## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-259-TP2.bam --OUTPUT POC-259-TP2.md.bam --METRICS_FILE POC-259-TP2.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 02:48:05 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	216	13966606	3501236	0	147	7409836	3651976	0.530541	10454757

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.175274	3259936	0	4228612
2.0	1.484276	1618183	979874	1591113
3.0	1.565519	786357	393155	496217
4.0	1.586879	391672	196561	146265
5.0	1.592495	205415	105275	46172
6.0	1.593971	113731	58704	17653
7.0	1.59436	66214	33185	8560
8.0	1.594462	39563	18867	4966
9.0	1.594488	24734	10860	3350
10.0	1.594496	15496	6145	2365
11.0	1.594497	10035	3444	1785
12.0	1.594498	6366	2044	1321
13.0	1.594498	4419	1250	1023
14.0	1.594498	2908	782	838
15.0	1.594498	2086	486	703
16.0	1.594498	1540	265	555
17.0	1.594498	1187	181	491
18.0	1.594498	803	119	427
19.0	1.594498	620	69	337
20.0	1.594498	561	62	296
21.0	1.594498	460	34	274
22.0	1.594498	404	25	235
23.0	1.594498	300	26	196
24.0	1.594498	249	14	191
25.0	1.594498	238	16	143
26.0	1.594498	194	10	117
27.0	1.594498	179	10	129
28.0	1.594498	160	6	135
29.0	1.594498	152	10	125
30.0	1.594498	134	4	83
31.0	1.594498	128	7	79
32.0	1.594498	89	3	98
33.0	1.594498	107	5	94
34.0	1.594498	103	5	90
35.0	1.594498	99	0	63
36.0	1.594498	89	0	60
37.0	1.594498	72	0	54
38.0	1.594498	63	2	44
39.0	1.594498	73	0	52
40.0	1.594498	57	2	43
41.0	1.594498	44	1	36
42.0	1.594498	44	3	28
43.0	1.594498	42	4	36
44.0	1.594498	42	4	39
45.0	1.594498	45	2	52
46.0	1.594498	47	3	47
47.0	1.594498	33	3	47
48.0	1.594498	46	2	25
49.0	1.594498	41	1	25
50.0	1.594498	32	0	28
51.0	1.594498	25	2	26
52.0	1.594498	33	1	21
53.0	1.594498	31	1	27
54.0	1.594498	23	1	21
55.0	1.594498	31	0	26
56.0	1.594498	27	1	29
57.0	1.594498	22	0	20
58.0	1.594498	24	1	18
59.0	1.594498	17	3	21
60.0	1.594498	22	0	21
61.0	1.594498	26	0	18
62.0	1.594498	24	0	12
63.0	1.594498	22	1	12
64.0	1.594498	15	1	20
65.0	1.594498	13	1	13
66.0	1.594498	22	0	13
67.0	1.594498	13	0	18
68.0	1.594498	12	1	10
69.0	1.594498	13	0	10
70.0	1.594498	5	1	14
71.0	1.594498	21	0	18
72.0	1.594498	10	0	8
73.0	1.594498	11	2	15
74.0	1.594498	15	0	15
75.0	1.594498	14	0	8
76.0	1.594498	14	1	10
77.0	1.594498	10	0	10
78.0	1.594498	5	0	6
79.0	1.594498	14	0	9
80.0	1.594498	13	1	11
81.0	1.594498	18	0	9
82.0	1.594498	12	0	11
83.0	1.594498	11	0	10
84.0	1.594498	8	0	10
85.0	1.594498	5	1	11
86.0	1.594498	15	0	8
87.0	1.594498	9	1	4
88.0	1.594498	5	0	12
89.0	1.594498	4	0	5
