## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[one.sorted.bam] OUTPUT=one.markdup.bam METRICS_FILE=one.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.bfq8ROwoxh] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false 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 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> MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Jun 08 19:30:54 UTC 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
one 5 875093 3 1675 4 696570 4600 0.795995 179949
## HISTOGRAM java.lang.Double
BIN CoverageMult all_sets optical_sets non_optical_sets
1.0 1.000199 48274 0 48511
2.0 1.007928 45768 4129 46000
3.0 1.007987 23129 203 22994
4.0 1.007988 14312 19 14246
5.0 1.007988 9564 2 9540
6.0 1.007988 6676 0 6626
7.0 1.007988 5071 0 5054
8.0 1.007988 3747 0 3730
9.0 1.007988 2810 0 2792
10.0 1.007988 2284 0 2283
11.0 1.007988 1876 0 1834
12.0 1.007988 1663 0 1659
13.0 1.007988 1387 0 1372
14.0 1.007988 1051 0 1051
15.0 1.007988 973 0 974
16.0 1.007988 872 0 880
17.0 1.007988 736 0 711
18.0 1.007988 655 0 649
19.0 1.007988 514 0 495
20.0 1.007988 485 0 495
21.0 1.007988 440 0 438
22.0 1.007988 419 0 424
23.0 1.007988 380 0 379
24.0 1.007988 331 0 319
25.0 1.007988 268 0 267
26.0 1.007988 282 0 282
27.0 1.007988 226 0 225
28.0 1.007988 274 0 283
29.0 1.007988 239 0 226
30.0 1.007988 183 0 179
31.0 1.007988 189 0 194
32.0 1.007988 173 0 163
33.0 1.007988 168 0 169
34.0 1.007988 135 0 143
35.0 1.007988 123 0 110
36.0 1.007988 126 0 137
37.0 1.007988 132 0 123
38.0 1.007988 149 0 151
39.0 1.007988 89 0 86
40.0 1.007988 110 0 118
41.0 1.007988 94 0 86
42.0 1.007988 73 0 78
43.0 1.007988 75 0 65
44.0 1.007988 59 0 62
45.0 1.007988 70 0 68
46.0 1.007988 76 0 82
47.0 1.007988 94 0 89
48.0 1.007988 88 0 94
49.0 1.007988 70 0 72
50.0 1.007988 54 0 43
51.0 1.007988 54 0 58
52.0 1.007988 48 0 48
53.0 1.007988 60 0 60
54.0 1.007988 53 0 56
55.0 1.007988 53 0 45
56.0 1.007988 62 0 64
57.0 1.007988 50 0 58
58.0 1.007988 62 0 45
59.0 1.007988 42 0 45
60.0 1.007988 39 0 49
61.0 1.007988 39 0 34
62.0 1.007988 25 0 26
63.0 1.007988 42 0 36
64.0 1.007988 34 0 33
65.0 1.007988 34 0 37
66.0 1.007988 28 0 30
67.0 1.007988 39 0 38
68.0 1.007988 35 0 43
69.0 1.007988 40 0 33
70.0 1.007988 35 0 41
71.0 1.007988 32 0 24
72.0 1.007988 25 0 26
73.0 1.007988 29 0 30
74.0 1.007988 21 0 25
75.0 1.007988 36 0 38
76.0 1.007988 35 0 30
77.0 1.007988 28 0 28
78.0 1.007988 27 0 24
79.0 1.007988 32 0 29
80.0 1.007988 22 0 20
81.0 1.007988 15 0 14
82.0 1.007988 13 0 11
83.0 1.007988 10 0 14
84.0 1.007988 17 0 22
85.0 1.007988 28 0 27
86.0 1.007988 13 0 14
87.0 1.007988 31 0 28
88.0 1.007988 11 0 11
89.0 1.007988 17 0 18
90.0 1.007988 19 0 15
91.0 1.007988 16 0 13
92.0 1.007988 7 0 7
93.0 1.007988 10 0 11
94.0 1.007988 16 0 28
95.0 1.007988 28 0 23
96.0 1.007988 16 0 10
97.0 1.007988 9 0 5
98.0 1.007988 7 0 11
99.0 1.007988 12 0 10
100.0 1.007988 12 0 16
101.0 0 7 0 1
102.0 0 1 0 3
103.0 0 3 0 1
104.0 0 2 0 1
105.0 0 1 0 0
107.0 0 1 0 2
108.0 0 1 0 0
110.0 0 1 0 1
115.0 0 0 0 1
116.0 0 1 0 0
120.0 0 1 0 1