## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-53-TP3.bam --OUTPUT POC-53-TP3.md.bam --METRICS_FILE POC-53-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 02:43:47 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	245	15146479	3288843	0	165	8701612	4294914	0.574498	9425355

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.169251	2825928	0	3774828
2.0	1.403674	1612595	1042021	1697496
3.0	1.450673	873172	433709	626020
4.0	1.460096	469796	224733	210676
5.0	1.461985	259979	126177	72025
6.0	1.462364	149491	73037	27357
7.0	1.46244	89234	43569	12309
8.0	1.462455	55422	26161	6487
9.0	1.462458	34838	15712	4003
10.0	1.462459	22963	9663	2727
11.0	1.462459	15111	5801	2000
12.0	1.462459	10227	3609	1453
13.0	1.462459	6695	2262	1068
14.0	1.462459	4615	1383	843
15.0	1.462459	3365	894	715
16.0	1.462459	2316	560	611
17.0	1.462459	1706	336	480
18.0	1.462459	1258	217	386
19.0	1.462459	922	144	347
20.0	1.462459	734	99	300
21.0	1.462459	514	63	224
22.0	1.462459	463	55	191
23.0	1.462459	344	32	178
24.0	1.462459	305	20	174
25.0	1.462459	259	20	141
26.0	1.462459	220	16	126
27.0	1.462459	195	10	99
28.0	1.462459	176	9	118
29.0	1.462459	136	10	113
30.0	1.462459	132	6	78
31.0	1.462459	119	1	72
32.0	1.462459	120	3	71
33.0	1.462459	92	1	64
34.0	1.462459	84	2	58
35.0	1.462459	77	3	61
36.0	1.462459	84	4	46
37.0	1.462459	54	3	37
38.0	1.462459	47	0	40
39.0	1.462459	55	2	44
40.0	1.462459	55	1	33
41.0	1.462459	29	0	39
42.0	1.462459	46	0	26
43.0	1.462459	44	0	32
44.0	1.462459	48	1	17
45.0	1.462459	35	1	23
46.0	1.462459	26	0	26
47.0	1.462459	24	2	23
48.0	1.462459	29	0	25
49.0	1.462459	26	0	15
50.0	1.462459	22	2	20
51.0	1.462459	22	1	18
52.0	1.462459	21	1	13
53.0	1.462459	19	0	20
54.0	1.462459	29	0	15
55.0	1.462459	14	1	13
56.0	1.462459	25	0	10
57.0	1.462459	9	0	12
58.0	1.462459	22	0	7
59.0	1.462459	9	0	13
60.0	1.462459	11	1	9
61.0	1.462459	16	0	18
62.0	1.462459	18	0	9
63.0	1.462459	10	0	9
64.0	1.462459	13	0	11
65.0	1.462459	12	0	4
66.0	1.462459	4	0	5
67.0	1.462459	15	0	11
68.0	1.462459	7	0	7
69.0	1.462459	10	0	9
70.0	1.462459	4	0	4
71.0	1.462459	11	0	5
72.0	1.462459	10	0	5
73.0	1.462459	3	1	9
74.0	1.462459	8	0	14
75.0	1.462459	9	0	4
76.0	1.462459	9	0	6
77.0	1.462459	5	0	3
78.0	1.462459	8	0	3
79.0	1.462459	4	0	4
80.0	1.462459	5	0	3
81.0	1.462459	5	0	3
82.0	1.462459	5	0	10
83.0	1.462459	4	0	2
84.0	1.462459	2	0	4
85.0	1.462459	10	0	11
86.0	1.462459	5	0	6
87.0	1.462459	4	0	2
88.0	1.462459	3	0	3
89.0	1.462459	5	0	3
90.0	1.462459	8	0	4
91.0	1.462459	3	0	0
92.0	1.462459	3	0	5
93.0	1.462459	5	0	6
94.0	1.462459	2	0	3
95.0	1.462459	0	0	2
