## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-42-TP4.bam --OUTPUT POC-42-TP4.md.bam --METRICS_FILE POC-42-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 02:42:44 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	278	9400028	2221113	0	197	6091963	2004608	0.64808	3888634

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.070692	1094173	0	1359705
2.0	1.166156	811328	520644	937996
3.0	1.174668	543281	199534	527727
4.0	1.175427	336324	99657	255374
5.0	1.175494	199202	55180	113716
6.0	1.1755	117983	32486	50848
7.0	1.175501	71043	19608	24157
8.0	1.175501	43973	11940	12435
9.0	1.175501	27999	7538	7064
10.0	1.175501	18206	4686	4424
11.0	1.175501	11990	2908	2915
12.0	1.175501	8319	1913	2075
13.0	1.175501	5784	1176	1546
14.0	1.175501	3956	764	1182
15.0	1.175501	2953	535	947
16.0	1.175501	2214	334	716
17.0	1.175501	1597	222	623
18.0	1.175501	1220	141	522
19.0	1.175501	973	103	431
20.0	1.175501	735	68	373
21.0	1.175501	583	33	293
22.0	1.175501	480	22	235
23.0	1.175501	389	15	222
24.0	1.175501	306	17	186
25.0	1.175501	273	4	165
26.0	1.175501	235	8	166
27.0	1.175501	175	8	156
28.0	1.175501	184	4	123
29.0	1.175501	156	4	87
30.0	1.175501	124	2	100
31.0	1.175501	126	0	91
32.0	1.175501	118	4	85
33.0	1.175501	107	0	71
34.0	1.175501	68	1	60
35.0	1.175501	79	1	69
36.0	1.175501	69	0	55
37.0	1.175501	59	1	39
38.0	1.175501	67	0	51
39.0	1.175501	41	1	59
40.0	1.175501	53	0	30
41.0	1.175501	55	0	35
42.0	1.175501	55	0	35
43.0	1.175501	24	0	30
44.0	1.175501	45	1	35
45.0	1.175501	33	0	35
46.0	1.175501	41	1	27
47.0	1.175501	35	1	33
48.0	1.175501	38	0	28
49.0	1.175501	26	0	25
50.0	1.175501	33	0	20
51.0	1.175501	27	0	25
52.0	1.175501	30	0	24
53.0	1.175501	15	0	22
54.0	1.175501	23	1	16
55.0	1.175501	23	0	21
56.0	1.175501	26	0	20
57.0	1.175501	19	0	14
58.0	1.175501	21	0	17
59.0	1.175501	11	1	12
60.0	1.175501	18	0	12
61.0	1.175501	19	0	20
62.0	1.175501	14	0	12
63.0	1.175501	10	0	16
64.0	1.175501	13	0	8
65.0	1.175501	12	0	11
66.0	1.175501	24	0	10
67.0	1.175501	9	0	11
68.0	1.175501	15	0	5
69.0	1.175501	14	0	5
70.0	1.175501	3	0	5
71.0	1.175501	4	0	5
72.0	1.175501	7	0	5
73.0	1.175501	10	0	9
74.0	1.175501	10	0	7
75.0	1.175501	4	0	5
76.0	1.175501	4	0	6
77.0	1.175501	5	0	11
78.0	1.175501	6	0	6
79.0	1.175501	5	0	11
80.0	1.175501	10	1	7
81.0	1.175501	13	0	10
82.0	1.175501	3	0	6
83.0	1.175501	7	0	5
84.0	1.175501	5	0	3
85.0	1.175501	4	0	3
86.0	1.175501	10	0	3
87.0	1.175501	8	0	2
88.0	1.175501	3	0	6
89.0	1.175501	4	0	9
90.0	1.175501	2	0	3
91.0	1.175501	5	0	3
92.0	1.175501	6	0	4
93.0	1.175501	9	0	5
94.0	1.175501	4	1	4
95.0	1.175501	6	0	3
96.0	1.175501	6	0	4
97.0	1.175501	4	0	3
98.0	1.175501	2	0	4
99.0	1.175501	4	0	5
100.0	1.175501	1	0	1
101.0	0	2	0	2
102.0	0	4	0	1
103.0	0	0	0	2
104.0	0	1	0	1
105.0	0	4	0	5
106.0	0	5	0	3
107.0	0	4	0	4
108.0	0	0	0	3
