## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-201-TP2.bam --OUTPUT POC-201-TP2.md.bam --METRICS_FILE POC-201-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 03:06:50 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	177	15247061	4542578	0	110	8081439	3494665	0.530033	10811325

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.140525	3526539	0	4469756
2.0	1.418896	1797567	1075449	1771340
3.0	1.486839	879763	400313	588602
4.0	1.503423	432807	185681	188989
5.0	1.50747	221853	93716	65333
6.0	1.508458	119249	49648	27700
7.0	1.508699	67183	26385	14368
8.0	1.508758	39872	14478	8755
9.0	1.508772	23939	7892	5973
10.0	1.508776	15531	4351	4276
11.0	1.508777	9875	2500	3222
12.0	1.508777	6779	1398	2565
13.0	1.508777	4682	851	1933
14.0	1.508777	3237	502	1564
15.0	1.508777	2472	314	1341
16.0	1.508777	1876	204	1080
17.0	1.508777	1477	140	913
18.0	1.508777	1235	83	753
19.0	1.508777	982	64	681
20.0	1.508777	878	52	577
21.0	1.508777	748	30	478
22.0	1.508777	609	25	439
23.0	1.508777	508	27	397
24.0	1.508777	482	17	341
25.0	1.508777	409	17	297
26.0	1.508777	381	14	261
27.0	1.508777	315	12	229
28.0	1.508777	250	7	234
29.0	1.508777	284	7	196
30.0	1.508777	237	10	165
31.0	1.508777	223	10	180
32.0	1.508777	186	3	186
33.0	1.508777	200	2	132
34.0	1.508777	164	3	125
35.0	1.508777	148	2	124
36.0	1.508777	134	3	101
37.0	1.508777	133	4	116
38.0	1.508777	130	1	94
39.0	1.508777	121	2	75
40.0	1.508777	108	3	76
41.0	1.508777	110	4	75
42.0	1.508777	88	5	64
43.0	1.508777	65	1	58
44.0	1.508777	86	2	76
45.0	1.508777	74	1	56
46.0	1.508777	74	1	45
47.0	1.508777	65	2	55
48.0	1.508777	58	0	46
49.0	1.508777	64	0	47
50.0	1.508777	56	0	45
51.0	1.508777	49	0	45
52.0	1.508777	48	0	32
53.0	1.508777	46	1	36
54.0	1.508777	39	0	23
55.0	1.508777	35	0	31
56.0	1.508777	41	0	37
57.0	1.508777	32	0	28
58.0	1.508777	40	2	31
59.0	1.508777	28	0	23
60.0	1.508777	31	0	19
61.0	1.508777	35	0	26
62.0	1.508777	31	0	22
63.0	1.508777	24	1	16
64.0	1.508777	29	0	20
65.0	1.508777	15	0	15
66.0	1.508777	20	1	20
67.0	1.508777	23	1	16
68.0	1.508777	12	1	13
69.0	1.508777	17	0	22
70.0	1.508777	18	0	24
71.0	1.508777	19	0	18
72.0	1.508777	25	1	18
73.0	1.508777	18	0	15
74.0	1.508777	21	0	15
75.0	1.508777	19	0	12
76.0	1.508777	9	0	4
77.0	1.508777	16	0	17
78.0	1.508777	22	0	11
79.0	1.508777	11	0	6
80.0	1.508777	8	0	16
81.0	1.508777	14	0	7
82.0	1.508777	13	0	9
83.0	1.508777	13	0	7
84.0	1.508777	8	0	11
85.0	1.508777	14	0	4
86.0	1.508777	4	0	8
87.0	1.508777	13	0	10
88.0	1.508777	14	0	7
89.0	1.508777	8	0	7
90.0	1.508777	3	0	6
91.0	1.508777	5	0	9
92.0	1.508777	5	0	7
93.0	1.508777	6	0	6
94.0	1.508777	9	0	6
95.0	1.508777	10	0	4
96.0	1.508777	6	0	6
97.0	1.508777	10	0	10
98.0	1.508777	7	0	7
99.0	1.508777	7	0	11
100.0	1.508777	7	0	1
101.0	0	9	0	3
102.0	0	5	0	5
103.0	0	10	0	6
104.0	0	7	0	5
105.0	0	6	0	6
106.0	0	3	0	7
107.0	0	6	0	3
108.0	0	5	0	2
109.0	0	2	0	3
110.0	0	7	0	5
111.0	0	3	0	7
112.0	0	5	0	5
113.0	0	7	0	4
114.0	0	3	0	2
115.0	0	7	0	4
116.0	0	2	0	3
117.0	0	1	0	1
118.0	0	1	0	4
119.0	0	4	0	2
