## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-219-TP2.bam --OUTPUT POC-219-TP2.md.bam --METRICS_FILE POC-219-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 03:00:58 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	205	12744049	2916404	0	136	6683951	3184860	0.524477	9625883

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.165752	3014089	0	3859083
2.0	1.475942	1499213	899476	1477904
3.0	1.558479	730850	345178	479282
4.0	1.580441	364055	169173	147278
5.0	1.586285	188780	89706	48778
6.0	1.58784	103291	48687	18952
7.0	1.588254	58934	27486	8792
8.0	1.588364	34968	15733	5200
9.0	1.588393	21753	9077	3341
10.0	1.588401	13789	5324	2295
11.0	1.588403	8808	3077	1657
12.0	1.588404	5929	1859	1207
13.0	1.588404	3894	1065	912
14.0	1.588404	2611	619	717
15.0	1.588404	1795	395	641
16.0	1.588404	1364	234	488
17.0	1.588404	954	147	412
18.0	1.588404	758	86	312
19.0	1.588404	567	46	271
20.0	1.588404	416	47	249
21.0	1.588404	374	24	198
22.0	1.588404	271	23	181
23.0	1.588404	224	12	153
24.0	1.588404	226	10	133
25.0	1.588404	205	6	121
26.0	1.588404	146	5	107
27.0	1.588404	132	5	107
28.0	1.588404	164	3	92
29.0	1.588404	100	3	78
30.0	1.588404	86	4	61
31.0	1.588404	87	1	53
32.0	1.588404	52	1	58
33.0	1.588404	59	2	36
34.0	1.588404	76	0	56
35.0	1.588404	56	1	46
36.0	1.588404	45	0	38
37.0	1.588404	48	2	38
38.0	1.588404	39	1	35
39.0	1.588404	47	0	23
40.0	1.588404	42	0	28
41.0	1.588404	34	2	19
42.0	1.588404	27	0	22
43.0	1.588404	26	0	21
44.0	1.588404	20	0	18
45.0	1.588404	29	0	24
46.0	1.588404	20	2	21
47.0	1.588404	24	0	24
48.0	1.588404	19	0	15
49.0	1.588404	26	1	13
50.0	1.588404	20	0	19
51.0	1.588404	11	0	13
52.0	1.588404	19	0	9
53.0	1.588404	19	0	15
54.0	1.588404	13	0	7
55.0	1.588404	18	0	12
56.0	1.588404	7	1	12
57.0	1.588404	16	0	8
58.0	1.588404	11	0	14
59.0	1.588404	6	0	11
60.0	1.588404	10	0	7
61.0	1.588404	14	0	17
62.0	1.588404	11	0	6
63.0	1.588404	11	0	5
64.0	1.588404	8	0	3
65.0	1.588404	10	0	7
66.0	1.588404	3	0	5
67.0	1.588404	4	0	9
68.0	1.588404	10	0	10
69.0	1.588404	8	0	10
70.0	1.588404	7	0	9
71.0	1.588404	5	0	3
72.0	1.588404	6	1	6
73.0	1.588404	7	0	7
74.0	1.588404	8	0	5
75.0	1.588404	8	0	2
76.0	1.588404	7	0	4
77.0	1.588404	8	0	4
78.0	1.588404	5	0	5
79.0	1.588404	2	0	5
80.0	1.588404	3	0	7
81.0	1.588404	5	0	4
82.0	1.588404	6	0	3
83.0	1.588404	6	0	4
84.0	1.588404	1	0	6
85.0	1.588404	2	0	1
86.0	1.588404	5	1	3
87.0	1.588404	4	0	6
88.0	1.588404	1	0	1
89.0	1.588404	8	0	1
90.0	1.588404	2	0	7
91.0	1.588404	7	1	4
92.0	1.588404	3	0	3
93.0	1.588404	7	0	3
94.0	1.588404	2	0	2
95.0	1.588404	1	0	3
96.0	1.588404	1	0	2
