## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Uma_22_Sep_2018/UA_Uma_22_Sep_2018.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Uma_22_Sep_2018/UA_Uma_22_Sep_2018.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Uma_22_Sep_2018/UA_Uma_22_Sep_2018.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: Wed Dec 21 03:47:45 UTC 2022

## 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	5082863	15043743	0	0	2450164	3436444	155379	0.265083	28608921

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.007934	8796614	0	8889926
2.0	1.603681	2015061	151579	1964246
3.0	1.955802	442731	1711	414111
4.0	2.163926	93396	18	83409
5.0	2.28694	19444	10	16509
6.0	2.359648	4358	5	3629
7.0	2.402623	1074	2	926
8.0	2.428023	419	6	370
9.0	2.443036	238	1	223
10.0	2.45191	138	0	128
11.0	2.457155	107	0	110
12.0	2.460255	94	1	94
13.0	2.462087	69	0	65
14.0	2.46317	58	0	56
15.0	2.46381	56	0	57
16.0	2.464189	46	0	48
17.0	2.464412	41	0	40
18.0	2.464544	40	0	39
19.0	2.464623	36	0	38
20.0	2.464669	30	1	27
21.0	2.464696	34	0	37
22.0	2.464712	17	0	17
23.0	2.464722	22	0	21
24.0	2.464727	26	0	25
25.0	2.464731	16	0	17
26.0	2.464733	17	0	18
27.0	2.464734	31	0	29
28.0	2.464734	20	0	19
29.0	2.464735	9	0	8
30.0	2.464735	14	0	16
31.0	2.464735	21	0	19
32.0	2.464735	6	0	8
33.0	2.464735	12	0	11
34.0	2.464735	8	0	7
35.0	2.464735	6	0	6
36.0	2.464735	8	0	8
37.0	2.464735	6	0	7
38.0	2.464735	7	0	8
39.0	2.464735	8	0	7
40.0	2.464735	4	0	4
41.0	2.464735	8	0	7
42.0	2.464735	9	0	9
43.0	2.464735	11	0	11
44.0	2.464735	8	0	9
45.0	2.464735	8	0	8
46.0	2.464735	6	0	6
47.0	2.464735	4	0	4
48.0	2.464735	10	0	10
49.0	2.464735	12	0	11
50.0	2.464735	12	0	12
51.0	2.464735	7	0	8
52.0	2.464735	3	0	4
53.0	2.464735	2	0	0
54.0	2.464735	5	0	5
55.0	2.464735	5	0	5
56.0	2.464735	1	1	1
57.0	2.464735	3	0	3
58.0	2.464735	5	0	5
59.0	2.464735	3	0	5
60.0	2.464735	5	0	5
61.0	2.464735	3	0	1
62.0	2.464735	3	0	3
63.0	2.464735	4	0	4
64.0	2.464735	4	0	5
65.0	2.464735	3	0	3
66.0	2.464735	4	0	3
67.0	2.464735	6	0	6
68.0	2.464735	3	0	3
69.0	2.464735	2	0	2
70.0	2.464735	2	0	2
71.0	2.464735	4	0	5
72.0	2.464735	1	0	1
73.0	2.464735	1	0	1
74.0	2.464735	2	0	1
75.0	2.464735	2	0	2
76.0	2.464735	1	0	1
77.0	2.464735	2	0	3
78.0	2.464735	2	0	3
79.0	2.464735	5	0	4
80.0	2.464735	7	0	6
81.0	2.464735	3	0	4
82.0	2.464735	2	0	2
83.0	2.464735	1	0	1
84.0	2.464735	5	0	4
85.0	2.464735	0	0	0
86.0	2.464735	0	0	0
87.0	2.464735	3	0	3
88.0	2.464735	2	0	2
89.0	2.464735	1	0	1
90.0	2.464735	3	0	4
91.0	2.464735	1	0	3
92.0	2.464735	4	0	2
93.0	2.464735	1	0	0
94.0	2.464735	2	0	2
95.0	2.464735	1	0	2
96.0	2.464735	1	0	0
97.0	2.464735	2	0	2
98.0	2.464735	0	0	0
99.0	2.464735	0	0	0
100.0	2.464735	2	0	3
101.0	0	5	0	4
102.0	0	1	0	1
103.0	0	2	0	2
104.0	0	3	0	3
105.0	0	2	0	2
107.0	0	0	0	1
108.0	0	2	0	1
109.0	0	1	0	1
110.0	0	2	0	2
111.0	0	1	0	1
112.0	0	1	0	2
113.0	0	2	1	1
