## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/RU_Vla_Ale_1_2018-10-13/RU_Vla_Ale_1_2018-10-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/RU_Vla_Ale_1_2018-10-13/RU_Vla_Ale_1_2018-10-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/RU_Vla_Ale_1_2018-10-13/RU_Vla_Ale_1_2018-10-13.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: Thu Feb 16 08:54:23 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	6049260	48355093	0	0	4052501	21484680	393298	0.457592	36978023

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.00398	14286363	0	14400970
2.0	1.275505	6346267	379450	6340347
3.0	1.348939	2834221	6086	2799629
4.0	1.368799	1233585	134	1202750
5.0	1.37417	530508	18	510305
6.0	1.375623	230458	19	219350
7.0	1.376016	101724	4	95920
8.0	1.376122	46451	5	43445
9.0	1.376151	22177	3	20836
10.0	1.376158	11618	5	10826
11.0	1.376161	6636	2	6269
12.0	1.376161	4272	1	4082
13.0	1.376161	2885	4	2738
14.0	1.376161	2045	2	1994
15.0	1.376161	1625	1	1596
16.0	1.376161	1232	1	1215
17.0	1.376161	1094	0	1055
18.0	1.376161	859	1	825
19.0	1.376161	738	0	707
20.0	1.376161	631	1	622
21.0	1.376161	476	0	469
22.0	1.376161	497	0	501
23.0	1.376161	423	1	413
24.0	1.376161	357	0	342
25.0	1.376161	312	0	316
26.0	1.376161	290	0	277
27.0	1.376161	265	1	268
28.0	1.376161	247	0	248
29.0	1.376161	224	0	212
30.0	1.376161	212	1	204
31.0	1.376161	167	0	163
32.0	1.376161	148	0	151
33.0	1.376161	153	1	149
34.0	1.376161	144	0	139
35.0	1.376161	129	0	133
36.0	1.376161	118	1	111
37.0	1.376161	126	0	128
38.0	1.376161	106	0	108
39.0	1.376161	96	0	83
40.0	1.376161	80	0	81
41.0	1.376161	75	0	80
42.0	1.376161	85	0	84
43.0	1.376161	78	0	76
44.0	1.376161	60	1	56
45.0	1.376161	64	0	75
46.0	1.376161	61	0	54
47.0	1.376161	59	0	58
48.0	1.376161	57	0	45
49.0	1.376161	38	0	42
50.0	1.376161	56	0	54
51.0	1.376161	37	0	38
52.0	1.376161	39	0	39
53.0	1.376161	33	0	40
54.0	1.376161	46	0	50
55.0	1.376161	44	0	40
56.0	1.376161	39	0	34
57.0	1.376161	29	0	29
58.0	1.376161	36	0	32
59.0	1.376161	24	0	27
60.0	1.376161	35	0	32
61.0	1.376161	20	0	20
62.0	1.376161	29	0	33
63.0	1.376161	31	0	26
64.0	1.376161	22	0	21
65.0	1.376161	26	1	27
66.0	1.376161	14	0	15
67.0	1.376161	22	0	24
68.0	1.376161	29	0	30
69.0	1.376161	19	0	18
70.0	1.376161	24	0	17
71.0	1.376161	13	0	16
72.0	1.376161	16	0	17
