## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-40-TP2.bam --OUTPUT POC-40-TP2.md.bam --METRICS_FILE POC-40-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 02:43:50 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	247	15746250	3286088	0	162	8186809	3784933	0.519922	11955440

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.157807	3776035	0	4817642
2.0	1.468003	1887089	1140280	1841297
3.0	1.55111	912211	425427	592505
4.0	1.573376	446512	199878	182312
5.0	1.579341	228633	102878	61105
6.0	1.580939	122288	54515	24105
7.0	1.581368	69211	30079	12204
8.0	1.581482	40946	16911	6966
9.0	1.581513	25126	9472	4643
10.0	1.581521	15483	5310	3178
11.0	1.581524	9782	3050	2319
12.0	1.581524	6625	1794	1778
13.0	1.581524	4393	1012	1367
14.0	1.581524	3052	582	1073
15.0	1.581524	2159	399	859
16.0	1.581524	1556	234	674
17.0	1.581524	1174	138	559
18.0	1.581524	962	88	468
19.0	1.581524	771	55	421
20.0	1.581524	616	27	372
21.0	1.581524	479	22	337
22.0	1.581524	371	20	288
23.0	1.581524	367	11	252
24.0	1.581524	298	12	213
25.0	1.581524	292	9	165
26.0	1.581524	268	11	182
27.0	1.581524	195	2	176
28.0	1.581524	204	7	145
29.0	1.581524	164	5	110
30.0	1.581524	157	6	92
31.0	1.581524	116	2	98
32.0	1.581524	104	2	81
33.0	1.581524	95	0	72
34.0	1.581524	95	0	73
35.0	1.581524	98	0	69
36.0	1.581524	82	2	54
37.0	1.581524	76	2	66
38.0	1.581524	72	1	62
39.0	1.581524	68	2	43
40.0	1.581524	54	1	41
41.0	1.581524	51	0	50
42.0	1.581524	44	0	40
43.0	1.581524	51	1	35
44.0	1.581524	46	0	38
45.0	1.581524	38	0	31
46.0	1.581524	43	0	28
47.0	1.581524	33	2	31
48.0	1.581524	42	0	34
49.0	1.581524	30	2	29
50.0	1.581524	28	0	27
51.0	1.581524	26	0	18
52.0	1.581524	23	0	24
53.0	1.581524	31	0	19
54.0	1.581524	29	0	27
55.0	1.581524	23	0	15
56.0	1.581524	21	1	17
57.0	1.581524	17	1	10
58.0	1.581524	19	1	11
59.0	1.581524	17	0	17
60.0	1.581524	14	0	13
61.0	1.581524	25	0	15
62.0	1.581524	11	0	12
63.0	1.581524	10	0	8
64.0	1.581524	11	0	8
65.0	1.581524	18	0	16
66.0	1.581524	11	0	13
67.0	1.581524	11	0	8
68.0	1.581524	17	0	18
69.0	1.581524	9	0	12
70.0	1.581524	13	0	9
71.0	1.581524	9	0	6
72.0	1.581524	4	0	5
73.0	1.581524	10	0	4
74.0	1.581524	9	0	8
75.0	1.581524	11	0	10
76.0	1.581524	8	0	6
77.0	1.581524	4	0	4
78.0	1.581524	5	0	9
79.0	1.581524	9	0	7
80.0	1.581524	14	0	6
81.0	1.581524	7	0	9
82.0	1.581524	6	1	8
83.0	1.581524	4	0	5
84.0	1.581524	2	0	2
85.0	1.581524	5	0	5
86.0	1.581524	7	0	5
87.0	1.581524	3	0	5
88.0	1.581524	8	0	3
89.0	1.581524	10	0	4
90.0	1.581524	7	0	6
91.0	1.581524	2	0	4
92.0	1.581524	3	0	4
93.0	1.581524	5	0	5
94.0	1.581524	5	0	2
95.0	1.581524	7	0	3
96.0	1.581524	4	1	1
97.0	1.581524	4	0	4
98.0	1.581524	3	0	3
99.0	1.581524	3	0	2
