## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-259-TP4.bam --OUTPUT POC-259-TP4.md.bam --METRICS_FILE POC-259-TP4.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 02:42:04 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	369	14350100	2990053	0	252	6726160	3984183	0.468721	15960082

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.241551	4358506	0	5734796
2.0	1.746771	1733864	1140526	1424030
3.0	1.952357	751121	452801	324366
4.0	2.036016	356089	220242	80972
5.0	2.070059	182008	113602	25964
6.0	2.083912	98825	61018	11237
7.0	2.089549	55746	32422	6196
8.0	2.091843	32301	17393	3840
9.0	2.092776	19006	9420	2607
10.0	2.093156	11669	5185	1853
11.0	2.09331	7193	2869	1419
12.0	2.093373	4600	1598	1078
13.0	2.093399	3105	925	782
14.0	2.093409	2064	516	642
15.0	2.093414	1417	324	524
16.0	2.093415	1052	182	407
17.0	2.093416	803	130	369
18.0	2.093416	611	83	315
19.0	2.093416	496	44	269
20.0	2.093416	402	27	203
21.0	2.093417	325	20	193
22.0	2.093417	264	15	178
23.0	2.093417	227	12	151
24.0	2.093417	212	14	117
25.0	2.093417	171	8	109
26.0	2.093417	164	6	99
27.0	2.093417	113	6	97
28.0	2.093417	120	6	69
29.0	2.093417	109	9	63
30.0	2.093417	96	2	78
31.0	2.093417	87	2	49
32.0	2.093417	79	1	45
33.0	2.093417	60	0	37
34.0	2.093417	65	1	46
35.0	2.093417	54	1	44
36.0	2.093417	55	3	40
37.0	2.093417	51	3	30
38.0	2.093417	30	1	31
39.0	2.093417	42	2	22
40.0	2.093417	36	1	20
41.0	2.093417	34	0	12
42.0	2.093417	31	1	19
43.0	2.093417	18	1	19
44.0	2.093417	25	0	15
45.0	2.093417	16	0	20
46.0	2.093417	27	0	17
47.0	2.093417	22	2	16
48.0	2.093417	22	0	16
49.0	2.093417	14	2	13
50.0	2.093417	12	1	11
51.0	2.093417	17	0	20
52.0	2.093417	20	0	9
53.0	2.093417	17	2	18
54.0	2.093417	12	0	12
55.0	2.093417	12	0	8
56.0	2.093417	10	0	11
57.0	2.093417	11	0	11
58.0	2.093417	16	0	7
59.0	2.093417	17	0	13
60.0	2.093417	4	0	9
61.0	2.093417	14	0	7
62.0	2.093417	13	0	9
63.0	2.093417	8	0	7
64.0	2.093417	6	0	5
65.0	2.093417	8	0	12
66.0	2.093417	9	0	6
67.0	2.093417	6	0	5
68.0	2.093417	9	0	4
69.0	2.093417	12	0	10
70.0	2.093417	8	0	5
71.0	2.093417	5	0	5
72.0	2.093417	7	0	3
73.0	2.093417	8	0	1
74.0	2.093417	8	0	2
75.0	2.093417	3	0	9
76.0	2.093417	1	1	7
77.0	2.093417	5	0	1
78.0	2.093417	9	0	3
79.0	2.093417	6	0	2
80.0	2.093417	4	0	1
81.0	2.093417	3	0	5
82.0	2.093417	4	0	2
83.0	2.093417	6	0	0
84.0	2.093417	0	0	2
85.0	2.093417	3	0	3
86.0	2.093417	4	0	3
87.0	2.093417	3	0	4
