## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/MA_Ori_Ber_1_2020-09-21/MA_Ori_Ber_1_2020-09-21.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/MA_Ori_Ber_1_2020-09-21/MA_Ori_Ber_1_2020-09-21.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/MA_Ori_Ber_1_2020-09-21/MA_Ori_Ber_1_2020-09-21.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 04:13:11 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	3744292	27589583	0	0	2196587	10358749	245564	0.388879	27141157

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.00518	10194875	0	10284848
2.0	1.368906	4003285	238026	3989505
3.0	1.500521	1499533	3163	1466772
4.0	1.548146	528412	65	505641
5.0	1.565379	176836	23	164571
6.0	1.571615	56765	10	51524
7.0	1.573871	18008	11	16071
8.0	1.574688	5884	6	5099
9.0	1.574983	2122	4	1853
10.0	1.57509	938	2	847
11.0	1.575129	526	2	487
12.0	1.575143	339	5	341
13.0	1.575148	266	5	260
14.0	1.575149	274	4	263
15.0	1.57515	199	0	200
16.0	1.57515	175	1	173
17.0	1.57515	173	2	162
18.0	1.57515	127	0	129
19.0	1.575151	127	1	130
20.0	1.575151	123	0	117
21.0	1.575151	98	0	99
22.0	1.575151	76	0	77
23.0	1.575151	80	0	84
24.0	1.575151	82	0	80
25.0	1.575151	88	1	87
26.0	1.575151	66	1	66
27.0	1.575151	75	0	73
28.0	1.575151	54	0	51
29.0	1.575151	52	0	50
30.0	1.575151	44	0	47
31.0	1.575151	53	0	52
32.0	1.575151	50	0	52
33.0	1.575151	41	0	39
34.0	1.575151	34	1	33
35.0	1.575151	36	0	47
36.0	1.575151	44	0	38
37.0	1.575151	30	0	26
38.0	1.575151	30	0	30
39.0	1.575151	32	0	35
40.0	1.575151	38	1	36
41.0	1.575151	30	0	32
42.0	1.575151	29	0	28
43.0	1.575151	21	0	18
44.0	1.575151	30	0	33
45.0	1.575151	22	0	19
46.0	1.575151	18	0	17
47.0	1.575151	23	0	29
48.0	1.575151	20	0	15
49.0	1.575151	21	0	25
50.0	1.575151	26	0	21
51.0	1.575151	21	0	25
52.0	1.575151	15	1	13
53.0	1.575151	20	0	16
54.0	1.575151	16	0	19
55.0	1.575151	19	0	21
56.0	1.575151	21	0	22
57.0	1.575151	24	0	20
58.0	1.575151	11	0	12
59.0	1.575151	12	0	18
60.0	1.575151	13	0	9
61.0	1.575151	25	0	23
62.0	1.575151	15	0	16
63.0	1.575151	13	0	12
64.0	1.575151	9	0	11
65.0	1.575151	17	0	16
66.0	1.575151	7	0	4
67.0	1.575151	3	0	4
68.0	1.575151	14	0	13
69.0	1.575151	12	0	14
70.0	1.575151	8	0	9
71.0	1.575151	15	0	12
72.0	1.575151	6	0	6
73.0	1.575151	10	0	10
74.0	1.575151	8	0	9
75.0	1.575151	10	0	10
