## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/UA_Zap_Zap_1_2019-06-17/UA_Zap_Zap_1_2019-06-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/UA_Zap_Zap_1_2019-06-17/UA_Zap_Zap_1_2019-06-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/UA_Zap_Zap_1_2019-06-17/UA_Zap_Zap_1_2019-06-17.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 07:49:15 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	6430902	40762526	0	0	4063840	23216762	725410	0.574121	20420228

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.005718	6384228	0	6488347
2.0	1.142347	4029463	616067	4077059
3.0	1.160909	2471203	45394	2465829
4.0	1.16343	1427592	4461	1395875
5.0	1.163773	788623	489	753816
6.0	1.163819	422160	77	393946
7.0	1.163826	220528	23	200480
8.0	1.163827	113930	11	100962
9.0	1.163827	58175	12	49957
10.0	1.163827	28681	11	24023
11.0	1.163827	14321	6	11652
12.0	1.163827	7071	6	5710
13.0	1.163827	3654	3	2873
14.0	1.163827	1910	7	1501
15.0	1.163827	1063	5	806
16.0	1.163827	623	4	514
17.0	1.163827	408	0	354
18.0	1.163827	282	1	262
19.0	1.163827	234	3	223
20.0	1.163827	238	5	219
21.0	1.163827	173	0	172
22.0	1.163827	166	3	168
23.0	1.163827	151	1	142
24.0	1.163827	111	1	119
25.0	1.163827	118	0	117
26.0	1.163827	138	0	135
27.0	1.163827	105	0	107
28.0	1.163827	104	0	109
29.0	1.163827	94	1	88
30.0	1.163827	104	0	94
31.0	1.163827	64	0	66
32.0	1.163827	84	0	91
33.0	1.163827	72	0	69
34.0	1.163827	70	0	63
35.0	1.163827	67	0	79
36.0	1.163827	57	0	56
37.0	1.163827	58	0	56
38.0	1.163827	65	0	58
39.0	1.163827	47	0	50
40.0	1.163827	55	0	55
41.0	1.163827	53	0	55
42.0	1.163827	38	0	35
43.0	1.163827	52	0	52
44.0	1.163827	33	0	30
45.0	1.163827	46	0	44
46.0	1.163827	39	0	41
47.0	1.163827	27	0	29
48.0	1.163827	40	0	36
49.0	1.163827	39	1	42
50.0	1.163827	33	0	35
51.0	1.163827	31	1	25
52.0	1.163827	16	0	17
53.0	1.163827	31	1	37
54.0	1.163827	30	0	23
55.0	1.163827	27	0	28
56.0	1.163827	27	1	26
57.0	1.163827	17	0	20
58.0	1.163827	23	0	24
59.0	1.163827	29	0	26
60.0	1.163827	28	1	28
61.0	1.163827	32	0	34
62.0	1.163827	32	0	35
63.0	1.163827	22	0	20
64.0	1.163827	20	0	17
65.0	1.163827	10	0	12
66.0	1.163827	28	0	29
67.0	1.163827	22	0	18
68.0	1.163827	12	0	10
69.0	1.163827	16	0	17
70.0	1.163827	19	0	20
71.0	1.163827	17	0	18
72.0	1.163827	14	0	13
