## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-07-07/UA_Kie_Cho_1_2015-07-07.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-07-07/UA_Kie_Cho_1_2015-07-07.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-07-07/UA_Kie_Cho_1_2015-07-07.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: Fri Jan 20 08:53:08 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	28864839	12006169	0	0	6878746	1012458	0	0.168384	67126211

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9962651	9962651
2.0	1.836223	700465	700465
3.0	2.535493	55835	55835
4.0	3.120238	6236	6236
5.0	3.609216	1866	1866
6.0	4.01811	986	986
7.0	4.360037	687	687
8.0	4.645965	551	551
9.0	4.885064	384	384
10.0	5.085004	291	291
11.0	5.252199	267	267
12.0	5.392011	220	220
13.0	5.508925	170	170
14.0	5.606691	188	188
15.0	5.688446	145	145
16.0	5.756811	134	134
17.0	5.813979	121	121
18.0	5.861785	127	127
19.0	5.901761	118	118
20.0	5.93519	114	114
21.0	5.963144	96	96
22.0	5.98652	105	105
23.0	6.006067	102	102
24.0	6.022413	77	77
25.0	6.036082	76	76
26.0	6.047512	87	87
27.0	6.05707	80	80
28.0	6.065063	64	64
29.0	6.071747	55	55
30.0	6.077336	69	69
31.0	6.08201	48	48
32.0	6.085918	65	65
33.0	6.089187	49	49
34.0	6.09192	39	39
35.0	6.094205	40	40
36.0	6.096116	42	42
37.0	6.097714	37	37
38.0	6.09905	30	30
39.0	6.100168	31	31
40.0	6.101102	31	31
41.0	6.101884	27	27
42.0	6.102537	37	37
43.0	6.103084	21	21
44.0	6.103541	20	20
45.0	6.103923	24	24
46.0	6.104242	21	21
47.0	6.104509	22	22
48.0	6.104733	14	14
49.0	6.10492	15	15
50.0	6.105076	17	17
51.0	6.105207	17	17
52.0	6.105316	24	24
53.0	6.105407	15	15
54.0	6.105484	20	20
55.0	6.105548	16	16
56.0	6.105601	16	16
57.0	6.105646	6	6
58.0	6.105683	7	7
59.0	6.105714	12	12
60.0	6.10574	17	17
61.0	6.105762	19	19
62.0	6.10578	12	12
63.0	6.105796	8	8
64.0	6.105808	14	14
65.0	6.105819	16	16
66.0	6.105828	11	11
67.0	6.105836	20	20
68.0	6.105842	13	13
69.0	6.105847	10	10
70.0	6.105851	11	11
71.0	6.105855	5	5
72.0	6.105858	8	8
73.0	6.105861	9	9
74.0	6.105863	9	9
75.0	6.105865	11	11
76.0	6.105866	16	16
77.0	6.105867	16	16
78.0	6.105868	7	7
79.0	6.105869	11	11
80.0	6.10587	13	13
81.0	6.105871	8	8
82.0	6.105871	9	9
83.0	6.105872	12	12
84.0	6.105872	11	11
85.0	6.105872	8	8
86.0	6.105872	12	12
87.0	6.105873	10	10
88.0	6.105873	9	9
89.0	6.105873	8	8
90.0	6.105873	11	11
91.0	6.105873	9	9
92.0	6.105873	14	14
93.0	6.105873	9	9
94.0	6.105873	8	8
95.0	6.105873	5	5
96.0	6.105873	5	5
97.0	6.105874	11	11
98.0	6.105874	7	7
99.0	6.105874	6	6
100.0	6.105874	10	10
101.0	0	2	2
102.0	0	6	6
103.0	0	8	8
104.0	0	3	3
105.0	0	8	8
106.0	0	3	3
107.0	0	6	6
108.0	0	3	3
109.0	0	3	3
110.0	0	3	3
111.0	0	6	6
112.0	0	5	5
113.0	0	6	6
114.0	0	8	8
115.0	0	4	4
116.0	0	6	6
117.0	0	6	6
118.0	0	1	1
119.0	0	2	2
120.0	0	3	3
121.0	0	4	4
122.0	0	3	3
123.0	0	4	4
124.0	0	2	2
125.0	0	9	9
126.0	0	2	2
127.0	0	4	4
128.0	0	2	2
129.0	0	3	3
130.0	0	1	1
131.0	0	3	3
132.0	0	3	3
134.0	0	3	3
135.0	0	1	1
137.0	0	1	1
138.0	0	2	2
139.0	0	3	3
140.0	0	2	2
141.0	0	1	1
142.0	0	1	1
143.0	0	2	2
144.0	0	3	3
145.0	0	3	3
146.0	0	1	1
147.0	0	3	3
148.0	0	1	1
149.0	0	1	1
151.0	0	1	1
152.0	0	2	2
154.0	0	2	2
157.0	0	2	2
158.0	0	1	1
160.0	0	4	4
162.0	0	1	1
164.0	0	4	4
166.0	0	1	1
171.0	0	1	1
172.0	0	2	2
175.0	0	2	2
176.0	0	1	1
178.0	0	4	4
179.0	0	1	1
180.0	0	1	1
182.0	0	1	1
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
189.0	0	1	1
190.0	0	1	1
191.0	0	4	4
192.0	0	2	2
193.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	1	1
199.0	0	1	1
200.0	0	1	1
202.0	0	1	1
204.0	0	2	2
205.0	0	1	1
214.0	0	1	1
218.0	0	1	1
219.0	0	1	1
225.0	0	1	1
227.0	0	1	1
228.0	0	1	1
231.0	0	1	1
234.0	0	1	1
242.0	0	1	1
245.0	0	1	1
249.0	0	1	1
251.0	0	1	1
252.0	0	1	1
253.0	0	1	1
256.0	0	1	1
258.0	0	1	1
261.0	0	1	1
262.0	0	2	2
264.0	0	1	1
268.0	0	2	2
269.0	0	1	1
271.0	0	1	1
275.0	0	2	2
276.0	0	1	1
283.0	0	1	1
286.0	0	1	1
291.0	0	1	1
293.0	0	1	1
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
305.0	0	1	1
311.0	0	1	1
320.0	0	1	1
336.0	0	2	2
337.0	0	2	2
338.0	0	1	1
342.0	0	1	1
343.0	0	1	1
357.0	0	1	1
359.0	0	1	1
362.0	0	1	1
363.0	0	1	1
371.0	0	1	1
373.0	0	1	1
374.0	0	1	1
375.0	0	1	1
424.0	0	1	1
466.0	0	1	1
554.0	0	1	1
555.0	0	1	1
578.0	0	1	1
588.0	0	1	1
649.0	0	1	1
935.0	0	1	1
1390.0	0	1	1