## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-259-TP3.bam --OUTPUT POC-259-TP3.md.bam --METRICS_FILE POC-259-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 02:46:11 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	314	15110288	2990418	0	247	9506521	3642439	0.629144	6926516

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.096533	2026854	0	2595771
2.0	1.220299	1402541	931131	1606398
3.0	1.234269	874706	369566	792765
4.0	1.235846	517474	185716	340528
5.0	1.236024	299896	102235	137909
6.0	1.236044	176213	59306	58106
7.0	1.236046	105878	35677	26333
8.0	1.236046	65771	21431	13763
9.0	1.236046	41591	13088	7935
10.0	1.236046	27337	8062	5037
11.0	1.236046	17899	4976	3523
12.0	1.236046	12185	3187	2602
13.0	1.236046	8523	2017	1863
14.0	1.236046	5929	1301	1540
15.0	1.236046	4201	836	1181
16.0	1.236046	3073	512	978
17.0	1.236046	2291	340	804
18.0	1.236046	1750	206	612
19.0	1.236046	1324	137	596
20.0	1.236046	976	90	461
21.0	1.236046	808	75	438
22.0	1.236046	680	51	372
23.0	1.236046	553	28	305
24.0	1.236046	463	30	253
25.0	1.236046	378	15	221
26.0	1.236046	320	12	222
27.0	1.236046	272	21	193
28.0	1.236046	248	7	160
29.0	1.236046	235	13	145
30.0	1.236046	204	7	157
31.0	1.236046	185	5	132
32.0	1.236046	162	1	123
33.0	1.236046	137	7	128
34.0	1.236046	127	2	95
35.0	1.236046	124	2	93
36.0	1.236046	100	3	77
37.0	1.236046	99	1	76
38.0	1.236046	97	3	66
39.0	1.236046	88	2	83
40.0	1.236046	102	1	73
41.0	1.236046	76	1	58
42.0	1.236046	85	4	64
43.0	1.236046	76	1	42
44.0	1.236046	76	2	46
45.0	1.236046	43	1	52
46.0	1.236046	45	1	37
47.0	1.236046	60	0	39
48.0	1.236046	54	1	53
49.0	1.236046	50	0	45
50.0	1.236046	44	0	54
51.0	1.236046	35	3	23
52.0	1.236046	46	1	36
53.0	1.236046	42	2	20
54.0	1.236046	35	1	36
55.0	1.236046	29	1	31
56.0	1.236046	35	0	26
57.0	1.236046	29	0	19
58.0	1.236046	29	3	27
59.0	1.236046	30	2	21
60.0	1.236046	18	0	19
61.0	1.236046	22	0	16
62.0	1.236046	26	0	15
63.0	1.236046	20	2	17
64.0	1.236046	22	0	20
65.0	1.236046	27	0	22
66.0	1.236046	17	2	17
67.0	1.236046	20	0	12
68.0	1.236046	11	2	14
69.0	1.236046	21	0	8
70.0	1.236046	17	0	11
71.0	1.236046	17	0	11
72.0	1.236046	19	0	11
73.0	1.236046	18	0	16
74.0	1.236046	15	0	11
75.0	1.236046	9	1	10
76.0	1.236046	10	0	17
77.0	1.236046	6	1	5
78.0	1.236046	12	0	21
79.0	1.236046	13	1	15
80.0	1.236046	19	1	16
81.0	1.236046	16	0	14
82.0	1.236046	15	0	13
83.0	1.236046	12	0	10
84.0	1.236046	14	0	10
85.0	1.236046	7	0	7
86.0	1.236046	11	0	11
87.0	1.236046	14	0	10