73.0	1.163827	23	0	24
74.0	1.163827	16	0	15
75.0	1.163827	18	0	21
76.0	1.163827	14	0	7
77.0	1.163827	11	0	14
78.0	1.163827	13	0	14
79.0	1.163827	16	0	14
80.0	1.163827	10	0	11
81.0	1.163827	17	0	21
82.0	1.163827	12	0	11
83.0	1.163827	18	0	17
84.0	1.163827	13	0	14
85.0	1.163827	12	0	9
86.0	1.163827	11	0	13
87.0	1.163827	13	0	8
88.0	1.163827	6	0	9
89.0	1.163827	14	0	11
90.0	1.163827	9	0	12
91.0	1.163827	8	0	8
92.0	1.163827	14	0	16
93.0	1.163827	10	0	11
94.0	1.163827	12	0	14
95.0	1.163827	21	0	19
96.0	1.163827	10	0	7
97.0	1.163827	11	0	16
98.0	1.163827	17	0	13
99.0	1.163827	9	0	6
100.0	1.163827	7	1	5
101.0	0	8	0	10
102.0	0	6	0	9
103.0	0	7	0	3
104.0	0	6	0	6
105.0	0	3	0	5
106.0	0	8	0	6
107.0	0	6	0	10
108.0	0	7	0	7
109.0	0	8	0	9
110.0	0	6	0	6
111.0	0	12	0	7
112.0	0	6	0	9
113.0	0	8	0	5
114.0	0	6	0	8
115.0	0	7	1	6
116.0	0	3	0	4
117.0	0	6	0	8
118.0	0	7	0	5
119.0	0	6	0	6
120.0	0	6	0	7
121.0	0	5	0	5
122.0	0	8	0	5
123.0	0	8	0	8
124.0	0	7	0	10
125.0	0	8	0	6
126.0	0	6	0	4
127.0	0	5	0	7
128.0	0	6	0	8
129.0	0	9	0	8
130.0	0	3	0	1
131.0	0	3	0	2
132.0	0	3	0	4
133.0	0	2	0	5
134.0	0	4	0	6
135.0	0	6	0	5
136.0	0	7	0	6
137.0	0	3	0	3
138.0	0	6	0	6
139.0	0	7	0	6
140.0	0	3	0	4
141.0	0	5	0	6
142.0	0	3	0	2
143.0	0	5	0	3
144.0	0	3	0	4
145.0	0	5	0	5
146.0	0	5	0	4
147.0	0	4	0	3
148.0	0	3	0	6
149.0	0	5	0	5
150.0	0	5	0	2
151.0	0	4	0	7
152.0	0	3	0	5
153.0	0	8	0	4
154.0	0	2	0	1
155.0	0	4	0	4
156.0	0	2	0	2
157.0	0	2	0	2
158.0	0	5	0	5
159.0	0	4	0	6
160.0	0	4	0	3
161.0	0	6	0	4
162.0	0	4	0	5
163.0	0	2	0	2
164.0	0	4	0	5
165.0	0	5	0	4
166.0	0	4	0	4
167.0	0	2	0	2
168.0	0	2	0	4
169.0	0	2	0	0
170.0	0	3	0	2
171.0	0	1	0	2
172.0	0	4	0	4
173.0	0	3	0	4
174.0	0	3	0	2
176.0	0	4	0	4
177.0	0	2	0	1
178.0	0	2	0	2
180.0	0	2	0	3
182.0	0	2	0	6
183.0	0	4	0	2
184.0	0	7	0	5
185.0	0	2	0	2
186.0	0	1	0	2
187.0	0	3	0	4
188.0	0	3	0	3
189.0	0	3	0	3
190.0	0	3	0	2
191.0	0	4	0	4
192.0	0	4	0	4
193.0	0	3	0	2
194.0	0	2	0	3
195.0	0	3	0	3
196.0	0	3	0	2
197.0	0	3	0	4
198.0	0	2	0	4
199.0	0	6	0	5
200.0	0	4	0	4
201.0	0	0	0	1
202.0	0	3	0	2
203.0	0	3	0	1
204.0	0	0	0	1
205.0	0	1	0	1
206.0	0	3	0	3
207.0	0	2	0	3
208.0	0	4	0	4
209.0	0	2	0	1
210.0	0	3	0	4
211.0	0	2	0	1
212.0	0	1	0	0
213.0	0	4	0	3
214.0	0	2	0	3
215.0	0	1	0	0
216.0	0	4	0	5
217.0	0	2	0	1
218.0	0	1	0	1
219.0	0	1	0	2
221.0	0	2	0	2
