## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-173-TP1.bam --OUTPUT ACR-173-TP1.md.bam --METRICS_FILE ACR-173-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 18:13:40 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	699	12777304	4561141	0	443	7238432	2726051	0.566509	7506164

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.108165	2421050	0	2944670
2.0	1.310155	1400975	777535	1512501
3.0	1.346972	770935	278135	654401
4.0	1.353683	411429	133433	254319
5.0	1.354907	221178	72793	95773
6.0	1.355129	122295	41849	37708
7.0	1.35517	70083	25104	16015
8.0	1.355178	41840	15233	7800
9.0	1.355179	25971	9075	4322
10.0	1.355179	16427	5662	2688
11.0	1.355179	10899	3535	1768
12.0	1.355179	7308	2216	1295
13.0	1.355179	4979	1356	1001
14.0	1.355179	3400	852	734
15.0	1.355179	2409	534	546
16.0	1.355179	1680	358	478
17.0	1.355179	1195	209	333
18.0	1.355179	860	132	325
19.0	1.355179	674	98	263
20.0	1.355179	493	54	231
21.0	1.355179	406	28	174
22.0	1.355179	332	14	142
23.0	1.355179	233	12	137
24.0	1.355179	193	12	108
25.0	1.355179	167	8	81
26.0	1.355179	122	5	74
27.0	1.355179	129	6	95
28.0	1.355179	107	2	70
29.0	1.355179	85	4	61
30.0	1.355179	84	1	61
31.0	1.355179	82	0	56
32.0	1.355179	78	1	53
33.0	1.355179	50	2	30
34.0	1.355179	47	2	47
35.0	1.355179	53	2	23
36.0	1.355179	36	0	24
37.0	1.355179	40	1	32
38.0	1.355179	29	0	20
39.0	1.355179	24	0	27
40.0	1.355179	29	0	13
41.0	1.355179	29	0	24
42.0	1.355179	19	0	17
43.0	1.355179	13	0	18
44.0	1.355179	26	0	12
45.0	1.355179	22	0	9
46.0	1.355179	20	1	16
47.0	1.355179	20	0	18
48.0	1.355179	6	1	15
49.0	1.355179	17	0	10
50.0	1.355179	18	0	7
51.0	1.355179	10	0	20
52.0	1.355179	15	0	8
53.0	1.355179	17	0	7
54.0	1.355179	14	0	9
55.0	1.355179	7	0	10
56.0	1.355179	11	0	8
57.0	1.355179	8	0	10
58.0	1.355179	12	0	6
59.0	1.355179	7	0	9
60.0	1.355179	9	0	11
61.0	1.355179	5	0	4
62.0	1.355179	7	0	4
63.0	1.355179	9	0	8
64.0	1.355179	7	0	5
65.0	1.355179	7	0	4
66.0	1.355179	6	0	4
67.0	1.355179	4	0	7
68.0	1.355179	3	0	1
69.0	1.355179	4	0	5
70.0	1.355179	4	0	3
71.0	1.355179	4	0	1
72.0	1.355179	6	0	1
73.0	1.355179	6	0	3
74.0	1.355179	2	0	2
75.0	1.355179	1	0	2
76.0	1.355179	3	0	0
77.0	1.355179	2	0	2
78.0	1.355179	2	0	3
79.0	1.355179	2	0	2
80.0	1.355179	3	0	4
81.0	1.355179	2	0	0
82.0	1.355179	3	0	1
83.0	1.355179	2	0	3
84.0	1.355179	4	0	2
85.0	1.355179	1	0	0
86.0	1.355179	1	0	0
87.0	1.355179	1	0	1
88.0	1.355179	2	0	1
89.0	1.355179	1	0	1
90.0	1.355179	2	0	2
91.0	1.355179	1	0	1
92.0	1.355179	3	0	3
93.0	1.355179	1	0	2
94.0	1.355179	0	0	4
95.0	1.355179	2	0	0
96.0	1.355179	0	0	2
97.0	1.355179	2	0	1
98.0	1.355179	2	0	0
99.0	1.355179	2	0	2
100.0	1.355179	1	0	1
101.0	0	2	0	0
102.0	0	0	0	2
103.0	0	0	0	1
104.0	0	3	0	2
105.0	0	1	0	0
106.0	0	0	0	1
107.0	0	2	0	1
108.0	0	0	0	1
109.0	0	1	0	2
110.0	0	1	0	1
112.0	0	2	0	0
113.0	0	0	0	2
114.0	0	2	0	0
115.0	0	0	0	1
116.0	0	1	0	1
117.0	0	1	0	0
118.0	0	3	0	0
120.0	0	1	0	0
121.0	0	0	0	1
122.0	0	1	0	0
124.0	0	0	0	1
126.0	0	0	0	2
127.0	0	0	0	1
128.0	0	0	0	1
129.0	0	0	0	1
130.0	0	1	0	0
131.0	0	1	0	0
133.0	0	1	0	0
135.0	0	1	0	0
137.0	0	1	0	0
138.0	0	1	0	0
140.0	0	1	0	0
143.0	0	0	0	1
145.0	0	0	0	1
146.0	0	2	0	1
150.0	0	2	0	0
151.0	0	1	0	0
155.0	0	0	0	1
156.0	0	1	0	0
157.0	0	0	0	1
160.0	0	0	0	1
161.0	0	1	0	0
163.0	0	1	0	0
167.0	0	1	0	0
178.0	0	0	0	1
189.0	0	0	0	1
196.0	0	1	0	0
198.0	0	0	0	1
201.0	0	1	0	0
215.0	0	1	0	0
223.0	0	0	0	1
226.0	0	1	0	0
247.0	0	0	0	1
264.0	0	1	0	0
280.0	0	0	0	1
284.0	0	1	0	0
322.0	0	0	0	1
332.0	0	1	0	0
336.0	0	0	0	1
340.0	0	1	0	0
418.0	0	0	0	1
442.0	0	1	0	0