## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-53-TP1.bam --OUTPUT POC-53-TP1.md.bam --METRICS_FILE POC-53-TP1.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 02:44:21 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	243	13951063	3083295	0	127	6855512	4134976	0.491397	14258211

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.254122	3876695	0	5188231
2.0	1.725535	1649503	1088065	1422577
3.0	1.902734	743084	443782	344314
4.0	1.969341	363334	224108	85717
5.0	1.994379	190870	121471	26162
6.0	2.00379	107649	68127	10395
7.0	2.007327	62456	38302	5338
8.0	2.008657	37265	21462	3305
9.0	2.009157	22489	12588	2127
10.0	2.009345	14141	7132	1447
11.0	2.009415	8911	4108	1067
12.0	2.009442	5642	2313	829
13.0	2.009452	3676	1375	604
14.0	2.009456	2463	859	508
15.0	2.009457	1640	530	366
16.0	2.009458	1197	298	332
17.0	2.009458	828	167	268
18.0	2.009458	565	111	242
19.0	2.009458	464	64	193
20.0	2.009458	382	53	141
21.0	2.009458	282	38	143
22.0	2.009458	242	24	92
23.0	2.009458	199	12	106
24.0	2.009458	145	11	105
25.0	2.009458	144	3	74
26.0	2.009458	101	6	71
27.0	2.009458	97	5	57
28.0	2.009458	89	2	52
29.0	2.009458	73	3	45
30.0	2.009458	83	4	43
31.0	2.009458	59	2	38
32.0	2.009458	58	0	39
33.0	2.009458	51	1	31
34.0	2.009458	47	1	34
35.0	2.009458	37	1	24
36.0	2.009458	32	0	31
37.0	2.009458	40	1	26
38.0	2.009458	38	0	17
39.0	2.009458	30	0	19
40.0	2.009458	28	1	17
41.0	2.009458	19	0	15
42.0	2.009458	17	0	14
43.0	2.009458	23	1	17
44.0	2.009458	15	0	12
45.0	2.009458	18	0	12
46.0	2.009458	14	0	10
47.0	2.009458	22	0	9
48.0	2.009458	9	0	8
49.0	2.009458	13	0	11
50.0	2.009458	8	0	11
51.0	2.009458	8	0	6
52.0	2.009458	11	1	4
53.0	2.009458	8	0	7
54.0	2.009458	7	0	5
55.0	2.009458	4	1	7
56.0	2.009458	15	0	7
57.0	2.009458	10	0	4
58.0	2.009458	14	0	5
59.0	2.009458	2	0	6
60.0	2.009458	5	0	4
61.0	2.009458	3	0	6
62.0	2.009458	7	0	3
63.0	2.009458	7	0	2
64.0	2.009458	3	0	3
65.0	2.009458	6	0	2
66.0	2.009458	3	0	6
67.0	2.009458	9	0	2
68.0	2.009458	2	0	3
69.0	2.009458	3	0	6
70.0	2.009458	6	0	6
71.0	2.009458	4	0	0
72.0	2.009458	4	0	2
73.0	2.009458	3	0	4
74.0	2.009458	5	0	2
75.0	2.009458	4	0	4
76.0	2.009458	2	0	0
77.0	2.009458	1	0	3
78.0	2.009458	1	0	3
79.0	2.009458	3	0	2
80.0	2.009458	3	0	3
81.0	2.009458	1	0	3
82.0	2.009458	3	0	3
83.0	2.009458	1	0	3
84.0	2.009458	5	0	3
85.0	2.009458	5	0	1
86.0	2.009458	3	0	1
87.0	2.009458	2	0	0
88.0	2.009458	1	0	0
89.0	2.009458	0	0	1
90.0	2.009458	0	0	1
91.0	2.009458	0	0	0
92.0	2.009458	3	0	2
93.0	2.009458	1	0	3
94.0	2.009458	0	0	2
95.0	2.009458	1	0	3
96.0	2.009458	2	0	2
97.0	2.009458	2	0	1
98.0	2.009458	3	0	0
99.0	2.009458	3	0	1
100.0	2.009458	0	0	1
101.0	0	1	0	1
102.0	0	0	0	1
103.0	0	3	0	2
104.0	0	0	0	1
105.0	0	0	0	1
106.0	0	1	0	2
107.0	0	2	0	0
108.0	0	0	0	3
109.0	0	1	0	1
110.0	0	1	0	0
111.0	0	2	0	0
112.0	0	1	0	0
113.0	0	0	0	1
114.0	0	1	0	2
115.0	0	2	0	0
116.0	0	1	0	3
117.0	0	1	0	0
118.0	0	2	0	3
119.0	0	1	0	3
120.0	0	1	0	1
121.0	0	4	0	0
123.0	0	1	0	0
124.0	0	1	0	0
125.0	0	1	0	0
127.0	0	0	0	2
130.0	0	1	0	0
132.0	0	1	0	2
134.0	0	1	0	0
136.0	0	1	0	0
140.0	0	1	0	0
142.0	0	0	0	1
143.0	0	1	0	1
145.0	0	0	0	1
146.0	0	1	0	0
148.0	0	1	0	0
149.0	0	2	0	1
150.0	0	0	0	1
154.0	0	1	0	0
155.0	0	2	0	1
156.0	0	1	0	0
157.0	0	0	0	2
158.0	0	1	0	0
160.0	0	0	0	1
161.0	0	0	0	1
163.0	0	0	0	1
168.0	0	0	0	1
169.0	0	1	0	0
175.0	0	1	0	0
176.0	0	2	0	0
179.0	0	1	0	0
182.0	0	1	0	1
184.0	0	0	0	1
188.0	0	1	0	0
193.0	0	0	0	1
194.0	0	0	0	1
199.0	0	1	0	1
205.0	0	1	0	1
206.0	0	0	0	1
210.0	0	1	0	0
214.0	0	0	0	1
216.0	0	1	0	0
218.0	0	1	0	0
221.0	0	0	0	1
223.0	0	2	0	0
224.0	0	1	0	0
235.0	0	0	0	1
264.0	0	0	0	1
269.0	0	1	0	0
271.0	0	1	0	0
288.0	0	0	0	1
297.0	0	0	0	1
299.0	0	1	0	0
301.0	0	0	0	1
311.0	0	1	0	0
348.0	0	1	0	0
356.0	0	0	0	1
410.0	0	1	0	0
411.0	0	0	0	1
431.0	0	1	0	0