100.0	1.581524	3	0	2
101.0	0	3	0	2
102.0	0	2	0	4
103.0	0	7	0	3
104.0	0	3	0	5
105.0	0	5	0	3
106.0	0	1	0	2
107.0	0	2	0	5
108.0	0	1	0	2
109.0	0	4	0	2
110.0	0	4	0	2
111.0	0	4	0	1
112.0	0	6	0	7
113.0	0	2	0	4
114.0	0	2	0	1
115.0	0	2	0	1
116.0	0	1	0	3
117.0	0	4	0	5
118.0	0	2	0	1
119.0	0	1	0	0
120.0	0	2	0	2
121.0	0	4	0	2
122.0	0	3	0	1
123.0	0	4	0	4
124.0	0	1	0	3
125.0	0	0	0	1
126.0	0	4	0	2
127.0	0	1	0	0
128.0	0	2	0	0
129.0	0	1	0	0
130.0	0	3	0	3
131.0	0	1	0	2
132.0	0	2	0	1
133.0	0	3	0	0
134.0	0	2	0	3
135.0	0	2	0	3
136.0	0	0	0	1
137.0	0	1	0	3
138.0	0	0	0	2
139.0	0	3	0	0
140.0	0	2	0	0
141.0	0	3	0	1
142.0	0	0	0	1
143.0	0	1	0	1
144.0	0	0	0	2
145.0	0	1	0	1
146.0	0	1	0	1
147.0	0	2	0	2
148.0	0	2	0	0
149.0	0	2	0	0
151.0	0	2	0	0
152.0	0	3	0	1
153.0	0	0	0	1
154.0	0	3	0	0
155.0	0	1	0	3
157.0	0	1	0	2
158.0	0	1	0	4
159.0	0	0	0	2
160.0	0	0	0	2
161.0	0	4	0	1
162.0	0	2	0	1
165.0	0	2	0	0
166.0	0	0	0	1
167.0	0	1	0	0
169.0	0	2	0	0
170.0	0	0	0	2
171.0	0	1	0	1
172.0	0	0	0	1
173.0	0	1	0	0
174.0	0	1	0	0
176.0	0	1	0	1
178.0	0	1	0	0
179.0	0	0	0	2
180.0	0	2	0	3
181.0	0	1	0	3
182.0	0	1	0	1
183.0	0	2	0	2
185.0	0	1	0	1
186.0	0	3	0	0
187.0	0	1	0	0
190.0	0	3	0	1
192.0	0	0	0	1
193.0	0	0	0	2
194.0	0	1	0	1
196.0	0	1	0	0
198.0	0	0	0	1
199.0	0	1	0	0
200.0	0	1	0	1
201.0	0	0	0	1
202.0	0	1	0	0
203.0	0	1	0	0
204.0	0	1	0	1
205.0	0	2	0	0
206.0	0	1	0	2
208.0	0	1	0	0
209.0	0	0	0	1
211.0	0	1	0	1
212.0	0	1	0	0
213.0	0	2	0	0
214.0	0	0	0	2
215.0	0	0	0	1
216.0	0	0	0	1
217.0	0	0	0	1
220.0	0	1	0	3
221.0	0	1	0	0
224.0	0	0	0	1
227.0	0	1	0	0
228.0	0	0	0	1
229.0	0	1	0	0
231.0	0	1	0	0
233.0	0	1	0	1
234.0	0	0	0	1
235.0	0	1	0	1
236.0	0	1	0	0
239.0	0	1	0	0
242.0	0	0	0	1
243.0	0	0	0	1
244.0	0	0	0	1
245.0	0	1	0	1
246.0	0	0	0	2
247.0	0	1	0	0
249.0	0	1	0	0
250.0	0	0	0	1
251.0	0	1	0	1
253.0	0	1	0	0
256.0	0	1	0	0
257.0	0	1	0	0
259.0	0	1	0	0
260.0	0	1	0	0
262.0	0	0	0	1
263.0	0	0	0	1
264.0	0	1	0	0
266.0	0	0	0	1
270.0	0	1	0	0
271.0	0	1	0	1
273.0	0	1	0	0
275.0	0	2	0	0
276.0	0	0	0	1
279.0	0	2	0	0
282.0	0	0	0	1
285.0	0	1	0	1
286.0	0	1	0	0
289.0	0	0	0	1
293.0	0	0	0	1
294.0	0	1	0	0
301.0	0	0	0	1
302.0	0	1	0	0
304.0	0	0	0	1
307.0	0	1	0	0
308.0	0	0	0	2
309.0	0	1	0	0
322.0	0	0	0	1
324.0	0	0	0	1
326.0	0	1	0	1
329.0	0	1	0	0
331.0	0	1	0	0
339.0	0	2	0	0
344.0	0	1	0	0
366.0	0	0	0	1
372.0	0	1	0	0
381.0	0	0	0	1
386.0	0	1	0	0
389.0	0	0	0	1
394.0	0	1	0	0
395.0	0	0	0	1
396.0	0	0	0	1
398.0	0	0	0	1
407.0	0	1	0	0
424.0	0	1	0	0
430.0	0	0	0	1
431.0	0	1	0	0
432.0	0	1	0	0
448.0	0	0	0	1
466.0	0	0	0	1
472.0	0	1	0	0
491.0	0	1	0	0
494.0	0	1	0	0
523.0	0	0	0	1
573.0	0	0	0	1
580.0	0	1	0	0
591.0	0	1	0	0
616.0	0	0	0	1
617.0	0	0	0	1
641.0	0	1	0	0
664.0	0	1	0	0
728.0	0	0	0	1
809.0	0	1	0	0
966.0	0	0	0	1
1061.0	0	1	0	0