114.0	0	1	0	1
115.0	0	0	0	1
116.0	0	2	0	1
118.0	0	2	0	2
119.0	0	1	0	1
120.0	0	0	0	1
121.0	0	2	0	1
122.0	0	2	0	3
124.0	0	1	0	1
125.0	0	1	0	1
126.0	0	3	0	2
127.0	0	1	0	1
128.0	0	3	0	3
130.0	0	1	0	2
131.0	0	2	0	1
132.0	0	2	0	4
133.0	0	2	0	0
135.0	0	4	0	4
136.0	0	0	0	1
137.0	0	2	0	1
138.0	0	1	0	1
140.0	0	0	0	1
142.0	0	2	0	1
144.0	0	1	0	1
145.0	0	1	0	1
146.0	0	1	0	1
147.0	0	1	0	1
151.0	0	1	0	1
152.0	0	2	0	2
153.0	0	4	0	4
155.0	0	1	0	1
156.0	0	1	0	1
157.0	0	1	0	2
159.0	0	1	0	1
160.0	0	2	0	1
162.0	0	1	0	1
163.0	0	0	0	2
166.0	0	1	0	2
167.0	0	2	0	1
168.0	0	4	0	2
169.0	0	1	0	1
170.0	0	1	0	1
172.0	0	0	0	1
173.0	0	1	0	1
174.0	0	1	0	1
175.0	0	2	0	1
177.0	0	1	0	2
178.0	0	1	0	0
179.0	0	1	0	1
180.0	0	1	0	1
183.0	0	2	0	2
184.0	0	1	0	1
185.0	0	2	0	2
186.0	0	2	0	2
187.0	0	1	0	1
190.0	0	1	0	2
191.0	0	2	0	2
192.0	0	1	0	1
193.0	0	2	0	1
194.0	0	1	0	1
199.0	0	1	0	1
209.0	0	0	0	1
211.0	0	1	0	0
213.0	0	0	0	1
214.0	0	2	0	2
215.0	0	1	0	0
217.0	0	1	0	1
218.0	0	0	0	1
220.0	0	2	0	1
221.0	0	0	0	1
222.0	0	1	0	0
233.0	0	1	0	1
234.0	0	2	0	3
236.0	0	1	0	0
239.0	0	1	0	1
241.0	0	0	0	1
243.0	0	1	0	0
246.0	0	1	0	1
249.0	0	1	0	1
271.0	0	0	0	1
272.0	0	1	0	1
273.0	0	1	0	0
282.0	0	1	0	1
285.0	0	1	0	1
289.0	0	0	0	1
290.0	0	1	0	2
291.0	0	2	0	0
295.0	0	1	0	1
308.0	0	0	0	1
309.0	0	1	0	0
310.0	0	0	0	1
312.0	0	1	0	0
315.0	0	0	0	1
316.0	0	1	0	0
317.0	0	1	0	1
318.0	0	1	0	1
321.0	0	0	0	1
322.0	0	1	0	0
335.0	0	1	0	1
344.0	0	1	0	1
347.0	0	1	0	2
349.0	0	1	0	1
351.0	0	1	0	0
353.0	0	1	0	1
373.0	0	1	0	1
376.0	0	0	0	1
378.0	0	1	0	1
380.0	0	1	0	0
382.0	0	0	0	1
383.0	0	1	0	0
393.0	0	0	0	1
394.0	0	1	0	1
395.0	0	1	0	0
397.0	0	0	0	1
398.0	0	1	0	0
401.0	0	0	0	1
403.0	0	1	0	0
408.0	0	0	0	1
409.0	0	0	0	1
411.0	0	1	0	0
412.0	0	1	0	0
417.0	0	1	0	1
422.0	0	1	0	1
438.0	0	2	0	3
442.0	0	1	0	0
454.0	0	0	0	1
457.0	0	1	0	0
459.0	0	0	0	1
463.0	0	1	0	0
471.0	0	0	0	1
478.0	0	1	0	0
484.0	0	0	0	1
486.0	0	1	0	0
488.0	0	0	0	1
489.0	0	1	0	0
491.0	0	0	0	1
492.0	0	1	0	0
499.0	0	0	0	1
500.0	0	2	0	1
502.0	0	0	0	1
506.0	0	1	0	0
509.0	0	0	0	1
514.0	0	1	0	0
517.0	0	1	0	1
530.0	0	0	0	1
531.0	0	1	0	0
534.0	0	0	0	1
536.0	0	1	0	1
538.0	0	1	0	0
543.0	0	0	0	1
549.0	0	1	0	0
611.0	0	1	0	1
614.0	0	0	0	1
615.0	0	1	0	0
620.0	0	1	0	1
677.0	0	0	0	1
684.0	0	1	0	0
705.0	0	1	0	1
784.0	0	0	0	1
791.0	0	1	0	0
823.0	0	0	0	1
829.0	0	1	0	0
844.0	0	0	0	1
846.0	0	1	0	0
984.0	0	0	0	1
988.0	0	1	0	0
1008.0	0	0	0	1
1012.0	0	1	0	0
1013.0	0	0	0	1
1016.0	0	1	0	0
1097.0	0	0	0	1
1105.0	0	1	0	0
1160.0	0	0	0	1
1167.0	0	1	0	0
1192.0	0	1	0	1
1197.0	0	1	0	1
1211.0	0	0	0	1
1216.0	0	1	0	0
1261.0	0	0	0	1
1266.0	0	1	0	0
1294.0	0	0	0	1
1305.0	0	1	0	0
1344.0	0	0	0	1
1348.0	0	1	0	0
1355.0	0	1	0	1
1424.0	0	0	0	1
1425.0	0	1	0	0
2596.0	0	0	0	1
2603.0	0	1	0	0
2861.0	0	0	0	1
2866.0	0	1	0	0
5840.0	0	0	0	1
5847.0	0	1	0	0
6090.0	0	0	0	1
6109.0	0	1	0	0
11217.0	0	0	0	1
11272.0	0	1	0	0
25883.0	0	0	0	1
25995.0	0	1	0	0