## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-40-TP1.bam --OUTPUT POC-40-TP1.md.bam --METRICS_FILE POC-40-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 02:41:55 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	241	13536184	3027226	0	152	6894712	4236563	0.509355	12991995

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.26607	3514395	0	4804581
2.0	1.712725	1553843	1070918	1361879
3.0	1.8703	726544	445258	337566
4.0	1.92589	363575	227124	84321
5.0	1.945502	194582	125812	25355
6.0	1.952421	111663	71369	10028
7.0	1.954862	65522	40981	5022
8.0	1.955723	39891	23476	3042
9.0	1.956026	24433	13688	1972
10.0	1.956134	15365	8120	1458
11.0	1.956171	9945	4836	1032
12.0	1.956185	6368	2839	740
13.0	1.95619	4183	1636	609
14.0	1.956191	2675	975	531
15.0	1.956192	1823	656	417
16.0	1.956192	1386	384	326
17.0	1.956192	929	244	275
18.0	1.956192	726	150	227
19.0	1.956192	516	86	204
20.0	1.956192	385	58	170
21.0	1.956192	297	45	149
22.0	1.956192	260	30	120
23.0	1.956192	229	22	123
24.0	1.956192	180	26	108
25.0	1.956192	157	9	84
26.0	1.956192	120	10	73
27.0	1.956192	122	9	64
28.0	1.956192	94	7	62
29.0	1.956192	89	1	51
30.0	1.956192	78	2	50
31.0	1.956192	58	2	49
32.0	1.956192	64	4	36
33.0	1.956192	58	1	43
34.0	1.956192	59	0	44
35.0	1.956192	42	0	30
36.0	1.956192	30	2	33
37.0	1.956192	42	1	27
38.0	1.956192	35	1	27
39.0	1.956192	31	2	29
40.0	1.956192	40	1	18
41.0	1.956192	20	1	18
42.0	1.956192	23	2	20
43.0	1.956192	43	0	16
44.0	1.956192	18	2	16
45.0	1.956192	18	1	17
46.0	1.956192	23	1	19
47.0	1.956192	24	0	13
48.0	1.956192	12	0	14
49.0	1.956192	19	0	7
50.0	1.956192	12	1	7
51.0	1.956192	14	1	10
52.0	1.956192	12	0	6
53.0	1.956192	8	0	9
54.0	1.956192	8	0	5
55.0	1.956192	9	0	6
56.0	1.956192	11	1	8
57.0	1.956192	11	0	9
58.0	1.956192	9	0	5
59.0	1.956192	11	0	7
60.0	1.956192	7	0	13
61.0	1.956192	8	0	9
62.0	1.956192	13	1	8
63.0	1.956192	10	0	6
64.0	1.956192	5	0	7
65.0	1.956192	10	0	4
66.0	1.956192	5	1	7
67.0	1.956192	8	0	7
68.0	1.956192	9	1	7
69.0	1.956192	5	0	4
70.0	1.956192	10	0	4
71.0	1.956192	5	0	3
72.0	1.956192	8	0	5
73.0	1.956192	1	0	5
74.0	1.956192	5	0	4
75.0	1.956192	2	0	5
76.0	1.956192	4	0	2
77.0	1.956192	2	0	3
78.0	1.956192	5	0	3
79.0	1.956192	10	0	2
80.0	1.956192	1	0	3
81.0	1.956192	3	0	2
82.0	1.956192	4	0	1
83.0	1.956192	2	0	2
84.0	1.956192	4	0	4
85.0	1.956192	7	0	2
86.0	1.956192	2	1	4
87.0	1.956192	7	0	3
88.0	1.956192	1	0	2
