## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-40-TP4.bam --OUTPUT POC-40-TP4.md.bam --METRICS_FILE POC-40-TP4.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 02:39:54 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	297	14724046	2883998	0	175	7347680	4338997	0.499027	14261969

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.244861	3949233	0	5312764
2.0	1.68822	1740816	1176651	1519587
3.0	1.846123	799475	474043	381612
4.0	1.90236	391547	234895	97626
5.0	1.922389	206237	125681	30105
6.0	1.929522	114317	68929	12456
7.0	1.932063	65993	38689	6467
8.0	1.932968	39098	21591	3772
9.0	1.93329	23812	12282	2554
10.0	1.933405	14884	7122	1822
11.0	1.933446	9609	4156	1384
12.0	1.93346	6101	2304	1022
13.0	1.933465	4019	1431	749
14.0	1.933467	2593	809	591
15.0	1.933468	1781	468	510
16.0	1.933468	1308	288	395
17.0	1.933468	964	186	360
18.0	1.933468	663	120	253
19.0	1.933468	537	78	236
20.0	1.933468	396	55	204
21.0	1.933468	351	37	172
22.0	1.933468	274	16	144
23.0	1.933468	232	17	133
24.0	1.933468	196	13	102
25.0	1.933468	187	9	96
26.0	1.933468	150	7	91
27.0	1.933468	121	8	70
28.0	1.933468	111	3	85
29.0	1.933468	85	7	70
30.0	1.933468	80	3	66
31.0	1.933468	80	5	53
32.0	1.933468	74	4	56
33.0	1.933468	77	3	45
34.0	1.933468	53	1	36
35.0	1.933468	60	0	42
36.0	1.933468	45	1	35
37.0	1.933468	45	1	31
38.0	1.933468	44	1	31
39.0	1.933468	42	2	21
40.0	1.933468	29	1	24
41.0	1.933468	36	0	21
42.0	1.933468	31	0	14
43.0	1.933468	27	0	25
44.0	1.933468	25	0	24
45.0	1.933468	19	0	17
46.0	1.933468	28	0	16
47.0	1.933468	16	2	11
48.0	1.933468	26	0	12
49.0	1.933468	15	0	13
50.0	1.933468	12	0	11
51.0	1.933468	13	0	17
52.0	1.933468	15	0	8
53.0	1.933468	9	0	7
54.0	1.933468	18	0	12
55.0	1.933468	15	1	10
56.0	1.933468	9	0	15
57.0	1.933468	8	0	6
58.0	1.933468	10	0	5
59.0	1.933468	8	0	11
60.0	1.933468	13	0	7
61.0	1.933468	7	0	10
62.0	1.933468	6	0	3
63.0	1.933468	11	0	7
64.0	1.933468	9	0	5
65.0	1.933468	6	0	4
66.0	1.933468	9	0	5
67.0	1.933468	13	0	10
68.0	1.933468	8	1	5
69.0	1.933468	6	0	4
70.0	1.933468	4	0	5
71.0	1.933468	8	0	4
72.0	1.933468	8	0	1
73.0	1.933468	1	0	2
74.0	1.933468	1	0	2
75.0	1.933468	5	0	4
76.0	1.933468	3	0	5
77.0	1.933468	4	0	3
78.0	1.933468	3	0	5
79.0	1.933468	5	0	3
80.0	1.933468	5	0	2
81.0	1.933468	6	0	6
82.0	1.933468	2	0	2
83.0	1.933468	5	0	3
84.0	1.933468	3	0	2
85.0	1.933468	4	0	5
86.0	1.933468	8	0	6
87.0	1.933468	2	0	3
88.0	1.933468	5	0	4
89.0	1.933468	6	0	4
90.0	1.933468	0	0	0
91.0	1.933468	3	0	1
92.0	1.933468	3	0	1
93.0	1.933468	3	0	1
94.0	1.933468	1	0	7
95.0	1.933468	2	0	2
96.0	1.933468	5	0	0
97.0	1.933468	2	0	1
98.0	1.933468	4	0	0
99.0	1.933468	3	0	2
100.0	1.933468	3	0	3
101.0	0	2	1	2
102.0	0	1	0	3
103.0	0	0	0	1
104.0	0	2	0	0
105.0	0	2	0	1
106.0	0	1	0	1
107.0	0	2	0	3
108.0	0	0	0	1
109.0	0	1	0	4
110.0	0	1	0	1
111.0	0	0	0	2
112.0	0	3	0	2
113.0	0	1	0	1
114.0	0	1	0	2
115.0	0	0	0	2
116.0	0	2	0	1
118.0	0	3	0	1
119.0	0	0	0	3
120.0	0	1	0	4
121.0	0	2	0	1
122.0	0	1	0	1
123.0	0	5	0	0
124.0	0	1	0	0
125.0	0	2	0	1
126.0	0	0	0	2
127.0	0	4	0	1
128.0	0	2	0	3
129.0	0	1	0	0
130.0	0	2	0	0
132.0	0	4	0	0
133.0	0	1	0	0
134.0	0	1	0	2
135.0	0	2	0	0
136.0	0	1	0	0
139.0	0	0	0	1
140.0	0	0	0	1
141.0	0	1	0	0
142.0	0	2	0	0
143.0	0	0	0	1
146.0	0	1	0	0
148.0	0	0	0	1
149.0	0	0	0	1
151.0	0	1	0	0
152.0	0	1	0	0
153.0	0	1	0	0
154.0	0	1	0	2
155.0	0	1	0	0
157.0	0	2	0	1
162.0	0	0	0	2
163.0	0	0	0	1
165.0	0	0	0	1
171.0	0	1	0	0
172.0	0	1	0	2
173.0	0	0	0	2
175.0	0	3	0	0
177.0	0	0	0	1
178.0	0	1	0	1
179.0	0	1	0	0
181.0	0	1	0	0
183.0	0	0	0	1
185.0	0	0	0	1
187.0	0	1	0	1
188.0	0	1	0	0
189.0	0	0	0	1
191.0	0	0	0	1
192.0	0	1	0	1
195.0	0	1	0	0
196.0	0	1	0	0
200.0	0	1	0	1
202.0	0	0	0	1
203.0	0	1	0	0
205.0	0	1	0	1
207.0	0	0	0	1
208.0	0	0	0	1
209.0	0	1	0	0
210.0	0	1	0	0
211.0	0	1	0	0
216.0	0	1	0	0
218.0	0	0	0	1
219.0	0	1	0	0
222.0	0	1	0	0
223.0	0	1	0	1
231.0	0	1	0	0
232.0	0	1	0	0
234.0	0	0	0	1
235.0	0	0	0	1
242.0	0	1	0	0
261.0	0	1	0	0
262.0	0	1	0	0
267.0	0	0	0	1
275.0	0	0	0	1
278.0	0	0	0	1
280.0	0	0	0	1
297.0	0	1	0	0
308.0	0	1	0	0
313.0	0	1	0	0
314.0	0	1	0	0
319.0	0	0	0	1
335.0	0	1	0	0
343.0	0	0	0	1
379.0	0	1	0	0
408.0	0	0	0	1
410.0	0	0	0	1
412.0	0	0	0	1
422.0	0	1	0	0
426.0	0	1	0	0
429.0	0	0	0	1
462.0	0	1	0	0
496.0	0	1	0	0
615.0	0	0	0	1
715.0	0	1	0	0