## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-222-TP3.bam --OUTPUT POC-222-TP3.md.bam --METRICS_FILE POC-222-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 02:45:29 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	290	17373055	3873706	0	176	9191263	4863941	0.529053	13611939

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.19941	4098566	0	5419440
2.0	1.534123	1979051	1261909	1898546
3.0	1.62753	965110	515388	574141
4.0	1.653597	488760	260357	170412
5.0	1.660871	262393	141978	56581
6.0	1.662901	146957	79572	23086
7.0	1.663467	86198	45533	11598
8.0	1.663626	52767	26348	7030
9.0	1.66367	33152	15503	4612
10.0	1.663682	21221	9053	3114
11.0	1.663685	13600	5313	2408
12.0	1.663686	9183	3075	1860
13.0	1.663687	6158	1922	1353
14.0	1.663687	4200	1192	1105
15.0	1.663687	2886	683	826
16.0	1.663687	2094	453	690
17.0	1.663687	1558	292	588
18.0	1.663687	1180	200	504
19.0	1.663687	923	112	412
20.0	1.663687	730	80	362
21.0	1.663687	592	60	306
22.0	1.663687	493	45	271
23.0	1.663687	417	28	204
24.0	1.663687	350	34	223
25.0	1.663687	300	19	184
26.0	1.663687	271	24	139
27.0	1.663687	216	20	127
28.0	1.663687	182	14	133
29.0	1.663687	175	8	101
30.0	1.663687	138	8	104
31.0	1.663687	146	11	90
32.0	1.663687	127	7	64
33.0	1.663687	103	4	67
34.0	1.663687	96	3	73
35.0	1.663687	91	3	74
36.0	1.663687	86	0	70
37.0	1.663687	90	2	56
38.0	1.663687	68	4	47
39.0	1.663687	60	4	28
40.0	1.663687	59	3	33
41.0	1.663687	55	0	32
42.0	1.663687	56	1	43
43.0	1.663687	61	1	16
44.0	1.663687	33	0	34
45.0	1.663687	37	1	23
46.0	1.663687	43	2	28
47.0	1.663687	38	0	19
48.0	1.663687	35	1	29
49.0	1.663687	33	0	22
50.0	1.663687	22	0	12
51.0	1.663687	21	1	24
52.0	1.663687	28	2	14
53.0	1.663687	35	0	13
54.0	1.663687	19	0	19
55.0	1.663687	24	0	21
56.0	1.663687	24	0	14
57.0	1.663687	16	0	15
58.0	1.663687	20	0	15
59.0	1.663687	25	0	11
60.0	1.663687	16	0	19
61.0	1.663687	10	0	6
62.0	1.663687	14	0	15
63.0	1.663687	16	0	7
64.0	1.663687	16	0	9
65.0	1.663687	12	1	5
66.0	1.663687	13	0	9
67.0	1.663687	6	0	9
68.0	1.663687	10	0	5
69.0	1.663687	10	0	9
70.0	1.663687	7	0	11
71.0	1.663687	13	0	5
72.0	1.663687	6	0	2
73.0	1.663687	5	0	4
74.0	1.663687	8	0	6
75.0	1.663687	6	0	1
76.0	1.663687	8	0	9
77.0	1.663687	13	0	9
78.0	1.663687	3	0	4
79.0	1.663687	6	0	5
80.0	1.663687	7	0	4
81.0	1.663687	4	0	5
82.0	1.663687	2	0	4
83.0	1.663687	2	0	3
84.0	1.663687	6	0	6
85.0	1.663687	7	0	7
86.0	1.663687	9	0	4
87.0	1.663687	1	0	2
88.0	1.663687	9	0	1
89.0	1.663687	3	0	7
90.0	1.663687	7	0	4
91.0	1.663687	2	0	4
92.0	1.663687	5	0	4
93.0	1.663687	2	0	2
94.0	1.663687	2	0	6
95.0	1.663687	3	0	6
96.0	1.663687	6	0	2
97.0	1.663687	3	0	2
98.0	1.663687	8	0	4
99.0	1.663687	5	0	1
100.0	1.663687	0	0	1
101.0	0	5	0	1
102.0	0	3	0	1
103.0	0	5	0	5
104.0	0	1	0	2
105.0	0	4	0	1
106.0	0	0	0	2
107.0	0	3	0	2
108.0	0	3	0	1
109.0	0	3	0	1
110.0	0	3	0	2
111.0	0	1	0	1
112.0	0	2	0	3
113.0	0	1	0	1
114.0	0	2	0	1
115.0	0	3	0	1
116.0	0	6	0	3
117.0	0	0	0	1
118.0	0	1	0	2
119.0	0	2	0	0
120.0	0	3	0	0
121.0	0	2	0	3
122.0	0	0	0	2
123.0	0	2	0	0
124.0	0	4	0	2
125.0	0	0	0	1
126.0	0	3	0	1
127.0	0	0	0	2
128.0	0	1	0	0
129.0	0	1	0	1
130.0	0	0	0	1
131.0	0	0	0	3
132.0	0	0	0	2
134.0	0	3	0	2
135.0	0	2	0	0
136.0	0	0	0	1
137.0	0	2	0	1
138.0	0	2	0	0
139.0	0	1	0	0
140.0	0	2	0	0
141.0	0	1	0	0
143.0	0	0	0	2
144.0	0	1	0	1
146.0	0	1	0	1
147.0	0	1	0	1
148.0	0	0	0	1
149.0	0	0	0	2
151.0	0	1	0	0
152.0	0	1	0	0
153.0	0	2	0	1
155.0	0	2	0	1
156.0	0	1	0	1
158.0	0	1	0	0
159.0	0	0	0	2
160.0	0	0	0	1
161.0	0	1	0	0
164.0	0	2	0	2
166.0	0	1	0	0
167.0	0	1	0	1
168.0	0	2	0	2
169.0	0	1	0	0
171.0	0	0	0	1
173.0	0	1	0	3
174.0	0	0	0	1
177.0	0	1	0	0
178.0	0	0	0	2
181.0	0	2	0	0
182.0	0	1	0	1
183.0	0	1	0	0
184.0	0	2	0	0
188.0	0	1	0	0
190.0	0	1	0	0
192.0	0	1	0	0
193.0	0	0	0	1
195.0	0	1	0	0
198.0	0	1	0	0
200.0	0	1	0	0
202.0	0	0	0	1
203.0	0	0	0	1
206.0	0	1	0	0
207.0	0	0	0	1
219.0	0	1	0	0
221.0	0	1	0	0
229.0	0	1	0	0
231.0	0	0	0	1
237.0	0	1	0	0
239.0	0	0	0	1
247.0	0	0	0	1
255.0	0	0	0	1
257.0	0	2	0	0
274.0	0	1	0	0
275.0	0	0	0	1
279.0	0	1	0	0
285.0	0	0	0	1
290.0	0	0	0	1
300.0	0	0	0	1
301.0	0	0	0	1
303.0	0	1	0	0
306.0	0	1	0	0
318.0	0	1	0	0
319.0	0	1	0	0
321.0	0	0	0	1
330.0	0	1	0	0
357.0	0	1	0	0
393.0	0	0	0	1
438.0	0	0	0	1
443.0	0	1	0	0
459.0	0	1	0	0
554.0	0	0	0	1
584.0	0	1	0	0
658.0	0	0	0	1
722.0	0	1	0	0