97.0	1.588404	4	0	5
98.0	1.588404	2	0	3
99.0	1.588404	5	0	4
100.0	1.588404	2	0	2
101.0	0	9	0	2
102.0	0	4	0	6
103.0	0	4	0	5
104.0	0	0	0	5
105.0	0	3	0	5
106.0	0	5	0	0
107.0	0	3	0	2
108.0	0	2	0	6
109.0	0	4	0	2
110.0	0	1	0	4
111.0	0	4	0	2
112.0	0	4	0	1
113.0	0	6	0	0
114.0	0	1	0	2
115.0	0	2	0	2
116.0	0	4	0	0
117.0	0	1	0	4
118.0	0	0	0	5
119.0	0	2	0	1
120.0	0	0	0	2
121.0	0	5	0	1
122.0	0	3	0	3
123.0	0	2	0	2
124.0	0	2	0	1
125.0	0	1	0	2
126.0	0	1	0	1
127.0	0	0	1	3
128.0	0	2	0	1
129.0	0	1	0	2
130.0	0	1	0	1
131.0	0	2	0	3
132.0	0	4	0	2
133.0	0	2	0	1
134.0	0	2	0	1
135.0	0	4	0	1
136.0	0	2	0	2
137.0	0	2	0	1
138.0	0	3	0	4
139.0	0	1	0	0
140.0	0	1	0	0
141.0	0	1	0	1
142.0	0	2	0	1
143.0	0	2	0	1
144.0	0	2	0	0
145.0	0	1	0	0
146.0	0	1	0	0
148.0	0	0	0	2
150.0	0	1	0	1
151.0	0	0	0	1
152.0	0	1	0	1
153.0	0	2	0	0
154.0	0	1	0	0
156.0	0	0	0	1
157.0	0	2	0	2
159.0	0	1	0	1
160.0	0	0	0	1
161.0	0	0	0	1
162.0	0	0	0	1
163.0	0	2	0	2
164.0	0	2	0	0
165.0	0	0	0	1
166.0	0	1	0	2
167.0	0	0	0	1
168.0	0	0	0	1
169.0	0	2	0	2
170.0	0	2	0	1
171.0	0	0	0	1
172.0	0	1	0	0
173.0	0	0	0	1
174.0	0	1	0	2
175.0	0	0	0	1
176.0	0	3	0	1
177.0	0	1	0	1
178.0	0	0	0	2
179.0	0	1	0	1
180.0	0	2	0	1
184.0	0	3	0	2
185.0	0	1	0	0
186.0	0	1	0	1
187.0	0	3	0	1
188.0	0	0	0	1
190.0	0	1	0	1
191.0	0	1	0	1
192.0	0	0	0	1
194.0	0	2	0	1
196.0	0	0	0	2
197.0	0	1	0	0
198.0	0	1	0	2
199.0	0	0	0	1
200.0	0	1	0	0
201.0	0	1	0	0
203.0	0	0	0	1
204.0	0	1	0	0
206.0	0	1	0	1
207.0	0	1	0	0
209.0	0	0	0	1
213.0	0	0	0	1
214.0	0	1	0	1
215.0	0	1	0	0
217.0	0	2	0	0
218.0	0	0	0	1
220.0	0	1	0	1
221.0	0	1	0	0
222.0	0	1	0	0
223.0	0	0	0	1
225.0	0	1	0	1
226.0	0	0	0	1
227.0	0	1	0	0
228.0	0	3	0	0
229.0	0	1	0	0
230.0	0	0	0	1
233.0	0	1	0	0
238.0	0	1	0	0
242.0	0	1	0	0
244.0	0	1	0	0
245.0	0	0	0	1
250.0	0	0	0	2
251.0	0	0	0	1
252.0	0	0	0	1
253.0	0	0	0	1
254.0	0	1	0	0
258.0	0	0	0	1
261.0	0	0	0	1
264.0	0	1	0	0
268.0	0	0	0	1
272.0	0	2	0	0
273.0	0	1	0	0
274.0	0	0	0	1
278.0	0	1	0	0
280.0	0	2	0	1
281.0	0	0	0	1
284.0	0	0	0	2
286.0	0	0	0	1
287.0	0	2	0	0
289.0	0	1	0	1
293.0	0	1	0	0
299.0	0	1	0	0
304.0	0	0	0	1
305.0	0	1	0	0
309.0	0	0	0	1
313.0	0	0	0	1
314.0	0	0	0	1
316.0	0	1	0	0
317.0	0	1	0	0
320.0	0	1	0	0
321.0	0	0	0	1
332.0	0	1	0	1
334.0	0	0	0	1
335.0	0	0	0	1
340.0	0	1	0	0
349.0	0	1	0	0
351.0	0	1	0	0
353.0	0	2	0	0
363.0	0	0	0	1
378.0	0	0	0	1
382.0	0	1	0	0
387.0	0	1	0	0
399.0	0	0	0	1
408.0	0	1	0	1
413.0	0	0	0	1
414.0	0	1	0	0
426.0	0	0	0	1
439.0	0	1	0	0
458.0	0	1	0	0
461.0	0	0	0	1
466.0	0	1	0	0
509.0	0	0	0	1
516.0	0	1	0	0
522.0	0	1	0	0
642.0	0	0	0	1
655.0	0	0	0	1
703.0	0	0	0	1
713.0	0	1	0	0
745.0	0	1	0	0
788.0	0	1	0	0
1039.0	0	0	0	1
1165.0	0	1	0	0