## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-139-TP1.bam --OUTPUT ACR-139-TP1.md.bam --METRICS_FILE ACR-139-TP1.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 18:14:16 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	172	13989069	3690467	0	95	8372980	4070321	0.598537	7808263

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.158572	2264126	0	3028162
2.0	1.351703	1402943	923741	1567902
3.0	1.383898	814069	400155	649726
4.0	1.389265	458010	212726	232861
5.0	1.390159	259939	122896	79633
6.0	1.390308	153061	72326	28351
7.0	1.390333	92800	43424	11570
8.0	1.390337	57781	26377	5488
9.0	1.390338	37192	15885	3252
10.0	1.390338	24167	9874	2029
11.0	1.390338	16036	5984	1434
12.0	1.390338	10635	3853	1008
13.0	1.390338	7129	2364	767
14.0	1.390338	4752	1444	558
15.0	1.390338	3410	903	493
16.0	1.390338	2369	583	363
17.0	1.390338	1716	372	286
18.0	1.390338	1195	232	278
19.0	1.390338	834	162	206
20.0	1.390338	657	105	174
21.0	1.390338	500	76	145
22.0	1.390338	373	39	113
23.0	1.390338	298	27	93
24.0	1.390338	230	29	109
25.0	1.390338	207	22	97
26.0	1.390338	168	10	84
27.0	1.390338	157	10	70
28.0	1.390338	115	6	58
29.0	1.390338	95	5	54
30.0	1.390338	78	5	36
31.0	1.390338	61	4	34
32.0	1.390338	60	4	53
33.0	1.390338	59	3	39
34.0	1.390338	54	3	39
35.0	1.390338	57	2	36
36.0	1.390338	41	3	24
37.0	1.390338	50	3	27
38.0	1.390338	41	1	23
39.0	1.390338	43	1	26
40.0	1.390338	32	1	23
41.0	1.390338	28	2	32
42.0	1.390338	31	2	28
43.0	1.390338	33	1	12
44.0	1.390338	27	2	14
45.0	1.390338	25	1	15
46.0	1.390338	21	1	15
47.0	1.390338	20	1	16
48.0	1.390338	28	2	12
49.0	1.390338	18	1	15
50.0	1.390338	20	1	16
51.0	1.390338	13	0	12
52.0	1.390338	11	2	8
53.0	1.390338	9	1	6
54.0	1.390338	13	1	7
55.0	1.390338	15	0	9
56.0	1.390338	11	1	5
57.0	1.390338	7	2	5
58.0	1.390338	6	0	7
59.0	1.390338	8	0	3
60.0	1.390338	7	0	2
61.0	1.390338	10	0	9
62.0	1.390338	7	0	2
63.0	1.390338	10	0	5
64.0	1.390338	5	0	5
65.0	1.390338	6	0	4
66.0	1.390338	3	0	3
67.0	1.390338	5	0	4
68.0	1.390338	8	0	5
69.0	1.390338	8	0	5
70.0	1.390338	4	0	3
71.0	1.390338	4	1	2
72.0	1.390338	10	0	1
73.0	1.390338	3	0	0
74.0	1.390338	4	0	7
75.0	1.390338	2	0	4
76.0	1.390338	6	0	3
77.0	1.390338	3	0	1
78.0	1.390338	5	0	3
79.0	1.390338	5	2	1
80.0	1.390338	0	0	1
81.0	1.390338	4	0	1
82.0	1.390338	1	0	1
83.0	1.390338	1	1	1
84.0	1.390338	2	0	3
85.0	1.390338	0	0	1
86.0	1.390338	1	0	1
87.0	1.390338	2	1	2
88.0	1.390338	2	0	3
89.0	1.390338	2	0	1
90.0	1.390338	0	1	2
91.0	1.390338	0	0	2
92.0	1.390338	3	0	1
93.0	1.390338	2	0	1
94.0	1.390338	2	0	0
95.0	1.390338	0	0	0
96.0	1.390338	2	0	1
97.0	1.390338	2	0	1
98.0	1.390338	0	0	0
99.0	1.390338	3	0	2
100.0	1.390338	0	0	0
101.0	0	1	0	0
102.0	0	1	0	1
103.0	0	0	0	1
104.0	0	0	0	2
105.0	0	1	0	2
106.0	0	4	0	1
107.0	0	1	1	1
108.0	0	0	0	1
109.0	0	2	0	0
110.0	0	0	0	1
111.0	0	1	0	0
112.0	0	1	0	0
113.0	0	3	0	0
114.0	0	2	0	0
115.0	0	0	0	2
116.0	0	0	0	1
117.0	0	2	0	1
118.0	0	1	1	0
119.0	0	1	0	0
120.0	0	1	0	0
123.0	0	2	0	2
125.0	0	1	0	0
126.0	0	2	0	1
127.0	0	1	0	0
129.0	0	2	0	0
130.0	0	0	0	1
131.0	0	1	1	0
132.0	0	2	0	1
134.0	0	0	0	1
135.0	0	2	0	0
136.0	0	1	0	0
138.0	0	1	0	0
140.0	0	0	0	2
141.0	0	2	0	0
142.0	0	0	0	2
143.0	0	0	1	0
146.0	0	1	0	1
149.0	0	2	1	0
150.0	0	1	0	0
151.0	0	1	0	0
156.0	0	0	0	1
157.0	0	0	0	1
158.0	0	0	1	0
159.0	0	1	0	1
160.0	0	1	0	0
162.0	0	1	0	0
165.0	0	1	0	0
166.0	0	1	0	0
172.0	0	0	0	1
178.0	0	1	0	0
179.0	0	0	0	1
180.0	0	1	0	0
185.0	0	0	0	1
186.0	0	0	0	1
188.0	0	1	0	0
192.0	0	1	0	0
206.0	0	2	0	1
207.0	0	1	0	0
212.0	0	1	0	0
233.0	0	1	0	0
234.0	0	1	0	0
241.0	0	1	0	0
449.0	0	0	0	1
606.0	0	1	0	0