109.0	0	5	0	0
110.0	0	4	0	6
111.0	0	2	0	3
112.0	0	1	0	4
113.0	0	2	0	0
114.0	0	2	0	6
115.0	0	1	0	1
116.0	0	4	0	1
117.0	0	3	0	1
118.0	0	3	0	4
119.0	0	5	0	5
120.0	0	1	0	0
121.0	0	3	0	1
122.0	0	2	0	3
123.0	0	5	0	2
124.0	0	3	0	0
125.0	0	2	0	2
126.0	0	1	0	2
127.0	0	1	0	0
128.0	0	1	0	2
129.0	0	1	0	3
131.0	0	1	0	0
132.0	0	0	0	2
134.0	0	1	0	0
135.0	0	1	0	1
136.0	0	1	0	2
137.0	0	3	0	1
138.0	0	2	0	3
139.0	0	1	0	2
140.0	0	1	0	1
141.0	0	3	0	2
142.0	0	2	0	3
143.0	0	1	0	1
144.0	0	3	0	3
145.0	0	0	0	1
146.0	0	2	0	3
147.0	0	2	0	1
148.0	0	4	0	1
149.0	0	1	0	1
150.0	0	1	0	1
151.0	0	2	0	1
153.0	0	1	0	2
154.0	0	1	0	1
155.0	0	1	0	1
156.0	0	4	0	3
157.0	0	1	0	0
158.0	0	1	0	0
159.0	0	3	0	1
160.0	0	3	0	2
161.0	0	0	0	1
164.0	0	1	0	2
165.0	0	1	0	1
166.0	0	2	0	0
167.0	0	1	0	0
170.0	0	1	0	1
171.0	0	0	0	2
172.0	0	0	0	1
173.0	0	1	0	0
174.0	0	1	0	2
176.0	0	1	0	1
178.0	0	1	0	0
179.0	0	1	0	2
180.0	0	2	0	2
181.0	0	2	0	1
182.0	0	3	0	1
185.0	0	2	0	0
186.0	0	1	0	1
188.0	0	0	0	1
190.0	0	0	0	1
192.0	0	0	0	1
193.0	0	2	0	0
195.0	0	0	0	1
197.0	0	2	0	1
198.0	0	0	0	2
201.0	0	1	0	0
202.0	0	2	0	2
203.0	0	1	0	1
204.0	0	0	0	1
205.0	0	0	0	1
206.0	0	2	0	1
207.0	0	1	0	1
211.0	0	1	0	0
212.0	0	0	0	1
213.0	0	1	0	1
214.0	0	1	0	0
216.0	0	1	0	0
217.0	0	1	0	0
220.0	0	1	0	0
222.0	0	0	0	1
224.0	0	0	0	1
226.0	0	0	0	1
228.0	0	3	0	0
229.0	0	1	0	0
232.0	0	0	0	1
233.0	0	1	0	0
234.0	0	0	0	1
237.0	0	0	0	1
241.0	0	0	0	1
242.0	0	0	0	1
243.0	0	1	0	0
245.0	0	0	0	1
251.0	0	0	0	1
254.0	0	1	0	0
255.0	0	0	0	1
256.0	0	0	0	1
257.0	0	0	0	1
258.0	0	0	0	1
259.0	0	1	0	0
260.0	0	2	0	0
261.0	0	1	0	0
265.0	0	1	0	0
267.0	0	1	0	0
268.0	0	1	0	0
272.0	0	0	0	1
274.0	0	1	0	0
275.0	0	1	0	0
282.0	0	0	0	1
283.0	0	1	0	0
284.0	0	0	0	1
285.0	0	0	0	1
287.0	0	2	0	1
291.0	0	1	0	1
293.0	0	1	0	0
301.0	0	0	0	1
302.0	0	0	0	1
304.0	0	0	0	1
305.0	0	1	0	0
307.0	0	1	0	0
309.0	0	1	0	0
312.0	0	0	0	1
322.0	0	1	0	0
324.0	0	0	0	1
327.0	0	0	0	1
328.0	0	1	0	0
329.0	0	0	0	1
334.0	0	1	0	0
335.0	0	1	0	0
336.0	0	1	0	0
338.0	0	0	0	1
341.0	0	1	0	0
345.0	0	0	0	1
358.0	0	1	0	0
370.0	0	0	0	1
371.0	0	0	0	1
376.0	0	1	0	0
377.0	0	1	0	0
394.0	0	0	0	1
398.0	0	1	0	0
401.0	0	0	0	1
403.0	0	1	0	0
404.0	0	0	0	1
406.0	0	0	0	1
411.0	0	0	0	1
416.0	0	1	0	0
418.0	0	0	0	1
419.0	0	1	0	0
421.0	0	1	0	1
423.0	0	1	0	0
434.0	0	1	0	0
440.0	0	0	0	1
443.0	0	0	0	1
448.0	0	0	0	1
454.0	0	1	0	0
457.0	0	1	0	0
458.0	0	1	0	0
462.0	0	0	0	1
464.0	0	1	0	1
476.0	0	1	0	0
487.0	0	0	0	1
490.0	0	0	0	1
493.0	0	0	0	1
501.0	0	1	0	0
507.0	0	0	0	1
510.0	0	1	0	0
513.0	0	0	0	1
520.0	0	1	0	0
523.0	0	1	0	0
526.0	0	1	0	0
540.0	0	1	0	0
543.0	0	0	0	1
571.0	0	0	0	1
579.0	0	1	0	0
616.0	0	0	0	1
620.0	0	0	0	1
622.0	0	1	0	0
624.0	0	1	0	0
628.0	0	0	0	1
647.0	0	0	0	1
653.0	0	1	0	0
661.0	0	1	0	0
665.0	0	1	0	0
687.0	0	0	0	1
697.0	0	1	0	0
791.0	0	0	0	1
795.0	0	0	0	1
804.0	0	1	0	0
884.0	0	1	0	1
893.0	0	1	0	0