76.0	1.575151	11	0	15
77.0	1.575151	8	0	6
78.0	1.575151	15	0	13
79.0	1.575151	8	0	10
80.0	1.575151	12	0	8
81.0	1.575151	4	0	4
82.0	1.575151	2	0	7
83.0	1.575151	7	0	4
84.0	1.575151	10	0	11
85.0	1.575151	9	0	10
86.0	1.575151	7	0	5
87.0	1.575151	9	0	7
88.0	1.575151	6	0	7
89.0	1.575151	5	0	9
90.0	1.575151	8	0	6
91.0	1.575151	11	0	9
92.0	1.575151	7	0	7
93.0	1.575151	2	0	3
94.0	1.575151	2	0	2
95.0	1.575151	4	1	3
96.0	1.575151	5	0	5
97.0	1.575151	5	0	5
98.0	1.575151	3	0	4
99.0	1.575151	4	0	2
100.0	1.575151	4	0	5
101.0	0	4	0	3
102.0	0	4	0	7
103.0	0	5	0	7
104.0	0	11	0	9
105.0	0	6	0	4
106.0	0	6	0	7
107.0	0	4	0	3
108.0	0	3	0	3
109.0	0	3	0	4
110.0	0	3	0	3
111.0	0	6	0	5
112.0	0	2	0	2
113.0	0	5	0	5
114.0	0	2	0	3
115.0	0	5	0	5
116.0	0	3	0	1
117.0	0	1	0	1
118.0	0	3	0	4
119.0	0	7	0	7
120.0	0	1	0	1
121.0	0	4	0	5
122.0	0	3	0	1
123.0	0	3	0	4
124.0	0	4	0	7
125.0	0	5	0	4
126.0	0	4	0	3
127.0	0	2	0	1
128.0	0	2	0	2
129.0	0	4	0	3
130.0	0	3	0	3
131.0	0	1	0	1
132.0	0	4	0	4
133.0	0	0	0	1
134.0	0	2	0	3
135.0	0	3	0	1
137.0	0	0	0	3
138.0	0	6	0	5
139.0	0	3	0	4
140.0	0	3	0	4
141.0	0	5	0	4
142.0	0	2	0	1
143.0	0	3	0	2
144.0	0	1	0	2
145.0	0	3	0	2
146.0	0	2	0	3
147.0	0	1	0	0
148.0	0	4	0	4
149.0	0	1	0	1
150.0	0	4	0	3
151.0	0	3	0	3
152.0	0	1	0	2
153.0	0	5	0	4
154.0	0	1	0	4
155.0	0	3	0	1
156.0	0	1	0	0
157.0	0	2	0	3
158.0	0	4	0	4
159.0	0	4	0	4
160.0	0	1	0	1
161.0	0	1	0	0
162.0	0	1	0	1
163.0	0	1	0	1
164.0	0	1	0	2
165.0	0	2	0	3
166.0	0	2	0	3
167.0	0	4	0	2
168.0	0	6	0	7
169.0	0	2	0	0
170.0	0	1	0	2
171.0	0	1	0	0
172.0	0	2	0	2
173.0	0	0	0	1
174.0	0	2	0	2
175.0	0	0	0	1
176.0	0	2	0	3
177.0	0	4	0	2
178.0	0	2	0	1
179.0	0	2	0	4
180.0	0	1	0	3
181.0	0	2	0	0
182.0	0	4	0	4
183.0	0	1	0	0
184.0	0	3	0	3
185.0	0	2	0	3
186.0	0	5	0	3
187.0	0	1	0	1
188.0	0	1	0	1
189.0	0	0	0	2
190.0	0	3	0	4
191.0	0	4	0	2
192.0	0	3	0	2
194.0	0	0	0	1
195.0	0	1	0	3
196.0	0	3	0	2
197.0	0	4	0	2
198.0	0	1	0	1
199.0	0	1	0	2
200.0	0	1	1	1
202.0	0	3	0	3
203.0	0	1	0	2
204.0	0	3	0	1
205.0	0	0	0	1
207.0	0	1	0	1
209.0	0	5	0	4
210.0	0	1	0	2
211.0	0	3	0	3
212.0	0	2	0	2
213.0	0	1	0	1
214.0	0	3	0	3
215.0	0	2	0	1
216.0	0	1	0	1
217.0	0	2	0	4
218.0	0	3	0	1
219.0	0	1	0	1
220.0	0	0	0	1
221.0	0	1	0	1
222.0	0	3	0	2
224.0	0	2	0	4
225.0	0	3	0	2
226.0	0	1	0	1
227.0	0	1	0	1
228.0	0	2	0	2
229.0	0	2	0	2
230.0	0	2	0	2
231.0	0	2	0	2
