## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-229-TP1.bam --OUTPUT ACR-229-TP1.md.bam --METRICS_FILE ACR-229-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 18:14:43 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	241	17484271	4003606	0	157	8155394	4329168	0.466443	17975796

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.198381	5287576	0	6736998
2.0	1.651462	2184756	1364901	1903508
3.0	1.822762	934438	495908	472650
4.0	1.887527	428712	228668	123750
5.0	1.912013	212577	115019	40697
6.0	1.92127	113246	60232	17640
7.0	1.92477	63656	32280	9445
8.0	1.926094	37120	17556	5857
9.0	1.926594	22180	9578	4084
10.0	1.926783	13771	5316	2868
11.0	1.926855	8531	2944	1951
12.0	1.926882	5467	1693	1592
13.0	1.926892	3854	991	1187
14.0	1.926896	2700	555	965
15.0	1.926897	1867	324	801
16.0	1.926898	1301	219	594
17.0	1.926898	1024	132	506
18.0	1.926898	856	105	426
19.0	1.926898	671	51	375
20.0	1.926898	513	39	334
21.0	1.926898	454	23	278
22.0	1.926898	371	23	251
23.0	1.926898	327	15	179
24.0	1.926898	240	13	184
25.0	1.926898	244	10	171
26.0	1.926898	239	6	143
27.0	1.926898	209	7	131
28.0	1.926898	172	8	127
29.0	1.926898	144	4	100
30.0	1.926898	140	2	94
31.0	1.926898	138	4	79
32.0	1.926898	110	4	82
33.0	1.926898	97	3	59
34.0	1.926898	85	0	40
35.0	1.926898	78	1	48
36.0	1.926898	72	0	40
37.0	1.926898	50	1	35
38.0	1.926898	42	1	33
39.0	1.926898	57	3	28
40.0	1.926898	53	3	40
41.0	1.926898	41	1	29
42.0	1.926898	45	1	30
43.0	1.926898	41	2	28
44.0	1.926898	37	1	22
45.0	1.926898	34	1	14
46.0	1.926898	20	0	21
47.0	1.926898	31	0	17
48.0	1.926898	24	0	26
49.0	1.926898	27	1	14
50.0	1.926898	25	0	14
51.0	1.926898	25	0	12
52.0	1.926898	17	0	11
53.0	1.926898	20	0	14
54.0	1.926898	16	0	15
55.0	1.926898	13	0	17
56.0	1.926898	16	0	7
57.0	1.926898	16	1	13
58.0	1.926898	12	0	5
59.0	1.926898	13	0	8
60.0	1.926898	11	0	14
61.0	1.926898	17	1	2
62.0	1.926898	21	0	7
63.0	1.926898	8	0	10
64.0	1.926898	9	0	6
65.0	1.926898	7	0	5
66.0	1.926898	10	0	4
67.0	1.926898	5	0	4
68.0	1.926898	5	0	9
69.0	1.926898	8	0	5
70.0	1.926898	7	0	1
71.0	1.926898	5	0	1
72.0	1.926898	3	0	5
73.0	1.926898	5	0	6
74.0	1.926898	4	0	3
75.0	1.926898	4	0	5
76.0	1.926898	3	0	7
77.0	1.926898	7	0	4
78.0	1.926898	5	0	3
79.0	1.926898	2	0	6
80.0	1.926898	3	0	2
81.0	1.926898	8	0	3
82.0	1.926898	8	0	2
83.0	1.926898	3	0	3
84.0	1.926898	3	0	3
85.0	1.926898	3	0	2
86.0	1.926898	4	0	2
87.0	1.926898	3	0	3
88.0	1.926898	5	0	4
89.0	1.926898	2	0	3
90.0	1.926898	4	0	1
91.0	1.926898	3	0	3
92.0	1.926898	2	0	2
93.0	1.926898	1	0	3
94.0	1.926898	3	0	0
95.0	1.926898	5	0	1
96.0	1.926898	2	0	2
97.0	1.926898	1	0	1
98.0	1.926898	2	0	2
99.0	1.926898	3	0	3
100.0	1.926898	1	0	2
101.0	0	1	0	2
102.0	0	0	0	2
103.0	0	1	0	1
104.0	0	1	0	2
105.0	0	4	0	0
106.0	0	2	0	2
107.0	0	1	0	2
108.0	0	4	0	0
109.0	0	3	0	0
110.0	0	2	0	0
111.0	0	1	0	0
112.0	0	1	0	1
113.0	0	2	0	0
114.0	0	0	0	1
115.0	0	1	0	0
116.0	0	1	0	0
119.0	0	1	0	0
120.0	0	0	0	2
121.0	0	1	0	1
122.0	0	0	0	1
124.0	0	1	0	2
126.0	0	1	0	1
128.0	0	1	0	0
132.0	0	1	0	0
133.0	0	0	0	2
135.0	0	1	0	0
139.0	0	0	0	1
140.0	0	1	0	0
142.0	0	1	0	0
145.0	0	0	0	1
146.0	0	0	0	1
147.0	0	0	0	1
148.0	0	1	0	0
149.0	0	1	0	0
150.0	0	1	0	1
154.0	0	0	0	1
155.0	0	1	0	0
156.0	0	1	0	0
161.0	0	1	0	1
162.0	0	1	0	0
164.0	0	1	0	0
168.0	0	0	0	1
169.0	0	1	0	0
174.0	0	1	0	0
176.0	0	1	0	0
210.0	0	0	0	1
215.0	0	1	0	0
220.0	0	0	0	1
228.0	0	0	0	1
231.0	0	1	0	0
240.0	0	0	0	1
253.0	0	1	0	0
258.0	0	0	0	1
264.0	0	1	0	0
267.0	0	1	0	0
292.0	0	0	0	1
299.0	0	1	0	0