## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT ACR-145-TP2.bam --OUTPUT ACR-145-TP2.md.bam --METRICS_FILE ACR-145-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 18:14:47 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	120	10795674	2614507	0	83	6655251	2761805	0.616474	5309947

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.114554	1574730	0	2054296
2.0	1.26048	1040705	660579	1169572
3.0	1.279586	628374	275667	535428
4.0	1.282088	360571	142970	215510
5.0	1.282416	205198	80736	83744
6.0	1.282458	119163	47154	34013
7.0	1.282464	71756	28242	15881
8.0	1.282465	44497	16908	8555
9.0	1.282465	28470	10223	5249
10.0	1.282465	18764	6411	3484
11.0	1.282465	12781	3907	2512
12.0	1.282465	8587	2425	1884
13.0	1.282465	6074	1584	1448
14.0	1.282465	4357	932	1253
15.0	1.282465	3169	658	934
16.0	1.282465	2246	411	792
17.0	1.282465	1712	290	692
18.0	1.282465	1339	180	550
19.0	1.282465	1049	125	432
20.0	1.282465	833	79	394
21.0	1.282465	648	65	347
22.0	1.282465	550	53	335
23.0	1.282465	475	43	257
24.0	1.282465	414	39	258
25.0	1.282465	332	22	198
26.0	1.282465	300	18	173
27.0	1.282465	270	13	171
28.0	1.282465	220	10	166
29.0	1.282465	240	12	129
30.0	1.282465	176	10	126
31.0	1.282465	151	8	118
32.0	1.282465	145	10	104
33.0	1.282465	124	7	105
34.0	1.282465	145	6	91
35.0	1.282465	115	4	67
36.0	1.282465	103	5	76
37.0	1.282465	103	5	64
38.0	1.282465	95	6	54
39.0	1.282465	92	2	59
40.0	1.282465	76	1	41
41.0	1.282465	84	5	42
42.0	1.282465	61	3	49
43.0	1.282465	51	1	46
44.0	1.282465	58	5	36
45.0	1.282465	59	1	28
46.0	1.282465	39	4	29
47.0	1.282465	42	3	20
48.0	1.282465	36	2	31
49.0	1.282465	45	1	24
50.0	1.282465	36	3	30
51.0	1.282465	33	0	31
52.0	1.282465	26	0	27
53.0	1.282465	31	1	20
54.0	1.282465	31	1	16
55.0	1.282465	31	1	21
56.0	1.282465	32	0	14
57.0	1.282465	20	4	18
58.0	1.282465	26	1	18
59.0	1.282465	16	3	12
60.0	1.282465	15	1	11
61.0	1.282465	25	2	16
62.0	1.282465	24	1	20
63.0	1.282465	11	0	6
64.0	1.282465	16	0	11
65.0	1.282465	23	1	13
66.0	1.282465	9	1	14
67.0	1.282465	20	0	5
68.0	1.282465	12	0	5
69.0	1.282465	12	2	6
70.0	1.282465	9	1	12
71.0	1.282465	12	0	13
72.0	1.282465	12	1	11
73.0	1.282465	21	0	8
74.0	1.282465	7	0	5
75.0	1.282465	5	0	11
76.0	1.282465	11	0	11
77.0	1.282465	10	0	5
78.0	1.282465	13	0	3
79.0	1.282465	6	0	4
80.0	1.282465	5	0	3
81.0	1.282465	7	1	5
82.0	1.282465	7	0	7
83.0	1.282465	7	0	3
84.0	1.282465	6	0	3
85.0	1.282465	10	0	6
86.0	1.282465	2	0	4
87.0	1.282465	6	0	5
88.0	1.282465	4	0	0
89.0	1.282465	9	0	5
90.0	1.282465	12	0	2
91.0	1.282465	5	0	2
92.0	1.282465	6	0	2
93.0	1.282465	6	0	4
94.0	1.282465	5	0	5
95.0	1.282465	3	0	1
96.0	1.282465	3	0	1
97.0	1.282465	4	0	5
98.0	1.282465	5	0	1
99.0	1.282465	4	0	2
100.0	1.282465	2	0	1
101.0	0	5	0	7
102.0	0	3	0	1
103.0	0	1	0	0
104.0	0	4	0	2
105.0	0	3	0	1
106.0	0	2	0	2
107.0	0	2	0	2
108.0	0	2	0	2
109.0	0	2	0	1
110.0	0	2	0	4
111.0	0	1	0	5
112.0	0	1	0	2
113.0	0	3	0	1
114.0	0	4	0	0
115.0	0	0	0	1
116.0	0	3	0	1
117.0	0	2	0	2
118.0	0	1	0	1
119.0	0	6	0	3
120.0	0	1	0	4
121.0	0	1	0	1
122.0	0	3	0	1
123.0	0	6	0	0
124.0	0	3	0	0
125.0	0	3	0	4
126.0	0	1	0	0
127.0	0	0	0	1
128.0	0	3	0	2
129.0	0	2	1	2
130.0	0	2	0	0
131.0	0	5	0	1
132.0	0	1	0	1
133.0	0	1	0	2
134.0	0	1	0	2
135.0	0	2	0	1
136.0	0	0	1	0
137.0	0	1	0	0
138.0	0	2	0	3
139.0	0	0	0	2
140.0	0	1	0	0
143.0	0	1	0	0
144.0	0	1	0	0
145.0	0	3	0	2
146.0	0	2	0	1
147.0	0	0	0	1
149.0	0	1	0	0
151.0	0	1	0	0
152.0	0	1	0	0
153.0	0	2	0	1
159.0	0	0	0	1
160.0	0	1	0	0
161.0	0	2	0	0
163.0	0	1	0	1
164.0	0	0	0	1
165.0	0	1	0	2
168.0	0	1	0	0
170.0	0	1	0	0
171.0	0	0	0	1
174.0	0	1	0	0
175.0	0	1	0	0
176.0	0	0	0	1
180.0	0	1	1	0
184.0	0	0	0	1
185.0	0	0	0	2
190.0	0	1	0	0
191.0	0	1	0	0
202.0	0	0	0	2
206.0	0	0	0	1
208.0	0	1	0	0
212.0	0	1	0	0
217.0	0	0	0	1
219.0	0	0	0	1
221.0	0	0	0	1
225.0	0	2	0	0
228.0	0	0	0	1
230.0	0	1	0	1
232.0	0	1	0	0
240.0	0	1	0	0
247.0	0	1	0	0
251.0	0	1	0	0
261.0	0	0	0	1
265.0	0	1	0	0
269.0	0	1	0	0
278.0	0	0	0	1
279.0	0	0	0	1
288.0	0	2	0	0
290.0	0	1	0	0
325.0	0	1	0	0
468.0	0	0	0	1
494.0	0	1	0	0