232.0	0	3	0	2
233.0	0	2	0	2
234.0	0	0	0	1
237.0	0	2	0	1
238.0	0	1	0	2
239.0	0	1	0	0
240.0	0	3	0	4
241.0	0	2	0	1
243.0	0	0	0	1
244.0	0	5	0	4
246.0	0	0	0	2
247.0	0	3	0	1
248.0	0	2	0	2
249.0	0	1	0	2
251.0	0	1	0	0
254.0	0	2	0	2
255.0	0	0	0	1
256.0	0	2	0	3
257.0	0	2	0	1
258.0	0	1	0	1
259.0	0	1	0	0
260.0	0	1	0	1
261.0	0	0	0	1
262.0	0	3	0	3
263.0	0	3	0	3
264.0	0	2	0	1
265.0	0	1	0	1
266.0	0	1	0	1
268.0	0	1	0	2
269.0	0	1	0	0
270.0	0	1	0	1
272.0	0	1	0	1
273.0	0	1	0	1
274.0	0	1	0	1
275.0	0	1	0	2
276.0	0	1	0	1
277.0	0	2	0	1
278.0	0	1	0	1
279.0	0	1	0	1
280.0	0	1	0	2
281.0	0	1	0	1
282.0	0	2	0	2
283.0	0	2	0	1
284.0	0	1	0	2
285.0	0	1	0	1
286.0	0	0	0	1
287.0	0	1	0	2
288.0	0	1	0	0
289.0	0	1	0	2
290.0	0	4	0	1
291.0	0	0	0	2
292.0	0	1	0	2
293.0	0	5	0	2
294.0	0	1	0	1
295.0	0	1	0	1
296.0	0	0	0	1
297.0	0	3	0	2
299.0	0	1	0	2
302.0	0	2	0	3
303.0	0	2	0	2
304.0	0	1	0	2
305.0	0	2	0	0
306.0	0	0	0	1
307.0	0	2	0	1
308.0	0	3	0	2
311.0	0	1	0	2
312.0	0	1	0	1
313.0	0	0	0	1
314.0	0	1	0	0
315.0	0	0	0	1
316.0	0	0	0	1
317.0	0	2	0	1
318.0	0	1	0	0
319.0	0	3	0	3
321.0	0	1	0	0
326.0	0	0	0	1
328.0	0	1	0	1
329.0	0	1	0	2
331.0	0	1	0	0
332.0	0	2	0	2
333.0	0	1	0	1
334.0	0	1	0	0
335.0	0	2	0	2
336.0	0	1	0	1
337.0	0	0	0	2
338.0	0	3	0	3
340.0	0	2	0	1
341.0	0	3	0	3
342.0	0	2	0	1
345.0	0	1	0	2
347.0	0	1	0	0
348.0	0	0	0	1
349.0	0	0	0	1
350.0	0	2	0	2
351.0	0	1	0	0
353.0	0	3	0	2
354.0	0	1	0	2
356.0	0	2	0	1
357.0	0	1	0	2
360.0	0	1	0	1
361.0	0	3	0	3
363.0	0	2	0	1
364.0	0	1	0	1
367.0	0	1	0	1
368.0	0	0	0	1
369.0	0	2	0	1
371.0	0	2	0	2
372.0	0	2	0	3
375.0	0	2	0	2
376.0	0	1	0	0
380.0	0	1	0	1
381.0	0	0	0	1
382.0	0	2	0	2
383.0	0	2	0	1
387.0	0	1	0	1
391.0	0	1	0	1
392.0	0	1	0	1
393.0	0	0	0	1
397.0	0	1	0	0
401.0	0	0	0	1
404.0	0	2	0	1
407.0	0	0	0	1
410.0	0	1	0	0
411.0	0	1	0	1
412.0	0	0	0	1
413.0	0	1	0	0
414.0	0	1	0	1
416.0	0	1	0	1
418.0	0	1	0	1
419.0	0	0	0	1
422.0	0	1	0	0
423.0	0	0	0	1
424.0	0	0	0	1
425.0	0	1	0	1
427.0	0	2	0	2
428.0	0	1	0	1
430.0	0	1	0	0
431.0	0	1	0	1
432.0	0	1	0	1
434.0	0	1	0	2
435.0	0	1	0	0
438.0	0	1	0	0
443.0	0	1	0	2
444.0	0	0	0	1
445.0	0	2	0	0
446.0	0	1	0	1
447.0	0	0	0	1
448.0	0	0	0	2
449.0	0	1	0	0
450.0	0	1	0	0
452.0	0	1	0	1
453.0	0	1	0	1
454.0	0	0	0	2
455.0	0	1	0	1
456.0	0	3	0	1
457.0	0	1	0	1
458.0	0	2	0	1
462.0	0	1	0	1
467.0	0	0	0	2
468.0	0	1	0	1
469.0	0	2	0	1