222.0	0	1	0	2
223.0	0	2	0	1
224.0	0	4	0	3
225.0	0	0	0	2
226.0	0	3	0	3
227.0	0	1	0	1
228.0	0	3	0	2
229.0	0	2	0	1
230.0	0	1	0	2
231.0	0	5	0	5
232.0	0	3	0	3
233.0	0	0	0	2
234.0	0	1	0	1
235.0	0	3	0	0
236.0	0	1	0	3
237.0	0	1	0	2
238.0	0	3	0	3
239.0	0	2	0	2
240.0	0	4	0	4
241.0	0	1	0	3
242.0	0	3	0	2
243.0	0	1	0	0
244.0	0	2	0	1
245.0	0	4	0	4
246.0	0	2	0	3
247.0	0	1	0	1
248.0	0	1	0	0
249.0	0	4	0	4
250.0	0	3	0	6
251.0	0	1	0	1
252.0	0	2	0	1
253.0	0	2	0	1
254.0	0	2	0	0
255.0	0	1	0	1
256.0	0	3	0	4
257.0	0	1	0	2
258.0	0	2	0	1
259.0	0	3	0	3
260.0	0	1	0	3
261.0	0	1	0	1
262.0	0	6	0	2
263.0	0	0	0	1
264.0	0	1	0	0
265.0	0	0	0	2
266.0	0	2	0	3
267.0	0	2	0	0
268.0	0	2	0	3
270.0	0	1	0	0
271.0	0	1	0	0
272.0	0	2	0	4
273.0	0	3	0	3
274.0	0	1	0	2
275.0	0	1	0	1
276.0	0	4	0	3
278.0	0	5	0	5
279.0	0	1	0	2
280.0	0	1	0	0
282.0	0	3	0	3
283.0	0	3	0	3
284.0	0	4	0	6
285.0	0	3	0	5
286.0	0	2	0	0
287.0	0	7	0	3
288.0	0	1	0	2
291.0	0	3	0	2
292.0	0	0	0	2
293.0	0	4	0	3
295.0	0	2	0	4
296.0	0	1	0	1
297.0	0	2	0	1
298.0	0	2	0	1
299.0	0	1	0	0
300.0	0	1	0	1
301.0	0	2	0	4
302.0	0	1	0	2
303.0	0	2	0	3
304.0	0	1	0	0
305.0	0	0	0	1
306.0	0	2	0	1
307.0	0	2	0	3
309.0	0	1	0	1
310.0	0	3	0	1
311.0	0	2	0	1
312.0	0	0	0	1
313.0	0	1	0	1
314.0	0	1	0	0
316.0	0	1	0	1
318.0	0	1	0	1
319.0	0	1	0	0
320.0	0	2	0	4
321.0	0	1	0	0
322.0	0	1	0	3
323.0	0	3	0	4
324.0	0	3	0	0
325.0	0	1	0	2
327.0	0	1	0	0
328.0	0	0	0	1
329.0	0	1	0	1
330.0	0	3	0	2
331.0	0	2	0	1
332.0	0	3	0	4
334.0	0	1	0	0
335.0	0	1	0	3
336.0	0	1	0	1
337.0	0	0	0	1
338.0	0	2	0	3
339.0	0	5	0	3
341.0	0	0	0	2
342.0	0	1	0	0
343.0	0	2	0	0
344.0	0	1	0	0
346.0	0	3	0	3
348.0	0	1	0	1
349.0	0	0	0	1
350.0	0	1	0	2
351.0	0	1	0	1
352.0	0	1	0	0
353.0	0	0	0	1
355.0	0	2	0	0
357.0	0	1	0	1
360.0	0	0	0	1
362.0	0	0	0	1
363.0	0	1	0	2
364.0	0	2	0	1
366.0	0	2	0	0
367.0	0	0	0	1
368.0	0	2	0	4
369.0	0	1	0	0
370.0	0	2	1	1
372.0	0	1	0	0
373.0	0	1	0	1
374.0	0	0	0	1
375.0	0	2	0	3
376.0	0	1	0	1
377.0	0	1	0	2
378.0	0	3	0	4
379.0	0	1	0	0
380.0	0	1	0	1
381.0	0	1	0	0
382.0	0	1	0	1
383.0	0	0	0	1
384.0	0	1	0	0
385.0	0	3	0	2
387.0	0	1	0	0
388.0	0	0	0	1
391.0	0	1	0	1
395.0	0	0	0	1
396.0	0	1	0	2
397.0	0	1	0	1
398.0	0	1	0	0
399.0	0	1	0	0
400.0	0	0	0	1
401.0	0	1	0	0
404.0	0	1	0	0
405.0	0	1	0	1
406.0	0	0	0	1
407.0	0	0	0	2
408.0	0	2	0	1
410.0	0	1	0	0
412.0	0	2	0	2
