## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-40-TP3.bam --OUTPUT POC-40-TP3.md.bam --METRICS_FILE POC-40-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 02:43:19 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	255	15267292	3709466	0	154	8033906	3920547	0.526217	11580427

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.172596	3596270	0	4640988
2.0	1.486349	1789233	1081124	1758300
3.0	1.5703	872376	424457	560343
4.0	1.592763	432666	208853	167868
5.0	1.598773	225803	111937	53731
6.0	1.600382	124050	61857	20539
7.0	1.600812	71587	34664	9555
8.0	1.600927	42589	19800	5455
9.0	1.600958	26541	11254	3554
10.0	1.600966	16207	6444	2459
11.0	1.600968	10603	3806	1787
12.0	1.600969	6736	2216	1343
13.0	1.600969	4583	1346	934
14.0	1.600969	3242	744	832
15.0	1.600969	2031	444	617
16.0	1.600969	1525	307	513
17.0	1.600969	1044	192	429
18.0	1.600969	854	112	358
19.0	1.600969	634	57	339
20.0	1.600969	485	68	259
21.0	1.600969	425	37	229
22.0	1.600969	365	29	231
23.0	1.600969	288	17	170
24.0	1.600969	266	14	174
25.0	1.600969	215	12	155
26.0	1.600969	188	8	120
27.0	1.600969	155	6	119
28.0	1.600969	160	6	96
29.0	1.600969	111	6	80
30.0	1.600969	115	2	84
31.0	1.600969	106	3	73
32.0	1.600969	91	4	89
33.0	1.600969	87	4	65
34.0	1.600969	71	7	54
35.0	1.600969	72	5	52
36.0	1.600969	66	3	47
37.0	1.600969	67	2	48
38.0	1.600969	52	5	54
39.0	1.600969	57	2	64
40.0	1.600969	65	0	44
41.0	1.600969	50	0	36
42.0	1.600969	43	0	43
43.0	1.600969	40	0	31
44.0	1.600969	38	0	34
45.0	1.600969	33	0	35
46.0	1.600969	29	0	35
47.0	1.600969	40	1	26
48.0	1.600969	32	2	23
49.0	1.600969	38	1	28
50.0	1.600969	34	1	21
51.0	1.600969	25	0	21
52.0	1.600969	26	1	15
53.0	1.600969	22	1	21
54.0	1.600969	21	0	19
55.0	1.600969	17	0	17
56.0	1.600969	35	0	23
57.0	1.600969	17	0	17
58.0	1.600969	17	2	18
59.0	1.600969	18	2	16
60.0	1.600969	22	0	13
61.0	1.600969	16	0	18
62.0	1.600969	11	1	10
63.0	1.600969	15	0	13
64.0	1.600969	16	0	17
65.0	1.600969	17	1	9
66.0	1.600969	5	1	10
67.0	1.600969	24	1	16
68.0	1.600969	9	0	7
69.0	1.600969	11	0	7
70.0	1.600969	15	0	9
71.0	1.600969	11	0	11
72.0	1.600969	11	0	18
73.0	1.600969	13	0	14
74.0	1.600969	9	0	10
