## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-225-TP4.bam --OUTPUT ACR-225-TP4.md.bam --METRICS_FILE ACR-225-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 18:13:22 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	287	11452673	2421211	0	180	7122796	2341354	0.621933	5260683

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.077222	1536793	0	1887694
2.0	1.199355	1100368	650594	1245080
3.0	1.213202	702273	240479	658470
4.0	1.214772	411065	116709	298669
5.0	1.21495	233279	63324	125809
6.0	1.21497	132322	36405	53583
7.0	1.214973	76980	21669	24212
8.0	1.214973	46733	13224	12105
9.0	1.214973	28850	7828	6587
10.0	1.214973	18588	4758	4266
11.0	1.214973	12159	2981	2820
12.0	1.214973	7997	1920	1930
13.0	1.214973	5571	1184	1526
14.0	1.214973	3948	674	1114
15.0	1.214973	2806	466	883
16.0	1.214973	2034	336	712
17.0	1.214973	1485	165	522
18.0	1.214973	1066	136	477
19.0	1.214973	866	82	378
20.0	1.214973	674	45	330
21.0	1.214973	545	33	276
22.0	1.214973	385	19	246
23.0	1.214973	361	17	195
24.0	1.214973	267	17	177
25.0	1.214973	254	8	160
26.0	1.214973	190	6	110
27.0	1.214973	165	5	120
28.0	1.214973	137	7	121
29.0	1.214973	130	5	106
30.0	1.214973	111	5	83
31.0	1.214973	109	4	63
32.0	1.214973	95	1	75
33.0	1.214973	86	2	67
34.0	1.214973	68	1	42
35.0	1.214973	67	3	54
36.0	1.214973	62	1	52
37.0	1.214973	53	2	52
38.0	1.214973	68	3	50
39.0	1.214973	50	1	44
40.0	1.214973	49	0	29
41.0	1.214973	44	0	24
42.0	1.214973	35	1	22
43.0	1.214973	42	0	29
44.0	1.214973	31	0	23
45.0	1.214973	20	0	19
46.0	1.214973	28	0	15
47.0	1.214973	27	0	23
48.0	1.214973	27	0	19
49.0	1.214973	21	1	14
50.0	1.214973	18	1	18
51.0	1.214973	14	0	17
52.0	1.214973	22	0	11
53.0	1.214973	11	0	19
54.0	1.214973	21	0	23
55.0	1.214973	20	0	9
56.0	1.214973	17	0	10
57.0	1.214973	15	0	9
58.0	1.214973	11	0	14
59.0	1.214973	20	0	10
60.0	1.214973	8	0	7
61.0	1.214973	10	0	12
62.0	1.214973	17	0	7
63.0	1.214973	13	0	10
64.0	1.214973	7	0	8
65.0	1.214973	8	0	9
66.0	1.214973	12	1	9
67.0	1.214973	12	0	10
68.0	1.214973	8	0	8
69.0	1.214973	12	0	7
70.0	1.214973	13	0	4
71.0	1.214973	5	0	8
72.0	1.214973	12	0	8
73.0	1.214973	7	0	3
74.0	1.214973	7	0	3
75.0	1.214973	6	0	6
76.0	1.214973	4	0	2
77.0	1.214973	6	0	1
78.0	1.214973	3	0	3
79.0	1.214973	1	0	5
80.0	1.214973	3	0	5
81.0	1.214973	2	0	3
82.0	1.214973	4	0	5
83.0	1.214973	4	0	5
84.0	1.214973	6	0	4
85.0	1.214973	3	0	2
86.0	1.214973	5	0	1
87.0	1.214973	1	0	5
88.0	1.214973	6	0	5
89.0	1.214973	2	0	4
90.0	1.214973	4	0	4
91.0	1.214973	2	0	1
92.0	1.214973	2	0	0
93.0	1.214973	1	0	4
94.0	1.214973	2	0	2
95.0	1.214973	6	0	3
96.0	1.214973	2	0	2
97.0	1.214973	4	0	2
98.0	1.214973	5	0	2
99.0	1.214973	3	0	1
100.0	1.214973	0	0	0
101.0	0	3	0	1
103.0	0	2	0	2
105.0	0	0	0	4
106.0	0	4	0	3
107.0	0	1	0	1
108.0	0	2	0	1
109.0	0	1	0	0
110.0	0	2	0	1
111.0	0	3	0	1
112.0	0	2	0	3
113.0	0	1	0	1
114.0	0	2	0	0
115.0	0	0	0	2
116.0	0	3	0	0
118.0	0	1	0	0
119.0	0	0	0	1
121.0	0	3	0	1
122.0	0	1	0	0
123.0	0	0	0	2
124.0	0	1	0	1
125.0	0	0	0	1
126.0	0	1	0	1
127.0	0	0	0	1
128.0	0	4	0	0
129.0	0	0	0	2
130.0	0	1	0	1
132.0	0	1	0	0
133.0	0	3	0	1
134.0	0	0	0	1
135.0	0	1	0	0
136.0	0	2	0	1
137.0	0	0	0	1
138.0	0	0	0	1
139.0	0	1	0	1
140.0	0	2	0	1
145.0	0	1	0	1
147.0	0	0	0	2
148.0	0	0	0	2
149.0	0	1	0	0
151.0	0	1	0	1
152.0	0	1	0	0
153.0	0	2	0	0
155.0	0	1	0	1
156.0	0	2	0	0
158.0	0	1	0	1
159.0	0	1	0	0
161.0	0	1	0	0
163.0	0	1	0	0
164.0	0	1	0	0
165.0	0	0	0	1
169.0	0	0	0	1
172.0	0	1	0	0
174.0	0	0	0	1
175.0	0	0	0	1
180.0	0	0	0	1
181.0	0	1	0	1
184.0	0	1	0	0
185.0	0	1	0	0
189.0	0	1	0	1
193.0	0	0	0	1
197.0	0	0	0	1
199.0	0	1	0	1
206.0	0	1	0	0
211.0	0	0	0	1
212.0	0	1	0	0
214.0	0	1	0	0
217.0	0	0	0	1
221.0	0	1	0	0
223.0	0	1	0	0
234.0	0	0	0	1
237.0	0	1	0	0
241.0	0	1	0	1
248.0	0	1	0	0
251.0	0	0	0	1
254.0	0	0	0	1
257.0	0	1	0	0
258.0	0	0	0	1
263.0	0	1	0	0
274.0	0	1	0	0
293.0	0	0	0	1
309.0	0	0	0	1
316.0	0	0	0	1
317.0	0	1	0	0
320.0	0	1	0	0
343.0	0	1	0	0
364.0	0	0	0	1
377.0	0	0	0	1
378.0	0	1	0	0
382.0	0	0	0	1
394.0	0	1	0	0
414.0	0	0	0	1
425.0	0	1	0	0
426.0	0	1	0	0