## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-42-TP2.bam --OUTPUT POC-42-TP2.md.bam --METRICS_FILE POC-42-TP2.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	361	16689138	2971743	0	267	9235661	4929958	0.553396	11836192

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.200311	3514158	0	4748668
2.0	1.493356	1822456	1225276	1820056
3.0	1.564901	938205	515868	586270
4.0	1.582368	493594	265014	179151
5.0	1.586632	270487	145841	58783
6.0	1.587673	155563	82243	23331
7.0	1.587927	92262	48098	11125
8.0	1.587989	56421	27960	6419
9.0	1.588005	35857	16406	4307
10.0	1.588008	22942	9978	2980
11.0	1.588009	15160	5727	2096
12.0	1.588009	9921	3475	1630
13.0	1.588009	6720	2104	1241
14.0	1.588009	4438	1260	1021
15.0	1.588009	3143	800	784
16.0	1.588009	2260	495	647
17.0	1.588009	1652	334	506
18.0	1.588009	1265	209	456
19.0	1.588009	950	142	401
20.0	1.588009	711	102	312
21.0	1.588009	582	68	296
22.0	1.588009	510	41	257
23.0	1.588009	414	38	249
24.0	1.588009	373	34	199
25.0	1.588009	265	23	178
26.0	1.588009	272	20	142
27.0	1.588009	215	9	134
28.0	1.588009	193	10	128
29.0	1.588009	176	10	116
30.0	1.588009	157	2	96
31.0	1.588009	153	5	111
32.0	1.588009	141	7	78
33.0	1.588009	125	5	78
34.0	1.588009	103	8	71
35.0	1.588009	104	2	76
36.0	1.588009	70	7	53
37.0	1.588009	94	7	59
38.0	1.588009	80	4	55
39.0	1.588009	67	2	41
40.0	1.588009	77	3	46
41.0	1.588009	61	2	39
42.0	1.588009	66	2	46
43.0	1.588009	47	1	34
44.0	1.588009	46	0	30
45.0	1.588009	33	2	16
46.0	1.588009	33	1	24
47.0	1.588009	28	2	27
48.0	1.588009	38	0	22
49.0	1.588009	46	0	29
50.0	1.588009	22	2	24
51.0	1.588009	27	1	17
52.0	1.588009	22	0	23
53.0	1.588009	30	0	18
54.0	1.588009	28	2	17
55.0	1.588009	21	0	18
56.0	1.588009	23	0	17
57.0	1.588009	20	0	7
58.0	1.588009	20	0	6
59.0	1.588009	20	0	13
60.0	1.588009	13	0	17
61.0	1.588009	19	1	12
62.0	1.588009	14	0	8
63.0	1.588009	17	1	11
64.0	1.588009	13	0	10
65.0	1.588009	12	1	7
66.0	1.588009	14	0	12
67.0	1.588009	14	0	8
68.0	1.588009	12	0	10
69.0	1.588009	9	1	10
70.0	1.588009	6	0	4
71.0	1.588009	11	3	4
72.0	1.588009	5	0	3
73.0	1.588009	10	0	7
74.0	1.588009	6	0	7
75.0	1.588009	5	0	5
76.0	1.588009	4	0	6
77.0	1.588009	3	0	3
78.0	1.588009	12	0	5
79.0	1.588009	8	0	5
80.0	1.588009	6	0	7
81.0	1.588009	5	0	3
82.0	1.588009	4	0	7
83.0	1.588009	3	0	4
84.0	1.588009	6	0	4
85.0	1.588009	8	0	13
86.0	1.588009	8	0	3
87.0	1.588009	3	0	1
88.0	1.588009	8	0	5
89.0	1.588009	5	0	2
90.0	1.588009	2	0	3
91.0	1.588009	4	0	6
92.0	1.588009	4	0	4
93.0	1.588009	4	0	2
94.0	1.588009	8	0	7
95.0	1.588009	5	0	3
96.0	1.588009	2	0	2
97.0	1.588009	7	0	2
