## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_5_2015-08-26/UA_Kie_Cho_5_2015-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_5_2015-08-26/UA_Kie_Cho_5_2015-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_5_2015-08-26/UA_Kie_Cho_5_2015-08-26.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 17:14:38 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	31027121	14042172	0	0	9168308	1251915	0	0.19746	73998596

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	11483708	11483708
2.0	1.827155	812444	812444
3.0	2.511341	64792	64792
4.0	3.07727	7865	7865
5.0	3.54538	2543	2543
6.0	3.93258	1522	1522
7.0	4.252855	1030	1030
8.0	4.517772	764	764
9.0	4.7369	610	610
10.0	4.918152	445	445
11.0	5.068076	408	408
12.0	5.192087	322	322
13.0	5.294663	274	274
14.0	5.379509	248	248
15.0	5.44969	217	217
16.0	5.50774	196	196
17.0	5.555757	178	178
18.0	5.595475	124	124
19.0	5.628327	135	135
20.0	5.655501	135	135
21.0	5.677978	103	103
22.0	5.696571	106	106
23.0	5.711949	114	114
24.0	5.72467	123	123
25.0	5.735191	94	94
26.0	5.743895	96	96
27.0	5.751094	87	87
28.0	5.757048	75	75
29.0	5.761974	77	77
30.0	5.766048	65	65
31.0	5.769417	61	61
32.0	5.772205	64	64
33.0	5.77451	70	70
34.0	5.776418	61	61
35.0	5.777995	50	50
36.0	5.7793	57	57
37.0	5.780379	63	63
38.0	5.781272	48	48
39.0	5.78201	38	38
40.0	5.782621	44	44
41.0	5.783126	38	38
42.0	5.783544	46	46
43.0	5.78389	29	29
44.0	5.784176	43	43
45.0	5.784412	34	34
46.0	5.784608	28	28
47.0	5.78477	29	29
48.0	5.784904	28	28
49.0	5.785014	34	34
50.0	5.785106	25	25
51.0	5.785182	19	19
52.0	5.785244	33	33
53.0	5.785296	21	21
54.0	5.785339	24	24
55.0	5.785374	25	25
56.0	5.785404	19	19
57.0	5.785428	19	19
58.0	5.785448	24	24
59.0	5.785465	24	24
60.0	5.785478	20	20
61.0	5.78549	25	25
62.0	5.785499	22	22
63.0	5.785507	17	17
64.0	5.785513	17	17
65.0	5.785519	19	19
66.0	5.785523	20	20
67.0	5.785527	12	12
68.0	5.78553	11	11
69.0	5.785532	12	12
70.0	5.785534	9	9
71.0	5.785536	18	18
72.0	5.785537	17	17
73.0	5.785539	16	16
74.0	5.785539	15	15
75.0	5.78554	9	9
76.0	5.785541	20	20
77.0	5.785541	12	12
78.0	5.785542	9	9
79.0	5.785542	13	13
80.0	5.785543	9	9
81.0	5.785543	19	19
82.0	5.785543	9	9
83.0	5.785543	10	10
84.0	5.785543	13	13
85.0	5.785544	10	10
86.0	5.785544	12	12
87.0	5.785544	8	8
88.0	5.785544	8	8
89.0	5.785544	10	10
90.0	5.785544	8	8
91.0	5.785544	4	4
92.0	5.785544	9	9
93.0	5.785544	6	6
94.0	5.785544	8	8
95.0	5.785544	7	7
96.0	5.785544	8	8
97.0	5.785544	6	6
98.0	5.785544	11	11
99.0	5.785544	4	4
100.0	5.785544	11	11
101.0	0	12	12
102.0	0	11	11
103.0	0	11	11
104.0	0	10	10
105.0	0	13	13
106.0	0	9	9
107.0	0	7	7
108.0	0	12	12
109.0	0	11	11
