## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT POC-219-TP4.bam --OUTPUT POC-219-TP4.md.bam --METRICS_FILE POC-219-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 03:01:25 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	233	11165651	2448923	0	162	6666474	2852424	0.597053	6000774

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.126267	1812129	0	2361913
2.0	1.301473	1134675	716211	1242941
3.0	1.328728	658487	288563	535515
4.0	1.332968	368991	146053	208707
5.0	1.333628	207270	81583	79802
6.0	1.33373	119135	47720	32480
7.0	1.333746	70336	28423	14366
8.0	1.333749	43427	17163	7223
9.0	1.333749	27088	10394	4110
10.0	1.333749	17863	6468	2687
11.0	1.333749	11607	4109	1892
12.0	1.333749	7885	2393	1310
13.0	1.333749	5391	1552	940
14.0	1.333749	3600	875	756
15.0	1.333749	2586	544	584
16.0	1.333749	1765	374	462
17.0	1.333749	1332	218	369
18.0	1.333749	950	159	321
19.0	1.333749	660	110	252
20.0	1.333749	539	60	258
21.0	1.333749	444	45	191
22.0	1.333749	355	30	202
23.0	1.333749	281	14	148
24.0	1.333749	227	16	135
25.0	1.333749	206	7	105
26.0	1.333749	161	7	97
27.0	1.333749	125	3	89
28.0	1.333749	105	1	76
29.0	1.333749	89	2	60
30.0	1.333749	98	3	69
31.0	1.333749	74	3	65
32.0	1.333749	82	0	60
33.0	1.333749	76	0	53
34.0	1.333749	66	2	42
35.0	1.333749	56	1	42
36.0	1.333749	54	1	36
37.0	1.333749	41	3	32
38.0	1.333749	41	0	29
39.0	1.333749	35	2	29
40.0	1.333749	32	1	30
41.0	1.333749	49	2	15
42.0	1.333749	30	1	29
43.0	1.333749	28	0	28
44.0	1.333749	15	0	22
45.0	1.333749	28	2	30
46.0	1.333749	26	0	20
47.0	1.333749	25	0	23
48.0	1.333749	31	0	18
49.0	1.333749	19	0	12
50.0	1.333749	16	0	13
51.0	1.333749	22	2	13
52.0	1.333749	16	0	10
53.0	1.333749	13	0	10
54.0	1.333749	7	1	8
55.0	1.333749	8	0	9
56.0	1.333749	12	0	9
57.0	1.333749	13	0	15
58.0	1.333749	8	0	7
59.0	1.333749	10	0	9
60.0	1.333749	12	0	15
61.0	1.333749	8	0	6
62.0	1.333749	7	0	6
63.0	1.333749	10	1	9
64.0	1.333749	14	0	12
65.0	1.333749	7	0	9
66.0	1.333749	12	0	11
67.0	1.333749	5	0	6
68.0	1.333749	7	0	9
69.0	1.333749	10	0	8
70.0	1.333749	8	1	6
71.0	1.333749	6	0	5
72.0	1.333749	2	0	2
73.0	1.333749	7	0	2
74.0	1.333749	5	0	11
75.0	1.333749	4	0	8
76.0	1.333749	8	0	2
77.0	1.333749	10	0	7
78.0	1.333749	6	0	8
79.0	1.333749	5	0	6
80.0	1.333749	7	0	1
81.0	1.333749	5	0	7
82.0	1.333749	7	0	4
83.0	1.333749	5	0	5
84.0	1.333749	4	0	3
85.0	1.333749	7	0	6
86.0	1.333749	6	0	2
87.0	1.333749	3	0	8
88.0	1.333749	5	0	6
89.0	1.333749	6	0	3
90.0	1.333749	7	0	4
91.0	1.333749	1	0	4
92.0	1.333749	8	0	3
93.0	1.333749	1	0	1
94.0	1.333749	4	0	3
95.0	1.333749	3	0	5
96.0	1.333749	5	0	4
97.0	1.333749	1	0	1
98.0	1.333749	1	0	0
99.0	1.333749	4	0	3
100.0	1.333749	1	0	5
101.0	0	1	0	2
102.0	0	4	0	1
