1
158.0	0	4	0	1
159.0	0	2	0	0
160.0	0	0	0	1
161.0	0	0	0	2
162.0	0	2	0	1
164.0	0	2	0	1
165.0	0	0	0	1
166.0	0	0	0	2
167.0	0	1	0	1
169.0	0	1	0	0
170.0	0	0	0	1
171.0	0	1	0	1
172.0	0	1	0	0
173.0	0	2	0	3
174.0	0	1	0	1
175.0	0	3	0	0
177.0	0	1	0	0
178.0	0	1	0	0
179.0	0	0	0	1
180.0	0	2	0	0
181.0	0	0	0	1
182.0	0	0	0	1
185.0	0	1	0	1
186.0	0	1	0	1
187.0	0	1	0	0
191.0	0	1	0	0
192.0	0	2	0	0
193.0	0	0	0	2
195.0	0	1	0	0
197.0	0	0	0	1
201.0	0	0	0	2
204.0	0	1	0	0
205.0	0	1	0	0
207.0	0	0	0	2
209.0	0	0	0	1
210.0	0	0	0	1
211.0	0	0	0	2
212.0	0	0	0	2
214.0	0	1	0	0
215.0	0	0	0	1
217.0	0	1	0	2
218.0	0	1	0	2
219.0	0	3	0	0
220.0	0	3	0	1
221.0	0	1	0	0
223.0	0	0	0	2
224.0	0	1	0	0
226.0	0	2	0	0
228.0	0	1	0	0
229.0	0	2	0	0
231.0	0	1	0	2
232.0	0	1	0	0
233.0	0	1	0	0
235.0	0	0	0	1
237.0	0	0	0	1
239.0	0	1	0	0
243.0	0	1	0	0
244.0	0	1	0	0
245.0	0	1	0	0
246.0	0	1	0	0
247.0	0	0	0	1
252.0	0	0	0	1
260.0	0	0	0	2
265.0	0	2	0	0
271.0	0	1	0	0
288.0	0	0	0	1
289.0	0	0	0	1
290.0	0	0	0	1
293.0	0	1	0	0
299.0	0	1	0	0
303.0	0	1	0	1
311.0	0	1	0	0
312.0	0	1	0	0
325.0	0	0	0	1
332.0	0	0	0	1
339.0	0	1	0	0
341.0	0	0	0	1
342.0	0	0	0	1
352.0	0	0	0	1
355.0	0	1	0	0
360.0	0	1	0	0
362.0	0	1	0	0
365.0	0	1	0	0
369.0	0	0	0	1
391.0	0	0	0	1
399.0	0	1	0	0
408.0	0	1	0	0
446.0	0	0	0	1
455.0	0	0	0	1
461.0	0	1	0	0
464.0	0	0	0	1
480.0	0	1	0	0
501.0	0	1	0	0
773.0	0	0	0	1
833.0	0	1	0	0