470.0	0	1	0	0
472.0	0	0	0	1
473.0	0	1	0	1
475.0	0	1	0	0
477.0	0	0	0	1
478.0	0	1	0	1
479.0	0	1	0	0
480.0	0	0	0	1
481.0	0	2	0	1
483.0	0	0	0	2
484.0	0	1	0	0
485.0	0	1	0	1
486.0	0	1	0	2
487.0	0	1	0	0
489.0	0	1	0	0
490.0	0	0	0	1
492.0	0	1	0	0
493.0	0	2	0	3
495.0	0	1	0	1
496.0	0	1	0	0
497.0	0	2	0	2
500.0	0	1	0	1
501.0	0	0	0	1
502.0	0	1	0	0
505.0	0	1	0	1
507.0	0	0	0	1
509.0	0	1	0	0
511.0	0	1	0	1
512.0	0	1	0	2
514.0	0	1	0	0
519.0	0	1	0	1
534.0	0	1	0	1
536.0	0	2	0	2
559.0	0	1	0	1
562.0	0	1	0	1
568.0	0	1	0	1
569.0	0	1	0	1
572.0	0	0	0	1
573.0	0	1	0	1
574.0	0	1	0	1
577.0	0	1	0	0
584.0	0	1	0	1
587.0	0	1	0	1
589.0	0	1	0	1
600.0	0	0	0	1
602.0	0	0	0	1
603.0	0	0	0	1
604.0	0	2	0	0
606.0	0	1	0	0
614.0	0	1	0	1
615.0	0	1	0	1
619.0	0	1	0	1
628.0	0	0	0	1
630.0	0	1	0	0
658.0	0	1	0	1
670.0	0	1	0	1
678.0	0	1	0	1
690.0	0	1	0	1
709.0	0	1	0	1
722.0	0	0	0	1
723.0	0	1	0	1
725.0	0	1	0	0
732.0	0	0	0	1
737.0	0	0	0	1
738.0	0	1	0	0
741.0	0	1	0	0
742.0	0	1	0	1
745.0	0	0	0	1
748.0	0	1	0	0
752.0	0	1	0	1
756.0	0	0	0	1
759.0	0	2	0	1
763.0	0	0	0	1
767.0	0	1	0	1
770.0	0	1	0	0
772.0	0	1	0	2
776.0	0	1	0	0
777.0	0	0	0	1
778.0	0	1	0	0
780.0	0	0	0	2
782.0	0	1	0	0
783.0	0	0	0	2
784.0	0	1	0	1
788.0	0	1	0	0
789.0	0	1	0	1
790.0	0	1	0	1
791.0	0	2	0	0
796.0	0	1	0	1
802.0	0	0	0	1
806.0	0	1	0	0
811.0	0	0	0	1
818.0	0	1	0	0
821.0	0	0	0	1
824.0	0	1	0	1
826.0	0	1	0	1
827.0	0	1	0	0
830.0	0	1	0	1
833.0	0	0	0	1
839.0	0	1	0	0
841.0	0	0	0	1
843.0	0	1	0	0
847.0	0	1	0	1
854.0	0	0	0	1
857.0	0	1	0	0
860.0	0	1	0	1
886.0	0	1	0	1
915.0	0	1	0	1
917.0	0	1	0	1
948.0	0	0	0	1
954.0	0	1	0	1
958.0	0	0	0	1
961.0	0	1	0	0
962.0	0	1	0	0
963.0	0	1	0	1
966.0	0	1	0	1
974.0	0	1	0	1
1006.0	0	0	0	1
1011.0	0	1	0	0
1034.0	0	1	0	1
1049.0	0	1	0	1
1058.0	0	1	0	1
1061.0	0	1	0	1
1064.0	0	0	0	1
1066.0	0	0	0	1
1069.0	0	1	0	0
1070.0	0	1	0	0
1075.0	0	0	0	1
1077.0	0	1	0	0
1078.0	0	0	0	1
1080.0	0	1	0	2
1081.0	0	1	0	0
1084.0	0	1	0	1
1087.0	0	1	0	0
1095.0	0	1	0	1
1110.0	0	0	0	1
1116.0	0	0	0	1
1117.0	0	1	0	0
1122.0	0	1	0	0
1125.0	0	0	0	1
1128.0	0	0	0	1
1133.0	0	2	0	0
1136.0	0	1	0	2
1144.0	0	1	0	0
1151.0	0	0	0	1
1152.0	0	1	0	0
1164.0	0	1	0	1
1165.0	0	0	0	1
1172.0	0	0	0	1
1173.0	0	1	0	0
1174.0	0	0	0	1
1175.0	0	1	0	0
1179.0	0	0	0	1
1180.0	0	1	0	0
1182.0	0	1	0	0
1222.0	0	1	0	1
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