110.0	0	5	5
111.0	0	4	4
112.0	0	7	7
113.0	0	6	6
114.0	0	12	12
115.0	0	10	10
116.0	0	5	5
117.0	0	4	4
118.0	0	2	2
119.0	0	7	7
120.0	0	11	11
121.0	0	8	8
122.0	0	4	4
123.0	0	2	2
124.0	0	7	7
125.0	0	2	2
126.0	0	4	4
127.0	0	6	6
128.0	0	4	4
129.0	0	3	3
130.0	0	4	4
131.0	0	2	2
132.0	0	4	4
133.0	0	4	4
134.0	0	5	5
135.0	0	6	6
136.0	0	4	4
137.0	0	2	2
138.0	0	3	3
139.0	0	3	3
140.0	0	5	5
141.0	0	2	2
142.0	0	3	3
143.0	0	2	2
144.0	0	1	1
145.0	0	4	4
146.0	0	7	7
147.0	0	3	3
148.0	0	3	3
149.0	0	3	3
150.0	0	4	4
151.0	0	2	2
152.0	0	1	1
153.0	0	4	4
154.0	0	2	2
155.0	0	3	3
156.0	0	4	4
157.0	0	3	3
158.0	0	4	4
159.0	0	2	2
160.0	0	2	2
161.0	0	1	1
162.0	0	2	2
163.0	0	2	2
164.0	0	4	4
165.0	0	1	1
166.0	0	1	1
167.0	0	1	1
168.0	0	2	2
169.0	0	2	2
170.0	0	2	2
172.0	0	3	3
173.0	0	1	1
174.0	0	1	1
175.0	0	3	3
177.0	0	5	5
178.0	0	5	5
179.0	0	4	4
180.0	0	4	4
181.0	0	3	3
182.0	0	2	2
183.0	0	1	1
184.0	0	3	3
185.0	0	1	1
186.0	0	1	1
188.0	0	2	2
189.0	0	2	2
190.0	0	2	2
191.0	0	1	1
193.0	0	1	1
194.0	0	2	2
196.0	0	1	1
197.0	0	1	1
198.0	0	3	3
201.0	0	2	2
202.0	0	4	4
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	1	1
208.0	0	4	4
209.0	0	2	2
211.0	0	3	3
212.0	0	1	1
214.0	0	2	2
215.0	0	1	1
217.0	0	1	1
218.0	0	2	2
219.0	0	2	2
220.0	0	1	1
221.0	0	3	3
223.0	0	1	1
225.0	0	1	1
226.0	0	3	3
227.0	0	1	1
228.0	0	1	1
230.0	0	1	1
231.0	0	1	1
234.0	0	2	2
235.0	0	1	1
236.0	0	1	1
237.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	2	2
246.0	0	1	1
249.0	0	1	1
253.0	0	1	1
254.0	0	1	1
255.0	0	1	1
256.0	0	2	2
266.0	0	1	1
267.0	0	1	1
272.0	0	1	1
273.0	0	1	1
274.0	0	4	4
278.0	0	2	2
281.0	0	1	1
284.0	0	1	1
287.0	0	1	1
294.0	0	1	1
296.0	0	1	1
299.0	0	1	1
300.0	0	1	1
306.0	0	1	1
307.0	0	2	2
308.0	0	1	1
312.0	0	1	1
313.0	0	2	2
314.0	0	1	1
315.0	0	2	2
317.0	0	1	1
318.0	0	1	1
319.0	0	1	1
321.0	0	1	1
323.0	0	2	2
325.0	0	1	1
326.0	0	1	1
328.0	0	2	2
332.0	0	1	1
333.0	0	1	1
336.0	0	1	1
337.0	0	1	1
338.0	0	2	2
343.0	0	2	2
344.0	0	1	1
345.0	0	1	1
347.0	0	1	1
348.0	0	1	1
352.0	0	1	1
358.0	0	1	1
359.0	0	1	1
360.0	0	1	1
363.0	0	1	1
365.0	0	1	1
367.0	0	1	1
371.0	0	1	1
378.0	0	1	1
385.0	0	1	1
388.0	0	1	1
390.0	0	1	1
392.0	0	1	1
395.0	0	1	1
397.0	0	1	1
400.0	0	1	1
406.0	0	1	1
407.0	0	1	1
409.0	0	2	2
412.0	0	1	1
413.0	0	1	1
414.0	0	2	2
421.0	0	1	1
429.0	0	1	1
431.0	0	1	1
437.0	0	1	1
447.0	0	1	1
449.0	0	1	1
454.0	0	1	1
464.0	0	1	1
466.0	0	1	1
478.0	0	1	1
494.0	0	1	1
504.0	0	1	1
509.0	0	1	1
526.0	0	1	1
535.0	0	1	1
536.0	0	1	1
541.0	0	1	1
542.0	0	1	1
554.0	0	1	1
559.0	0	1	1
563.0	0	1	1
575.0	0	1	1
617.0	0	1	1
654.0	0	2	2
666.0	0	1	1
667.0	0	1	1
734.0	0	1	1
737.0	0	1	1
845.0	0	1	1
901.0	0	1	1
939.0	0	1	1
1018.0	0	1	1
1710.0	0	1	1
3776.0	0	1	1