88.0	2.093417	2	0	7
89.0	2.093417	1	0	2
90.0	2.093417	3	0	1
91.0	2.093417	2	0	2
92.0	2.093417	2	0	3
93.0	2.093417	1	1	1
94.0	2.093417	1	0	3
95.0	2.093417	3	0	1
96.0	2.093417	3	0	2
97.0	2.093417	4	0	6
98.0	2.093417	4	0	2
99.0	2.093417	5	0	2
100.0	2.093417	3	0	1
101.0	0	5	0	0
102.0	0	1	0	1
103.0	0	2	0	0
104.0	0	1	0	2
105.0	0	3	0	3
106.0	0	2	0	0
107.0	0	2	0	2
108.0	0	2	0	1
109.0	0	0	0	1
110.0	0	2	0	3
111.0	0	1	0	4
112.0	0	1	0	2
113.0	0	2	0	1
114.0	0	1	0	0
115.0	0	3	0	1
116.0	0	1	0	0
117.0	0	1	0	0
118.0	0	2	0	1
119.0	0	1	0	0
120.0	0	1	0	2
122.0	0	2	0	1
123.0	0	1	0	0
124.0	0	1	0	3
125.0	0	0	0	2
126.0	0	2	0	2
127.0	0	2	0	1
128.0	0	2	0	0
129.0	0	2	0	2
130.0	0	0	0	1
131.0	0	1	0	1
132.0	0	2	0	4
133.0	0	1	0	0
134.0	0	1	0	2
135.0	0	2	0	1
136.0	0	1	0	0
137.0	0	1	0	1
138.0	0	0	0	2
139.0	0	1	0	0
140.0	0	1	0	2
141.0	0	0	0	1
142.0	0	2	0	2
143.0	0	0	0	1
144.0	0	1	0	1
145.0	0	1	0	2
146.0	0	1	0	1
147.0	0	0	0	1
149.0	0	1	0	1
150.0	0	1	0	0
151.0	0	3	0	0
152.0	0	0	0	3
153.0	0	1	0	1
154.0	0	1	0	2
155.0	0	2	0	0
156.0	0	2	0	3
157.0	0	1	0	0
158.0	0	1	0	0
159.0	0	2	0	0
160.0	0	1	0	0
161.0	0	1	0	1
162.0	0	1	0	0
163.0	0	1	0	0
164.0	0	1	0	0
167.0	0	0	0	1
169.0	0	2	0	1
170.0	0	1	0	2
171.0	0	0	0	1
173.0	0	1	0	1
176.0	0	2	0	0
178.0	0	1	0	0
182.0	0	0	0	1
184.0	0	3	0	0
188.0	0	0	0	1
190.0	0	0	0	1
191.0	0	0	0	1
192.0	0	0	0	1
194.0	0	1	0	0
195.0	0	1	0	1
197.0	0	0	0	1
199.0	0	1	0	1
203.0	0	0	0	1
205.0	0	1	0	0
209.0	0	0	0	1
211.0	0	1	0	1
213.0	0	1	0	0
214.0	0	1	0	1
215.0	0	0	0	1
216.0	0	0	0	1
217.0	0	2	0	0
219.0	0	1	0	0
220.0	0	2	0	1
222.0	0	0	0	1
223.0	0	0	0	1
224.0	0	1	0	1
226.0	0	0	0	1
227.0	0	0	0	1
230.0	0	0	0	1
231.0	0	1	0	0
232.0	0	0	0	1
233.0	0	1	0	0
234.0	0	1	0	1
236.0	0	1	0	1
237.0	0	0	0	1
238.0	0	1	0	1
239.0	0	0	0	1
241.0	0	1	0	0
244.0	0	1	0	0
245.0	0	0	0	1
246.0	0	1	0	0
249.0	0	1	0	0
250.0	0	2	0	0
251.0	0	1	0	1
252.0	0	1	0	0
256.0	0	1	0	0
258.0	0	1	0	0
263.0	0	1	0	0
264.0	0	1	0	0
290.0	0	0	0	1
301.0	0	0	0	1
303.0	0	0	0	1
311.0	0	0	0	1
315.0	0	1	0	0
318.0	0	1	0	0
320.0	0	0	0	1
338.0	0	1	0	0
340.0	0	1	0	0
345.0	0	1	0	0
347.0	0	0	0	1
349.0	0	0	0	1
351.0	0	0	0	1
358.0	0	1	0	0
377.0	0	1	0	0
384.0	0	1	0	0
385.0	0	0	0	1
392.0	0	1	0	0
396.0	0	0	0	1
434.0	0	1	0	0
435.0	0	0	0	1
443.0	0	0	0	1
450.0	0	0	0	1
461.0	0	0	0	1
469.0	0	1	0	0
481.0	0	1	0	0
495.0	0	1	0	0
502.0	0	0	0	1
509.0	0	1	0	0
528.0	0	1	0	0
587.0	0	0	0	1
662.0	0	1	0	0
756.0	0	0	0	1
848.0	0	1	0	0