73.0	1.376161	17	0	14
74.0	1.376161	18	0	21
75.0	1.376161	17	0	18
76.0	1.376161	14	0	11
77.0	1.376161	18	0	23
78.0	1.376161	21	0	19
79.0	1.376161	19	0	13
80.0	1.376161	8	0	8
81.0	1.376161	13	0	15
82.0	1.376161	14	0	14
83.0	1.376161	11	0	9
84.0	1.376161	9	0	11
85.0	1.376161	15	0	18
86.0	1.376161	7	0	6
87.0	1.376161	12	0	9
88.0	1.376161	10	0	10
89.0	1.376161	12	0	14
90.0	1.376161	10	0	10
91.0	1.376161	9	0	6
92.0	1.376161	12	0	14
93.0	1.376161	9	0	6
94.0	1.376161	7	0	6
95.0	1.376161	10	0	12
96.0	1.376161	17	0	19
97.0	1.376161	8	0	6
98.0	1.376161	6	0	7
99.0	1.376161	8	0	9
100.0	1.376161	10	0	8
101.0	0	6	0	7
102.0	0	9	0	9
103.0	0	3	0	4
104.0	0	6	0	5
105.0	0	6	0	4
106.0	0	5	0	6
107.0	0	6	0	9
108.0	0	8	0	6
109.0	0	4	0	3
110.0	0	8	0	8
111.0	0	6	0	5
112.0	0	4	0	6
113.0	0	9	0	10
114.0	0	8	0	6
115.0	0	6	0	5
116.0	0	3	0	3
117.0	0	2	0	2
118.0	0	4	0	5
119.0	0	4	0	3
120.0	0	6	0	6
121.0	0	3	0	3
122.0	0	4	0	5
123.0	0	3	0	4
124.0	0	4	0	3
125.0	0	7	0	9
126.0	0	9	0	6
127.0	0	5	0	7
128.0	0	13	0	12
129.0	0	4	0	4
130.0	0	6	0	6
131.0	0	4	0	3
132.0	0	8	0	7
133.0	0	4	0	5
134.0	0	3	0	3
135.0	0	6	0	7
136.0	0	3	0	3
137.0	0	3	0	3
138.0	0	6	0	5
139.0	0	4	0	3
140.0	0	4	0	5
141.0	0	6	0	6
142.0	0	3	0	3
143.0	0	2	0	3
144.0	0	2	0	2
145.0	0	4	0	2
146.0	0	2	0	4
147.0	0	4	0	5
148.0	0	4	0	2
149.0	0	4	1	3
150.0	0	0	0	2
151.0	0	2	0	3
152.0	0	5	0	3
153.0	0	4	0	4
154.0	0	5	0	5
155.0	0	7	0	8
156.0	0	2	0	1
157.0	0	3	0	3
158.0	0	3	0	3
159.0	0	3	0	4
160.0	0	2	0	1
161.0	0	2	0	2
162.0	0	5	0	4
163.0	0	1	0	1
164.0	0	4	0	5
165.0	0	1	0	0
166.0	0	2	0	3
167.0	0	2	0	3
168.0	0	4	0	2
169.0	0	1	0	1
170.0	0	1	0	2
171.0	0	4	0	5
172.0	0	3	0	1
173.0	0	3	0	4
174.0	0	1	0	2
175.0	0	6	0	4
176.0	0	1	0	1
177.0	0	1	0	1
178.0	0	4	0	4
179.0	0	1	0	2
180.0	0	1	0	1
181.0	0	3	0	2
182.0	0	0	0	1
183.0	0	2	0	2
184.0	0	3	0	2
186.0	0	1	0	1
187.0	0	2	0	3
188.0	0	3	0	2
189.0	0	3	0	3
190.0	0	2	0	2
191.0	0	2	0	2
192.0	0	0	0	2
193.0	0	2	0	3
194.0	0	4	0	1
195.0	0	2	0	2
196.0	0	1	0	1
197.0	0	1	0	2
198.0	0	2	0	2
199.0	0	2	0	1
200.0	0	1	0	1
201.0	0	0	0	1
202.0	0	2	0	3
203.0	0	2	0	2
204.0	0	3	0	2
205.0	0	4	0	4
206.0	0	2	0	1
207.0	0	1	0	1
209.0	0	1	0	1
210.0	0	3	0	4
211.0	0	1	0	2
212.0	0	1	0	1
213.0	0	2	0	2
214.0	0	5	0	4
215.0	0	1	0	1
216.0	0	3	0	3
217.0	0	1	0	1
218.0	0	1	0	0
220.0	0	2	0	2
221.0	0	0	0	1
222.0	0	1	0	0
