## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[three.sorted.bam] OUTPUT=three.markdup.bam METRICS_FILE=three.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.KC4GAAfXa2] 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 19:34:27 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
three 6 870998 0 1606 6 692528 4598 0.795098 179928
## HISTOGRAM java.lang.Double
BIN CoverageMult all_sets optical_sets non_optical_sets
1.0 1.000204 48739 0 48971
2.0 1.008107 45752 4142 45988
3.0 1.008169 23198 201 23104
4.0 1.008169 14311 18 14210
5.0 1.008169 9540 0 9535
6.0 1.008169 6694 0 6612
7.0 1.008169 4630 0 4600
8.0 1.008169 3629 0 3630
9.0 1.008169 2801 0 2757
10.0 1.008169 2349 0 2370
11.0 1.008169 1808 0 1791
12.0 1.008169 1633 0 1611
13.0 1.008169 1347 0 1350
14.0 1.008169 1179 0 1178
15.0 1.008169 927 0 894
16.0 1.008169 814 0 819
17.0 1.008169 715 0 714
18.0 1.008169 614 0 606
19.0 1.008169 567 0 554
20.0 1.008169 471 0 480
21.0 1.008169 463 0 451
22.0 1.008169 411 0 415
23.0 1.008169 330 0 325
24.0 1.008169 343 0 336
25.0 1.008169 321 0 320
26.0 1.008169 285 0 290
27.0 1.008169 268 0 269
28.0 1.008169 237 0 229
29.0 1.008169 248 0 252
30.0 1.008169 197 0 192
31.0 1.008169 175 0 174
32.0 1.008169 209 0 211
33.0 1.008169 165 0 159
34.0 1.008169 166 0 186
35.0 1.008169 136 0 108
36.0 1.008169 129 0 141
37.0 1.008169 142 0 136
38.0 1.008169 117 0 122
39.0 1.008169 101 0 100
40.0 1.008169 130 0 123
41.0 1.008169 77 0 72
42.0 1.008169 91 0 90
43.0 1.008169 81 0 90
44.0 1.008169 74 0 66
45.0 1.008169 69 0 70
46.0 1.008169 65 0 64
47.0 1.008169 61 0 59
48.0 1.008169 60 0 61
49.0 1.008169 72 0 73
50.0 1.008169 44 0 43
51.0 1.008169 63 0 66
52.0 1.008169 51 0 45
53.0 1.008169 60 0 63
54.0 1.008169 38 0 46
55.0 1.008169 59 0 46
56.0 1.008169 65 0 69
57.0 1.008169 29 0 30
58.0 1.008169 47 0 42
59.0 1.008169 40 0 44
60.0 1.008169 56 0 66
61.0 1.008169 53 0 46
62.0 1.008169 48 0 45
63.0 1.008169 35 0 32
64.0 1.008169 34 0 33
65.0 1.008169 33 0 37
66.0 1.008169 62 0 66
67.0 1.008169 37 0 29
68.0 1.008169 25 0 27
69.0 1.008169 27 0 30
70.0 1.008169 38 0 30
71.0 1.008169 27 0 26
72.0 1.008169 13 0 15
73.0 1.008169 22 0 34
74.0 1.008169 34 0 27
75.0 1.008169 31 0 33
76.0 1.008169 26 0 26
77.0 1.008169 21 0 15
78.0 1.008169 32 0 40
79.0 1.008169 38 0 31
80.0 1.008169 23 0 29
81.0 1.008169 27 0 14
82.0 1.008169 14 0 14
83.0 1.008169 11 0 14
84.0 1.008169 23 0 39
85.0 1.008169 25 0 12
86.0 1.008169 16 0 15
87.0 1.008169 15 0 9
88.0 1.008169 17 0 26
89.0 1.008169 20 0 21
90.0 1.008169 13 0 10
91.0 1.008169 17 0 16
92.0 1.008169 12 0 11
93.0 1.008169 16 0 25
94.0 1.008169 23 0 18
95.0 1.008169 14 0 9
96.0 1.008169 13 0 12
97.0 1.008169 10 0 8
98.0 1.008169 10 0 6
99.0 1.008169 7 0 10
100.0 1.008169 5 0 4
101.0 0 3 0 1
102.0 0 1 0 2
103.0 0 1 0 0
104.0 0 0 0 1
106.0 0 1 0 1
107.0 0 2 0 1
114.0 0 1 0 1
116.0 0 1 0 1