88.0	1.236046	13	1	1
89.0	1.236046	11	0	9
90.0	1.236046	8	0	9
91.0	1.236046	7	0	10
92.0	1.236046	11	0	12
93.0	1.236046	7	0	7
94.0	1.236046	7	0	8
95.0	1.236046	14	0	8
96.0	1.236046	7	1	6
97.0	1.236046	6	2	4
98.0	1.236046	10	0	5
99.0	1.236046	10	0	3
100.0	1.236046	3	0	12
101.0	0	4	0	7
102.0	0	11	1	6
103.0	0	3	0	11
104.0	0	5	0	4
105.0	0	5	0	7
106.0	0	6	0	2
107.0	0	4	0	9
108.0	0	6	0	5
109.0	0	11	0	5
110.0	0	3	0	9
111.0	0	6	0	3
112.0	0	9	0	8
113.0	0	8	0	4
114.0	0	2	0	7
115.0	0	6	0	2
116.0	0	1	0	2
117.0	0	10	0	3
118.0	0	5	0	2
119.0	0	8	0	3
120.0	0	6	0	8
121.0	0	5	0	4
122.0	0	5	0	3
123.0	0	0	1	4
124.0	0	5	0	8
125.0	0	2	0	6
126.0	0	4	0	3
127.0	0	2	0	6
128.0	0	5	0	6
129.0	0	5	0	4
130.0	0	7	0	7
131.0	0	5	0	2
132.0	0	3	0	0
133.0	0	3	1	3
134.0	0	4	0	1
135.0	0	4	0	5
136.0	0	3	0	4
137.0	0	3	0	3
138.0	0	4	0	4
139.0	0	2	0	2
140.0	0	3	0	4
141.0	0	4	0	3
142.0	0	10	0	2
143.0	0	2	0	5
144.0	0	5	0	2
145.0	0	1	0	2
146.0	0	6	0	7
147.0	0	1	0	1
148.0	0	1	0	2
149.0	0	2	0	3
150.0	0	3	0	0
151.0	0	5	0	1
152.0	0	4	0	2
153.0	0	2	0	0
154.0	0	1	0	3
156.0	0	0	0	3
157.0	0	0	0	2
158.0	0	1	0	2
159.0	0	2	0	3
160.0	0	8	0	1
161.0	0	4	0	6
162.0	0	1	0	3
163.0	0	3	0	2
164.0	0	1	0	0
165.0	0	5	0	0
166.0	0	2	0	2
167.0	0	0	0	4
168.0	0	5	1	2
169.0	0	2	0	0
170.0	0	2	0	0
171.0	0	2	0	1
172.0	0	0	0	2
173.0	0	1	0	3
174.0	0	1	0	1
175.0	0	2	0	0
176.0	0	2	0	2
177.0	0	2	0	0
178.0	0	2	0	2
179.0	0	1	0	1
180.0	0	1	0	1
183.0	0	1	0	4
184.0	0	4	0	1
186.0	0	3	0	4
187.0	0	0	0	2
188.0	0	1	0	2
189.0	0	0	0	1
190.0	0	2	0	0
191.0	0	3	0	1
192.0	0	2	0	5
193.0	0	1	0	1
194.0	0	3	0	3
195.0	0	1	0	2
196.0	0	1	0	0
197.0	0	2	0	1
198.0	0	1	0	0
199.0	0	1	0	0
200.0	0	1	0	0
202.0	0	2	0	0
203.0	0	1	0	0
204.0	0	3	0	2
206.0	0	2	0	1
207.0	0	2	0	0
209.0	0	1	0	0
211.0	0	0	0	1
212.0	0	0	0	1
213.0	0	0	0	1
214.0	0	0	0	2
215.0	0	2	0	0
216.0	0	1	0	0
217.0	0	0	0	1
218.0	0	1	0	2
219.0	0	0	0	1
220.0	0	2	0	1
221.0	0	1	0	0
222.0	0	1	0	1
223.0	0	0	0	1
224.0	0	1	0	0
225.0	0	1	0	0
226.0	0	0	0	2
228.0	0	0	0	2
229.0	0	0	0	1
232.0	0	2	0	0
233.0	0	0	0	1
234.0	0	0	0	1
235.0	0	2	0	1
237.0	0	1	0	1
238.0	0	1	0	2
239.0	0	0	0	2
240.0	0	1	0	2
241.0	0	1	0	1
242.0	0	1	0	0
243.0	0	2	0	1
244.0	0	2	0	0
245.0	0	1	0	1
246.0	0	0	0	2
247.0	0	1	0	1
248.0	0	0	0	1
249.0	0	0	0	1
250.0	0	1	0	0
251.0	0	2	0	2
252.0	0	1	0	0
254.0	0	2	0	1
256.0	0	1	0	1
257.0	0	1	0	0
258.0	0	3	0	1
259.0	0	0	0	1
261.0	0	0	0	2
262.0	0	1	0	1
263.0	0	2	0	0
264.0	0	0	0	1
265.0	0	2	0	0
267.0	0	0	0	1
268.0	0	1	0	0
270.0	0	0	0	1
271.0	0	2	0	0
272.0	0	0	0	1
273.0	0	0	0	2
274.0	0	1	0	1
