## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-150-TP3.bam --OUTPUT ACR-150-TP3.md.bam --METRICS_FILE ACR-150-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 18:14:34 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	189	14112489	3220565	0	102	7914204	3751951	0.560794	9141217

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.159838	2787674	0	3652061
2.0	1.407534	1561618	978919	1626702
3.0	1.460433	830944	397655	594917
4.0	1.47173	437399	199627	197882
5.0	1.474143	234732	109081	66186
6.0	1.474658	132204	61545	25299
7.0	1.474768	77473	35323	11656
8.0	1.474791	47036	20349	6262
9.0	1.474796	29066	11866	3822
10.0	1.474797	18617	6999	2653
11.0	1.474798	12200	4139	1945
12.0	1.474798	8031	2459	1478
13.0	1.474798	5443	1415	1174
14.0	1.474798	3657	848	883
15.0	1.474798	2512	552	667
16.0	1.474798	1795	309	610
17.0	1.474798	1310	189	455
18.0	1.474798	1029	145	413
19.0	1.474798	765	95	349
20.0	1.474798	581	71	308
21.0	1.474798	481	46	274
22.0	1.474798	443	35	200
23.0	1.474798	361	22	192
24.0	1.474798	309	11	167
25.0	1.474798	267	9	173
26.0	1.474798	208	10	130
27.0	1.474798	170	12	119
28.0	1.474798	178	4	111
29.0	1.474798	142	5	113
30.0	1.474798	131	3	76
31.0	1.474798	103	10	93
32.0	1.474798	106	4	67
33.0	1.474798	108	4	56
34.0	1.474798	96	0	47
35.0	1.474798	78	3	43
36.0	1.474798	60	1	52
37.0	1.474798	64	2	38
38.0	1.474798	50	0	42
39.0	1.474798	49	2	38
40.0	1.474798	52	1	30
41.0	1.474798	38	2	29
42.0	1.474798	51	3	23
43.0	1.474798	26	1	36
44.0	1.474798	36	2	17
45.0	1.474798	47	1	20
46.0	1.474798	23	0	22
47.0	1.474798	23	0	18
48.0	1.474798	26	0	16
49.0	1.474798	31	0	15
50.0	1.474798	18	1	6
51.0	1.474798	22	0	18
52.0	1.474798	14	1	17
53.0	1.474798	19	1	17
54.0	1.474798	18	0	15
55.0	1.474798	16	0	8
56.0	1.474798	10	0	9
57.0	1.474798	17	0	13
58.0	1.474798	25	0	4
59.0	1.474798	11	0	9
60.0	1.474798	9	0	10
61.0	1.474798	7	0	6
62.0	1.474798	7	0	8
63.0	1.474798	18	0	6
64.0	1.474798	9	1	6
65.0	1.474798	10	0	4
66.0	1.474798	7	0	8
67.0	1.474798	15	0	5
68.0	1.474798	4	0	7
69.0	1.474798	10	0	6
70.0	1.474798	3	0	4
71.0	1.474798	11	0	6
72.0	1.474798	11	0	8
73.0	1.474798	2	0	4
74.0	1.474798	8	0	3
75.0	1.474798	6	0	3
76.0	1.474798	6	0	3
77.0	1.474798	4	0	3
78.0	1.474798	2	0	1
79.0	1.474798	6	0	2
80.0	1.474798	6	0	2
81.0	1.474798	3	0	2
82.0	1.474798	2	1	1
83.0	1.474798	1	0	1
84.0	1.474798	1	0	2
85.0	1.474798	4	0	1
86.0	1.474798	3	0	3
87.0	1.474798	3	1	1
88.0	1.474798	3	0	2
89.0	1.474798	2	0	4
90.0	1.474798	0	0	2
91.0	1.474798	2	0	4
92.0	1.474798	2	0	0
93.0	1.474798	2	0	2
94.0	1.474798	3	0	4
95.0	1.474798	0	0	0
96.0	1.474798	2	0	1
97.0	1.474798	1	0	2
98.0	1.474798	1	0	0
99.0	1.474798	2	0	1
100.0	1.474798	4	0	1
101.0	0	1	0	1
102.0	0	4	0	2
103.0	0	6	0	2
104.0	0	3	0	2
105.0	0	2	0	3
106.0	0	2	0	0
109.0	0	1	0	0
111.0	0	2	0	1
112.0	0	2	0	0
113.0	0	0	0	2
115.0	0	0	0	2
116.0	0	1	0	0
117.0	0	1	0	0
119.0	0	3	0	0
120.0	0	0	0	1
121.0	0	0	0	2
122.0	0	0	0	2
123.0	0	1	0	0
124.0	0	1	0	2
125.0	0	1	0	1
126.0	0	1	0	1
127.0	0	2	0	0
129.0	0	0	0	2
130.0	0	1	0	2
131.0	0	3	0	0
132.0	0	0	0	1
133.0	0	4	0	0
136.0	0	1	0	1
138.0	0	2	0	0
139.0	0	1	0	0
145.0	0	1	0	0
149.0	0	1	0	0
150.0	0	0	0	3
151.0	0	1	0	0
152.0	0	0	0	1
154.0	0	1	0	0
155.0	0	2	0	0
162.0	0	0	0	1
171.0	0	1	0	0
179.0	0	0	0	1
183.0	0	0	0	1
185.0	0	1	0	1
188.0	0	0	0	1
198.0	0	1	0	0
199.0	0	1	0	0
200.0	0	1	0	0
202.0	0	0	0	1
208.0	0	0	0	1
209.0	0	1	0	0
211.0	0	1	0	0
214.0	0	0	0	1
220.0	0	1	0	0
223.0	0	1	0	0
230.0	0	0	0	1
236.0	0	1	0	0
243.0	0	0	0	1
247.0	0	0	0	1
248.0	0	0	0	1
254.0	0	1	0	0
256.0	0	1	0	0
257.0	0	0	0	1
258.0	0	1	0	0
263.0	0	0	0	1
278.0	0	0	0	1
282.0	0	1	0	0
293.0	0	1	0	0
338.0	0	1	0	0
348.0	0	0	0	1
362.0	0	1	0	0
412.0	0	0	0	1
438.0	0	1	0	0