## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Ode_Ode_1_2020-09-28/UA_Ode_Ode_1_2020-09-28.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Ode_Ode_1_2020-09-28/UA_Ode_Ode_1_2020-09-28.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Ode_Ode_1_2020-09-28/UA_Ode_Ode_1_2020-09-28.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 Jan 18 04:21:32 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	3116371	26383442	0	0	1837069	9577891	252577	0.375655	27252182

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.005735	10137082	0	10234883
2.0	1.387708	3782989	244453	3763281
3.0	1.53278	1358484	3318	1323146
4.0	1.587878	461637	75	438292
5.0	1.608803	149777	23	138260
6.0	1.616751	46903	17	41932
7.0	1.619769	14851	7	12951
8.0	1.620916	4864	10	4205
9.0	1.621351	1853	4	1656
10.0	1.621517	906	6	807
11.0	1.621579	562	5	527
12.0	1.621603	395	1	388
13.0	1.621612	327	2	324
14.0	1.621616	271	4	277
15.0	1.621617	233	1	221
16.0	1.621618	198	2	197
17.0	1.621618	180	1	178
18.0	1.621618	137	0	137
19.0	1.621618	128	0	122
20.0	1.621618	111	0	113
21.0	1.621618	113	0	112
22.0	1.621618	96	0	96
23.0	1.621618	79	1	78
24.0	1.621618	77	0	79
25.0	1.621618	67	0	67
26.0	1.621618	98	1	95
27.0	1.621618	73	1	73
28.0	1.621618	64	0	64
29.0	1.621618	61	0	62
30.0	1.621618	50	0	47
31.0	1.621618	53	0	57
32.0	1.621618	47	0	51
33.0	1.621618	36	0	30
34.0	1.621618	44	0	45
35.0	1.621618	44	1	47
36.0	1.621618	38	1	33
37.0	1.621618	37	0	42
38.0	1.621618	41	0	38
39.0	1.621618	27	0	27
40.0	1.621618	30	1	29
41.0	1.621618	28	2	26
42.0	1.621618	28	0	29
43.0	1.621618	20	0	22
44.0	1.621618	29	0	26
45.0	1.621618	27	0	23
46.0	1.621618	16	0	19
47.0	1.621618	26	0	26
48.0	1.621618	30	0	28
49.0	1.621618	23	0	24
50.0	1.621618	18	0	20
51.0	1.621618	19	0	19
52.0	1.621618	16	0	16
53.0	1.621618	24	0	25
54.0	1.621618	20	0	20
55.0	1.621618	24	0	24
56.0	1.621618	14	0	13
57.0	1.621618	13	0	10
58.0	1.621618	9	0	9
59.0	1.621618	13	0	14
60.0	1.621618	16	0	17
61.0	1.621618	14	0	13
62.0	1.621618	12	0	14
63.0	1.621618	13	0	12
64.0	1.621618	10	0	10
65.0	1.621618	9	0	10
66.0	1.621618	11	0	9
67.0	1.621618	8	0	9
68.0	1.621618	9	0	8
69.0	1.621618	7	0	7
70.0	1.621618	4	0	6
71.0	1.621618	11	0	10
72.0	1.621618	5	0	4
73.0	1.621618	15	0	14
