## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-225-TP3.bam --OUTPUT ACR-225-TP3.md.bam --METRICS_FILE ACR-225-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 18:14:52 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	372	15630593	3292804	0	250	8940959	4284700	0.572018	9703548

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.160826	2914705	0	3877557
2.0	1.392673	1677692	1068713	1759091
3.0	1.438978	921717	440709	666841
4.0	1.448227	497042	225135	233156
5.0	1.450074	273530	125531	82864
6.0	1.450443	154677	71775	31775
7.0	1.450517	90395	42029	13990
8.0	1.450531	55148	25035	7199
9.0	1.450534	34677	15057	4157
10.0	1.450535	22123	9022	2787
11.0	1.450535	14497	5468	2016
12.0	1.450535	9594	3311	1426
13.0	1.450535	6330	2000	1063
14.0	1.450535	4327	1248	832
15.0	1.450535	3013	771	685
16.0	1.450535	2139	474	515
17.0	1.450535	1551	294	468
18.0	1.450535	1106	210	374
19.0	1.450535	868	134	310
20.0	1.450535	660	83	246
21.0	1.450535	494	74	234
22.0	1.450535	408	33	188
23.0	1.450535	322	27	178
24.0	1.450535	266	19	134
25.0	1.450535	240	15	113
26.0	1.450535	192	11	137
27.0	1.450535	178	5	113
28.0	1.450535	145	10	81
29.0	1.450535	115	7	84
30.0	1.450535	114	1	61
31.0	1.450535	96	2	59
32.0	1.450535	92	1	54
33.0	1.450535	64	3	53
34.0	1.450535	77	6	55
35.0	1.450535	70	4	43
36.0	1.450535	70	3	35
37.0	1.450535	60	4	41
38.0	1.450535	36	4	30
39.0	1.450535	45	3	36
40.0	1.450535	41	2	25
41.0	1.450535	32	3	30
42.0	1.450535	37	1	27
43.0	1.450535	29	1	23
44.0	1.450535	32	1	29
45.0	1.450535	23	2	14
46.0	1.450535	28	1	17
47.0	1.450535	29	1	15
48.0	1.450535	23	1	17
49.0	1.450535	20	0	17
50.0	1.450535	18	2	14
51.0	1.450535	20	0	17
52.0	1.450535	17	2	10
53.0	1.450535	22	0	11
54.0	1.450535	14	0	14
55.0	1.450535	12	1	17
56.0	1.450535	21	0	8
57.0	1.450535	16	0	13
58.0	1.450535	13	2	8
59.0	1.450535	11	0	9
60.0	1.450535	11	0	11
61.0	1.450535	10	0	6
62.0	1.450535	7	1	10
63.0	1.450535	11	0	6
64.0	1.450535	20	0	13
65.0	1.450535	14	0	11
66.0	1.450535	7	0	3
67.0	1.450535	4	0	9
68.0	1.450535	5	0	4
69.0	1.450535	10	1	3
70.0	1.450535	7	0	4
71.0	1.450535	9	0	4
72.0	1.450535	10	1	1
73.0	1.450535	3	0	3
74.0	1.450535	4	1	2
75.0	1.450535	2	0	5
76.0	1.450535	5	0	5
77.0	1.450535	4	0	2
78.0	1.450535	4	0	3
79.0	1.450535	2	1	6
80.0	1.450535	3	0	3
81.0	1.450535	2	0	3
82.0	1.450535	2	0	2
83.0	1.450535	4	0	4
84.0	1.450535	4	0	3
85.0	1.450535	2	0	2
86.0	1.450535	1	0	4
87.0	1.450535	4	0	5
88.0	1.450535	1	0	1
89.0	1.450535	1	0	4
90.0	1.450535	6	0	5
91.0	1.450535	2	0	1
92.0	1.450535	4	1	5
93.0	1.450535	5	1	4
94.0	1.450535	4	0	1
95.0	1.450535	3	0	0
96.0	1.450535	1	0	2
97.0	1.450535	3	0	1
98.0	1.450535	3	0	1
99.0	1.450535	4	0	1
100.0	1.450535	6	0	0
101.0	0	3	0	1
102.0	0	7	0	3
103.0	0	3	0	1
104.0	0	3	0	2
105.0	0	1	0	0
106.0	0	0	0	1
108.0	0	1	0	2
109.0	0	2	0	3
110.0	0	1	0	1
111.0	0	1	0	4
112.0	0	1	0	1
113.0	0	2	1	1
114.0	0	2	1	0
115.0	0	2	0	0
116.0	0	2	0	1
117.0	0	2	0	2
118.0	0	3	0	0
119.0	0	1	0	2
120.0	0	0	0	1
121.0	0	1	0	1
122.0	0	0	0	1
123.0	0	1	0	0
124.0	0	2	0	1
125.0	0	1	0	1
126.0	0	1	1	1
127.0	0	3	0	0
128.0	0	1	0	1
130.0	0	4	0	0
131.0	0	1	0	0
133.0	0	1	0	2
135.0	0	1	0	0
137.0	0	1	0	0
138.0	0	0	0	1
139.0	0	1	0	0
142.0	0	1	0	0
143.0	0	1	0	0
146.0	0	1	1	0
147.0	0	1	0	1
151.0	0	0	0	1
153.0	0	1	0	0
154.0	0	1	0	0
155.0	0	1	0	0
156.0	0	0	0	1
157.0	0	1	0	1
158.0	0	1	1	0
160.0	0	1	0	0
162.0	0	0	0	1
166.0	0	1	0	0
167.0	0	0	0	2
173.0	0	1	0	0
179.0	0	1	0	0
184.0	0	0	0	1
186.0	0	1	0	0
188.0	0	0	0	1
190.0	0	0	0	1
193.0	0	1	0	0
198.0	0	0	0	1
199.0	0	1	0	0
203.0	0	1	0	1
205.0	0	1	0	0
206.0	0	0	0	1
210.0	0	1	0	1
212.0	0	1	0	0
214.0	0	1	0	1
217.0	0	1	0	0
218.0	0	1	0	0
226.0	0	1	0	0
227.0	0	0	0	1
229.0	0	0	0	1
233.0	0	1	0	0
238.0	0	1	0	0
241.0	0	2	0	0
264.0	0	0	0	1
280.0	0	1	0	0
352.0	0	0	0	1
366.0	0	0	0	1
371.0	0	1	0	0
509.0	0	1	0	0