## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-150-TP1.bam --OUTPUT ACR-150-TP1.md.bam --METRICS_FILE ACR-150-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 18:16:00 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	682	13963917	3581079	0	513	11874480	2352301	0.850366	2097711

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.002669	215546	0	236166
2.0	1.003958	144787	399373	177161
3.0	1.00396	170052	178359	220169
4.0	1.00396	198378	97026	255658
5.0	1.00396	213982	59784	263813
6.0	1.00396	210916	40199	242509
7.0	1.00396	193531	28127	200967
8.0	1.00396	166399	19806	153595
9.0	1.00396	135219	14235	109581
10.0	1.00396	106777	10553	74141
11.0	1.00396	81214	7475	48470
12.0	1.00396	61040	5519	31383
13.0	1.00396	45515	3987	20720
14.0	1.00396	34084	2986	14084
15.0	1.00396	25458	2039	9798
16.0	1.00396	19329	1549	7032
17.0	1.00396	14665	1115	5212
18.0	1.00396	11089	814	3798
19.0	1.00396	8657	602	2817
20.0	1.00396	6472	440	2153
21.0	1.00396	5102	264	1608
22.0	1.00396	4021	228	1247
23.0	1.00396	3077	145	1038
24.0	1.00396	2433	109	844
25.0	1.00396	1962	91	608
26.0	1.00396	1483	62	529
27.0	1.00396	1196	44	456
28.0	1.00396	972	32	378
29.0	1.00396	770	21	334
30.0	1.00396	647	17	280
31.0	1.00396	503	9	242
32.0	1.00396	490	7	273
33.0	1.00396	411	4	191
34.0	1.00396	332	3	185
35.0	1.00396	285	2	158
36.0	1.00396	248	2	145
37.0	1.00396	191	5	120
38.0	1.00396	174	2	119
39.0	1.00396	175	0	100
40.0	1.00396	140	1	80
41.0	1.00396	128	3	81
42.0	1.00396	91	0	80
43.0	1.00396	128	0	73
44.0	1.00396	77	0	57
45.0	1.00396	80	0	54
46.0	1.00396	62	0	58
47.0	1.00396	83	0	50
48.0	1.00396	57	0	45
49.0	1.00396	57	0	38
50.0	1.00396	62	0	40
51.0	1.00396	50	0	35
52.0	1.00396	42	1	33
53.0	1.00396	43	0	39
54.0	1.00396	38	0	25
55.0	1.00396	33	0	26
56.0	1.00396	34	0	21
57.0	1.00396	28	0	20
58.0	1.00396	25	0	27
59.0	1.00396	34	0	24
60.0	1.00396	24	0	18
61.0	1.00396	34	1	20
62.0	1.00396	16	0	18
63.0	1.00396	20	0	20
64.0	1.00396	26	0	16
65.0	1.00396	12	0	16
66.0	1.00396	20	0	12
67.0	1.00396	15	0	14
68.0	1.00396	26	0	5
69.0	1.00396	17	0	12
70.0	1.00396	14	0	13
71.0	1.00396	12	0	12
72.0	1.00396	11	0	10
73.0	1.00396	21	0	6
74.0	1.00396	6	0	10
75.0	1.00396	7	0	15
76.0	1.00396	11	0	9
77.0	1.00396	4	0	5
78.0	1.00396	9	0	6
79.0	1.00396	6	0	3
80.0	1.00396	10	0	5
81.0	1.00396	3	0	6
82.0	1.00396	4	0	5
83.0	1.00396	10	0	6
84.0	1.00396	6	0	7
85.0	1.00396	6	0	7
86.0	1.00396	7	0	6
87.0	1.00396	6	0	6
88.0	1.00396	4	0	9
89.0	1.00396	5	0	6
90.0	1.00396	10	0	8
91.0	1.00396	3	0	3
92.0	1.00396	8	0	2
93.0	1.00396	3	0	2
94.0	1.00396	8	0	7
95.0	1.00396	8	0	4
96.0	1.00396	5	0	4
97.0	1.00396	3	0	4
98.0	1.00396	4	0	1
99.0	1.00396	4	0	3
100.0	1.00396	7	0	4
101.0	0	5	0	4
102.0	0	5	0	2
103.0	0	7	0	6
104.0	0	3	0	5
105.0	0	7	0	2
106.0	0	4	0	0
107.0	0	3	0	1
108.0	0	3	0	3
109.0	0	4	0	2
110.0	0	2	0	1
111.0	0	1	0	1
112.0	0	1	0	0
113.0	0	1	0	0
114.0	0	1	0	1
115.0	0	1	0	1
116.0	0	0	0	1
117.0	0	1	0	4
118.0	0	0	0	2
119.0	0	1	0	1
120.0	0	0	0	4
121.0	0	2	0	2
122.0	0	1	0	2
123.0	0	2	0	2
124.0	0	2	0	6
125.0	0	7	0	0
126.0	0	0	0	1
127.0	0	2	0	0
128.0	0	5	0	1
129.0	0	1	0	1
130.0	0	1	0	1
131.0	0	0	0	2
132.0	0	1	0	0
133.0	0	1	0	2
134.0	0	0	0	1
135.0	0	1	0	2
136.0	0	4	0	1
137.0	0	0	0	2
139.0	0	3	0	0
141.0	0	2	0	0
143.0	0	2	0	1
144.0	0	0	0	1
146.0	0	0	0	1
147.0	0	1	0	0
148.0	0	2	0	0
150.0	0	1	0	0
152.0	0	0	0	1
153.0	0	1	0	0
154.0	0	0	0	1
155.0	0	0	0	1
156.0	0	1	0	0
158.0	0	0	0	1
160.0	0	1	0	0
161.0	0	1	0	1
162.0	0	0	0	2
163.0	0	0	0	1
164.0	0	1	0	1
167.0	0	1	0	0
169.0	0	2	0	0
170.0	0	2	0	1
174.0	0	0	0	1
177.0	0	1	0	1
178.0	0	1	0	2
179.0	0	1	0	0
180.0	0	0	0	2
181.0	0	2	0	0
182.0	0	0	0	1
183.0	0	1	0	0
184.0	0	0	0	1
185.0	0	1	0	1
189.0	0	1	0	0
190.0	0	1	0	1
193.0	0	3	0	0
194.0	0	0	0	1
202.0	0	1	0	0
209.0	0	0	0	1
210.0	0	0	0	1
214.0	0	1	0	0
215.0	0	0	0	1
217.0	0	1	0	1
221.0	0	1	0	0
225.0	0	1	0	0
232.0	0	1	0	0
235.0	0	0	0	1
237.0	0	0	0	1
240.0	0	1	0	0
250.0	0	0	0	1
255.0	0	1	0	0
264.0	0	1	0	0
269.0	0	0	0	1
286.0	0	0	0	1
289.0	0	1	0	0
299.0	0	1	0	0
318.0	0	0	0	1
321.0	0	0	0	1
336.0	0	1	0	0
338.0	0	1	0	0
344.0	0	0	0	1
367.0	0	1	0	0
554.0	0	0	0	1
576.0	0	1	0	0