74.0	1.621618	8	0	8
75.0	1.621618	6	0	6
76.0	1.621618	6	0	7
77.0	1.621618	6	0	4
78.0	1.621618	8	0	10
79.0	1.621618	11	0	12
80.0	1.621618	12	0	11
81.0	1.621618	8	0	8
82.0	1.621618	5	0	6
83.0	1.621618	6	0	5
84.0	1.621618	4	0	4
85.0	1.621618	9	0	7
86.0	1.621618	3	0	4
87.0	1.621618	5	0	6
88.0	1.621618	10	0	8
89.0	1.621618	7	0	7
90.0	1.621618	5	0	5
91.0	1.621618	8	0	8
92.0	1.621618	3	0	6
93.0	1.621618	6	0	4
94.0	1.621618	6	0	6
95.0	1.621618	6	0	6
96.0	1.621618	1	0	3
97.0	1.621618	7	0	8
98.0	1.621618	6	0	5
99.0	1.621618	6	0	8
100.0	1.621618	9	0	6
101.0	0	7	0	7
102.0	0	8	0	7
103.0	0	5	0	4
104.0	0	3	0	6
105.0	0	5	0	5
106.0	0	7	0	6
107.0	0	5	0	3
108.0	0	4	0	6
109.0	0	6	0	8
110.0	0	5	0	2
111.0	0	3	0	3
112.0	0	3	0	3
113.0	0	2	0	2
114.0	0	6	0	6
115.0	0	3	0	2
116.0	0	5	0	5
117.0	0	2	0	2
118.0	0	3	0	5
119.0	0	4	0	2
120.0	0	3	0	3
121.0	0	2	0	3
122.0	0	3	0	2
123.0	0	1	0	3
124.0	0	3	0	3
125.0	0	4	0	5
126.0	0	4	0	1
127.0	0	1	0	1
128.0	0	2	0	4
129.0	0	2	0	4
130.0	0	5	0	4
131.0	0	5	0	4
132.0	0	3	1	3
133.0	0	6	0	6
134.0	0	3	0	2
135.0	0	2	0	2
136.0	0	4	0	3
137.0	0	1	0	2
138.0	0	5	0	5
139.0	0	3	0	6
140.0	0	5	0	3
141.0	0	0	0	2
142.0	0	10	0	6
143.0	0	2	0	2
144.0	0	1	0	3
146.0	0	6	0	5
147.0	0	2	0	2
148.0	0	7	0	8
149.0	0	2	0	2
150.0	0	1	0	0
151.0	0	0	0	2
152.0	0	4	0	3
153.0	0	2	0	1
154.0	0	4	0	3
156.0	0	1	0	2
157.0	0	1	0	3
158.0	0	3	0	1
159.0	0	4	0	3
161.0	0	2	0	4
162.0	0	6	0	4
163.0	0	0	0	2
164.0	0	3	0	3
165.0	0	2	0	1
166.0	0	3	0	4
167.0	0	1	0	1
168.0	0	4	0	2
169.0	0	1	0	2
170.0	0	1	0	0
171.0	0	1	0	1
172.0	0	0	0	1
173.0	0	0	0	1
174.0	0	2	0	3
175.0	0	2	0	2
176.0	0	2	0	2
177.0	0	2	0	1
178.0	0	4	0	2
179.0	0	2	0	2
180.0	0	2	0	2
181.0	0	1	0	2
182.0	0	3	0	3
183.0	0	1	0	0
184.0	0	3	0	5
185.0	0	2	0	2
186.0	0	1	0	2
187.0	0	2	0	2
188.0	0	3	0	2
189.0	0	1	0	1
190.0	0	1	0	0
191.0	0	2	0	2
192.0	0	3	0	3
193.0	0	3	0	3
194.0	0	1	0	3
195.0	0	1	0	0
196.0	0	2	0	1
197.0	0	2	0	1
198.0	0	1	0	1
200.0	0	0	0	1
201.0	0	1	0	1
202.0	0	2	0	1
203.0	0	1	0	1
204.0	0	1	0	2
205.0	0	1	0	2
206.0	0	1	0	3
207.0	0	3	0	2
208.0	0	4	0	3
209.0	0	2	0	0
210.0	0	3	0	3
213.0	0	2	0	3
214.0	0	3	0	2
215.0	0	2	0	2
217.0	0	1	0	2
219.0	0	1	0	0
221.0	0	1	0	1
222.0	0	2	0	2
224.0	0	1	0	2
225.0	0	0	0	2
226.0	0	1	0	0
227.0	0	1	0	0
228.0	0	2	0	1
229.0	0	2	0	2
230.0	0	0	0	1
