## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-201-TP1.bam --OUTPUT POC-201-TP1.md.bam --METRICS_FILE POC-201-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 02:42:05 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	270	14867017	3108298	0	184	7142620	4273318	0.480436	15837524

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.248386	4286804	0	5710108
2.0	1.736664	1792714	1175308	1510966
3.0	1.927644	796894	475633	356537
4.0	2.002341	383380	236807	88921
5.0	2.031557	198915	124730	27284
6.0	2.042984	108207	67492	11114
7.0	2.047454	61515	36644	5771
8.0	2.049202	35835	20389	3494
9.0	2.049886	21724	11025	2320
10.0	2.050153	13027	6198	1598
11.0	2.050258	8121	3466	1112
12.0	2.050299	4997	1911	890
13.0	2.050315	3267	1137	684
14.0	2.050321	2177	662	508
15.0	2.050323	1516	363	389
16.0	2.050324	1039	207	331
17.0	2.050325	734	138	259
18.0	2.050325	527	78	210
19.0	2.050325	393	50	175
20.0	2.050325	325	41	149
21.0	2.050325	246	26	166
22.0	2.050325	211	10	122
23.0	2.050325	182	10	107
24.0	2.050325	157	4	100
25.0	2.050325	131	9	93
26.0	2.050325	104	3	63
27.0	2.050325	100	6	52
28.0	2.050325	79	3	75
29.0	2.050325	91	7	40
30.0	2.050325	57	1	44
31.0	2.050325	74	0	47
32.0	2.050325	53	1	42
33.0	2.050325	55	1	34
34.0	2.050325	47	0	38
35.0	2.050325	49	0	33
36.0	2.050325	36	0	39
37.0	2.050325	38	0	25
38.0	2.050325	42	0	19
39.0	2.050325	30	0	20
40.0	2.050325	26	0	25
41.0	2.050325	20	0	17
42.0	2.050325	25	0	18
43.0	2.050325	18	1	15
44.0	2.050325	20	0	11
45.0	2.050325	17	0	12
46.0	2.050325	12	0	5
47.0	2.050325	16	1	16
48.0	2.050325	9	0	8
49.0	2.050325	20	1	16
50.0	2.050325	13	1	8
51.0	2.050325	9	0	8
52.0	2.050325	7	0	6
53.0	2.050325	10	0	8
54.0	2.050325	8	0	7
55.0	2.050325	7	0	6
56.0	2.050325	8	0	6
57.0	2.050325	4	0	4
58.0	2.050325	6	0	6
59.0	2.050325	6	0	5
60.0	2.050325	7	0	7
61.0	2.050325	7	0	6
62.0	2.050325	6	0	3
63.0	2.050325	9	0	2
64.0	2.050325	10	0	9
65.0	2.050325	5	0	3
66.0	2.050325	3	0	4
67.0	2.050325	3	0	4
68.0	2.050325	3	0	6
69.0	2.050325	6	0	4
70.0	2.050325	2	0	4
71.0	2.050325	3	0	8
72.0	2.050325	6	0	4
73.0	2.050325	5	0	4
74.0	2.050325	3	0	0
75.0	2.050325	4	0	3
76.0	2.050325	2	0	6
77.0	2.050325	6	0	1
78.0	2.050325	2	0	4
79.0	2.050325	4	0	1
80.0	2.050325	4	0	3
81.0	2.050325	4	0	1
82.0	2.050325	1	0	3
83.0	2.050325	3	0	1
84.0	2.050325	3	0	6
85.0	2.050325	1	0	4
86.0	2.050325	1	0	5
87.0	2.050325	4	0	2
88.0	2.050325	2	0	2
89.0	2.050325	2	0	2
90.0	2.050325	4	0	3
91.0	2.050325	5	0	4
92.0	2.050325	2	0	1
93.0	2.050325	2	0	4
94.0	2.050325	2	0	0
95.0	2.050325	4	0	1
96.0	2.050325	5	0	1
97.0	2.050325	3	0	0
98.0	2.050325	2	0	2
99.0	2.050325	0	0	2
100.0	2.050325	2	0	0
101.0	0	3	0	3
102.0	0	1	0	1
103.0	0	1	0	2
104.0	0	1	0	0
105.0	0	4	0	1
106.0	0	1	0	3
107.0	0	0	0	2
108.0	0	1	0	2
109.0	0	1	0	0
110.0	0	0	0	2
111.0	0	3	0	1
112.0	0	2	0	1
113.0	0	2	0	2
115.0	0	2	0	0
116.0	0	1	0	1
117.0	0	2	0	2
119.0	0	2	0	2
120.0	0	0	0	2
121.0	0	0	0	2
122.0	0	2	0	1
123.0	0	1	0	3
124.0	0	4	0	2
125.0	0	0	0	2
126.0	0	1	0	0
127.0	0	1	0	0
128.0	0	1	0	0
129.0	0	1	0	0
130.0	0	0	0	1
131.0	0	2	0	1
132.0	0	3	0	0
135.0	0	1	0	0
136.0	0	1	0	0
138.0	0	2	0	0
140.0	0	0	0	1
141.0	0	1	0	1
142.0	0	1	0	0
144.0	0	1	0	0
145.0	0	0	0	1
146.0	0	0	0	2
147.0	0	0	0	1
148.0	0	2	0	1
149.0	0	1	0	3
151.0	0	0	0	1
152.0	0	2	0	1
153.0	0	2	0	0
155.0	0	0	0	1
156.0	0	0	0	2
158.0	0	0	0	1
159.0	0	2	0	2
161.0	0	0	0	1
162.0	0	1	0	0
163.0	0	1	0	0
165.0	0	1	0	1
166.0	0	1	0	0
169.0	0	1	0	0
172.0	0	0	0	1
173.0	0	1	0	0
174.0	0	1	0	0
175.0	0	0	0	1
177.0	0	0	0	1
180.0	0	1	0	0
181.0	0	0	0	1
183.0	0	1	0	0
184.0	0	2	0	0
186.0	0	1	0	0
193.0	0	1	0	0
201.0	0	1	0	0
203.0	0	0	0	1
208.0	0	0	0	2
209.0	0	1	0	0
210.0	0	0	0	1
216.0	0	0	0	1
218.0	0	1	0	0
223.0	0	1	0	0
226.0	0	0	0	1
227.0	0	0	0	1
228.0	0	1	0	0
230.0	0	1	0	0
241.0	0	0	0	1
242.0	0	1	0	0
247.0	0	1	0	1
249.0	0	0	0	1
250.0	0	1	0	0
251.0	0	1	0	0
252.0	0	0	0	1
253.0	0	1	0	0
258.0	0	0	0	1
263.0	0	0	0	1
271.0	0	0	0	1
284.0	0	1	0	0
286.0	0	1	0	0
299.0	0	1	0	0
309.0	0	1	0	0
313.0	0	0	0	1
325.0	0	0	0	1
328.0	0	1	0	0
331.0	0	0	0	1
341.0	0	1	0	0
345.0	0	1	0	0
371.0	0	0	0	1
419.0	0	1	0	0