## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-139-TP3.bam --OUTPUT ACR-139-TP3.md.bam --METRICS_FILE ACR-139-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	181	14217207	3142491	0	119	8145913	3537842	0.572962	8475046

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.135116	2619485	0	3376241
2.0	1.347194	1548817	931865	1649910
3.0	1.386817	847506	370457	653228
4.0	1.39422	451744	186530	231968
5.0	1.395603	244526	101583	83132
6.0	1.395861	136801	57599	32817
7.0	1.39591	79791	33138	14892
8.0	1.395919	48461	19396	7876
9.0	1.39592	30313	11464	4949
10.0	1.395921	19407	6780	3263
11.0	1.395921	12594	3909	2377
12.0	1.395921	8367	2478	1712
13.0	1.395921	5744	1452	1343
14.0	1.395921	3987	935	1048
15.0	1.395921	2791	553	837
16.0	1.395921	1958	342	681
17.0	1.395921	1547	218	600
18.0	1.395921	1154	146	434
19.0	1.395921	852	95	402
20.0	1.395921	704	57	378
21.0	1.395921	520	36	292
22.0	1.395921	437	28	244
23.0	1.395921	342	20	207
24.0	1.395921	309	12	195
25.0	1.395921	272	17	191
26.0	1.395921	218	13	166
27.0	1.395921	226	8	138
28.0	1.395921	188	12	118
29.0	1.395921	147	5	107
30.0	1.395921	143	6	102
31.0	1.395921	135	4	80
32.0	1.395921	120	5	89
33.0	1.395921	119	1	78
34.0	1.395921	99	3	81
35.0	1.395921	87	2	72
36.0	1.395921	91	2	61
37.0	1.395921	76	2	65
38.0	1.395921	62	2	54
39.0	1.395921	58	3	46
40.0	1.395921	64	1	42
41.0	1.395921	67	3	38
42.0	1.395921	50	1	28
43.0	1.395921	38	0	22
44.0	1.395921	42	3	30
45.0	1.395921	23	0	30
46.0	1.395921	31	2	32
47.0	1.395921	29	2	27
48.0	1.395921	41	2	30
49.0	1.395921	35	3	18
50.0	1.395921	27	1	18
51.0	1.395921	36	0	17
52.0	1.395921	27	0	29
53.0	1.395921	29	1	14
54.0	1.395921	16	0	20
55.0	1.395921	21	0	12
56.0	1.395921	16	0	13
57.0	1.395921	20	1	17
58.0	1.395921	14	1	19
59.0	1.395921	18	0	14
60.0	1.395921	12	0	12
61.0	1.395921	15	0	9
62.0	1.395921	13	0	12
63.0	1.395921	17	0	11
64.0	1.395921	13	1	10
65.0	1.395921	14	0	8
66.0	1.395921	16	0	11
67.0	1.395921	5	0	4
68.0	1.395921	12	0	7
69.0	1.395921	11	0	9
70.0	1.395921	12	0	6
71.0	1.395921	8	0	7
72.0	1.395921	9	0	11
73.0	1.395921	9	1	5
74.0	1.395921	7	0	4
75.0	1.395921	7	2	4
76.0	1.395921	6	0	5
77.0	1.395921	8	1	3
78.0	1.395921	6	0	4
79.0	1.395921	3	0	6
80.0	1.395921	6	0	4
81.0	1.395921	2	0	2
82.0	1.395921	4	0	4
83.0	1.395921	5	0	6
84.0	1.395921	8	0	8
85.0	1.395921	6	0	8
86.0	1.395921	2	0	4
87.0	1.395921	7	0	5
88.0	1.395921	4	0	1
89.0	1.395921	4	0	2
90.0	1.395921	3	0	2
91.0	1.395921	5	0	5
92.0	1.395921	5	0	5
93.0	1.395921	4	0	7
94.0	1.395921	4	0	6
95.0	1.395921	6	0	1
96.0	1.395921	1	0	4
97.0	1.395921	5	0	2
98.0	1.395921	8	0	7
99.0	1.395921	3	0	3
100.0	1.395921	5	1	6
101.0	0	4	0	2
102.0	0	6	0	1
103.0	0	5	0	4
104.0	0	1	0	1
105.0	0	8	1	0
106.0	0	2	0	0
107.0	0	2	0	5
108.0	0	4	0	3
109.0	0	2	0	1
110.0	0	3	0	5
111.0	0	2	0	1
112.0	0	1	0	2
113.0	0	2	0	1
114.0	0	2	0	3
115.0	0	2	0	3
116.0	0	2	0	3
117.0	0	2	0	1
118.0	0	1	0	1
119.0	0	10	0	2
120.0	0	1	0	2
121.0	0	2	0	0
122.0	0	1	0	0
123.0	0	3	0	4
124.0	0	0	0	1
125.0	0	2	0	3
126.0	0	2	0	2
127.0	0	4	0	1
128.0	0	2	0	4
129.0	0	2	0	3
130.0	0	3	0	1
131.0	0	3	1	2
132.0	0	3	0	1
133.0	0	1	0	1
134.0	0	2	0	1
137.0	0	0	0	1
139.0	0	0	0	1
140.0	0	3	0	0
141.0	0	1	0	0
145.0	0	1	0	0
147.0	0	0	0	2
148.0	0	2	0	0
149.0	0	2	0	0
151.0	0	0	0	1
153.0	0	0	0	1
154.0	0	1	0	0
155.0	0	1	0	2
156.0	0	1	0	3
157.0	0	1	0	0
158.0	0	2	0	0
159.0	0	2	0	0
161.0	0	1	0	1
162.0	0	1	0	1
163.0	0	2	0	0
165.0	0	0	0	1
166.0	0	1	0	1
169.0	0	0	0	1
170.0	0	1	0	1
171.0	0	0	0	1
172.0	0	1	0	1
173.0	0	1	0	0
174.0	0	1	0	0
175.0	0	1	0	1
177.0	0	0	0	1
179.0	0	0	0	1
180.0	0	1	0	0
181.0	0	2	0	0
183.0	0	1	0	0
185.0	0	1	0	0
187.0	0	0	0	2
188.0	0	1	0	0
190.0	0	0	0	1
191.0	0	0	1	1
192.0	0	1	0	0
194.0	0	1	0	1
196.0	0	1	0	0
199.0	0	1	0	0
200.0	0	1	0	0
202.0	0	1	0	0
203.0	0	1	0	1
205.0	0	1	0	1
212.0	0	1	0	0
216.0	0	0	0	1
219.0	0	1	0	0
220.0	0	0	0	1
222.0	0	0	0	1
226.0	0	1	0	0
228.0	0	0	0	1
240.0	0	1	0	0
242.0	0	1	0	0
251.0	0	0	0	1
253.0	0	0	0	1
257.0	0	1	0	0
265.0	0	1	0	1
266.0	0	1	0	0
282.0	0	0	0	1
294.0	0	1	0	0
298.0	0	1	0	0
311.0	0	1	0	0
325.0	0	0	0	1
331.0	0	0	0	1
338.0	0	0	0	1
352.0	0	1	0	0
365.0	0	1	0	0
366.0	0	0	0	1
388.0	0	1	0	0
400.0	0	0	0	1
403.0	0	0	0	1
413.0	0	1	0	0
414.0	0	1	0	0
430.0	0	1	0	0
526.0	0	0	0	1
564.0	0	1	0	0
566.0	0	0	0	1
578.0	0	1	0	0