## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-145-TP1.bam --OUTPUT ACR-145-TP1.md.bam --METRICS_FILE ACR-145-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 18:15:11 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	459	15541786	4317734	0	305	10495029	3040963	0.675278	5673164

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.051501	1421630	0	1736920
2.0	1.119429	1173529	823402	1389102
3.0	1.123818	880516	314504	915458
4.0	1.124101	591118	153453	505404
5.0	1.124119	372723	83926	250961
6.0	1.124121	226512	48223	118112
7.0	1.124121	137404	28211	55620
8.0	1.124121	83966	17228	27880
9.0	1.124121	51873	10300	14806
10.0	1.124121	33333	6400	8646
11.0	1.124121	21637	3924	5382
12.0	1.124121	14408	2321	3819
13.0	1.124121	9793	1385	2563
14.0	1.124121	6694	906	1993
15.0	1.124121	4716	575	1519
16.0	1.124121	3369	387	1152
17.0	1.124121	2430	232	939
18.0	1.124121	1805	147	753
19.0	1.124121	1377	106	671
20.0	1.124121	1109	69	573
21.0	1.124121	871	38	454
22.0	1.124121	692	24	370
23.0	1.124121	541	14	355
24.0	1.124121	480	23	288
25.0	1.124121	415	11	251
26.0	1.124121	331	13	230
27.0	1.124121	308	5	207
28.0	1.124121	269	12	203
29.0	1.124121	261	8	168
30.0	1.124121	212	8	132
31.0	1.124121	168	3	128
32.0	1.124121	173	6	106
33.0	1.124121	162	3	93
34.0	1.124121	138	7	102
35.0	1.124121	105	4	104
36.0	1.124121	111	0	86
37.0	1.124121	107	0	56
38.0	1.124121	78	2	70
39.0	1.124121	72	3	55
40.0	1.124121	77	1	51
41.0	1.124121	50	0	45
42.0	1.124121	65	1	47
43.0	1.124121	61	2	36
44.0	1.124121	59	0	37
45.0	1.124121	35	0	40
46.0	1.124121	43	0	40
47.0	1.124121	42	0	36
48.0	1.124121	31	1	35
49.0	1.124121	44	1	19
50.0	1.124121	39	0	27
51.0	1.124121	25	1	38
52.0	1.124121	45	1	34
53.0	1.124121	32	1	20
54.0	1.124121	33	0	22
55.0	1.124121	30	0	23
56.0	1.124121	26	0	21
57.0	1.124121	19	0	17
58.0	1.124121	28	0	24
59.0	1.124121	19	0	15
60.0	1.124121	22	0	13
61.0	1.124121	15	2	19
62.0	1.124121	18	0	12
63.0	1.124121	24	0	13
64.0	1.124121	17	0	14
65.0	1.124121	13	0	11
66.0	1.124121	14	0	16
67.0	1.124121	15	0	6
68.0	1.124121	18	0	7
69.0	1.124121	11	0	11
70.0	1.124121	21	0	14
71.0	1.124121	13	0	10
72.0	1.124121	13	0	13
73.0	1.124121	12	0	5
74.0	1.124121	8	0	10
75.0	1.124121	7	0	12
76.0	1.124121	7	0	3
77.0	1.124121	4	0	5
78.0	1.124121	10	0	4
79.0	1.124121	6	0	10
80.0	1.124121	6	0	7
81.0	1.124121	10	0	3
82.0	1.124121	4	0	5
83.0	1.124121	6	0	3
84.0	1.124121	9	0	4
85.0	1.124121	11	0	4
86.0	1.124121	8	0	5
87.0	1.124121	2	0	6
88.0	1.124121	5	0	6
89.0	1.124121	4	0	5
90.0	1.124121	8	0	1
91.0	1.124121	8	0	3
92.0	1.124121	4	0	3
93.0	1.124121	2	0	6
94.0	1.124121	5	0	5
95.0	1.124121	2	0	1
96.0	1.124121	7	0	3
97.0	1.124121	3	0	6
98.0	1.124121	7	0	3
99.0	1.124121	4	0	5
100.0	1.124121	6	0	2
101.0	0	3	0	4
102.0	0	3	0	1
103.0	0	2	0	4
104.0	0	3	0	2
105.0	0	4	0	1
106.0	0	3	0	0
107.0	0	3	0	3
108.0	0	1	0	5
109.0	0	1	0	5
110.0	0	2	0	1
111.0	0	1	0	1
112.0	0	5	0	3
113.0	0	2	0	1
114.0	0	3	0	1
115.0	0	1	0	1
116.0	0	3	0	3
117.0	0	0	0	1
118.0	0	3	0	1
119.0	0	0	0	4
120.0	0	3	0	2
121.0	0	5	0	3
122.0	0	1	0	2
123.0	0	2	0	3
124.0	0	2	0	2
125.0	0	3	0	0
126.0	0	3	0	1
127.0	0	2	0	0
128.0	0	2	0	3
129.0	0	1	0	1
130.0	0	2	0	0
131.0	0	3	0	1
132.0	0	1	0	0
133.0	0	1	0	0
135.0	0	0	0	2
136.0	0	0	0	1
137.0	0	2	0	2
139.0	0	0	0	2
140.0	0	1	0	2
141.0	0	2	0	0
142.0	0	1	0	1
143.0	0	2	0	1
145.0	0	2	0	2
146.0	0	1	0	1
147.0	0	2	0	1
148.0	0	2	0	1
151.0	0	0	0	1
152.0	0	2	0	0
153.0	0	4	0	1
154.0	0	2	0	1
158.0	0	1	0	0
159.0	0	1	0	2
160.0	0	1	0	0
161.0	0	1	0	0
164.0	0	1	0	3
165.0	0	0	0	1
166.0	0	0	0	2
167.0	0	1	0	0
168.0	0	1	0	0
169.0	0	1	0	0
173.0	0	2	0	0
174.0	0	0	0	1
175.0	0	0	0	1
180.0	0	2	0	0
187.0	0	1	0	0
188.0	0	1	0	0
192.0	0	0	0	1
204.0	0	1	0	0
208.0	0	1	0	0
216.0	0	1	0	0
221.0	0	0	0	1
245.0	0	0	0	1
246.0	0	0	0	1
253.0	0	1	0	0
260.0	0	1	0	0
261.0	0	1	0	0
270.0	0	0	0	1
274.0	0	0	0	1
282.0	0	1	0	0
297.0	0	1	0	0
305.0	0	0	0	1
322.0	0	0	0	1
328.0	0	1	0	0
332.0	0	1	0	0
333.0	0	0	0	1
341.0	0	1	0	0
347.0	0	0	0	1
373.0	0	0	0	1
374.0	0	0	0	1
376.0	0	1	0	0
398.0	0	1	0	0
401.0	0	1	0	0
413.0	0	0	0	1
420.0	0	0	0	1
430.0	0	1	0	0
449.0	0	1	0	0
469.0	0	0	0	1
492.0	0	1	0	0
517.0	0	0	0	1
531.0	0	1	0	0