96.0	1.462459	4	0	1
97.0	1.462459	1	0	3
98.0	1.462459	5	0	3
99.0	1.462459	3	0	8
100.0	1.462459	4	0	5
101.0	0	8	0	1
102.0	0	4	0	3
103.0	0	4	0	1
104.0	0	2	0	2
105.0	0	2	0	3
106.0	0	5	1	2
107.0	0	3	0	0
108.0	0	1	0	3
109.0	0	2	0	2
110.0	0	2	0	2
111.0	0	3	0	1
112.0	0	5	0	1
113.0	0	0	0	1
114.0	0	2	0	1
115.0	0	3	0	0
116.0	0	1	0	2
117.0	0	1	0	2
118.0	0	1	0	0
119.0	0	1	0	0
120.0	0	1	0	4
121.0	0	1	0	2
122.0	0	2	0	1
123.0	0	3	0	2
124.0	0	1	1	4
125.0	0	1	0	0
126.0	0	0	0	3
127.0	0	0	0	2
128.0	0	1	0	2
129.0	0	2	0	2
130.0	0	1	0	2
131.0	0	2	0	3
132.0	0	1	0	0
133.0	0	2	0	0
134.0	0	2	0	2
136.0	0	1	0	1
137.0	0	1	0	1
138.0	0	1	0	2
139.0	0	2	0	1
140.0	0	1	0	0
141.0	0	1	0	1
142.0	0	6	0	1
143.0	0	2	0	4
144.0	0	3	0	2
145.0	0	0	0	1
146.0	0	3	0	0
147.0	0	3	0	1
148.0	0	2	0	2
149.0	0	2	0	2
150.0	0	1	0	0
151.0	0	2	0	0
153.0	0	2	0	1
154.0	0	0	0	2
155.0	0	2	0	2
156.0	0	1	0	2
157.0	0	0	0	2
159.0	0	2	0	1
160.0	0	1	0	0
162.0	0	3	0	1
163.0	0	0	0	1
164.0	0	0	0	1
165.0	0	2	0	2
166.0	0	0	0	2
167.0	0	1	0	1
168.0	0	0	0	1
170.0	0	1	0	1
171.0	0	0	0	1
172.0	0	2	0	1
173.0	0	0	0	1
174.0	0	1	0	1
176.0	0	1	0	1
177.0	0	1	0	0
179.0	0	2	0	0
180.0	0	1	0	1
181.0	0	2	0	1
182.0	0	0	0	1
184.0	0	1	0	1
185.0	0	1	0	1
187.0	0	1	0	0
189.0	0	0	0	2
190.0	0	1	0	1
192.0	0	2	0	0
193.0	0	1	0	0
194.0	0	1	0	0
195.0	0	2	0	0
196.0	0	1	0	1
197.0	0	0	0	1
198.0	0	1	0	1
202.0	0	1	0	0
203.0	0	1	0	1
204.0	0	0	0	2
206.0	0	0	0	1
207.0	0	1	0	0
208.0	0	0	0	1
210.0	0	1	0	1
212.0	0	3	0	3
214.0	0	0	0	1
215.0	0	1	0	0
216.0	0	0	0	1
219.0	0	0	0	1
220.0	0	1	0	0
223.0	0	0	0	1
225.0	0	1	0	0
227.0	0	1	0	1
228.0	0	1	0	0
230.0	0	0	0	1
231.0	0	1	0	0
235.0	0	1	0	0
236.0	0	0	0	1
237.0	0	0	0	1
238.0	0	1	0	2
240.0	0	1	0	0
241.0	0	0	0	2
243.0	0	1	0	0
245.0	0	1	0	0
246.0	0	0	0	1
249.0	0	1	0	0
252.0	0	1	0	0
258.0	0	1	0	0
260.0	0	2	0	1
263.0	0	0	0	1
264.0	0	1	0	1
265.0	0	0	0	1
266.0	0	1	0	1
269.0	0	1	0	0
270.0	0	1	0	0
271.0	0	1	0	0
276.0	0	0	0	1
277.0	0	1	0	0
278.0	0	0	0	1
282.0	0	1	0	0
284.0	0	1	0	0
286.0	0	1	0	1
301.0	0	0	0	1
302.0	0	0	0	1
308.0	0	1	0	0
309.0	0	2	0	0
317.0	0	0	0	1
321.0	0	0	0	1
323.0	0	0	0	1
329.0	0	1	0	0
330.0	0	1	0	0
332.0	0	1	0	2
335.0	0	1	0	0
343.0	0	0	0	1
347.0	0	1	0	1
348.0	0	0	0	1
351.0	0	1	0	0
353.0	0	0	0	1
354.0	0	0	0	1
358.0	0	0	0	1
362.0	0	2	0	0
368.0	0	1	0	0
382.0	0	1	0	0
389.0	0	1	0	0
391.0	0	1	0	0
392.0	0	1	0	0
415.0	0	0	0	1
421.0	0	0	0	2
423.0	0	0	0	1
426.0	0	1	0	0
431.0	0	1	0	0
435.0	0	1	0	0
447.0	0	1	0	0
488.0	0	0	0	1
516.0	0	0	0	1
533.0	0	0	0	1
539.0	0	1	0	0
554.0	0	1	0	0
555.0	0	0	0	1
571.0	0	1	0	0
588.0	0	1	0	0
613.0	0	0	0	1
640.0	0	1	0	0
679.0	0	0	0	1
729.0	0	0	0	1
784.0	0	1	0	0
852.0	0	1	0	0