## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-150-TP2.bam --OUTPUT ACR-150-TP2.md.bam --METRICS_FILE ACR-150-TP2.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 18:13:43 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	169	14295485	3174096	0	117	8116757	3893884	0.567785	9037970

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.161981	2773443	0	3671991
2.0	1.40091	1538886	974978	1588339
3.0	1.450039	821545	399473	576691
4.0	1.460141	436652	204730	197771
5.0	1.462218	239806	113641	71019
6.0	1.462645	135876	64926	28692
7.0	1.462733	81143	38411	13879
8.0	1.462751	50337	22594	7960
9.0	1.462755	31606	13446	4997
10.0	1.462756	20444	8048	3395
11.0	1.462756	13533	4875	2540
12.0	1.462756	9137	2888	1902
13.0	1.462756	6296	1803	1447
14.0	1.462756	4327	1157	1137
15.0	1.462756	3092	752	894
16.0	1.462756	2275	486	753
17.0	1.462756	1703	301	587
18.0	1.462756	1303	202	564
19.0	1.462756	1029	127	425
20.0	1.462756	765	91	381
21.0	1.462756	655	73	330
22.0	1.462756	493	58	277
23.0	1.462756	446	46	266
24.0	1.462756	386	19	213
25.0	1.462756	322	17	179
26.0	1.462756	326	18	185
27.0	1.462756	232	19	157
28.0	1.462756	219	11	137
29.0	1.462756	182	16	110
30.0	1.462756	168	10	114
31.0	1.462756	157	11	96
32.0	1.462756	146	9	83
33.0	1.462756	133	8	82
34.0	1.462756	105	4	79
35.0	1.462756	106	4	79
36.0	1.462756	84	1	61
37.0	1.462756	72	6	44
38.0	1.462756	63	2	52
39.0	1.462756	70	3	46
40.0	1.462756	75	4	44
41.0	1.462756	60	0	38
42.0	1.462756	62	1	43
43.0	1.462756	58	3	34
44.0	1.462756	55	3	30
45.0	1.462756	39	3	27
46.0	1.462756	50	1	32
47.0	1.462756	42	2	27
48.0	1.462756	34	0	27
49.0	1.462756	34	1	23
50.0	1.462756	33	1	28
51.0	1.462756	31	1	15
52.0	1.462756	32	0	28
53.0	1.462756	24	0	16
54.0	1.462756	27	0	12
55.0	1.462756	25	0	17
56.0	1.462756	24	1	14
57.0	1.462756	21	1	12
58.0	1.462756	18	1	10
59.0	1.462756	16	1	15
60.0	1.462756	19	0	18
61.0	1.462756	20	0	14
62.0	1.462756	16	0	5
63.0	1.462756	12	0	8
64.0	1.462756	10	0	10
65.0	1.462756	16	2	8
66.0	1.462756	9	0	7
67.0	1.462756	11	1	10
68.0	1.462756	9	0	12
69.0	1.462756	13	2	9
70.0	1.462756	10	0	6
71.0	1.462756	11	1	11
72.0	1.462756	9	1	4
73.0	1.462756	16	0	3
74.0	1.462756	5	1	7
75.0	1.462756	4	0	4
76.0	1.462756	8	0	3
77.0	1.462756	7	0	3
78.0	1.462756	4	0	5
79.0	1.462756	4	0	5
80.0	1.462756	4	0	4
81.0	1.462756	3	0	3
82.0	1.462756	6	1	5
83.0	1.462756	7	0	4
84.0	1.462756	3	0	5
85.0	1.462756	1	0	4
86.0	1.462756	7	0	2
87.0	1.462756	5	0	3
88.0	1.462756	6	0	4
89.0	1.462756	9	0	4
90.0	1.462756	3	0	1
91.0	1.462756	2	0	3
92.0	1.462756	2	0	2
93.0	1.462756	6	0	4
94.0	1.462756	9	1	2
95.0	1.462756	5	1	0
96.0	1.462756	0	0	0
97.0	1.462756	3	0	1
98.0	1.462756	3	0	5
99.0	1.462756	1	0	2
100.0	1.462756	6	0	1
101.0	0	1	0	3
102.0	0	4	0	3
103.0	0	2	0	1
104.0	0	4	0	2
105.0	0	1	0	3
106.0	0	3	0	2
107.0	0	1	0	1
108.0	0	3	0	1
109.0	0	2	0	2
110.0	0	1	0	2
111.0	0	3	0	1
112.0	0	0	0	1
113.0	0	0	0	1
114.0	0	1	0	3
115.0	0	4	0	2
116.0	0	2	0	1
117.0	0	0	0	3
118.0	0	3	1	4
119.0	0	2	0	4
120.0	0	3	0	1
121.0	0	3	0	0
122.0	0	3	0	3
123.0	0	3	0	1
124.0	0	3	0	0
126.0	0	2	0	0
127.0	0	1	0	0
128.0	0	1	1	0
129.0	0	1	0	1
131.0	0	0	0	1
132.0	0	2	1	0
133.0	0	0	0	1
134.0	0	1	0	0
135.0	0	3	0	0
136.0	0	0	0	1
138.0	0	0	0	1
139.0	0	2	0	0
140.0	0	1	0	0
141.0	0	0	0	1
142.0	0	0	0	1
143.0	0	2	0	0
144.0	0	1	0	2
145.0	0	1	0	0
146.0	0	1	0	0
147.0	0	1	0	1
149.0	0	2	1	0
154.0	0	1	0	0
155.0	0	1	0	0
156.0	0	1	0	0
157.0	0	2	0	0
160.0	0	0	1	0
164.0	0	0	0	2
166.0	0	0	0	1
167.0	0	2	0	0
169.0	0	1	0	0
170.0	0	0	0	1
171.0	0	0	0	1
172.0	0	2	0	0
173.0	0	0	0	1
177.0	0	2	0	0
179.0	0	0	0	1
180.0	0	0	0	2
181.0	0	0	0	1
182.0	0	1	0	0
183.0	0	0	0	1
186.0	0	1	0	1
187.0	0	1	0	0
188.0	0	1	0	0
189.0	0	1	0	0
190.0	0	1	0	0
204.0	0	1	0	0
211.0	0	1	0	0
212.0	0	1	0	0
230.0	0	1	0	0
232.0	0	0	0	1
241.0	0	0	0	1
248.0	0	1	0	0
258.0	0	1	0	0
270.0	0	1	0	0
312.0	0	0	0	1
333.0	0	1	0	0
374.0	0	0	0	1
491.0	0	1	0	0