## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-229-TP3.bam --OUTPUT ACR-229-TP3.md.bam --METRICS_FILE ACR-229-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 18:14:34 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	218	13955508	3216226	0	141	7496723	3937748	0.537188	10512390

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.19608	3113591	0	4150128
2.0	1.513199	1597631	1030919	1567910
3.0	1.597277	803303	420222	499832
4.0	1.619568	410639	211330	150188
5.0	1.625479	219594	114639	47731
6.0	1.627046	122517	64169	17790
7.0	1.627461	70923	36473	8119
8.0	1.627571	42714	21067	4515
9.0	1.627601	26296	12324	2887
10.0	1.627608	16542	6989	1956
11.0	1.62761	10543	4129	1387
12.0	1.627611	7001	2573	1030
13.0	1.627611	4591	1462	800
14.0	1.627611	3075	898	629
15.0	1.627611	2153	533	512
16.0	1.627611	1468	347	439
17.0	1.627611	1134	212	388
18.0	1.627611	825	136	293
19.0	1.627611	637	89	242
20.0	1.627611	515	56	182
21.0	1.627611	415	48	228
22.0	1.627611	313	21	164
23.0	1.627611	293	14	131
24.0	1.627611	182	19	94
25.0	1.627611	171	14	113
26.0	1.627611	151	5	81
27.0	1.627611	128	11	72
28.0	1.627611	124	5	57
29.0	1.627611	118	4	55
30.0	1.627611	83	7	60
31.0	1.627611	89	6	50
32.0	1.627611	66	6	40
33.0	1.627611	55	4	35
34.0	1.627611	39	1	39
35.0	1.627611	70	2	53
36.0	1.627611	55	7	28
37.0	1.627611	44	1	35
38.0	1.627611	42	2	31
39.0	1.627611	24	0	28
40.0	1.627611	25	0	20
41.0	1.627611	36	2	26
42.0	1.627611	32	1	22
43.0	1.627611	25	1	15
44.0	1.627611	20	3	11
45.0	1.627611	26	0	22
46.0	1.627611	25	0	18
47.0	1.627611	25	2	18
48.0	1.627611	18	0	12
49.0	1.627611	26	0	11
50.0	1.627611	19	0	5
51.0	1.627611	18	1	11
52.0	1.627611	15	1	7
53.0	1.627611	15	0	3
54.0	1.627611	7	0	14
55.0	1.627611	14	0	7
56.0	1.627611	6	0	19
57.0	1.627611	15	2	6
58.0	1.627611	7	0	3
59.0	1.627611	12	0	7
60.0	1.627611	7	0	10
61.0	1.627611	12	0	4
62.0	1.627611	9	0	5
63.0	1.627611	8	0	9
64.0	1.627611	9	0	6
65.0	1.627611	5	1	5
66.0	1.627611	4	0	3
67.0	1.627611	5	0	7
68.0	1.627611	5	0	8
69.0	1.627611	6	0	7
70.0	1.627611	13	2	7
71.0	1.627611	6	1	3
72.0	1.627611	11	0	4
73.0	1.627611	4	0	4
74.0	1.627611	1	0	2
75.0	1.627611	8	0	1
76.0	1.627611	8	0	3
77.0	1.627611	4	0	3
78.0	1.627611	1	0	2
79.0	1.627611	3	0	2
80.0	1.627611	3	1	3
81.0	1.627611	1	0	2
82.0	1.627611	1	0	1
83.0	1.627611	2	0	3
84.0	1.627611	2	0	1
85.0	1.627611	8	0	1
86.0	1.627611	2	0	3
87.0	1.627611	5	0	2
88.0	1.627611	4	0	2
89.0	1.627611	0	0	2
90.0	1.627611	3	0	1
91.0	1.627611	6	0	0
92.0	1.627611	2	0	1
93.0	1.627611	2	0	1
94.0	1.627611	0	0	3
95.0	1.627611	0	0	0
96.0	1.627611	2	0	4
97.0	1.627611	1	0	4
98.0	1.627611	2	0	1
99.0	1.627611	3	0	0
100.0	1.627611	2	0	2
101.0	0	2	0	1
102.0	0	3	0	0
103.0	0	0	0	1
104.0	0	2	0	0
105.0	0	1	0	0
106.0	0	5	1	2
107.0	0	0	0	1
108.0	0	2	0	0
109.0	0	1	0	0
111.0	0	2	0	3
113.0	0	1	0	0
115.0	0	1	0	1
116.0	0	1	0	0
117.0	0	1	0	0
119.0	0	2	0	1
120.0	0	1	0	0
122.0	0	1	0	1
123.0	0	1	0	1
124.0	0	0	0	1
125.0	0	1	0	0
126.0	0	1	0	0
127.0	0	0	0	1
128.0	0	1	0	1
129.0	0	1	0	0
131.0	0	1	0	0
132.0	0	1	0	1
133.0	0	0	0	3
134.0	0	0	0	1
135.0	0	0	0	1
136.0	0	1	0	0
138.0	0	0	0	1
140.0	0	1	0	1
141.0	0	1	0	2
142.0	0	1	0	1
143.0	0	1	0	1
145.0	0	1	0	0
146.0	0	1	0	0
147.0	0	2	0	1
148.0	0	0	0	1
150.0	0	2	0	0
152.0	0	1	0	0
153.0	0	2	0	0
154.0	0	0	0	1
157.0	0	0	0	1
160.0	0	1	0	0
161.0	0	0	0	1
162.0	0	1	0	0
166.0	0	1	0	0
167.0	0	1	0	0
173.0	0	0	0	1
174.0	0	1	0	0
181.0	0	0	0	1
188.0	0	1	0	0
189.0	0	1	0	0
206.0	0	1	0	0
212.0	0	0	0	1
214.0	0	0	0	1
217.0	0	0	0	1
218.0	0	0	0	2
228.0	0	1	0	0
229.0	0	0	0	2
231.0	0	1	0	0
236.0	0	1	0	0
238.0	0	1	0	0
250.0	0	1	0	0
251.0	0	1	0	0
254.0	0	0	0	1
277.0	0	1	0	0
278.0	0	0	0	1
285.0	0	1	0	0
308.0	0	1	0	0
335.0	0	0	0	1
343.0	0	1	0	0