## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-244-TP3.bam --OUTPUT ACR-244-TP3.md.bam --METRICS_FILE ACR-244-TP3.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 18:15:29 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	229	17901749	4784247	0	129	8944729	5006461	0.499657	16549606

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.221276	4770642	0	6251075
2.0	1.63531	2126186	1336650	1959055
3.0	1.775675	980091	542234	526542
4.0	1.823262	478659	270889	138312
5.0	1.839394	250125	146862	40990
6.0	1.844864	138598	80579	15566
7.0	1.846718	80357	45327	7528
8.0	1.847346	47544	25556	4535
9.0	1.847559	29382	14489	2971
10.0	1.847632	18144	8352	2097
11.0	1.847656	11504	4766	1498
12.0	1.847664	7395	2804	1065
13.0	1.847667	4856	1644	852
14.0	1.847668	3303	982	736
15.0	1.847669	2225	590	571
16.0	1.847669	1569	360	487
17.0	1.847669	1134	239	384
18.0	1.847669	840	159	296
19.0	1.847669	666	97	291
20.0	1.847669	473	61	228
21.0	1.847669	399	42	165
22.0	1.847669	331	28	157
23.0	1.847669	285	23	156
24.0	1.847669	237	12	143
25.0	1.847669	204	12	115
26.0	1.847669	180	15	103
27.0	1.847669	163	12	89
28.0	1.847669	120	6	77
29.0	1.847669	86	10	63
30.0	1.847669	118	5	65
31.0	1.847669	101	2	59
32.0	1.847669	78	4	50
33.0	1.847669	55	3	43
34.0	1.847669	52	1	38
35.0	1.847669	50	5	34
36.0	1.847669	64	3	30
37.0	1.847669	40	7	30
38.0	1.847669	50	1	36
39.0	1.847669	29	4	23
40.0	1.847669	39	0	30
41.0	1.847669	39	1	21
42.0	1.847669	30	0	17
43.0	1.847669	26	0	21
44.0	1.847669	25	1	22
45.0	1.847669	22	2	24
46.0	1.847669	34	1	21
47.0	1.847669	26	0	13
48.0	1.847669	27	0	11
49.0	1.847669	23	1	18
50.0	1.847669	21	0	14
51.0	1.847669	11	0	7
52.0	1.847669	11	1	14
53.0	1.847669	18	0	5
54.0	1.847669	15	1	11
55.0	1.847669	21	0	10
56.0	1.847669	16	0	11
57.0	1.847669	7	0	3
58.0	1.847669	10	0	10
59.0	1.847669	14	1	4
60.0	1.847669	12	2	6
61.0	1.847669	5	1	9
62.0	1.847669	13	1	6
63.0	1.847669	5	1	12
64.0	1.847669	9	1	6
65.0	1.847669	5	1	6
66.0	1.847669	4	0	4
67.0	1.847669	10	0	6
68.0	1.847669	9	0	3
69.0	1.847669	4	0	9
70.0	1.847669	8	0	3
71.0	1.847669	3	0	4
72.0	1.847669	5	1	3
73.0	1.847669	4	1	6
74.0	1.847669	6	0	4
75.0	1.847669	4	0	2
76.0	1.847669	9	0	5
77.0	1.847669	4	0	3
78.0	1.847669	4	0	6
79.0	1.847669	3	0	3
80.0	1.847669	5	0	4
81.0	1.847669	3	0	1
82.0	1.847669	4	0	1
83.0	1.847669	8	1	1
84.0	1.847669	6	0	1
85.0	1.847669	2	0	2
86.0	1.847669	4	0	2
87.0	1.847669	4	0	4
88.0	1.847669	4	0	3
89.0	1.847669	5	0	2
90.0	1.847669	2	0	2
91.0	1.847669	1	0	3
92.0	1.847669	3	0	2
93.0	1.847669	2	0	2
94.0	1.847669	1	0	2
95.0	1.847669	2	0	0
96.0	1.847669	0	2	2
97.0	1.847669	3	0	0
98.0	1.847669	3	0	0
99.0	1.847669	1	0	0
100.0	1.847669	1	1	0
102.0	0	2	0	1
103.0	0	2	0	0
104.0	0	1	0	0
105.0	0	2	0	1
106.0	0	2	0	1
108.0	0	2	0	1
110.0	0	0	0	1
112.0	0	2	0	1
113.0	0	0	0	2
116.0	0	1	0	0
117.0	0	0	0	2
118.0	0	1	0	0
119.0	0	1	0	0
120.0	0	1	0	0
121.0	0	2	0	0
122.0	0	2	0	1
123.0	0	1	0	0
124.0	0	0	0	2
125.0	0	0	0	1
127.0	0	0	0	1
128.0	0	2	0	0
130.0	0	1	0	0
131.0	0	1	0	2
132.0	0	2	0	0
133.0	0	1	0	0
134.0	0	2	0	0
135.0	0	2	0	0
139.0	0	0	0	1
140.0	0	1	0	0
141.0	0	0	1	0
142.0	0	1	0	0
146.0	0	0	0	1
147.0	0	1	0	0
148.0	0	1	0	0
149.0	0	1	0	1
152.0	0	1	0	0
154.0	0	1	0	0
155.0	0	0	0	1
157.0	0	1	0	0
159.0	0	0	0	1
160.0	0	0	0	1
161.0	0	1	0	0
163.0	0	0	0	1
165.0	0	0	0	1
168.0	0	1	0	0
170.0	0	1	0	1
175.0	0	0	0	1
176.0	0	0	0	2
180.0	0	1	0	1
183.0	0	2	0	1
184.0	0	1	0	1
185.0	0	0	0	1
188.0	0	2	0	0
195.0	0	1	0	1
197.0	0	1	0	0
201.0	0	0	0	1
202.0	0	1	0	0
209.0	0	2	0	0
213.0	0	1	0	0
227.0	0	1	0	0
271.0	0	0	0	1
284.0	0	1	0	0
288.0	0	0	0	1
298.0	0	1	0	0
331.0	0	0	0	1
430.0	0	1	0	0