## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/AU_Vic_Yer_1_NA/AU_Vic_Yer_1_NA.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/AU_Vic_Yer_1_NA/AU_Vic_Yer_1_NA.dedup.bam METRICS_FILE=./pipeline_output_destplus/AU_Vic_Yer_1_NA/AU_Vic_Yer_1_NA.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    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 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 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Jan 14 01:01:27 UTC 2023

## 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
lib1	18163211	711418	0	0	2629307	56623	0	0.140026	4228743

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	591519	591519
2.0	1.845156	11225	11225
3.0	2.559445	957	957
4.0	3.163131	249	249
5.0	3.673339	108	108
6.0	4.104545	83	83
7.0	4.468981	63	63
8.0	4.776987	44	44
9.0	5.0373	34	34
10.0	5.257305	36	36
11.0	5.443243	41	41
12.0	5.60039	29	29
13.0	5.733204	45	45
14.0	5.845452	34	34
15.0	5.94032	18	18
16.0	6.020498	18	18
17.0	6.08826	31	31
18.0	6.14553	18	18
19.0	6.193933	12	12
20.0	6.23484	20	20
21.0	6.269413	9	9
22.0	6.298633	14	14
23.0	6.323328	13	13
24.0	6.344199	12	12
25.0	6.361839	14	14
26.0	6.376747	7	7
27.0	6.389347	10	10
28.0	6.399995	4	4
29.0	6.408995	13	13
30.0	6.416602	4	4
31.0	6.42303	11	11
32.0	6.428463	3	3
33.0	6.433055	9	9
34.0	6.436936	11	11
35.0	6.440216	10	10
36.0	6.442988	4	4
37.0	6.44533	5	5
38.0	6.44731	6	6
39.0	6.448984	7	7
40.0	6.450398	7	7
41.0	6.451593	7	7
42.0	6.452604	6	6
43.0	6.453457	7	7
44.0	6.454179	7	7
45.0	6.454789	6	6
46.0	6.455304	6	6
47.0	6.45574	4	4
48.0	6.456108	8	8
49.0	6.456419	13	13
50.0	6.456682	8	8
51.0	6.456904	7	7
52.0	6.457092	8	8
53.0	6.457251	4	4
54.0	6.457385	7	7
55.0	6.457499	5	5
56.0	6.457594	11	11
57.0	6.457675	6	6
58.0	6.457744	4	4
59.0	6.457802	3	3
60.0	6.457851	5	5
61.0	6.457892	6	6
62.0	6.457927	7	7
63.0	6.457956	6	6
64.0	6.457981	4	4
65.0	6.458002	5	5
66.0	6.45802	5	5
67.0	6.458035	3	3
68.0	6.458048	1	1
69.0	6.458059	3	3
70.0	6.458068	5	5
71.0	6.458075	1	1
72.0	6.458082	7	7
73.0	6.458087	6	6
74.0	6.458092	1	1
75.0	6.458096	4	4
76.0	6.458099	4	4
77.0	6.458102	6	6
78.0	6.458105	4	4
79.0	6.458107	3	3
80.0	6.458108	5	5
81.0	6.45811	2	2
82.0	6.458111	4	4
83.0	6.458112	1	1
84.0	6.458113	3	3
85.0	6.458113	4	4
86.0	6.458114	0	0
87.0	6.458115	3	3
88.0	6.458115	1	1
89.0	6.458115	1	1
90.0	6.458116	6	6
91.0	6.458116	2	2
92.0	6.458116	0	0
93.0	6.458116	3	3
94.0	6.458117	3	3
95.0	6.458117	0	0
96.0	6.458117	2	2
97.0	6.458117	2	2
98.0	6.458117	2	2
99.0	6.458117	2	2
100.0	6.458117	0	0
101.0	0	3	3
102.0	0	3	3
103.0	0	2	2
104.0	0	2	2
105.0	0	1	1
106.0	0	2	2
107.0	0	2	2
111.0	0	1	1
112.0	0	1	1
113.0	0	2	2
115.0	0	2	2
116.0	0	3	3
117.0	0	1	1
118.0	0	1	1
119.0	0	1	1
120.0	0	2	2
122.0	0	1	1
123.0	0	1	1
124.0	0	1	1
125.0	0	3	3
126.0	0	2	2
133.0	0	3	3
135.0	0	1	1
143.0	0	1	1
144.0	0	1	1
145.0	0	1	1
146.0	0	1	1
147.0	0	1	1
150.0	0	1	1
167.0	0	1	1
170.0	0	1	1
171.0	0	1	1
173.0	0	1	1
174.0	0	1	1
179.0	0	1	1
182.0	0	1	1
188.0	0	1	1
196.0	0	1	1
199.0	0	1	1
210.0	0	1	1
212.0	0	1	1
215.0	0	1	1
222.0	0	1	1
226.0	0	1	1
229.0	0	1	1
237.0	0	1	1
238.0	0	1	1
242.0	0	1	1
243.0	0	1	1
249.0	0	1	1
251.0	0	1	1
256.0	0	1	1
259.0	0	1	1
260.0	0	1	1
275.0	0	2	2
312.0	0	1	1
327.0	0	1	1
334.0	0	1	1
363.0	0	1	1
379.0	0	2	2
515.0	0	1	1
542.0	0	1	1
667.0	0	1	1
843.0	0	1	1