## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-139-TP2.bam --OUTPUT ACR-139-TP2.md.bam --METRICS_FILE ACR-139-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 18:14:16 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	153	14682333	3185122	0	105	7657603	4319193	0.521553	12403966

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.225171	3570741	0	4806081
2.0	1.600257	1694912	1137860	1581622
3.0	1.715089	814635	471643	439063
4.0	1.750245	410312	237159	119262
5.0	1.761008	217956	126483	36957
6.0	1.764303	122672	69746	14801
7.0	1.765312	71586	38847	7626
8.0	1.765621	43203	21628	4662
9.0	1.765715	26397	12212	3049
10.0	1.765744	16239	7016	2272
11.0	1.765753	10603	4134	1574
12.0	1.765756	6802	2374	1205
13.0	1.765757	4550	1367	1008
14.0	1.765757	3050	895	793
15.0	1.765757	2169	512	602
16.0	1.765757	1593	297	504
17.0	1.765757	1184	212	427
18.0	1.765757	895	135	347
19.0	1.765757	655	90	278
20.0	1.765757	521	87	249
21.0	1.765757	459	64	221
22.0	1.765757	333	36	153
23.0	1.765757	323	32	157
24.0	1.765757	248	33	145
25.0	1.765757	229	22	127
26.0	1.765757	209	24	105
27.0	1.765757	152	14	87
28.0	1.765757	159	18	102
29.0	1.765757	130	9	80
30.0	1.765757	118	9	68
31.0	1.765757	107	8	75
32.0	1.765757	93	8	64
33.0	1.765757	96	7	74
34.0	1.765757	94	5	47
35.0	1.765757	72	5	37
36.0	1.765757	74	3	51
37.0	1.765757	59	3	44
38.0	1.765757	67	0	46
39.0	1.765757	55	7	39
40.0	1.765757	55	2	47
41.0	1.765757	60	1	27
42.0	1.765757	51	0	16
43.0	1.765757	39	4	18
44.0	1.765757	38	2	25
45.0	1.765757	34	1	21
46.0	1.765757	21	0	24
47.0	1.765757	27	1	21
48.0	1.765757	29	2	13
49.0	1.765757	22	0	24
50.0	1.765757	28	0	18
51.0	1.765757	27	2	7
52.0	1.765757	30	1	20
53.0	1.765757	15	3	14
54.0	1.765757	14	1	13
55.0	1.765757	27	0	9
56.0	1.765757	13	1	20
57.0	1.765757	16	1	11
58.0	1.765757	30	0	11
59.0	1.765757	9	0	10
60.0	1.765757	19	1	7
61.0	1.765757	12	0	10
62.0	1.765757	12	1	7
63.0	1.765757	19	0	15
64.0	1.765757	14	0	5
65.0	1.765757	10	0	8
66.0	1.765757	12	1	8
67.0	1.765757	4	0	9
68.0	1.765757	11	1	7
69.0	1.765757	10	0	7
70.0	1.765757	6	0	8
71.0	1.765757	11	0	7
72.0	1.765757	14	2	7
73.0	1.765757	5	0	9
74.0	1.765757	11	0	5
75.0	1.765757	17	0	5
76.0	1.765757	9	0	5
77.0	1.765757	7	0	1
78.0	1.765757	3	2	5
79.0	1.765757	9	0	4
80.0	1.765757	2	0	5
81.0	1.765757	5	0	0
82.0	1.765757	6	0	4
83.0	1.765757	2	0	7
84.0	1.765757	5	0	3
85.0	1.765757	7	0	6
86.0	1.765757	6	0	2
87.0	1.765757	3	0	5
88.0	1.765757	2	0	1
89.0	1.765757	4	0	2
90.0	1.765757	3	0	4
91.0	1.765757	3	0	3
92.0	1.765757	3	0	2
93.0	1.765757	3	0	2
94.0	1.765757	5	0	2
95.0	1.765757	3	0	2
96.0	1.765757	0	0	2
97.0	1.765757	3	0	1
98.0	1.765757	4	1	3
99.0	1.765757	2	0	1
100.0	1.765757	3	1	2
101.0	0	2	0	0
102.0	0	2	0	2
103.0	0	5	0	1
104.0	0	6	1	2
105.0	0	1	0	1
106.0	0	6	1	2
107.0	0	2	1	3
108.0	0	0	0	1
109.0	0	1	0	0
110.0	0	3	0	1
111.0	0	2	0	2
112.0	0	2	0	2
114.0	0	2	0	3
115.0	0	3	0	0
116.0	0	4	0	2
117.0	0	2	0	1
118.0	0	2	0	0
119.0	0	1	0	2
120.0	0	2	0	1
122.0	0	1	0	0
123.0	0	1	0	0
124.0	0	1	0	2
125.0	0	1	0	2
126.0	0	1	0	1
127.0	0	3	0	0
129.0	0	1	0	0
130.0	0	1	0	1
131.0	0	1	0	0
132.0	0	0	0	1
133.0	0	0	0	1
134.0	0	1	0	0
136.0	0	1	0	1
137.0	0	0	1	0
138.0	0	1	1	1
139.0	0	2	0	0
141.0	0	1	0	1
142.0	0	0	0	1
143.0	0	1	0	0
144.0	0	1	0	0
145.0	0	1	0	0
146.0	0	2	0	1
147.0	0	1	1	1
151.0	0	1	0	0
153.0	0	0	1	0
154.0	0	2	0	0
155.0	0	1	0	0
156.0	0	0	0	1
158.0	0	1	0	0
160.0	0	0	1	0
163.0	0	1	0	0
165.0	0	1	0	0
166.0	0	0	0	1
170.0	0	0	0	1
173.0	0	0	0	1
183.0	0	0	0	1
184.0	0	0	1	0
185.0	0	1	0	1
188.0	0	1	0	0
189.0	0	1	0	1
191.0	0	1	0	0
193.0	0	1	0	0
195.0	0	1	0	0
197.0	0	1	0	0
199.0	0	0	0	1
203.0	0	1	0	0
205.0	0	0	0	1
208.0	0	1	0	0
210.0	0	2	0	0
211.0	0	0	0	1
214.0	0	0	0	1
219.0	0	1	0	0
220.0	0	1	0	0
222.0	0	0	0	1
239.0	0	0	0	1
240.0	0	1	0	0
244.0	0	1	0	1
247.0	0	0	0	1
250.0	0	1	0	0
251.0	0	1	0	0
253.0	0	1	0	0
255.0	0	1	0	1
256.0	0	1	0	0
267.0	0	1	0	0
277.0	0	0	0	1
279.0	0	1	0	0
285.0	0	1	0	0
289.0	0	1	0	0
290.0	0	0	0	1
301.0	0	1	0	0
486.0	0	0	0	1
638.0	0	1	0	0