## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[in/r1.bam] OUTPUT=in/r1.marked.bam METRICS_FILE=picard/one_library.duplication_metrics    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 ASSUME_SORTED=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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Oct 24 21:42:08 HST 2026

## 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
Pond-492101	4	267	0	3	0	3	0	0.011152	11792

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	146	146
2.0	1.977611	3	3
3.0	2.933336	0	0
4.0	3.867664	0	0
5.0	4.781074	0	0
6.0	5.674035	0	0
7.0	6.547004	0	0
8.0	7.400429	0	0
9.0	8.234748	0	0
10.0	9.050387	0	0
11.0	9.847767	0	0
12.0	10.627294	0	0
13.0	11.389369	0	0
14.0	12.134383	0	0
15.0	12.862718	0	0
16.0	13.574746	0	0
17.0	14.270834	0	0
18.0	14.951337	0	0
19.0	15.616605	0	0
20.0	16.26698	0	0
21.0	16.902793	0	0
22.0	17.524372	0	0
23.0	18.132036	0	0
24.0	18.726094	0	0
25.0	19.306853	0	0
26.0	19.87461	0	0
27.0	20.429656	0	0
28.0	20.972275	0	0
29.0	21.502747	0	0
30.0	22.021342	0	0
31.0	22.528326	0	0
32.0	23.023961	0	0
33.0	23.508499	0	0
34.0	23.982189	0	0
35.0	24.445274	0	0
36.0	24.897992	0	0
37.0	25.340574	0	0
38.0	25.773247	0	0
39.0	26.196234	0	0
40.0	26.609751	0	0
41.0	27.014011	0	0
42.0	27.409219	0	0
43.0	27.79558	0	0
44.0	28.173291	0	0
45.0	28.542545	0	0
46.0	28.903533	0	0
47.0	29.256439	0	0
48.0	29.601444	0	0
49.0	29.938725	0	0
50.0	30.268455	0	0
51.0	30.590803	0	0
52.0	30.905934	0	0
53.0	31.21401	0	0
54.0	31.515189	0	0
55.0	31.809624	0	0
56.0	32.097469	0	0
57.0	32.378868	0	0
58.0	32.653968	0	0
59.0	32.922909	0	0
60.0	33.185829	0	0
61.0	33.442863	0	0
62.0	33.694142	0	0
63.0	33.939795	0	0
64.0	34.179949	0	0
65.0	34.414726	0	0
66.0	34.644247	0	0
67.0	34.86863	0	0
68.0	35.087989	0	0
69.0	35.302437	0	0
70.0	35.512083	0	0
71.0	35.717037	0	0
72.0	35.917402	0	0
73.0	36.113281	0	0
74.0	36.304774	0	0
75.0	36.491981	0	0
76.0	36.674996	0	0
77.0	36.853914	0	0
78.0	37.028826	0	0
79.0	37.199823	0	0
80.0	37.366991	0	0
81.0	37.530416	0	0
82.0	37.690183	0	0
83.0	37.846373	0	0
84.0	37.999066	0	0
85.0	38.148341	0	0
86.0	38.294273	0	0
87.0	38.436939	0	0
88.0	38.57641	0	0
89.0	38.712759	0	0
90.0	38.846056	0	0
91.0	38.976368	0	0
92.0	39.103762	0	0
93.0	39.228305	0	0
94.0	39.350059	0	0
95.0	39.469088	0	0
96.0	39.585451	0	0
97.0	39.69921	0	0
98.0	39.810422	0	0
99.0	39.919144	0	0
100.0	40.025431	0	0