231.0	0	1	0	1
233.0	0	1	0	2
234.0	0	2	0	1
235.0	0	2	0	2
236.0	0	3	0	3
237.0	0	0	0	4
238.0	0	5	0	0
240.0	0	0	0	2
241.0	0	0	0	1
242.0	0	2	0	2
243.0	0	3	0	4
244.0	0	4	0	1
245.0	0	1	0	2
246.0	0	4	0	3
247.0	0	2	0	2
248.0	0	0	0	1
249.0	0	2	0	0
250.0	0	0	0	1
251.0	0	3	0	3
252.0	0	2	0	4
253.0	0	3	0	2
254.0	0	1	0	0
255.0	0	2	0	1
256.0	0	3	0	3
257.0	0	0	0	2
258.0	0	3	0	3
259.0	0	0	0	1
260.0	0	4	0	2
261.0	0	1	0	1
262.0	0	0	0	1
263.0	0	2	0	1
264.0	0	2	0	1
265.0	0	0	0	1
266.0	0	1	0	2
267.0	0	1	0	2
268.0	0	3	0	2
270.0	0	1	0	0
271.0	0	1	0	1
272.0	0	2	0	2
273.0	0	1	0	0
274.0	0	1	0	1
275.0	0	3	0	3
277.0	0	1	0	2
278.0	0	1	0	0
280.0	0	1	0	1
281.0	0	0	0	2
282.0	0	1	0	0
283.0	0	1	0	0
284.0	0	0	0	2
285.0	0	1	0	1
286.0	0	2	0	0
287.0	0	0	0	1
288.0	0	2	0	1
290.0	0	3	0	3
292.0	0	0	0	2
293.0	0	2	0	2
294.0	0	1	0	2
295.0	0	1	0	1
296.0	0	3	0	1
297.0	0	1	0	1
298.0	0	1	0	1
299.0	0	2	0	1
300.0	0	0	1	2
301.0	0	2	0	0
302.0	0	1	0	2
303.0	0	2	0	2
304.0	0	0	0	2
305.0	0	1	0	0
307.0	0	1	0	0
308.0	0	1	0	2
309.0	0	2	0	1
310.0	0	1	0	1
311.0	0	1	0	0
312.0	0	1	0	1
313.0	0	1	0	1
314.0	0	1	0	1
318.0	0	1	0	1
320.0	0	0	0	1
322.0	0	1	0	0
323.0	0	1	0	1
324.0	0	1	0	1
325.0	0	1	0	2
326.0	0	1	0	1
327.0	0	1	0	1
328.0	0	1	0	1
330.0	0	1	0	1
331.0	0	1	0	0
333.0	0	1	0	1
334.0	0	0	0	1
335.0	0	1	0	2
336.0	0	1	0	0
337.0	0	3	0	2
338.0	0	0	0	2
339.0	0	1	0	2
340.0	0	2	0	0
342.0	0	1	0	2
345.0	0	3	0	1
346.0	0	3	0	5
347.0	0	2	0	2
349.0	0	1	0	0
351.0	0	1	0	0
353.0	0	1	0	2
354.0	0	1	0	1
357.0	0	1	0	0
358.0	0	2	0	2
362.0	0	1	0	1
363.0	0	1	0	2
364.0	0	1	0	1
365.0	0	3	0	2
366.0	0	2	0	2
370.0	0	1	0	1
371.0	0	0	0	1
372.0	0	1	0	1
374.0	0	1	0	0
375.0	0	1	0	2
376.0	0	1	0	0
378.0	0	1	0	2
380.0	0	1	0	1
381.0	0	1	0	1
382.0	0	1	0	2
383.0	0	1	0	0
385.0	0	2	0	1
386.0	0	2	0	2
388.0	0	0	0	1
389.0	0	1	0	0
393.0	0	1	0	2
395.0	0	2	0	1
397.0	0	0	0	1
398.0	0	3	0	3
399.0	0	1	0	1
400.0	0	1	0	2
401.0	0	1	0	1
402.0	0	0	0	1
403.0	0	3	0	0
407.0	0	0	0	1
409.0	0	3	0	2
411.0	0	1	0	3
412.0	0	1	0	1
413.0	0	1	0	1
414.0	0	1	0	0
415.0	0	1	0	1
416.0	0	2	0	1
419.0	0	1	0	1
420.0	0	1	0	1
422.0	0	1	0	1
425.0	0	1	0	1
427.0	0	0	0	2
428.0	0	1	0	1
429.0	0	1	0	0
430.0	0	1	0	1
434.0	0	1	0	0
436.0	0	1	0	1
438.0	0	0	0	1
439.0	0	2	0	1
441.0	0	1	0	2
442.0	0	0	0	1
443.0	0	1	0	0
445.0	0	2	0	1
454.0	0	0	0	1