120.0	0	4	0	8
121.0	0	3	0	2
122.0	0	5	0	5
123.0	0	2	0	4
124.0	0	3	0	2
125.0	0	1	0	1
126.0	0	5	0	5
127.0	0	2	0	1
128.0	0	8	0	3
129.0	0	3	0	2
130.0	0	2	0	1
131.0	0	5	0	2
132.0	0	2	0	1
133.0	0	4	0	0
134.0	0	5	0	3
135.0	0	3	0	2
136.0	0	1	0	3
137.0	0	1	0	3
138.0	0	2	0	2
139.0	0	1	0	4
140.0	0	3	0	4
141.0	0	3	0	4
142.0	0	3	0	2
143.0	0	1	0	3
144.0	0	1	0	0
145.0	0	1	0	5
146.0	0	2	0	0
147.0	0	0	0	2
148.0	0	3	0	2
150.0	0	5	0	1
151.0	0	5	0	0
152.0	0	3	0	0
153.0	0	3	0	0
154.0	0	3	0	2
156.0	0	2	0	4
157.0	0	3	0	3
158.0	0	0	0	3
159.0	0	2	0	0
160.0	0	0	0	3
161.0	0	1	0	3
162.0	0	3	0	3
164.0	0	3	0	2
165.0	0	0	0	1
166.0	0	3	0	0
167.0	0	1	0	0
168.0	0	2	0	3
169.0	0	1	0	2
170.0	0	2	0	1
171.0	0	0	0	2
172.0	0	1	0	2
173.0	0	1	0	1
174.0	0	1	0	2
175.0	0	3	0	1
176.0	0	1	0	2
177.0	0	2	0	2
178.0	0	1	0	1
179.0	0	2	0	2
180.0	0	2	0	1
181.0	0	2	0	2
183.0	0	1	0	1
184.0	0	0	0	4
185.0	0	3	0	0
186.0	0	0	0	2
187.0	0	3	0	2
188.0	0	1	0	1
189.0	0	1	0	0
190.0	0	1	0	1
191.0	0	1	0	0
192.0	0	1	0	0
193.0	0	2	0	1
194.0	0	2	0	0
195.0	0	0	0	4
196.0	0	1	0	1
197.0	0	1	0	0
198.0	0	1	0	2
199.0	0	3	0	1
201.0	0	3	0	3
202.0	0	1	0	1
204.0	0	2	0	1
205.0	0	0	0	2
207.0	0	5	0	1
208.0	0	1	0	0
209.0	0	2	0	1
210.0	0	0	0	1
211.0	0	2	0	2
212.0	0	0	0	1
213.0	0	1	0	0
215.0	0	2	0	1
216.0	0	1	0	0
217.0	0	1	0	1
218.0	0	1	0	0
219.0	0	1	0	0
221.0	0	1	0	2
223.0	0	1	0	2
225.0	0	1	0	0
226.0	0	0	0	1
227.0	0	1	0	1
228.0	0	1	0	0
231.0	0	0	0	1
232.0	0	3	0	1
233.0	0	2	0	0
234.0	0	0	0	1
235.0	0	1	0	1
236.0	0	0	0	1
237.0	0	0	0	2
238.0	0	1	0	1
239.0	0	1	0	1
241.0	0	1	0	0
242.0	0	1	0	0
244.0	0	1	0	0
245.0	0	0	0	3
247.0	0	1	0	0
248.0	0	1	0	1
249.0	0	0	0	1
250.0	0	0	0	1
251.0	0	1	0	1
252.0	0	0	0	2
253.0	0	1	0	0
254.0	0	0	0	1
255.0	0	0	0	1
256.0	0	1	0	0
257.0	0	1	0	0
259.0	0	1	0	0
261.0	0	1	0	0
262.0	0	1	0	1
263.0	0	1	0	4
265.0	0	0	0	1
267.0	0	1	0	0
268.0	0	1	0	3
270.0	0	1	0	0
271.0	0	1	0	0
272.0	0	1	0	1
274.0	0	0	0	1
275.0	0	0	0	1
276.0	0	1	0	0
277.0	0	1	0	0
278.0	0	1	0	0
279.0	0	0	0	1
280.0	0	0	0	1
282.0	0	1	0	0
284.0	0	2	0	0
287.0	0	1	0	0
288.0	0	1	0	0
289.0	0	1	0	0
290.0	0	1	0	0
291.0	0	2	0	0
292.0	0	0	0	1
294.0	0	0	0	1
295.0	0	1	0	0
297.0	0	2	0	1
298.0	0	1	0	1
301.0	0	0	0	1
317.0	0	1	0	0
321.0	0	0	0	1
322.0	0	1	0	0
325.0	0	1	0	0
329.0	0	1	0	0
330.0	0	1	0	0
331.0	0	1	0	1
338.0	0	0	0	1
339.0	0	0	0	2
340.0	0	0	0	1
345.0	0	0	0	1
346.0	0	2	0	0
352.0	0	2	0	0
354.0	0	0	0	1
358.0	0	0	0	1
362.0	0	1	0	0
364.0	0	1	0	0
368.0	0	1	0	0
369.0	0	0	0	1
372.0	0	0	0	1
374.0	0	0	0	1
381.0	0	0	0	1
383.0	0	0	0	1
384.0	0	1	0	0
386.0	0	1	0	0
389.0	0	0	0	1
390.0	0	0	0	1
391.0	0	1	0	0
396.0	0	1	0	0
400.0	0	1	0	0
410.0	0	1	0	0
415.0	0	0	0	1
421.0	0	1	0	0
431.0	0	1	0	0
436.0	0	0	0	1
443.0	0	1	0	0
467.0	0	1	0	0
477.0	0	0	0	2
484.0	0	0	0	2
485.0	0	0	0	1
500.0	0	1	0	0
512.0	0	0	0	1
520.0	0	1	0	0
522.0	0	0	0	1
525.0	0	1	0	0
531.0	0	2	0	0
542.0	0	1	0	0
545.0	0	1	0	1
581.0	0	1	0	0
593.0	0	0	0	1
594.0	0	0	0	1
610.0	0	0	0	1
651.0	0	1	0	0
660.0	0	1	0	0
676.0	0	1	0	0
699.0	0	0	0	1
718.0	0	0	0	1
727.0	0	1	0	0
758.0	0	1	0	0
938.0	0	0	0	1
963.0	0	1	0	0