## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-244-TP1.bam --OUTPUT ACR-244-TP1.md.bam --METRICS_FILE ACR-244-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 18:15:47 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	205	9439508	1758219	0	138	5508051	2100150	0.583511	5198075

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.107082	1597421	0	1990054
2.0	1.287184	1017380	590165	1116287
3.0	1.316483	586203	222889	501507
4.0	1.321249	317893	107711	194527
5.0	1.322025	171370	57911	71610
6.0	1.322151	94422	32277	27464
7.0	1.322171	54289	19101	11703
8.0	1.322175	32229	10916	5710
9.0	1.322175	20092	6502	3337
10.0	1.322175	12674	3816	2085
11.0	1.322175	8129	2346	1392
12.0	1.322175	5444	1385	1037
13.0	1.322175	3626	860	766
14.0	1.322175	2459	529	607
15.0	1.322175	1732	328	439
16.0	1.322175	1196	205	403
17.0	1.322175	890	126	297
18.0	1.322175	648	63	254
19.0	1.322175	519	57	215
20.0	1.322175	422	41	205
21.0	1.322175	329	25	170
22.0	1.322175	240	19	157
23.0	1.322175	212	13	106
24.0	1.322175	167	7	97
25.0	1.322175	130	4	81
26.0	1.322175	115	4	70
27.0	1.322175	96	5	61
28.0	1.322175	79	2	68
29.0	1.322175	82	4	45
30.0	1.322175	72	1	45
31.0	1.322175	63	0	50
32.0	1.322175	53	2	38
33.0	1.322175	60	0	45
34.0	1.322175	54	1	31
35.0	1.322175	44	2	40
36.0	1.322175	42	0	32
37.0	1.322175	54	1	28
38.0	1.322175	32	0	22
39.0	1.322175	39	0	23
40.0	1.322175	32	0	19
41.0	1.322175	20	0	25
42.0	1.322175	23	0	15
43.0	1.322175	24	0	19
44.0	1.322175	21	0	17
45.0	1.322175	24	0	18
46.0	1.322175	20	2	17
47.0	1.322175	21	0	11
48.0	1.322175	12	0	11
49.0	1.322175	15	0	7
50.0	1.322175	7	0	11
51.0	1.322175	13	0	11
52.0	1.322175	10	0	3
53.0	1.322175	12	0	7
54.0	1.322175	6	0	6
55.0	1.322175	6	0	13
56.0	1.322175	9	0	7
57.0	1.322175	10	0	3
58.0	1.322175	7	0	3
59.0	1.322175	4	0	3
60.0	1.322175	3	0	5
61.0	1.322175	9	1	3
62.0	1.322175	6	0	6
63.0	1.322175	7	0	2
64.0	1.322175	4	0	1
65.0	1.322175	2	0	4
66.0	1.322175	4	0	4
67.0	1.322175	7	0	4
68.0	1.322175	2	0	4
69.0	1.322175	7	0	2
70.0	1.322175	4	0	7
71.0	1.322175	5	0	1
72.0	1.322175	4	0	3
73.0	1.322175	2	0	2
74.0	1.322175	2	0	3
75.0	1.322175	4	0	1
76.0	1.322175	3	0	1
77.0	1.322175	3	0	0
78.0	1.322175	3	0	1
79.0	1.322175	1	0	3
80.0	1.322175	1	0	4
81.0	1.322175	1	0	2
82.0	1.322175	7	0	2
83.0	1.322175	2	0	1
84.0	1.322175	2	0	0
85.0	1.322175	4	0	1
86.0	1.322175	0	0	2
87.0	1.322175	2	0	2
88.0	1.322175	1	0	1
89.0	1.322175	3	0	1
90.0	1.322175	1	0	3
91.0	1.322175	0	0	0
92.0	1.322175	0	0	1
93.0	1.322175	0	0	0
94.0	1.322175	1	0	0
95.0	1.322175	0	0	1
96.0	1.322175	2	0	1
97.0	1.322175	1	0	2
98.0	1.322175	1	0	1
99.0	1.322175	0	0	2
100.0	1.322175	3	0	0
101.0	0	1	0	1
104.0	0	2	0	0
105.0	0	0	0	1
106.0	0	2	0	0
107.0	0	0	0	1
108.0	0	2	0	0
109.0	0	0	0	3
110.0	0	1	0	2
111.0	0	1	0	0
113.0	0	0	0	1
114.0	0	2	0	0
116.0	0	2	0	0
119.0	0	1	0	1
120.0	0	1	0	1
121.0	0	0	0	2
124.0	0	1	0	0
125.0	0	1	0	0
127.0	0	0	0	1
128.0	0	1	0	0
129.0	0	1	0	0
130.0	0	1	0	0
131.0	0	0	0	1
134.0	0	0	0	1
139.0	0	0	0	2
140.0	0	1	0	0
143.0	0	0	0	1
145.0	0	1	0	1
146.0	0	1	0	0
149.0	0	1	0	0
152.0	0	1	0	0
153.0	0	0	0	2
154.0	0	0	0	1
155.0	0	0	0	1
157.0	0	2	0	0
160.0	0	1	0	0
163.0	0	0	0	1
164.0	0	1	0	0
169.0	0	0	0	1
175.0	0	1	0	0
176.0	0	0	0	1
179.0	0	1	0	0
181.0	0	1	0	0
184.0	0	0	0	1
187.0	0	0	0	1
188.0	0	0	0	1
189.0	0	1	0	0
190.0	0	0	0	1
191.0	0	1	0	0
194.0	0	2	0	0
196.0	0	1	0	2
198.0	0	1	0	0
201.0	0	0	0	1
209.0	0	1	0	0
210.0	0	1	0	0
216.0	0	1	0	0
229.0	0	0	0	1
241.0	0	1	0	0
262.0	0	0	0	1
271.0	0	1	0	0
333.0	0	0	0	1
353.0	0	1	0	0
383.0	0	0	0	1
392.0	0	0	0	1
402.0	0	1	0	0
413.0	0	1	0	0