## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-237-TP3.bam --OUTPUT ACR-237-TP3.md.bam --METRICS_FILE ACR-237-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 18:13:22 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	188	14486885	2914256	0	121	7612857	4157652	0.525501	11759990

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.211675	3469649	0	4645293
2.0	1.565173	1659604	1083726	1554595
3.0	1.668304	804742	445564	450843
4.0	1.698392	405452	225285	130615
5.0	1.70717	216666	122021	42932
6.0	1.709731	121679	68326	17577
7.0	1.710478	70739	38510	9244
8.0	1.710696	43403	21973	5574
9.0	1.71076	26667	12413	3651
10.0	1.710778	17004	7275	2559
11.0	1.710784	10916	4272	1883
12.0	1.710785	7172	2365	1453
13.0	1.710786	4861	1491	1146
14.0	1.710786	3221	958	951
15.0	1.710786	2358	514	764
16.0	1.710786	1763	331	615
17.0	1.710786	1253	210	456
18.0	1.710786	986	145	425
19.0	1.710786	746	80	400
20.0	1.710786	660	70	316
21.0	1.710786	494	48	270
22.0	1.710786	443	42	231
23.0	1.710786	363	25	220
24.0	1.710786	314	30	165
25.0	1.710786	296	24	162
26.0	1.710786	212	12	149
27.0	1.710786	190	18	126
28.0	1.710786	186	13	112
29.0	1.710786	152	10	104
30.0	1.710786	148	10	76
31.0	1.710786	125	7	79
32.0	1.710786	102	4	92
33.0	1.710786	100	5	61
34.0	1.710786	72	1	56
35.0	1.710786	88	2	56
36.0	1.710786	85	6	51
37.0	1.710786	72	3	52
38.0	1.710786	64	1	39
39.0	1.710786	47	1	39
40.0	1.710786	60	0	33
41.0	1.710786	57	2	25
42.0	1.710786	47	2	29
43.0	1.710786	40	2	28
44.0	1.710786	41	2	31
45.0	1.710786	37	1	30
46.0	1.710786	33	1	27
47.0	1.710786	32	2	12
48.0	1.710786	43	3	25
49.0	1.710786	28	1	24
50.0	1.710786	27	1	11
51.0	1.710786	20	1	15
52.0	1.710786	19	1	14
53.0	1.710786	26	1	18
54.0	1.710786	30	0	17
55.0	1.710786	15	0	15
56.0	1.710786	18	0	12
57.0	1.710786	16	0	8
58.0	1.710786	10	0	11
59.0	1.710786	15	0	12
60.0	1.710786	16	0	9
61.0	1.710786	10	0	11
62.0	1.710786	10	0	8
63.0	1.710786	15	0	8
64.0	1.710786	14	0	7
65.0	1.710786	14	0	6
66.0	1.710786	12	0	5
67.0	1.710786	5	0	3
68.0	1.710786	10	0	4
69.0	1.710786	8	0	5
70.0	1.710786	5	0	3
71.0	1.710786	9	0	6
72.0	1.710786	7	0	3
73.0	1.710786	8	0	4
74.0	1.710786	8	0	6
75.0	1.710786	7	0	4
76.0	1.710786	6	0	7
77.0	1.710786	4	0	1
78.0	1.710786	5	0	6
79.0	1.710786	6	1	3
80.0	1.710786	7	0	3
81.0	1.710786	2	0	1
82.0	1.710786	5	0	2
83.0	1.710786	5	0	2
84.0	1.710786	5	0	3
85.0	1.710786	4	0	2
86.0	1.710786	5	1	1
87.0	1.710786	2	0	1
88.0	1.710786	3	0	0
89.0	1.710786	3	0	5
90.0	1.710786	5	0	4
91.0	1.710786	2	0	2
92.0	1.710786	1	0	2
93.0	1.710786	4	0	0
94.0	1.710786	5	1	1
95.0	1.710786	3	0	1
96.0	1.710786	3	0	2
97.0	1.710786	1	0	1
98.0	1.710786	2	0	1
99.0	1.710786	1	0	2
100.0	1.710786	1	0	0
101.0	0	1	0	1
102.0	0	1	0	3
103.0	0	1	0	2
104.0	0	3	0	1
105.0	0	2	0	3
106.0	0	2	0	2
107.0	0	1	0	1
108.0	0	1	0	3
109.0	0	4	0	2
110.0	0	3	0	1
111.0	0	2	0	1
112.0	0	2	0	1
114.0	0	2	0	0
115.0	0	2	0	0
116.0	0	2	0	1
118.0	0	2	0	0
119.0	0	2	0	0
120.0	0	0	0	1
121.0	0	1	0	0
122.0	0	0	0	1
124.0	0	1	1	3
125.0	0	2	1	0
126.0	0	1	0	1
127.0	0	1	0	1
128.0	0	0	0	2
130.0	0	1	0	0
132.0	0	1	0	0
133.0	0	1	0	1
134.0	0	1	0	1
135.0	0	1	0	0
136.0	0	1	0	1
137.0	0	1	0	1
140.0	0	3	0	0
145.0	0	0	0	1
147.0	0	0	0	1
150.0	0	1	0	0
151.0	0	0	0	1
152.0	0	1	0	0
155.0	0	1	0	1
156.0	0	2	0	0
158.0	0	0	0	1
160.0	0	0	0	1
161.0	0	1	0	0
162.0	0	2	0	1
163.0	0	0	0	1
165.0	0	1	0	0
166.0	0	2	0	0
179.0	0	0	0	1
181.0	0	0	0	1
182.0	0	1	0	0
183.0	0	1	0	0
185.0	0	1	0	0
191.0	0	0	0	1
204.0	0	1	0	0
212.0	0	0	0	1
221.0	0	0	0	1
224.0	0	1	0	0
228.0	0	0	0	1
231.0	0	0	0	1
233.0	0	1	0	0
237.0	0	1	0	0
241.0	0	1	0	0
243.0	0	0	0	1
255.0	0	0	0	1
270.0	0	1	0	0
338.0	0	0	0	1
352.0	0	0	0	1
356.0	0	1	0	0
367.0	0	1	0	0
375.0	0	1	0	0