90.0	1.594498	7	2	4
91.0	1.594498	11	0	7
92.0	1.594498	8	0	6
93.0	1.594498	9	1	7
94.0	1.594498	9	0	8
95.0	1.594498	4	0	8
96.0	1.594498	6	1	2
97.0	1.594498	9	0	8
98.0	1.594498	5	0	7
99.0	1.594498	6	0	7
100.0	1.594498	7	0	6
101.0	0	5	0	9
102.0	0	6	0	4
103.0	0	8	0	7
104.0	0	8	0	7
105.0	0	8	0	5
106.0	0	2	0	6
107.0	0	4	0	3
108.0	0	3	0	2
109.0	0	6	0	3
110.0	0	8	0	8
111.0	0	4	0	8
112.0	0	4	0	2
113.0	0	5	0	4
114.0	0	7	0	6
115.0	0	7	1	4
116.0	0	1	0	5
117.0	0	6	0	0
118.0	0	5	0	1
119.0	0	7	0	2
120.0	0	3	0	2
121.0	0	6	0	3
122.0	0	2	0	8
123.0	0	3	0	1
124.0	0	5	0	7
125.0	0	1	0	2
126.0	0	1	0	7
127.0	0	3	0	0
128.0	0	1	0	2
129.0	0	2	0	4
130.0	0	3	0	4
131.0	0	4	0	1
132.0	0	4	0	1
133.0	0	4	1	1
134.0	0	4	0	4
135.0	0	7	0	0
136.0	0	1	0	2
137.0	0	4	0	1
138.0	0	0	0	2
139.0	0	2	0	3
140.0	0	2	0	7
141.0	0	0	0	2
142.0	0	4	0	3
143.0	0	1	0	5
144.0	0	2	0	2
145.0	0	4	0	4
146.0	0	1	0	2
147.0	0	3	0	6
148.0	0	0	0	4
149.0	0	8	0	3
150.0	0	3	0	1
151.0	0	1	0	2
152.0	0	5	0	1
153.0	0	3	0	4
154.0	0	2	1	1
155.0	0	1	0	1
156.0	0	2	0	4
157.0	0	0	0	3
158.0	0	6	0	1
159.0	0	1	0	3
160.0	0	1	0	3
161.0	0	1	0	1
162.0	0	1	0	1
163.0	0	2	0	1
164.0	0	1	0	1
165.0	0	1	0	2
166.0	0	4	0	4
167.0	0	4	0	2
168.0	0	6	0	2
169.0	0	3	0	1
170.0	0	0	0	1
171.0	0	2	0	1
172.0	0	1	0	1
173.0	0	1	0	1
174.0	0	2	0	1
175.0	0	1	0	2
176.0	0	1	0	1
177.0	0	0	0	1
178.0	0	7	0	2
179.0	0	1	0	0
180.0	0	2	1	0
181.0	0	0	0	2
182.0	0	1	0	2
183.0	0	3	0	1
184.0	0	1	0	2
185.0	0	1	0	2
186.0	0	0	0	2
188.0	0	5	0	0
189.0	0	3	0	0
190.0	0	3	0	3
191.0	0	0	0	2
192.0	0	0	0	1
193.0	0	1	0	2
194.0	0	1	0	1
195.0	0	1	0	2
196.0	0	3	0	2
197.0	0	1	0	1
199.0	0	1	0	1
200.0	0	1	0	1
202.0	0	0	0	3
203.0	0	1	0	3
204.0	0	1	0	1
205.0	0	1	0	2
206.0	0	2	0	1
207.0	0	2	0	0
208.0	0	0	0	2
209.0	0	3	0	0
210.0	0	1	0	1
211.0	0	0	0	1
212.0	0	4	0	2
213.0	0	3	0	1
214.0	0	3	0	1
215.0	0	1	0	0
216.0	0	1	0	1
217.0	0	1	0	1
220.0	0	1	0	0
222.0	0	2	0	3
223.0	0	2	0	0
225.0	0	1	0	2
226.0	0	1	0	2
227.0	0	2	0	0
228.0	0	0	0	2
229.0	0	1	0	1
230.0	0	1	0	1
231.0	0	1	0	0
232.0	0	0	0	1
233.0	0	1	0	0
234.0	0	0	0	1
235.0	0	1	0	1
237.0	0	2	0	1
240.0	0	1	0	0
243.0	0	2	0	0
244.0	0	1	0	1
245.0	0	1	0	1
247.0	0	2	0	0
249.0	0	1	0	1
250.0	0	1	0	0
251.0	0	1	0	0
254.0	0	0	0	1
258.0	0	1	0	2
259.0	0	0	0	1
260.0	0	0	0	1
261.0	0	0	0	1
262.0	0	1	0	0
263.0	0	1	0	1
264.0	0	1	0	1
265.0	0	0	0	1
268.0	0	1	0	1
269.0	0	1	0	0
272.0	0	1	0	2
273.0	0	0	0	1
277.0	0	1	0	0
281.0	0	0	0	1
282.0	0	0	0	2
283.0	0	2	0	3
285.0	0	0	0	1
287.0	0	0	0	2
288.0	0	1	0	0
289.0	0	1	0	1
293.0	0	2	0	0
295.0	0	1	0	0
296.0	0	0	0	1
