## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT /mounts/lovelace/temporary/porter/PN_with/05_sam_sort_coord/2_3_S6.bam --OUTPUT /mounts/lovelace/temporary/porter/PN_with/06_picard_dedupe/2_3_S6.bam --METRICS_FILE /mounts/lovelace/temporary/porter/PN_with/06_picard_dedupe/input-dedupe-stats.txt --REMOVE_DUPLICATES true --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 --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 --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Jun 18 13:18:38 EDT 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	350101	396056	0	0	84355	57345	6575	0.174263	1361085

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.014546	289188	0	293975
2.0	1.772946	42712	6214	39403
3.0	2.33987	5944	170	4717
4.0	2.763661	757	4	552
5.0	3.080456	89	1	52
6.0	3.317268	15	1	8
7.0	3.494292	2	0	2
8.0	3.626622	2	0	0
9.0	3.725542	1	0	1
10.0	3.799487	1	0	1
11.0	3.854763	0	0	0
12.0	3.896084	0	0	0
13.0	3.926972	0	0	0
14.0	3.950062	0	0	0
15.0	3.967322	0	0	0
16.0	3.980224	0	0	0
17.0	3.989869	0	0	0
18.0	3.997079	0	0	0
19.0	4.002468	0	0	0
20.0	4.006497	0	0	0
21.0	4.009509	0	0	0
22.0	4.01176	0	0	0
23.0	4.013443	0	0	0
24.0	4.014701	0	0	0
25.0	4.015641	0	0	0
26.0	4.016344	0	0	0
27.0	4.01687	0	0	0
28.0	4.017263	0	0	0
29.0	4.017556	0	0	0
30.0	4.017776	0	0	0
31.0	4.01794	0	0	0
32.0	4.018063	0	0	0
33.0	4.018154	0	0	0
34.0	4.018223	0	0	0
35.0	4.018274	0	0	0
36.0	4.018312	0	0	0
37.0	4.018341	0	0	0
38.0	4.018362	0	0	0
39.0	4.018378	0	0	0
40.0	4.01839	0	0	0
41.0	4.018399	0	0	0
42.0	4.018406	0	0	0
43.0	4.018411	0	0	0
44.0	4.018415	0	0	0
45.0	4.018417	0	0	0
46.0	4.01842	0	0	0
47.0	4.018421	0	0	0
48.0	4.018422	0	0	0
49.0	4.018423	0	0	0
50.0	4.018424	0	0	0
51.0	4.018424	0	0	0
52.0	4.018425	0	0	0
53.0	4.018425	0	0	0
54.0	4.018425	0	0	0
55.0	4.018425	0	0	0
56.0	4.018425	0	0	0
57.0	4.018425	0	0	0
58.0	4.018426	0	0	0
59.0	4.018426	0	0	0
60.0	4.018426	0	0	0
61.0	4.018426	0	0	0
62.0	4.018426	0	0	0
63.0	4.018426	0	0	0
64.0	4.018426	0	0	0
65.0	4.018426	0	0	0
66.0	4.018426	0	0	0
67.0	4.018426	0	0	0
68.0	4.018426	0	0	0
69.0	4.018426	0	0	0
70.0	4.018426	0	0	0
71.0	4.018426	0	0	0
72.0	4.018426	0	0	0
73.0	4.018426	0	0	0
74.0	4.018426	0	0	0
75.0	4.018426	0	0	0
76.0	4.018426	0	0	0
77.0	4.018426	0	0	0
78.0	4.018426	0	0	0
79.0	4.018426	0	0	0
80.0	4.018426	0	0	0
81.0	4.018426	0	0	0
82.0	4.018426	0	0	0
83.0	4.018426	0	0	0
84.0	4.018426	0	0	0
85.0	4.018426	0	0	0
86.0	4.018426	0	0	0
87.0	4.018426	0	0	0
88.0	4.018426	0	0	0
89.0	4.018426	0	0	0
90.0	4.018426	0	0	0
91.0	4.018426	0	0	0
92.0	4.018426	0	0	0
93.0	4.018426	0	0	0
94.0	4.018426	0	0	0
95.0	4.018426	0	0	0
96.0	4.018426	0	0	0
97.0	4.018426	0	0	0
98.0	4.018426	0	0	0
99.0	4.018426	0	0	0
100.0	4.018426	0	0	0