## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-225-TP1.bam --OUTPUT ACR-225-TP1.md.bam --METRICS_FILE ACR-225-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 18:13:21 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	270	12569710	2785631	0	180	6900152	2753666	0.548952	8043105

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.12137	2601771	0	3233384
2.0	1.356353	1444257	821177	1501461
3.0	1.405594	754219	299990	580342
4.0	1.415912	387812	142066	208185
5.0	1.418074	202602	74570	75441
6.0	1.418528	110226	40662	30521
7.0	1.418622	62408	22995	13801
8.0	1.418642	36960	12836	7434
9.0	1.418647	22624	7495	4596
10.0	1.418647	14151	4408	3031
11.0	1.418648	9019	2618	2169
12.0	1.418648	6041	1434	1570
13.0	1.418648	4122	928	1131
14.0	1.418648	2807	549	942
15.0	1.418648	2051	342	750
16.0	1.418648	1511	218	631
17.0	1.418648	1075	121	494
18.0	1.418648	916	86	422
19.0	1.418648	629	65	343
20.0	1.418648	531	34	301
21.0	1.418648	440	33	249
22.0	1.418648	364	19	221
23.0	1.418648	293	18	203
24.0	1.418648	270	13	174
25.0	1.418648	220	8	133
26.0	1.418648	187	7	113
27.0	1.418648	165	2	100
28.0	1.418648	146	3	93
29.0	1.418648	117	5	91
30.0	1.418648	95	8	93
31.0	1.418648	110	3	68
32.0	1.418648	102	4	80
33.0	1.418648	89	0	66
34.0	1.418648	81	2	61
35.0	1.418648	50	1	54
36.0	1.418648	64	2	56
37.0	1.418648	76	0	38
38.0	1.418648	53	1	40
39.0	1.418648	54	0	41
40.0	1.418648	52	0	23
41.0	1.418648	39	2	31
42.0	1.418648	41	1	28
43.0	1.418648	46	0	30
44.0	1.418648	31	1	26
45.0	1.418648	33	2	23
46.0	1.418648	25	0	16
47.0	1.418648	29	2	28
48.0	1.418648	21	1	14
49.0	1.418648	27	0	15
50.0	1.418648	28	0	12
51.0	1.418648	22	1	16
52.0	1.418648	19	0	24
53.0	1.418648	16	1	15
54.0	1.418648	16	0	9
55.0	1.418648	8	1	13
56.0	1.418648	21	0	13
57.0	1.418648	13	1	12
58.0	1.418648	13	0	13
59.0	1.418648	18	1	12
60.0	1.418648	16	0	7
61.0	1.418648	15	1	8
62.0	1.418648	6	0	10
63.0	1.418648	6	0	7
64.0	1.418648	11	0	8
65.0	1.418648	8	0	6
66.0	1.418648	10	0	4
67.0	1.418648	9	0	5
68.0	1.418648	8	0	5
69.0	1.418648	8	0	10
70.0	1.418648	3	0	10
71.0	1.418648	10	0	4
72.0	1.418648	3	0	3
73.0	1.418648	3	0	7
74.0	1.418648	7	0	5
75.0	1.418648	7	0	2
76.0	1.418648	6	0	5
77.0	1.418648	4	0	5
78.0	1.418648	7	0	3
79.0	1.418648	4	0	3
80.0	1.418648	7	0	5
81.0	1.418648	4	0	1
82.0	1.418648	6	0	6
83.0	1.418648	4	0	2
84.0	1.418648	6	0	3
85.0	1.418648	6	0	2
86.0	1.418648	3	0	5
87.0	1.418648	3	0	2
88.0	1.418648	1	0	5
89.0	1.418648	3	0	5
90.0	1.418648	1	0	7
91.0	1.418648	3	0	5
92.0	1.418648	4	0	3
93.0	1.418648	5	0	2
94.0	1.418648	4	0	3
95.0	1.418648	3	0	2
96.0	1.418648	6	0	1
97.0	1.418648	3	0	4
98.0	1.418648	2	0	3
99.0	1.418648	6	0	6
100.0	1.418648	6	0	2
101.0	0	4	0	3
102.0	0	2	0	3
103.0	0	2	0	2
104.0	0	1	0	1
105.0	0	4	0	0
106.0	0	1	0	2
107.0	0	5	0	2
108.0	0	0	0	1
109.0	0	1	0	0
110.0	0	4	0	1
111.0	0	2	0	0
112.0	0	1	0	1
113.0	0	0	0	2
114.0	0	0	0	1
115.0	0	1	0	2
116.0	0	2	0	0
117.0	0	2	0	0
118.0	0	1	0	0
120.0	0	2	0	0
121.0	0	1	0	2
122.0	0	2	0	5
123.0	0	1	0	1
124.0	0	1	0	2
125.0	0	2	0	3
126.0	0	2	0	1
127.0	0	3	0	0
128.0	0	2	0	0
130.0	0	2	0	0
131.0	0	1	0	1
132.0	0	0	0	1
133.0	0	2	0	0
136.0	0	0	0	1
138.0	0	0	0	2
139.0	0	1	0	0
141.0	0	1	0	0
142.0	0	1	0	1
143.0	0	1	0	1
145.0	0	0	0	1
146.0	0	1	0	1
148.0	0	0	0	2
149.0	0	0	0	1
150.0	0	1	0	0
151.0	0	2	0	0
152.0	0	1	0	1
154.0	0	2	0	1
157.0	0	0	0	1
159.0	0	3	0	0
160.0	0	1	0	1
165.0	0	2	0	0
169.0	0	2	0	0
171.0	0	1	0	0
177.0	0	0	0	1
185.0	0	0	0	1
188.0	0	1	0	0
189.0	0	0	0	1
196.0	0	1	0	1
199.0	0	0	0	1
202.0	0	0	0	1
206.0	0	1	0	0
215.0	0	1	0	0
217.0	0	0	0	1
219.0	0	1	0	0
220.0	0	1	0	0
221.0	0	1	0	0
223.0	0	1	0	0
234.0	0	0	0	1
237.0	0	0	0	1
250.0	0	0	0	1
253.0	0	1	0	1
254.0	0	1	0	1
256.0	0	1	0	0
262.0	0	1	0	0
264.0	0	0	0	1
274.0	0	1	0	0
280.0	0	1	0	1
292.0	0	1	0	0
298.0	0	0	0	1
317.0	0	1	0	0
358.0	0	0	0	1
366.0	0	0	0	1
372.0	0	0	0	1
373.0	0	1	0	0
375.0	0	0	0	1
379.0	0	1	0	0
389.0	0	1	0	0
406.0	0	1	0	0
507.0	0	0	0	1
526.0	0	1	0	0