275.0	0	1	0	1
276.0	0	1	0	0
277.0	0	1	0	1
279.0	0	0	1	0
280.0	0	1	0	0
281.0	0	1	0	1
282.0	0	1	0	1
283.0	0	1	0	0
284.0	0	0	0	1
285.0	0	0	0	2
286.0	0	1	0	0
288.0	0	2	0	0
291.0	0	1	0	0
294.0	0	0	0	1
295.0	0	1	0	0
296.0	0	1	0	1
297.0	0	1	0	0
298.0	0	1	0	0
299.0	0	0	0	2
300.0	0	1	0	1
302.0	0	1	0	1
306.0	0	1	0	0
307.0	0	0	0	2
308.0	0	1	0	1
310.0	0	0	0	2
311.0	0	2	0	1
314.0	0	1	0	1
318.0	0	1	0	0
320.0	0	3	0	0
321.0	0	1	0	0
322.0	0	1	0	0
325.0	0	0	0	1
326.0	0	1	0	0
328.0	0	1	0	1
334.0	0	1	0	0
335.0	0	0	0	2
336.0	0	0	0	1
339.0	0	1	0	1
341.0	0	0	0	1
344.0	0	0	0	1
345.0	0	1	0	1
347.0	0	2	0	0
349.0	0	2	0	1
351.0	0	1	0	0
353.0	0	0	0	1
354.0	0	1	0	0
355.0	0	1	0	0
358.0	0	2	0	0
360.0	0	0	0	1
362.0	0	1	0	1
366.0	0	0	0	1
374.0	0	0	0	2
379.0	0	1	0	1
382.0	0	0	0	1
384.0	0	1	0	0
385.0	0	0	0	2
388.0	0	1	0	1
389.0	0	2	0	1
393.0	0	0	0	1
397.0	0	1	0	0
400.0	0	0	0	1
401.0	0	1	0	2
403.0	0	1	0	0
404.0	0	0	0	1
408.0	0	0	0	2
409.0	0	1	0	0
413.0	0	0	0	1
414.0	0	0	0	1
417.0	0	0	0	1
419.0	0	1	0	0
420.0	0	1	0	0
421.0	0	1	0	0
423.0	0	0	0	1
424.0	0	0	0	1
426.0	0	1	0	0
427.0	0	1	0	0
428.0	0	1	0	0
432.0	0	1	0	0
433.0	0	0	0	1
436.0	0	2	0	1
442.0	0	1	0	0
443.0	0	1	0	1
444.0	0	0	0	1
446.0	0	0	0	1
447.0	0	0	0	1
450.0	0	2	0	1
454.0	0	1	0	0
455.0	0	1	0	0
457.0	0	0	0	1
460.0	0	1	0	0
462.0	0	1	0	0
466.0	0	0	0	1
468.0	0	0	0	1
470.0	0	0	0	1
471.0	0	1	0	0
473.0	0	1	0	0
474.0	0	0	0	1
475.0	0	1	0	0
478.0	0	1	0	0
483.0	0	0	0	2
484.0	0	1	0	0
488.0	0	1	0	2
489.0	0	1	0	0
496.0	0	1	0	0
500.0	0	2	0	0
501.0	0	0	0	1
509.0	0	1	0	0
512.0	0	1	0	0
515.0	0	1	0	1
516.0	0	0	0	1
517.0	0	0	0	1
526.0	0	1	0	1
529.0	0	1	0	0
536.0	0	0	0	1
538.0	0	1	0	0
542.0	0	0	0	1
545.0	0	1	0	0
550.0	0	0	0	1
565.0	0	1	0	0
567.0	0	1	0	0
572.0	0	0	0	1
573.0	0	0	0	1
575.0	0	1	0	0
584.0	0	1	0	0
586.0	0	0	0	1
592.0	0	1	0	0
597.0	0	1	0	0
604.0	0	0	0	1
610.0	0	1	0	0
614.0	0	1	0	0
616.0	0	0	0	1
617.0	0	0	0	1
622.0	0	0	0	1
631.0	0	1	0	0
634.0	0	1	0	0
635.0	0	1	0	0
649.0	0	1	0	1
659.0	0	1	0	0
687.0	0	0	0	2
688.0	0	0	0	1
719.0	0	1	0	1
720.0	0	0	0	1
725.0	0	1	0	0
730.0	0	0	0	1
732.0	0	1	0	0
737.0	0	0	0	1
740.0	0	1	0	0
753.0	0	1	0	0
761.0	0	0	0	1
765.0	0	1	0	0
783.0	0	0	0	1
798.0	0	1	0	0
807.0	0	0	0	1
815.0	0	1	0	0
838.0	0	1	0	0
857.0	0	1	0	0
874.0	0	1	0	0
885.0	0	0	0	1
911.0	0	1	0	0
937.0	0	0	0	1
954.0	0	1	0	0
1033.0	0	0	0	1
1090.0	0	0	0	1
1099.0	0	0	0	1
1155.0	0	1	0	0
1164.0	0	0	0	1
1178.0	0	1	0	0
1185.0	0	1	0	0
1223.0	0	0	0	1
1226.0	0	1	0	0
1323.0	0	0	0	1
1355.0	0	1	0	0
1490.0	0	1	0	0
2142.0	0	0	0	1
2420.0	0	1	0	0