223.0	0	1	0	1
224.0	0	4	0	4
226.0	0	1	0	1
228.0	0	1	0	1
230.0	0	2	0	2
231.0	0	3	0	6
233.0	0	3	0	1
234.0	0	2	0	2
235.0	0	2	0	1
236.0	0	1	0	1
237.0	0	1	0	2
238.0	0	4	0	3
239.0	0	4	0	4
241.0	0	1	0	2
242.0	0	2	0	1
243.0	0	1	0	1
244.0	0	1	0	1
246.0	0	1	0	1
247.0	0	1	0	2
248.0	0	2	0	1
249.0	0	3	0	3
251.0	0	0	0	1
252.0	0	3	0	3
253.0	0	0	0	2
254.0	0	2	0	1
255.0	0	1	0	1
256.0	0	1	0	0
257.0	0	5	0	4
258.0	0	1	0	2
261.0	0	2	0	1
264.0	0	1	0	1
266.0	0	2	0	3
268.0	0	2	0	1
270.0	0	1	0	3
271.0	0	4	0	3
272.0	0	2	0	1
273.0	0	0	0	1
274.0	0	1	0	0
275.0	0	1	0	1
276.0	0	1	0	1
280.0	0	1	0	1
282.0	0	2	0	2
284.0	0	1	0	1
287.0	0	2	0	2
288.0	0	3	0	3
289.0	0	0	0	1
290.0	0	1	0	1
291.0	0	1	0	0
292.0	0	2	0	2
293.0	0	1	0	1
294.0	0	1	0	2
295.0	0	2	0	2
296.0	0	2	0	1
299.0	0	1	0	2
300.0	0	2	0	1
301.0	0	1	0	1
303.0	0	1	0	1
305.0	0	0	0	1
306.0	0	2	0	1
307.0	0	2	0	2
309.0	0	1	0	2
310.0	0	1	0	0
311.0	0	1	0	1
312.0	0	2	0	3
313.0	0	1	0	1
314.0	0	1	0	0
315.0	0	0	0	1
316.0	0	1	0	0
318.0	0	1	0	2
319.0	0	2	0	1
322.0	0	1	0	1
325.0	0	1	0	1
326.0	0	1	0	1
328.0	0	2	0	2
329.0	0	0	0	1
331.0	0	2	0	2
332.0	0	1	0	1
333.0	0	2	0	1
336.0	0	1	0	2
337.0	0	1	0	1
338.0	0	1	0	0
339.0	0	2	0	2
340.0	0	1	0	1
341.0	0	1	0	1
346.0	0	1	0	2
349.0	0	1	0	1
354.0	0	1	0	1
355.0	0	2	0	1
357.0	0	1	0	1
359.0	0	0	0	1
360.0	0	1	0	0
361.0	0	0	0	1
362.0	0	1	0	0
363.0	0	2	0	3
364.0	0	1	0	0
365.0	0	1	0	1
366.0	0	1	0	2
367.0	0	2	0	2
368.0	0	2	0	1
371.0	0	0	0	1
372.0	0	2	0	3
373.0	0	2	0	1
376.0	0	1	0	0
378.0	0	1	0	1
379.0	0	1	0	1
380.0	0	0	0	1
381.0	0	1	0	1
383.0	0	1	0	0
384.0	0	2	0	2
386.0	0	1	0	3
387.0	0	2	0	0
388.0	0	1	0	1
390.0	0	1	0	1
392.0	0	0	0	1
393.0	0	2	0	1
394.0	0	1	0	1
395.0	0	0	0	1
399.0	0	1	0	1
400.0	0	1	0	0
403.0	0	3	0	3
405.0	0	1	0	1
407.0	0	1	0	1
408.0	0	3	0	3
411.0	0	0	1	0
412.0	0	2	0	2
413.0	0	1	0	2
414.0	0	1	0	1
415.0	0	1	0	1
418.0	0	2	0	1
421.0	0	2	0	3
423.0	0	1	0	1
424.0	0	0	0	1
425.0	0	1	0	0
426.0	0	1	0	0
429.0	0	1	0	1
432.0	0	1	0	1
434.0	0	1	0	1
435.0	0	2	0	2
437.0	0	1	0	2
438.0	0	1	0	0
439.0	0	1	0	2
440.0	0	2	0	1
442.0	0	1	0	1
444.0	0	1	0	3
445.0	0	4	0	2
447.0	0	0	0	1
448.0	0	1	0	1
449.0	0	2	0	2
450.0	0	1	0	0
453.0	0	1	0	1
454.0	0	1	0	1
455.0	0	1	0	1
456.0	0	1	0	1
459.0	0	1	0	2
460.0	0	1	0	1
461.0	0	1	0	0
463.0	0	1	0	1
465.0	0	2	0	2
467.0	0	1	0	1
468.0	0	1	0	1
471.0	0	1	0	1
478.0	0	1	0	1