75.0	1.600969	8	1	5
76.0	1.600969	11	2	7
77.0	1.600969	6	0	6
78.0	1.600969	9	0	5
79.0	1.600969	9	0	8
80.0	1.600969	8	1	5
81.0	1.600969	7	0	7
82.0	1.600969	9	0	5
83.0	1.600969	2	0	6
84.0	1.600969	3	0	9
85.0	1.600969	7	0	9
86.0	1.600969	9	1	6
87.0	1.600969	9	0	5
88.0	1.600969	5	0	5
89.0	1.600969	4	0	6
90.0	1.600969	6	0	9
91.0	1.600969	10	0	10
92.0	1.600969	7	0	6
93.0	1.600969	5	0	8
94.0	1.600969	4	0	6
95.0	1.600969	8	0	5
96.0	1.600969	4	0	4
97.0	1.600969	1	0	6
98.0	1.600969	9	0	6
99.0	1.600969	7	0	4
100.0	1.600969	9	0	3
101.0	0	8	0	6
102.0	0	4	0	3
103.0	0	8	0	4
104.0	0	5	0	4
105.0	0	1	0	4
106.0	0	5	0	6
107.0	0	3	0	4
108.0	0	5	0	4
109.0	0	1	0	1
110.0	0	8	0	4
111.0	0	3	0	6
112.0	0	3	0	8
113.0	0	5	0	2
114.0	0	7	0	2
115.0	0	4	0	3
116.0	0	4	0	4
117.0	0	2	0	2
118.0	0	2	0	3
119.0	0	3	0	4
120.0	0	5	0	1
121.0	0	4	0	0
122.0	0	3	0	2
123.0	0	4	0	1
124.0	0	4	0	4
125.0	0	2	0	2
126.0	0	2	0	5
127.0	0	0	0	2
128.0	0	3	0	0
129.0	0	1	0	0
130.0	0	2	0	0
131.0	0	3	0	3
132.0	0	0	0	1
133.0	0	1	0	3
134.0	0	3	0	2
135.0	0	2	0	3
136.0	0	1	0	3
137.0	0	1	1	3
138.0	0	3	0	3
139.0	0	5	0	2
140.0	0	0	0	2
141.0	0	2	0	2
142.0	0	2	0	1
143.0	0	2	0	1
144.0	0	2	1	2
145.0	0	4	0	1
146.0	0	1	0	3
147.0	0	0	0	1
148.0	0	3	0	1
149.0	0	3	0	2
150.0	0	4	0	1
151.0	0	2	0	2
152.0	0	1	0	0
153.0	0	2	0	1
154.0	0	2	0	0
155.0	0	2	0	0
156.0	0	1	0	1
157.0	0	1	0	1
158.0	0	0	0	4
159.0	0	3	0	1
161.0	0	0	0	4
162.0	0	2	0	1
163.0	0	2	0	2
164.0	0	2	0	0
165.0	0	1	0	2
166.0	0	1	0	0
167.0	0	0	0	3
168.0	0	2	0	2
169.0	0	2	0	2
170.0	0	1	0	1
171.0	0	2	0	0
172.0	0	3	0	2
173.0	0	0	0	2
174.0	0	0	0	1
175.0	0	1	0	1
176.0	0	1	0	0
177.0	0	2	0	0
178.0	0	0	0	1
179.0	0	3	0	1
180.0	0	0	1	2
181.0	0	1	0	1
182.0	0	1	0	2
183.0	0	0	0	1
184.0	0	0	0	1
185.0	0	2	0	1
186.0	0	1	0	0
187.0	0	2	0	0
188.0	0	1	0	1
190.0	0	1	0	2
191.0	0	2	0	2
192.0	0	1	0	1
193.0	0	2	0	0
194.0	0	1	0	1
196.0	0	1	0	2
197.0	0	2	0	0
199.0	0	1	0	0
200.0	0	0	0	2
201.0	0	1	0	1
202.0	0	1	0	3
203.0	0	1	0	0
204.0	0	2	0	1
205.0	0	0	0	2
206.0	0	1	0	0
207.0	0	2	0	2
208.0	0	0	0	3
209.0	0	0	0	1
210.0	0	1	0	1
211.0	0	1	0	0
212.0	0	1	0	0
214.0	0	0	0	3
216.0	0	1	0	2
217.0	0	0	0	2
218.0	0	0	0	2
219.0	0	1	0	3
220.0	0	2	0	2
222.0	0	4	0	1
223.0	0	0	0	2
