## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-173-TP4.bam --OUTPUT ACR-173-TP4.md.bam --METRICS_FILE ACR-173-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 18:13:43 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	283	11523809	2731754	0	157	8129960	2166025	0.705491	3684498

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.038066	822815	0	986708
2.0	1.083555	732915	525073	878204
3.0	1.085549	599310	201814	655176
4.0	1.085636	431528	102087	406089
5.0	1.08564	288054	58826	222697
6.0	1.08564	183011	36328	113306
7.0	1.08564	114733	22770	56294
8.0	1.08564	72402	14700	28587
9.0	1.08564	46228	9529	15418
10.0	1.08564	30446	6108	9087
11.0	1.08564	20339	4008	5594
12.0	1.08564	13718	2698	3622
13.0	1.08564	9635	1779	2455
14.0	1.08564	6745	1190	1765
15.0	1.08564	4945	746	1378
16.0	1.08564	3564	507	1070
17.0	1.08564	2654	322	871
18.0	1.08564	1978	212	740
19.0	1.08564	1501	174	602
20.0	1.08564	1191	96	491
21.0	1.08564	925	67	387
22.0	1.08564	724	47	332
23.0	1.08564	579	24	280
24.0	1.08564	482	23	249
25.0	1.08564	395	12	232
26.0	1.08564	295	9	187
27.0	1.08564	272	10	174
28.0	1.08564	203	5	117
29.0	1.08564	186	5	148
30.0	1.08564	172	3	114
31.0	1.08564	130	3	103
32.0	1.08564	136	4	94
33.0	1.08564	128	1	75
34.0	1.08564	92	1	94
35.0	1.08564	96	1	79
36.0	1.08564	81	0	55
37.0	1.08564	89	2	69
38.0	1.08564	81	1	41
39.0	1.08564	64	2	56
40.0	1.08564	40	0	50
41.0	1.08564	56	0	34
42.0	1.08564	55	1	39
43.0	1.08564	37	0	29
44.0	1.08564	51	0	41
45.0	1.08564	40	0	31
46.0	1.08564	39	0	28
47.0	1.08564	39	0	32
48.0	1.08564	37	0	24
49.0	1.08564	38	0	31
50.0	1.08564	39	0	19
51.0	1.08564	29	0	32
52.0	1.08564	21	0	17
53.0	1.08564	25	0	19
54.0	1.08564	22	0	17
55.0	1.08564	19	0	14
56.0	1.08564	12	0	13
57.0	1.08564	19	0	17
58.0	1.08564	24	0	13
59.0	1.08564	14	0	12
60.0	1.08564	19	0	11
61.0	1.08564	12	0	7
62.0	1.08564	13	0	5
63.0	1.08564	7	0	8
64.0	1.08564	4	0	8
65.0	1.08564	9	0	12
66.0	1.08564	11	0	9
67.0	1.08564	5	0	12
68.0	1.08564	11	0	9
69.0	1.08564	7	0	8
70.0	1.08564	8	0	10
71.0	1.08564	12	0	7
72.0	1.08564	4	0	8
73.0	1.08564	10	0	4
74.0	1.08564	10	0	4
75.0	1.08564	6	0	7
76.0	1.08564	6	0	5
77.0	1.08564	5	0	5
78.0	1.08564	7	0	6
79.0	1.08564	7	0	7
80.0	1.08564	7	0	8
81.0	1.08564	1	0	3
82.0	1.08564	2	0	0
83.0	1.08564	4	0	4
84.0	1.08564	6	0	5
85.0	1.08564	3	0	3
86.0	1.08564	5	0	1
87.0	1.08564	4	0	4
88.0	1.08564	7	0	7
89.0	1.08564	4	0	5
90.0	1.08564	5	0	3
91.0	1.08564	7	0	1
92.0	1.08564	7	0	5
93.0	1.08564	5	0	1
94.0	1.08564	3	0	2
95.0	1.08564	3	0	4
96.0	1.08564	2	0	5
97.0	1.08564	2	0	1
98.0	1.08564	1	0	2
99.0	1.08564	3	0	4
100.0	1.08564	3	0	3
101.0	0	5	0	4
102.0	0	4	0	2
103.0	0	4	0	3
104.0	0	3	0	1
105.0	0	2	0	0
106.0	0	1	0	1
107.0	0	3	0	2
108.0	0	3	0	0
109.0	0	1	0	0
110.0	0	2	0	2
111.0	0	1	0	1
112.0	0	1	0	1
113.0	0	1	0	1
114.0	0	2	0	0
115.0	0	0	0	2
116.0	0	1	0	3
117.0	0	1	0	1
118.0	0	1	0	3
119.0	0	2	0	1
121.0	0	2	0	0
122.0	0	1	0	2
123.0	0	1	0	1
124.0	0	2	0	1
126.0	0	2	0	1
127.0	0	4	0	2
128.0	0	0	0	2
129.0	0	1	0	1
130.0	0	0	0	1
131.0	0	1	0	2
133.0	0	1	0	0
134.0	0	2	0	0
135.0	0	1	0	0
136.0	0	3	0	0
137.0	0	1	0	1
139.0	0	0	0	1
140.0	0	1	0	0
144.0	0	0	0	2
145.0	0	0	0	1
146.0	0	0	0	2
147.0	0	0	0	1
148.0	0	1	0	0
149.0	0	1	0	0
150.0	0	2	0	0
152.0	0	0	0	1
154.0	0	0	0	1
156.0	0	2	0	0
158.0	0	1	0	1
161.0	0	2	0	0
163.0	0	1	0	0
165.0	0	0	0	1
175.0	0	1	0	1
176.0	0	1	0	0
177.0	0	0	0	1
183.0	0	0	0	1
185.0	0	1	0	0
188.0	0	1	0	1
191.0	0	1	0	1
193.0	0	1	0	0
194.0	0	0	0	1
195.0	0	0	0	1
198.0	0	1	0	0
221.0	0	0	0	2
223.0	0	0	0	1
226.0	0	1	0	0
229.0	0	2	0	0
236.0	0	1	0	0
237.0	0	1	0	0
257.0	0	0	0	1
260.0	0	0	0	1
270.0	0	1	0	0
278.0	0	1	0	0
283.0	0	0	0	1
287.0	0	0	0	1
288.0	0	1	0	0
293.0	0	0	0	1
296.0	0	0	0	1
299.0	0	1	0	0
309.0	0	1	0	0
316.0	0	1	0	0
317.0	0	0	0	1
333.0	0	1	0	0
342.0	0	0	0	1
350.0	0	1	0	0
354.0	0	0	0	1
374.0	0	1	0	0
459.0	0	0	0	1
472.0	0	1	0	0
542.0	0	0	0	1
575.0	0	1	0	0