480.0	0	1	0	1
484.0	0	1	0	1
485.0	0	1	0	1
486.0	0	1	0	1
488.0	0	1	0	1
491.0	0	2	0	2
492.0	0	1	0	1
493.0	0	1	0	1
497.0	0	1	0	2
498.0	0	1	0	0
508.0	0	0	0	1
511.0	0	1	0	0
512.0	0	1	0	1
513.0	0	1	0	1
515.0	0	1	0	1
520.0	0	1	0	1
521.0	0	1	0	1
522.0	0	0	0	1
526.0	0	1	0	1
527.0	0	1	0	0
531.0	0	0	0	1
536.0	0	1	0	0
537.0	0	1	0	1
540.0	0	0	0	1
543.0	0	1	0	0
544.0	0	2	0	2
547.0	0	1	0	1
558.0	0	1	0	2
560.0	0	2	0	1
561.0	0	2	0	3
564.0	0	1	0	0
571.0	0	1	0	1
574.0	0	1	0	1
576.0	0	0	0	1
578.0	0	1	0	1
581.0	0	1	0	0
586.0	0	1	0	1
589.0	0	1	0	1
592.0	0	0	0	1
593.0	0	1	0	0
597.0	0	1	0	1
601.0	0	1	0	1
605.0	0	1	0	1
611.0	0	0	0	2
612.0	0	1	0	0
615.0	0	1	0	0
619.0	0	0	0	1
621.0	0	1	0	0
625.0	0	1	0	1
626.0	0	0	0	1
627.0	0	1	0	0
629.0	0	1	0	1
635.0	0	1	0	1
638.0	0	1	0	1
640.0	0	0	0	1
643.0	0	2	0	1
645.0	0	1	0	1
648.0	0	1	0	1
650.0	0	1	0	1
651.0	0	1	0	1
654.0	0	1	0	1
657.0	0	1	0	1
659.0	0	1	0	1
662.0	0	0	0	1
665.0	0	1	0	0
672.0	0	1	0	1
673.0	0	0	0	1
674.0	0	1	0	2
675.0	0	1	0	1
676.0	0	2	0	1
677.0	0	2	0	1
685.0	0	2	0	2
693.0	0	0	0	1
694.0	0	1	0	0
697.0	0	0	0	1
698.0	0	1	0	0
702.0	0	1	0	1
707.0	0	2	0	3
710.0	0	1	0	0
711.0	0	2	0	2
717.0	0	1	0	1
719.0	0	1	0	1
724.0	0	1	0	1
725.0	0	1	0	1
730.0	0	1	0	1
733.0	0	2	0	2
734.0	0	0	0	1
736.0	0	1	0	1
737.0	0	0	0	1
738.0	0	1	0	0
739.0	0	1	0	0
742.0	0	0	0	1
743.0	0	1	0	0
749.0	0	1	0	1
750.0	0	1	0	1
752.0	0	1	0	1
757.0	0	1	0	1
758.0	0	0	0	1
760.0	0	1	0	0
761.0	0	0	0	1
762.0	0	1	0	0
763.0	0	2	0	2
769.0	0	0	0	1
772.0	0	1	0	1
774.0	0	2	0	1
778.0	0	1	0	1
797.0	0	1	0	1
800.0	0	1	0	1
808.0	0	1	0	1
812.0	0	0	0	1
815.0	0	1	0	0
816.0	0	1	0	1
823.0	0	1	0	1
828.0	0	0	0	1
831.0	0	1	0	1
835.0	0	1	0	0
842.0	0	0	0	1
844.0	0	1	0	2
846.0	0	1	0	0
850.0	0	1	0	1
852.0	0	1	0	0
853.0	0	1	0	1
857.0	0	0	0	1
863.0	0	1	0	0
870.0	0	0	0	1
874.0	0	1	0	1
876.0	0	0	0	1
877.0	0	1	0	0
879.0	0	1	0	0
882.0	0	2	0	2
886.0	0	1	0	1
888.0	0	0	0	1
890.0	0	1	0	0
893.0	0	1	0	1
895.0	0	1	0	1
909.0	0	1	0	1
910.0	0	1	0	1
915.0	0	0	0	1
916.0	0	1	0	1
922.0	0	1	0	1
927.0	0	2	0	1
936.0	0	1	0	1
953.0	0	1	0	1
960.0	0	1	0	1
965.0	0	0	0	1
966.0	0	1	0	0
1007.0	0	1	0	1
1009.0	0	1	0	1
1012.0	0	1	0	1
1014.0	0	0	0	1
1017.0	0	1	0	1
1018.0	0	2	0	1
1028.0	0	1	0	1
1036.0	0	1	0	1
1039.0	0	1	0	1
1068.0	0	0	0	1
1069.0	0	1	0	0
1078.0	0	1	0	1
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