89.0	1.956192	0	0	1
90.0	1.956192	1	0	4
91.0	1.956192	4	0	2
92.0	1.956192	2	0	2
93.0	1.956192	2	0	3
94.0	1.956192	3	0	4
95.0	1.956192	4	0	2
96.0	1.956192	1	0	3
97.0	1.956192	5	0	1
98.0	1.956192	2	0	1
99.0	1.956192	1	0	1
100.0	1.956192	0	0	0
101.0	0	1	0	3
102.0	0	3	0	0
103.0	0	2	0	0
104.0	0	2	0	2
105.0	0	0	0	2
106.0	0	3	0	0
107.0	0	3	0	3
108.0	0	0	0	2
109.0	0	1	0	2
110.0	0	0	0	1
111.0	0	2	0	2
112.0	0	0	0	1
113.0	0	3	0	3
114.0	0	4	0	1
115.0	0	1	0	2
116.0	0	2	0	1
118.0	0	0	0	1
119.0	0	1	0	2
120.0	0	2	0	1
121.0	0	0	0	1
122.0	0	2	0	1
123.0	0	2	0	1
124.0	0	1	0	2
125.0	0	1	0	2
126.0	0	0	0	1
127.0	0	2	0	2
128.0	0	5	0	4
129.0	0	1	1	0
130.0	0	4	0	2
131.0	0	2	0	2
132.0	0	1	0	0
133.0	0	2	0	1
134.0	0	1	0	3
135.0	0	1	0	1
136.0	0	3	0	1
137.0	0	0	0	5
138.0	0	1	0	0
140.0	0	1	0	1
141.0	0	0	0	1
142.0	0	2	0	2
144.0	0	2	0	0
145.0	0	2	0	1
146.0	0	0	0	1
147.0	0	1	0	1
148.0	0	2	0	1
149.0	0	0	0	1
150.0	0	2	0	0
151.0	0	1	0	0
154.0	0	0	0	1
155.0	0	3	0	0
157.0	0	1	0	1
159.0	0	0	0	1
160.0	0	1	0	0
161.0	0	1	0	1
163.0	0	1	0	0
164.0	0	1	0	2
166.0	0	1	0	1
167.0	0	1	0	0
168.0	0	1	0	0
169.0	0	1	0	0
172.0	0	0	0	2
173.0	0	0	0	1
174.0	0	0	0	2
175.0	0	0	0	1
177.0	0	2	0	0
179.0	0	2	0	0
181.0	0	1	0	0
182.0	0	0	0	1
183.0	0	0	0	1
184.0	0	1	0	0
185.0	0	0	0	1
188.0	0	0	0	1
189.0	0	2	0	1
190.0	0	1	0	0
191.0	0	1	0	1
192.0	0	0	0	1
193.0	0	1	0	1
196.0	0	1	0	0
197.0	0	1	0	1
201.0	0	1	0	0
203.0	0	1	0	2
205.0	0	0	0	1
207.0	0	0	0	2
208.0	0	1	0	0
210.0	0	1	0	0
211.0	0	0	0	1
214.0	0	1	0	1
218.0	0	0	0	1
219.0	0	0	0	1
221.0	0	1	0	0
222.0	0	0	0	1
223.0	0	1	0	0
225.0	0	1	0	1
227.0	0	2	0	1
228.0	0	2	0	0
229.0	0	0	0	1
233.0	0	1	0	0
234.0	0	0	0	1
236.0	0	2	0	0
237.0	0	1	0	1
241.0	0	0	0	1
242.0	0	1	0	0
243.0	0	0	0	1
245.0	0	2	0	0
250.0	0	1	0	0
254.0	0	1	0	0
256.0	0	1	0	1
257.0	0	1	0	1
258.0	0	1	0	0
262.0	0	0	0	1
266.0	0	1	0	0
274.0	0	0	0	1
281.0	0	0	0	1
282.0	0	1	0	0
288.0	0	0	0	1
292.0	0	1	0	0
294.0	0	1	0	1
295.0	0	1	0	0
296.0	0	0	0	1
298.0	0	1	0	1
299.0	0	0	0	2
301.0	0	1	0	0
305.0	0	1	0	0
307.0	0	1	0	0
310.0	0	1	0	0
320.0	0	0	0	1
332.0	0	0	0	1
340.0	0	0	0	1
341.0	0	1	0	0
351.0	0	0	0	1
356.0	0	1	0	0
359.0	0	1	0	0
364.0	0	0	0	1
366.0	0	0	0	1
382.0	0	0	0	1
385.0	0	1	0	0
393.0	0	1	0	0
398.0	0	0	0	1
403.0	0	1	0	0
405.0	0	0	0	1
419.0	0	1	0	0
421.0	0	1	0	0
429.0	0	1	0	0
455.0	0	1	0	0
460.0	0	0	0	1
474.0	0	1	0	0
505.0	0	0	0	1
566.0	0	0	0	1
572.0	0	1	0	0
651.0	0	1	0	0
765.0	0	0	0	1
893.0	0	1	0	0