224.0	0	3	0	0
225.0	0	1	0	0
226.0	0	2	0	0
229.0	0	1	0	2
230.0	0	1	0	1
231.0	0	1	0	0
234.0	0	3	0	1
235.0	0	0	0	1
236.0	0	1	0	0
237.0	0	1	0	0
238.0	0	0	0	1
239.0	0	2	0	2
240.0	0	1	0	1
241.0	0	1	0	1
242.0	0	2	0	1
243.0	0	1	0	1
244.0	0	1	0	0
245.0	0	1	0	1
246.0	0	0	0	2
247.0	0	1	0	0
249.0	0	0	0	1
250.0	0	1	0	1
251.0	0	2	0	0
252.0	0	1	0	1
253.0	0	1	0	0
254.0	0	1	0	0
255.0	0	0	0	1
256.0	0	0	0	1
257.0	0	1	0	0
258.0	0	1	0	0
259.0	0	1	0	1
260.0	0	0	0	1
262.0	0	2	0	1
263.0	0	0	0	1
264.0	0	3	0	0
266.0	0	1	0	1
267.0	0	2	0	0
269.0	0	0	0	2
271.0	0	0	0	1
274.0	0	3	0	0
276.0	0	1	0	0
277.0	0	0	0	1
278.0	0	1	0	1
281.0	0	0	0	1
283.0	0	2	0	2
284.0	0	1	0	2
287.0	0	1	0	0
291.0	0	0	0	1
292.0	0	1	0	1
296.0	0	2	0	2
297.0	0	1	0	1
299.0	0	1	0	1
300.0	0	0	0	1
301.0	0	1	0	1
302.0	0	0	0	1
303.0	0	1	0	0
306.0	0	2	0	0
311.0	0	0	0	2
312.0	0	1	0	0
314.0	0	1	0	0
316.0	0	0	0	1
317.0	0	1	0	0
321.0	0	1	0	0
329.0	0	1	0	0
331.0	0	1	0	2
334.0	0	0	0	1
335.0	0	0	0	1
337.0	0	1	0	2
338.0	0	2	0	0
340.0	0	0	0	1
341.0	0	1	0	0
343.0	0	0	0	1
349.0	0	1	0	0
352.0	0	1	0	0
354.0	0	0	0	1
357.0	0	0	0	1
362.0	0	2	0	0
364.0	0	0	0	1
368.0	0	2	0	0
370.0	0	1	0	1
373.0	0	1	0	0
378.0	0	0	0	1
383.0	0	0	0	1
385.0	0	0	0	1
388.0	0	0	0	1
389.0	0	1	0	0
394.0	0	2	0	0
396.0	0	1	0	0
398.0	0	0	0	1
399.0	0	0	0	1
401.0	0	1	0	0
405.0	0	1	0	0
407.0	0	0	0	1
410.0	0	0	0	2
411.0	0	1	0	0
414.0	0	0	0	1
415.0	0	1	0	0
416.0	0	0	0	1
419.0	0	0	0	1
421.0	0	0	0	1
423.0	0	0	0	1
424.0	0	0	0	1
429.0	0	1	0	0
435.0	0	1	0	1
440.0	0	2	0	0
444.0	0	1	0	0
447.0	0	1	0	0
450.0	0	1	0	0
452.0	0	0	0	3
453.0	0	0	0	1
454.0	0	0	0	1
462.0	0	1	0	0
463.0	0	1	0	0
467.0	0	1	0	0
470.0	0	1	0	0
471.0	0	1	0	0
477.0	0	1	0	0
478.0	0	0	0	1
480.0	0	1	0	1
481.0	0	1	0	0
483.0	0	2	0	0
500.0	0	0	0	1
505.0	0	1	0	0
512.0	0	0	0	1
513.0	0	1	0	0
517.0	0	0	0	1
525.0	0	1	0	0
527.0	0	0	0	1
538.0	0	0	0	1
539.0	0	0	0	1
547.0	0	1	0	0
571.0	0	1	0	1
578.0	0	1	0	0
602.0	0	1	0	0
617.0	0	1	0	0
635.0	0	1	0	0
669.0	0	0	0	1
703.0	0	0	0	1
743.0	0	1	0	0
778.0	0	1	0	0
808.0	0	0	0	1
811.0	0	0	0	1
837.0	0	1	0	0
853.0	0	0	0	1
893.0	0	1	0	0
918.0	0	1	0	0
1076.0	0	0	0	1
1124.0	0	0	0	1
1219.0	0	1	0	0
1260.0	0	1	0	0
1635.0	0	0	0	1
1814.0	0	1	0	0