## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-265-TP3.bam --OUTPUT ACR-265-TP3.md.bam --METRICS_FILE ACR-265-TP3.md.MarkDuplicates.metrics.txt --ASSUME_SORTED true --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE Apulcra-genome.fa --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 18:15:11 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	318	15662183	4374410	0	204	10230484	3092660	0.653196	6280532

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.060768	1697525	0	2085637
2.0	1.148385	1317048	849555	1526680
3.0	1.155622	924917	320543	918869
4.0	1.15622	589450	155330	471202
5.0	1.156269	355354	85111	219321
6.0	1.156274	209793	48410	100154
7.0	1.156274	124044	28712	46625
8.0	1.156274	74521	16928	22729
9.0	1.156274	46003	10250	12352
10.0	1.156274	28776	6345	7194
11.0	1.156274	18573	3799	4389
12.0	1.156274	12132	2390	3034
13.0	1.156274	8196	1454	2219
14.0	1.156274	5834	1015	1692
15.0	1.156274	4079	565	1363
16.0	1.156274	2897	341	981
17.0	1.156274	2108	234	820
18.0	1.156274	1625	149	720
19.0	1.156274	1238	95	618
20.0	1.156274	1012	80	509
21.0	1.156274	761	57	396
22.0	1.156274	603	33	379
23.0	1.156274	563	30	355
24.0	1.156274	419	26	287
25.0	1.156274	342	20	249
26.0	1.156274	330	10	224
27.0	1.156274	281	9	203
28.0	1.156274	253	4	182
29.0	1.156274	223	6	150
30.0	1.156274	202	6	154
31.0	1.156274	172	6	128
32.0	1.156274	157	2	103
33.0	1.156274	141	2	111
34.0	1.156274	133	4	110
35.0	1.156274	118	4	102
36.0	1.156274	97	1	76
37.0	1.156274	109	4	83
38.0	1.156274	96	1	70
39.0	1.156274	105	3	71
40.0	1.156274	66	1	52
41.0	1.156274	65	1	52
42.0	1.156274	56	2	54
43.0	1.156274	61	1	45
44.0	1.156274	62	0	35
45.0	1.156274	54	3	50
46.0	1.156274	60	1	35
47.0	1.156274	48	0	41
48.0	1.156274	49	0	34
49.0	1.156274	41	1	30
50.0	1.156274	31	0	25
51.0	1.156274	41	1	26
52.0	1.156274	53	0	35
53.0	1.156274	29	0	29
54.0	1.156274	36	0	32
55.0	1.156274	27	0	22
56.0	1.156274	24	1	22
57.0	1.156274	21	1	21
58.0	1.156274	34	0	33
59.0	1.156274	29	0	13
60.0	1.156274	13	1	12
61.0	1.156274	33	0	22
62.0	1.156274	20	0	15
63.0	1.156274	20	0	10
64.0	1.156274	14	0	15
65.0	1.156274	18	0	11
66.0	1.156274	9	1	14
67.0	1.156274	13	0	14
68.0	1.156274	11	0	8
69.0	1.156274	11	0	10
70.0	1.156274	12	0	9
71.0	1.156274	12	0	9
72.0	1.156274	8	0	12
73.0	1.156274	8	0	5
74.0	1.156274	12	0	5
75.0	1.156274	11	0	7
76.0	1.156274	10	0	13
77.0	1.156274	14	0	3
78.0	1.156274	10	0	10
79.0	1.156274	9	0	6
80.0	1.156274	6	0	5
81.0	1.156274	6	0	5
82.0	1.156274	4	0	8
83.0	1.156274	10	0	7