98.0	1.588009	1	0	6
99.0	1.588009	8	0	1
100.0	1.588009	3	0	4
101.0	0	2	0	2
102.0	0	3	0	1
103.0	0	3	0	4
104.0	0	2	0	3
105.0	0	3	0	1
106.0	0	3	0	0
107.0	0	5	0	6
108.0	0	7	0	2
109.0	0	6	0	4
110.0	0	4	0	1
111.0	0	1	0	3
112.0	0	1	0	3
113.0	0	5	0	3
114.0	0	2	0	3
115.0	0	3	1	3
116.0	0	4	0	1
117.0	0	0	0	1
118.0	0	4	0	1
119.0	0	1	0	1
120.0	0	2	0	1
121.0	0	1	0	1
122.0	0	2	0	3
123.0	0	2	0	2
124.0	0	0	0	3
125.0	0	2	0	1
126.0	0	2	0	1
127.0	0	1	0	4
128.0	0	2	0	1
129.0	0	1	0	0
130.0	0	3	0	0
131.0	0	4	0	2
132.0	0	3	0	0
133.0	0	1	0	4
134.0	0	2	0	0
135.0	0	1	0	3
136.0	0	5	0	1
137.0	0	1	0	0
138.0	0	0	1	1
139.0	0	1	0	2
140.0	0	1	0	1
141.0	0	1	0	0
142.0	0	1	0	0
143.0	0	1	0	1
144.0	0	1	0	0
145.0	0	1	0	3
146.0	0	2	0	0
147.0	0	1	0	0
148.0	0	2	0	0
149.0	0	1	0	0
150.0	0	1	0	1
151.0	0	0	0	1
152.0	0	1	0	1
153.0	0	2	0	0
155.0	0	1	0	1
156.0	0	0	0	1
157.0	0	2	0	0
158.0	0	1	0	2
159.0	0	0	0	1
160.0	0	3	0	1
161.0	0	3	0	1
162.0	0	0	0	1
164.0	0	1	0	1
165.0	0	1	0	1
166.0	0	0	0	1
167.0	0	1	0	0
169.0	0	1	0	0
170.0	0	0	0	1
172.0	0	2	0	0
173.0	0	0	0	1
176.0	0	0	0	1
177.0	0	0	0	1
178.0	0	0	0	1
179.0	0	2	0	2
180.0	0	2	0	0
181.0	0	0	0	1
182.0	0	1	0	0
183.0	0	0	0	1
184.0	0	0	0	1
186.0	0	0	0	1
190.0	0	2	0	0
191.0	0	1	0	2
192.0	0	1	0	1
194.0	0	0	0	1
196.0	0	0	0	1
197.0	0	0	0	1
198.0	0	1	0	0
200.0	0	1	0	0
201.0	0	1	0	1
202.0	0	0	0	3
203.0	0	1	0	0
204.0	0	2	0	1
205.0	0	1	0	0
208.0	0	2	0	0
209.0	0	0	0	2
210.0	0	1	0	0
211.0	0	0	0	1
213.0	0	1	0	0
214.0	0	2	0	0
215.0	0	0	0	1
217.0	0	1	0	0
218.0	0	0	0	1
222.0	0	1	0	0
224.0	0	1	0	0
231.0	0	0	0	1
233.0	0	2	0	0
235.0	0	1	0	0
236.0	0	1	0	0
237.0	0	0	0	1
239.0	0	0	0	1
240.0	0	1	0	0
242.0	0	1	0	1
244.0	0	0	0	1
245.0	0	0	0	1
246.0	0	0	0	1
247.0	0	0	0	2
249.0	0	1	0	0
252.0	0	0	0	1
255.0	0	1	0	0
256.0	0	2	0	0
257.0	0	0	0	1
261.0	0	1	0	0
262.0	0	0	0	2
263.0	0	0	0	1
266.0	0	1	0	0
270.0	0	0	0	1
272.0	0	2	0	0
273.0	0	1	0	0
274.0	0	1	0	0
277.0	0	1	0	0
279.0	0	2	0	0
280.0	0	1	0	0
288.0	0	1	0	0
299.0	0	0	0	1
303.0	0	0	0	1
311.0	0	0	0	2
313.0	0	0	0	1
314.0	0	1	0	0
317.0	0	0	0	1
318.0	0	1	0	0
320.0	0	0	0	1
330.0	0	0	0	1
338.0	0	1	0	0
339.0	0	1	0	2
342.0	0	0	0	1
347.0	0	1	0	0
355.0	0	1	0	0
356.0	0	1	0	0
360.0	0	1	0	0
361.0	0	1	0	1
362.0	0	1	0	0
372.0	0	1	0	0
386.0	0	1	0	0
389.0	0	0	0	1
390.0	0	0	0	1
398.0	0	0	0	1
400.0	0	0	0	1
411.0	0	1	0	0
420.0	0	1	0	0
427.0	0	1	0	0
433.0	0	0	0	1
443.0	0	0	0	1
451.0	0	1	0	0
455.0	0	0	0	1
462.0	0	1	0	0
465.0	0	0	0	1
471.0	0	0	0	1
475.0	0	1	0	0
479.0	0	2	0	0
523.0	0	0	0	1
533.0	0	1	0	0
535.0	0	0	0	1
539.0	0	1	0	0
584.0	0	1	0	0
613.0	0	0	0	1
658.0	0	0	0	1
675.0	0	1	0	0
772.0	0	1	0	0
1040.0	0	0	0	1
1177.0	0	1	0	0