## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-173-TP2.bam --OUTPUT ACR-173-TP2.md.bam --METRICS_FILE ACR-173-TP2.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 18:13:33 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	109	11770541	2880468	0	58	5546661	2991900	0.471233	11986894

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.20453	3450319	0	4441500
2.0	1.655722	1483144	915570	1311271
3.0	1.824729	652781	351806	334558
4.0	1.888036	302509	164710	84857
5.0	1.911749	148767	82600	25220
6.0	1.920632	78733	42278	9849
7.0	1.923959	43123	22164	5095
8.0	1.925206	24671	11486	3007
9.0	1.925672	14373	6014	1958
10.0	1.925847	8578	3235	1403
11.0	1.925913	5150	1783	918
12.0	1.925937	3298	955	714
13.0	1.925946	2103	495	536
14.0	1.92595	1367	300	457
15.0	1.925951	976	172	373
16.0	1.925952	690	108	293
17.0	1.925952	518	63	247
18.0	1.925952	412	24	198
19.0	1.925952	347	28	170
20.0	1.925952	271	17	117
21.0	1.925952	209	18	116
22.0	1.925952	167	11	121
23.0	1.925952	146	4	89
24.0	1.925952	136	6	55
25.0	1.925952	88	6	59
26.0	1.925952	88	2	57
27.0	1.925952	69	6	49
28.0	1.925952	78	2	31
29.0	1.925952	49	0	41
30.0	1.925952	59	2	36
31.0	1.925952	44	2	44
32.0	1.925952	39	1	25
33.0	1.925952	40	0	24
34.0	1.925952	37	0	34
35.0	1.925952	34	1	21
36.0	1.925952	28	1	20
37.0	1.925952	23	1	18
38.0	1.925952	22	1	15
39.0	1.925952	28	1	28
40.0	1.925952	30	0	14
41.0	1.925952	13	0	16
42.0	1.925952	22	0	8
43.0	1.925952	16	0	10
44.0	1.925952	14	0	18
45.0	1.925952	15	0	17
46.0	1.925952	10	1	16
47.0	1.925952	18	0	9
48.0	1.925952	17	1	8
49.0	1.925952	12	1	9
50.0	1.925952	18	1	7
51.0	1.925952	13	0	6
52.0	1.925952	11	0	4
53.0	1.925952	12	0	2
54.0	1.925952	9	0	2
55.0	1.925952	1	0	7
56.0	1.925952	8	0	3
57.0	1.925952	4	0	9
58.0	1.925952	7	0	4
59.0	1.925952	4	0	8
60.0	1.925952	5	0	6
61.0	1.925952	9	0	2
62.0	1.925952	6	0	2
63.0	1.925952	2	0	2
64.0	1.925952	7	0	2
65.0	1.925952	7	0	6
66.0	1.925952	0	0	3
67.0	1.925952	3	0	4
68.0	1.925952	2	0	1
69.0	1.925952	2	0	3
70.0	1.925952	5	0	1
71.0	1.925952	6	0	1
72.0	1.925952	1	0	3
73.0	1.925952	1	0	3
74.0	1.925952	1	0	0
75.0	1.925952	4	0	3
76.0	1.925952	2	0	1
77.0	1.925952	0	0	0
78.0	1.925952	2	0	0
79.0	1.925952	1	0	0
80.0	1.925952	0	0	0
81.0	1.925952	2	0	5
82.0	1.925952	1	0	1
83.0	1.925952	3	0	2
84.0	1.925952	3	0	1
85.0	1.925952	3	0	0
86.0	1.925952	2	0	2
87.0	1.925952	3	0	0
88.0	1.925952	0	0	0
89.0	1.925952	0	0	5
90.0	1.925952	1	0	0
91.0	1.925952	4	0	0
92.0	1.925952	1	0	0
93.0	1.925952	0	0	0
94.0	1.925952	1	0	0
95.0	1.925952	0	0	0
96.0	1.925952	0	0	0
97.0	1.925952	0	0	0
98.0	1.925952	0	0	0
99.0	1.925952	1	0	0
100.0	1.925952	0	0	0
107.0	0	0	0	1
108.0	0	1	0	0
109.0	0	0	0	1
110.0	0	0	0	1
111.0	0	0	0	1
112.0	0	1	0	0
114.0	0	1	0	1
116.0	0	0	0	1
120.0	0	1	0	3
121.0	0	2	0	1
122.0	0	1	0	0
124.0	0	1	0	0
126.0	0	1	0	0
129.0	0	1	0	2
132.0	0	1	0	0
137.0	0	2	0	0
157.0	0	0	0	1
177.0	0	1	0	1
185.0	0	1	0	0
187.0	0	0	0	2
194.0	0	1	0	1
196.0	0	0	0	1
198.0	0	1	0	0
199.0	0	1	0	0
201.0	0	0	0	1
205.0	0	1	0	0
207.0	0	0	0	1
216.0	0	1	0	0
228.0	0	1	0	0