103.0	0	3	0	1
104.0	0	2	1	4
105.0	0	1	0	1
106.0	0	3	0	2
107.0	0	3	0	1
108.0	0	2	0	1
109.0	0	2	0	2
110.0	0	2	0	2
111.0	0	2	0	1
112.0	0	0	0	3
113.0	0	4	0	0
114.0	0	0	0	3
115.0	0	2	0	3
116.0	0	4	0	2
117.0	0	1	0	1
118.0	0	1	0	2
119.0	0	1	0	3
120.0	0	3	0	0
121.0	0	1	0	2
122.0	0	1	0	1
123.0	0	4	0	2
124.0	0	2	0	0
125.0	0	2	0	3
126.0	0	3	0	1
127.0	0	0	0	2
128.0	0	0	0	1
129.0	0	1	0	0
130.0	0	2	0	1
131.0	0	1	0	1
132.0	0	0	0	1
133.0	0	2	0	1
134.0	0	0	0	4
135.0	0	0	0	1
136.0	0	1	0	0
137.0	0	3	0	0
138.0	0	1	0	1
139.0	0	3	0	2
140.0	0	1	0	2
141.0	0	2	0	2
142.0	0	4	0	1
143.0	0	0	0	1
144.0	0	1	0	0
146.0	0	0	0	2
147.0	0	2	0	2
148.0	0	0	0	1
149.0	0	1	0	3
150.0	0	1	0	0
152.0	0	3	0	3
153.0	0	1	0	1
154.0	0	1	0	1
155.0	0	2	0	1
156.0	0	3	0	0
157.0	0	1	0	0
158.0	0	1	0	2
160.0	0	2	0	0
161.0	0	1	0	2
163.0	0	1	0	0
164.0	0	0	1	0
165.0	0	0	0	2
168.0	0	2	0	1
169.0	0	1	0	0
170.0	0	1	0	0
171.0	0	3	0	0
172.0	0	1	0	2
173.0	0	1	0	1
174.0	0	1	0	2
175.0	0	1	0	1
176.0	0	0	0	1
177.0	0	1	0	1
178.0	0	1	0	1
180.0	0	2	0	0
181.0	0	0	0	1
184.0	0	0	0	1
185.0	0	0	0	1
186.0	0	2	0	1
187.0	0	1	0	1
190.0	0	2	0	2
191.0	0	1	0	0
192.0	0	0	0	1
193.0	0	0	0	1
194.0	0	0	0	1
195.0	0	2	0	0
196.0	0	1	0	0
197.0	0	2	0	1
198.0	0	1	0	0
201.0	0	0	0	2
205.0	0	1	0	0
206.0	0	0	0	1
209.0	0	0	0	1
210.0	0	1	0	0
211.0	0	0	0	2
215.0	0	1	0	0
216.0	0	1	0	0
217.0	0	0	0	1
218.0	0	1	0	0
219.0	0	1	0	1
220.0	0	1	0	2
221.0	0	0	0	2
223.0	0	0	0	3
225.0	0	1	0	0
227.0	0	2	0	0
228.0	0	1	0	1
233.0	0	2	0	0
234.0	0	1	0	0
236.0	0	1	0	0
237.0	0	0	0	1
239.0	0	0	0	1
241.0	0	1	0	0
245.0	0	0	0	1
246.0	0	1	0	0
247.0	0	1	0	1
248.0	0	0	0	1
250.0	0	0	0	1
251.0	0	1	0	0
253.0	0	0	0	1
254.0	0	0	0	1
257.0	0	1	0	3
258.0	0	1	0	0
259.0	0	0	0	2
262.0	0	1	0	0
263.0	0	0	0	1
264.0	0	0	0	1
266.0	0	1	0	0
267.0	0	0	0	1
270.0	0	2	0	0
272.0	0	1	0	1
273.0	0	0	0	1
274.0	0	1	0	0
277.0	0	1	0	0
278.0	0	2	0	2
281.0	0	1	0	2
282.0	0	0	0	1
283.0	0	1	0	0
286.0	0	1	0	0
289.0	0	3	0	0
293.0	0	0	0	1
296.0	0	1	0	0
297.0	0	1	0	0
298.0	0	1	0	0
299.0	0	1	0	0
300.0	0	1	0	0
301.0	0	1	0	0
311.0	0	0	0	2
316.0	0	1	0	0
320.0	0	1	0	1
322.0	0	0	0	1
323.0	0	1	0	0
326.0	0	0	0	2
328.0	0	1	0	0
338.0	0	1	0	1
340.0	0	0	0	1
344.0	0	0	0	1
346.0	0	0	0	1
347.0	0	0	0	1
350.0	0	1	0	0
352.0	0	1	0	0
357.0	0	0	0	1
359.0	0	0	0	1
361.0	0	1	0	0
365.0	0	1	0	0
370.0	0	1	0	0
373.0	0	0	0	1
376.0	0	0	0	1
381.0	0	2	0	1
386.0	0	1	0	0
388.0	0	1	0	0
391.0	0	1	0	0
407.0	0	1	0	0
412.0	0	1	0	0
413.0	0	0	0	1
422.0	0	1	0	1
428.0	0	0	0	1
432.0	0	1	0	0
433.0	0	1	0	0
443.0	0	0	0	1
450.0	0	0	0	1
460.0	0	1	0	0
466.0	0	0	0	1
484.0	0	1	0	0
487.0	0	1	0	0
511.0	0	0	0	1
573.0	0	1	0	0
619.0	0	0	0	1
631.0	0	0	0	1
639.0	0	1	0	0
669.0	0	0	0	1
688.0	0	1	0	0
772.0	0	1	0	0
955.0	0	0	0	1
1118.0	0	1	0	0