84.0	1.156274	4	0	4
85.0	1.156274	6	0	8
86.0	1.156274	4	1	5
87.0	1.156274	9	0	6
88.0	1.156274	5	0	2
89.0	1.156274	4	0	1
90.0	1.156274	8	0	6
91.0	1.156274	7	0	4
92.0	1.156274	4	0	8
93.0	1.156274	9	0	7
94.0	1.156274	6	0	3
95.0	1.156274	2	0	4
96.0	1.156274	3	0	3
97.0	1.156274	6	0	4
98.0	1.156274	4	0	1
99.0	1.156274	5	0	3
100.0	1.156274	3	0	4
101.0	0	3	0	4
102.0	0	4	0	4
103.0	0	5	0	3
104.0	0	4	0	3
105.0	0	5	0	1
106.0	0	3	0	6
107.0	0	5	0	0
108.0	0	2	0	2
109.0	0	3	0	0
110.0	0	4	0	2
111.0	0	4	0	5
112.0	0	1	0	4
113.0	0	5	0	1
114.0	0	2	0	2
115.0	0	1	0	0
116.0	0	1	0	1
117.0	0	3	0	4
118.0	0	3	0	1
119.0	0	4	0	1
120.0	0	1	0	2
121.0	0	1	0	3
122.0	0	5	0	2
123.0	0	2	0	1
125.0	0	2	0	1
126.0	0	2	0	1
127.0	0	3	0	2
128.0	0	2	0	2
129.0	0	2	0	1
130.0	0	3	0	2
131.0	0	1	0	2
132.0	0	2	0	6
133.0	0	3	0	5
134.0	0	1	0	1
135.0	0	1	0	1
136.0	0	1	0	1
137.0	0	0	0	3
138.0	0	6	0	2
139.0	0	2	0	2
140.0	0	2	0	1
141.0	0	0	0	2
142.0	0	2	0	0
143.0	0	0	0	1
144.0	0	2	0	1
145.0	0	2	0	2
146.0	0	2	0	2
147.0	0	3	0	1
149.0	0	3	0	0
150.0	0	2	0	1
151.0	0	1	0	3
152.0	0	1	0	1
153.0	0	1	0	0
154.0	0	1	0	0
156.0	0	2	0	0
157.0	0	0	0	1
159.0	0	3	0	0
160.0	0	1	0	1
161.0	0	1	0	2
163.0	0	0	0	3
164.0	0	0	0	2
165.0	0	2	0	0
166.0	0	1	0	2
168.0	0	0	0	1
169.0	0	2	0	1
170.0	0	1	0	0
171.0	0	1	0	1
172.0	0	1	0	1
173.0	0	1	0	1
174.0	0	1	0	0
175.0	0	1	0	0
176.0	0	1	0	1
177.0	0	2	0	2
179.0	0	0	0	1
181.0	0	1	0	0
182.0	0	1	0	0
183.0	0	1	0	0
185.0	0	1	0	0
186.0	0	0	0	2
187.0	0	1	0	0
189.0	0	1	0	1
190.0	0	2	0	1
191.0	0	1	0	1
196.0	0	0	0	1
197.0	0	0	0	1
198.0	0	1	0	0
199.0	0	1	0	0
201.0	0	0	0	1
202.0	0	1	0	2
203.0	0	2	0	0
204.0	0	1	0	0
206.0	0	1	0	0
209.0	0	0	0	2
212.0	0	0	0	1
213.0	0	1	0	0
214.0	0	0	0	1
215.0	0	1	0	1
217.0	0	2	0	0
221.0	0	1	0	1
222.0	0	1	0	0
224.0	0	1	0	1
230.0	0	1	0	0
233.0	0	0	0	1
234.0	0	1	0	0
237.0	0	0	0	1
239.0	0	0	0	1
243.0	0	0	0	2
244.0	0	1	0	0
245.0	0	1	0	0
247.0	0	2	0	0
255.0	0	0	0	1
256.0	0	0	0	1
258.0	0	1	0	0
262.0	0	1	0	0
268.0	0	0	0	1
272.0	0	1	0	0
273.0	0	1	0	0
274.0	0	0	0	1
281.0	0	1	0	1
283.0	0	0	0	1
284.0	0	0	0	1
288.0	0	1	0	1
298.0	0	0	0	1
299.0	0	0	0	1
303.0	0	1	0	0
306.0	0	1	0	0
307.0	0	1	0	1
318.0	0	1	0	0
319.0	0	2	0	0
333.0	0	0	0	1
344.0	0	0	0	1
350.0	0	1	0	0
362.0	0	1	0	0
368.0	0	0	0	1
369.0	0	1	0	0
386.0	0	0	0	1
433.0	0	1	0	0
445.0	0	1	0	0
448.0	0	0	0	1
458.0	0	0	0	1
471.0	0	1	0	0
483.0	0	0	0	1
488.0	0	1	0	0
531.0	0	1	0	0
559.0	0	0	0	1
585.0	0	1	0	0
651.0	0	0	0	1
695.0	0	1	0	0
700.0	0	0	0	1
721.0	0	1	0	0
735.0	0	0	0	1
785.0	0	1	0	0
799.0	0	0	0	1
818.0	0	1	0	0