## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-186-TP4.bam --OUTPUT ACR-186-TP4.md.bam --METRICS_FILE ACR-186-TP4.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 18:14:49 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	142	14841097	3139653	0	95	8588960	3672904	0.578729	8597667

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.130429	2612650	0	3361550
2.0	1.331604	1601624	973096	1736501
3.0	1.367406	902128	388102	718481
4.0	1.373777	487317	194944	263566
5.0	1.374911	264605	106483	94341
6.0	1.375113	148838	59697	35869
7.0	1.375149	86929	34000	15674
8.0	1.375155	51803	19867	8077
9.0	1.375156	32144	11731	4632
10.0	1.375156	20696	6752	3034
11.0	1.375157	13428	3986	2071
12.0	1.375157	8579	2419	1458
13.0	1.375157	5733	1374	1093
14.0	1.375157	3902	854	893
15.0	1.375157	2687	502	722
16.0	1.375157	1848	340	613
17.0	1.375157	1396	180	450
18.0	1.375157	1038	120	390
19.0	1.375157	746	80	290
20.0	1.375157	563	64	251
21.0	1.375157	442	33	237
22.0	1.375157	360	13	198
23.0	1.375157	301	23	154
24.0	1.375157	240	11	134
25.0	1.375157	226	4	134
26.0	1.375157	195	6	116
27.0	1.375157	143	7	102
28.0	1.375157	133	6	76
29.0	1.375157	123	2	91
30.0	1.375157	81	2	63
31.0	1.375157	106	1	55
32.0	1.375157	84	2	61
33.0	1.375157	71	2	60
34.0	1.375157	68	0	42
35.0	1.375157	56	1	44
36.0	1.375157	56	1	31
37.0	1.375157	57	0	37
38.0	1.375157	47	1	31
39.0	1.375157	41	0	28
40.0	1.375157	37	3	32
41.0	1.375157	46	0	22
42.0	1.375157	25	1	33
43.0	1.375157	29	0	29
44.0	1.375157	30	0	18
45.0	1.375157	30	0	12
46.0	1.375157	25	1	15
47.0	1.375157	27	1	15
48.0	1.375157	23	0	14
49.0	1.375157	17	0	10
50.0	1.375157	25	0	15
51.0	1.375157	10	0	10
52.0	1.375157	20	0	16
53.0	1.375157	16	0	10
54.0	1.375157	12	0	10
55.0	1.375157	14	0	6
56.0	1.375157	7	0	5
57.0	1.375157	12	0	12
58.0	1.375157	5	0	5
59.0	1.375157	7	0	4
60.0	1.375157	9	0	5
61.0	1.375157	6	0	6
62.0	1.375157	3	0	7
63.0	1.375157	10	0	8
64.0	1.375157	8	0	4
65.0	1.375157	7	0	6
66.0	1.375157	8	0	11
67.0	1.375157	4	0	7
68.0	1.375157	7	0	2
69.0	1.375157	8	0	2
70.0	1.375157	3	0	6
71.0	1.375157	11	0	4
72.0	1.375157	5	0	1
73.0	1.375157	5	0	2
74.0	1.375157	2	0	5
75.0	1.375157	3	0	6
76.0	1.375157	8	0	8
77.0	1.375157	4	0	4
78.0	1.375157	5	0	9
79.0	1.375157	9	0	8
80.0	1.375157	8	0	2
81.0	1.375157	2	0	4
82.0	1.375157	3	0	4
83.0	1.375157	4	0	3
84.0	1.375157	4	0	0
85.0	1.375157	5	0	2
86.0	1.375157	2	0	0
87.0	1.375157	4	0	0
88.0	1.375157	2	0	2
89.0	1.375157	1	0	1
90.0	1.375157	2	0	2
91.0	1.375157	2	0	2
92.0	1.375157	0	0	5
93.0	1.375157	2	0	1
94.0	1.375157	1	0	1
95.0	1.375157	4	0	1
96.0	1.375157	3	0	2
97.0	1.375157	1	0	1
98.0	1.375157	3	0	3
99.0	1.375157	1	0	1
100.0	1.375157	2	0	3
101.0	0	0	0	2
102.0	0	3	0	1
103.0	0	4	0	3
104.0	0	2	0	2
106.0	0	3	0	0
107.0	0	2	0	0
108.0	0	1	0	0
109.0	0	2	0	1
115.0	0	0	0	1
116.0	0	2	0	1
118.0	0	1	0	0
119.0	0	1	0	2
121.0	0	0	0	1
122.0	0	1	0	0
123.0	0	2	0	0
127.0	0	1	0	1
128.0	0	0	0	1
130.0	0	0	0	2
131.0	0	0	0	1
132.0	0	1	0	0
133.0	0	1	0	0
136.0	0	1	0	1
137.0	0	2	0	0
139.0	0	1	0	0
145.0	0	0	0	1
147.0	0	1	0	2
151.0	0	0	0	2
154.0	0	1	0	0
155.0	0	2	0	0
160.0	0	0	0	2
168.0	0	1	0	1
170.0	0	0	0	1
172.0	0	1	0	0
178.0	0	0	0	1
184.0	0	1	0	0
186.0	0	1	0	0
187.0	0	2	0	0
202.0	0	0	0	1
206.0	0	0	0	1
208.0	0	1	0	0
209.0	0	1	0	0
218.0	0	1	0	0
221.0	0	0	0	1
224.0	0	0	0	1
230.0	0	1	0	0
252.0	0	1	0	0
254.0	0	0	0	1
261.0	0	0	0	1
265.0	0	0	0	1
272.0	0	1	0	0
280.0	0	2	0	0
294.0	0	0	0	1
306.0	0	0	0	1
308.0	0	1	0	0
312.0	0	1	0	0
349.0	0	0	0	1
350.0	0	0	0	1
368.0	0	1	0	0
377.0	0	1	0	0
395.0	0	0	0	1
414.0	0	0	0	1
417.0	0	1	0	0
422.0	0	1	0	0