455.0	0	1	0	1
457.0	0	1	0	0
460.0	0	1	0	1
461.0	0	1	0	1
470.0	0	1	0	1
476.0	0	1	0	1
479.0	0	1	0	1
481.0	0	1	0	1
482.0	0	0	0	1
485.0	0	2	0	1
487.0	0	1	0	1
489.0	0	0	0	1
490.0	0	2	0	1
493.0	0	1	0	1
495.0	0	1	0	1
496.0	0	1	0	1
501.0	0	1	0	1
505.0	0	1	0	1
507.0	0	0	0	1
508.0	0	1	0	0
512.0	0	1	0	1
517.0	0	1	0	1
519.0	0	1	0	1
520.0	0	1	0	1
521.0	0	1	0	1
525.0	0	1	0	1
533.0	0	0	0	1
539.0	0	1	0	0
540.0	0	0	0	1
543.0	0	1	0	0
544.0	0	1	0	1
547.0	0	1	0	1
549.0	0	1	0	1
561.0	0	1	0	1
562.0	0	1	0	1
566.0	0	1	0	1
570.0	0	1	0	1
573.0	0	1	0	2
576.0	0	1	0	0
579.0	0	1	0	2
580.0	0	3	0	2
582.0	0	1	0	1
583.0	0	1	0	1
585.0	0	1	0	1
588.0	0	1	0	1
590.0	0	0	0	1
594.0	0	1	0	1
595.0	0	1	0	0
596.0	0	0	0	1
601.0	0	1	0	0
603.0	0	0	0	1
607.0	0	0	0	3
608.0	0	1	0	0
609.0	0	1	0	0
610.0	0	1	0	0
611.0	0	2	0	1
616.0	0	0	0	1
617.0	0	0	0	1
619.0	0	1	0	0
622.0	0	2	0	1
623.0	0	1	0	1
625.0	0	1	0	1
633.0	0	1	0	1
636.0	0	1	0	1
639.0	0	1	0	1
643.0	0	0	0	1
648.0	0	1	0	1
655.0	0	1	0	0
665.0	0	1	0	1
666.0	0	1	0	1
669.0	0	0	0	1
676.0	0	1	0	0
685.0	0	0	0	1
690.0	0	1	0	0
698.0	0	2	0	2
699.0	0	0	0	1
701.0	0	1	0	0
707.0	0	0	0	1
710.0	0	0	0	1
712.0	0	1	0	0
714.0	0	1	0	0
727.0	0	1	0	2
732.0	0	1	0	0
734.0	0	1	0	1
754.0	0	1	0	1
755.0	0	1	0	1
757.0	0	1	0	1
760.0	0	2	0	2
762.0	0	1	0	1
770.0	0	1	0	1
774.0	0	0	0	1
775.0	0	1	0	0
783.0	0	1	0	1
784.0	0	0	0	1
786.0	0	1	0	1
787.0	0	1	0	1
788.0	0	1	0	0
797.0	0	1	0	1
801.0	0	0	0	1
803.0	0	0	0	1
804.0	0	1	0	0
808.0	0	1	0	0
813.0	0	0	0	1
814.0	0	1	0	0
819.0	0	1	0	1
829.0	0	0	0	1
835.0	0	0	0	1
836.0	0	1	0	0
840.0	0	1	0	0
842.0	0	1	0	1
844.0	0	0	0	1
845.0	0	1	0	0
847.0	0	0	0	1
852.0	0	1	0	0
863.0	0	0	0	1
867.0	0	1	0	0
869.0	0	1	0	1
870.0	0	0	0	1
871.0	0	1	0	0
883.0	0	1	0	1
891.0	0	1	0	1
901.0	0	1	0	1
913.0	0	1	0	1
914.0	0	1	0	1
916.0	0	1	0	1
918.0	0	1	0	1
922.0	0	1	0	1
928.0	0	0	0	1
938.0	0	1	0	0
939.0	0	0	0	1
944.0	0	1	0	1
951.0	0	1	0	0
961.0	0	1	0	1
972.0	0	0	0	1
975.0	0	1	0	1
978.0	0	2	0	1
984.0	0	0	0	1
987.0	0	0	0	1
991.0	0	1	0	0
994.0	0	1	0	0
995.0	0	0	0	1
1005.0	0	1	0	0
1013.0	0	1	0	2
1017.0	0	0	0	1
1018.0	0	1	0	0
1021.0	0	0	0	1
1023.0	0	2	0	0
1032.0	0	1	0	1
1051.0	0	0	0	1
1053.0	0	1	0	0
1066.0	0	0	0	1
1072.0	0	1	0	0
1077.0	0	1	0	1
1093.0	0	0	0	1
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