413.0	0	1	0	1
414.0	0	1	0	0
417.0	0	3	0	3
418.0	0	1	0	1
419.0	0	0	0	1
420.0	0	1	0	2
421.0	0	1	0	0
422.0	0	1	0	1
423.0	0	1	0	1
424.0	0	1	0	0
425.0	0	2	0	2
426.0	0	0	0	2
427.0	0	1	0	1
428.0	0	0	0	1
429.0	0	0	0	1
430.0	0	2	0	0
431.0	0	1	0	1
433.0	0	2	0	1
435.0	0	1	0	2
437.0	0	1	0	1
438.0	0	2	0	3
439.0	0	1	0	3
440.0	0	2	0	0
441.0	0	1	0	0
442.0	0	1	0	1
443.0	0	1	0	1
445.0	0	2	0	2
446.0	0	1	0	0
448.0	0	0	0	1
450.0	0	1	0	1
451.0	0	0	0	1
452.0	0	1	0	3
453.0	0	4	0	2
455.0	0	0	0	1
457.0	0	2	0	0
458.0	0	1	0	0
459.0	0	1	0	1
460.0	0	1	0	0
464.0	0	0	0	1
465.0	0	0	0	1
466.0	0	1	0	1
467.0	0	1	0	1
468.0	0	1	0	1
470.0	0	2	0	0
471.0	0	0	0	1
472.0	0	0	0	1
475.0	0	1	0	0
476.0	0	2	0	3
477.0	0	1	0	1
478.0	0	2	0	1
479.0	0	1	0	0
480.0	0	1	0	2
481.0	0	1	0	1
483.0	0	1	0	1
484.0	0	0	0	1
485.0	0	1	0	1
487.0	0	1	0	0
488.0	0	1	0	1
491.0	0	1	0	2
494.0	0	1	0	0
495.0	0	1	0	0
496.0	0	1	0	1
497.0	0	1	0	1
498.0	0	0	0	1
499.0	0	1	0	0
500.0	0	0	0	1
502.0	0	0	0	1
504.0	0	1	0	0
506.0	0	2	0	1
507.0	0	0	0	1
508.0	0	1	0	2
511.0	0	2	0	0
513.0	0	2	0	3
516.0	0	1	0	1
519.0	0	2	0	1
520.0	0	1	0	1
523.0	0	2	0	2
524.0	0	1	0	1
526.0	0	0	0	1
527.0	0	1	0	0
530.0	0	0	0	1
531.0	0	1	0	2
532.0	0	1	0	0
536.0	0	1	0	0
538.0	0	2	0	3
540.0	0	1	0	0
543.0	0	1	0	1
545.0	0	1	0	1
549.0	0	1	0	1
550.0	0	1	0	1
552.0	0	1	0	1
556.0	0	1	0	1
560.0	0	1	0	1
565.0	0	1	0	1
566.0	0	1	0	1
568.0	0	0	0	1
569.0	0	1	0	1
571.0	0	3	0	4
572.0	0	1	0	1
573.0	0	0	0	1
574.0	0	2	0	1
575.0	0	0	0	1
576.0	0	1	0	0
577.0	0	0	0	1
578.0	0	1	0	1
579.0	0	0	0	1
580.0	0	1	0	0
581.0	0	1	0	0
582.0	0	3	0	1
587.0	0	1	0	1
588.0	0	1	0	2
589.0	0	2	0	1
592.0	0	1	0	1
594.0	0	1	0	1
596.0	0	1	0	1
597.0	0	1	0	1
602.0	0	1	0	1
603.0	0	2	0	2
606.0	0	1	0	1
611.0	0	2	0	2
612.0	0	0	0	1
613.0	0	1	0	1
614.0	0	1	0	1
615.0	0	0	0	1
616.0	0	2	0	1
619.0	0	0	0	1
621.0	0	1	0	0
623.0	0	2	0	2
624.0	0	1	0	0
628.0	0	0	0	1
629.0	0	1	0	0
632.0	0	1	0	1
634.0	0	0	0	1
637.0	0	1	0	1
639.0	0	2	0	2
640.0	0	1	0	0
642.0	0	1	0	1
644.0	0	0	0	1
645.0	0	2	0	1
652.0	0	1	0	1
655.0	0	0	0	1
656.0	0	1	0	1
657.0	0	1	0	0
659.0	0	0	0	1
661.0	0	2	0	2
662.0	0	1	0	0
663.0	0	1	0	1
668.0	0	1	0	1
672.0	0	1	0	1
675.0	0	1	0	1
677.0	0	1	0	1
678.0	0	0	0	1
679.0	0	0	0	1
680.0	0	3	0	2
682.0	0	2	0	2
691.0	0	1	0	0
694.0	0	1	0	1
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