## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-201-TP3.bam --OUTPUT POC-201-TP3.md.bam --METRICS_FILE POC-201-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 02:47:33 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	158	7117135	1739255	0	103	4276365	1549560	0.600855	3616440

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.095157	1101017	0	1378978
2.0	1.248191	723729	424516	798680
3.0	1.269576	433524	162408	377796
4.0	1.272564	245816	79499	160139
5.0	1.272981	136867	42869	65412
6.0	1.27304	77266	24603	27457
7.0	1.273048	44407	14314	12740
8.0	1.273049	26916	8469	6434
9.0	1.273049	16877	5045	3679
10.0	1.273049	10575	3037	2202
11.0	1.273049	6929	1855	1518
12.0	1.273049	4623	1109	1066
13.0	1.273049	3210	620	812
14.0	1.273049	2130	435	571
15.0	1.273049	1503	256	478
16.0	1.273049	1080	147	365
17.0	1.273049	771	104	305
18.0	1.273049	579	51	265
19.0	1.273049	432	31	207
20.0	1.273049	339	21	169
21.0	1.273049	304	24	178
22.0	1.273049	235	8	142
23.0	1.273049	176	6	118
24.0	1.273049	156	3	93
25.0	1.273049	127	2	85
26.0	1.273049	113	3	62
27.0	1.273049	84	5	70
28.0	1.273049	84	1	55
29.0	1.273049	82	1	54
30.0	1.273049	57	1	56
31.0	1.273049	58	0	38
32.0	1.273049	47	0	44
33.0	1.273049	55	0	35
34.0	1.273049	36	0	25
35.0	1.273049	40	0	34
36.0	1.273049	38	1	24
37.0	1.273049	21	0	20
38.0	1.273049	34	0	21
39.0	1.273049	23	1	26
40.0	1.273049	26	0	21
41.0	1.273049	28	0	14
42.0	1.273049	21	0	16
43.0	1.273049	15	0	17
44.0	1.273049	21	0	16
45.0	1.273049	20	0	13
46.0	1.273049	18	0	10
47.0	1.273049	14	0	15
48.0	1.273049	14	0	15
49.0	1.273049	15	0	3
50.0	1.273049	10	0	3
51.0	1.273049	10	0	7
52.0	1.273049	3	0	8
53.0	1.273049	10	0	7
54.0	1.273049	13	0	7
55.0	1.273049	8	0	12
56.0	1.273049	13	0	7
57.0	1.273049	6	0	3
58.0	1.273049	4	0	6
59.0	1.273049	8	0	2
60.0	1.273049	4	0	2
61.0	1.273049	8	0	3
62.0	1.273049	2	0	8
63.0	1.273049	5	0	2
64.0	1.273049	3	0	1
65.0	1.273049	3	0	4
66.0	1.273049	0	0	1
67.0	1.273049	5	0	3
68.0	1.273049	2	0	5
69.0	1.273049	2	0	4
70.0	1.273049	2	0	3
71.0	1.273049	6	0	5
72.0	1.273049	4	0	4
73.0	1.273049	3	0	1
74.0	1.273049	4	0	3
75.0	1.273049	3	0	1
76.0	1.273049	5	0	3
77.0	1.273049	0	0	3
78.0	1.273049	4	0	0
79.0	1.273049	2	0	2
80.0	1.273049	0	0	3
81.0	1.273049	2	0	2
82.0	1.273049	4	0	1
83.0	1.273049	3	0	3
84.0	1.273049	3	0	1
85.0	1.273049	0	0	2
86.0	1.273049	2	0	3
87.0	1.273049	0	0	1
88.0	1.273049	2	0	0
89.0	1.273049	3	0	3
90.0	1.273049	1	0	2
91.0	1.273049	2	0	1
92.0	1.273049	3	0	1
93.0	1.273049	4	0	0
94.0	1.273049	2	0	2
95.0	1.273049	0	0	0
96.0	1.273049	0	0	1
97.0	1.273049	0	0	0
98.0	1.273049	2	0	1
99.0	1.273049	0	0	0
100.0	1.273049	1	0	2
101.0	0	0	0	1
103.0	0	0	0	1
104.0	0	1	0	0
105.0	0	2	0	0
106.0	0	0	0	1
107.0	0	0	0	2
108.0	0	1	0	0
109.0	0	0	0	1
110.0	0	1	0	0
111.0	0	0	0	2
112.0	0	1	0	0
113.0	0	1	0	1
115.0	0	1	0	1
117.0	0	0	0	2
118.0	0	2	0	1
119.0	0	1	0	1
120.0	0	1	0	2
122.0	0	2	0	0
124.0	0	1	0	1
125.0	0	1	0	0
126.0	0	2	0	0
127.0	0	1	0	0
128.0	0	0	0	1
129.0	0	1	0	0
131.0	0	1	0	0
135.0	0	1	0	1
136.0	0	0	0	1
137.0	0	1	0	0
140.0	0	1	0	2
141.0	0	1	0	0
150.0	0	1	0	0
185.0	0	0	0	1
188.0	0	0	0	1
189.0	0	1	0	0
199.0	0	0	0	1
203.0	0	2	0	1
205.0	0	1	0	0
250.0	0	0	0	1
255.0	0	1	0	0
335.0	0	0	0	1
346.0	0	1	0	0