297.0	0	2	0	1
298.0	0	1	0	0
301.0	0	0	0	2
303.0	0	1	1	0
304.0	0	2	0	0
305.0	0	1	0	1
306.0	0	0	0	1
307.0	0	1	0	0
309.0	0	0	0	2
310.0	0	1	0	0
311.0	0	1	0	0
317.0	0	3	0	0
318.0	0	2	0	0
319.0	0	0	0	1
328.0	0	0	0	1
332.0	0	0	0	1
334.0	0	0	0	1
338.0	0	0	0	1
342.0	0	0	0	1
344.0	0	1	0	0
346.0	0	0	0	1
347.0	0	0	0	1
348.0	0	1	0	0
350.0	0	1	0	1
351.0	0	0	0	1
353.0	0	1	0	0
354.0	0	3	0	1
355.0	0	0	0	2
356.0	0	1	0	0
358.0	0	1	0	1
359.0	0	0	0	3
363.0	0	1	0	0
365.0	0	1	0	1
366.0	0	0	0	1
368.0	0	0	0	2
369.0	0	1	0	0
370.0	0	1	0	0
371.0	0	0	0	1
373.0	0	2	0	1
375.0	0	0	0	1
376.0	0	2	0	0
377.0	0	0	0	1
378.0	0	0	0	1
380.0	0	1	0	0
381.0	0	0	0	1
383.0	0	0	0	2
384.0	0	1	0	0
385.0	0	1	0	1
386.0	0	0	0	1
387.0	0	1	0	0
389.0	0	0	0	1
390.0	0	1	0	0
393.0	0	2	0	0
396.0	0	1	0	1
397.0	0	1	0	0
398.0	0	0	0	1
399.0	0	0	0	1
400.0	0	1	0	1
401.0	0	3	0	0
403.0	0	0	0	1
404.0	0	0	0	1
405.0	0	2	0	1
406.0	0	1	0	0
407.0	0	1	0	0
417.0	0	1	0	0
420.0	0	2	0	0
421.0	0	2	0	0
422.0	0	0	0	1
426.0	0	0	0	1
432.0	0	2	0	0
435.0	0	0	0	1
440.0	0	1	0	1
442.0	0	1	0	0
444.0	0	0	0	1
447.0	0	0	0	2
448.0	0	1	0	0
451.0	0	0	0	1
452.0	0	0	0	1
458.0	0	1	0	0
459.0	0	0	0	1
460.0	0	2	0	0
463.0	0	0	0	1
465.0	0	1	0	0
467.0	0	1	0	0
474.0	0	0	0	1
478.0	0	0	0	1
480.0	0	1	0	0
485.0	0	1	0	0
488.0	0	1	0	0
495.0	0	0	0	1
497.0	0	1	0	0
501.0	0	0	0	1
503.0	0	1	0	0
504.0	0	0	0	1
509.0	0	1	0	1
512.0	0	0	0	1
513.0	0	1	0	0
516.0	0	0	0	1
521.0	0	1	0	0
525.0	0	0	0	1
529.0	0	1	0	0
530.0	0	0	0	1
534.0	0	0	0	1
540.0	0	0	0	2
541.0	0	1	0	0
549.0	0	2	0	0
553.0	0	1	0	0
555.0	0	0	0	1
567.0	0	1	0	0
571.0	0	1	0	0
574.0	0	0	0	1
577.0	0	1	0	0
580.0	0	2	0	1
582.0	0	1	0	1
588.0	0	0	0	2
599.0	0	1	0	0
618.0	0	0	0	1
627.0	0	1	0	0
632.0	0	0	0	1
634.0	0	0	0	1
635.0	0	1	0	0
641.0	0	1	0	0
644.0	0	2	0	0
646.0	0	1	0	1
661.0	0	1	0	0
670.0	0	0	0	1
671.0	0	0	0	1
673.0	0	0	0	1
678.0	0	1	0	0
691.0	0	0	0	1
693.0	0	0	0	1
698.0	0	1	0	0
701.0	0	0	0	1
707.0	0	0	0	1
721.0	0	1	0	0
722.0	0	1	0	0
733.0	0	1	0	0
742.0	0	0	0	1
743.0	0	1	0	0
745.0	0	0	0	1
760.0	0	1	0	0
773.0	0	1	0	0
774.0	0	0	0	1
775.0	0	0	0	1
792.0	0	0	0	1
803.0	0	1	0	0
813.0	0	1	0	0
831.0	0	1	0	0
834.0	0	1	0	0
843.0	0	0	0	1
858.0	0	1	0	0
864.0	0	0	0	1
867.0	0	1	0	0
878.0	0	0	0	1
891.0	0	0	0	1
910.0	0	1	0	0
916.0	0	0	0	1
919.0	0	0	0	1
959.0	0	1	0	0
962.0	0	1	0	0
969.0	0	1	0	0
998.0	0	1	0	0
1049.0	0	0	0	1
1085.0	0	0	0	1
1163.0	0	1	0	0
1171.0	0	1	0	0
1310.0	0	0	0	1
1316.0	0	0	0	1
1365.0	0	0	0	1
1379.0	0	1	0	0
1442.0	0	1	0	0
1518.0	0	1	0	0
1562.0	0	0	0	1
1741.0	0	1	0	0
2421.0	0	0	0	1
2723.0	0	1	0	0