## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/DE_Bay_Mun_1_2017-06-20/DE_Bay_Mun_1_2017-06-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/DE_Bay_Mun_1_2017-06-20/DE_Bay_Mun_1_2017-06-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/DE_Bay_Mun_1_2017-06-20/DE_Bay_Mun_1_2017-06-20.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 09:28:53 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	3911990	53433396	0	0	2585646	29421025	916871	0.554508	28548299

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.00597	9609351	0	9752580
2.0	1.160753	5584923	780900	5638034
3.0	1.184569	3253913	56501	3239693
4.0	1.188233	1824190	5861	1783135
5.0	1.188797	989181	703	945354
6.0	1.188884	524369	89	490222
7.0	1.188897	275806	21	251070
8.0	1.188899	141214	7	125573
9.0	1.1889	72386	11	62479
10.0	1.1889	36956	8	31490
11.0	1.1889	18592	7	15296
12.0	1.1889	9682	5	7903
13.0	1.1889	5000	1	3994
14.0	1.1889	2663	6	2084
15.0	1.1889	1517	2	1193
16.0	1.1889	880	6	755
17.0	1.1889	602	1	500
18.0	1.1889	386	2	351
19.0	1.1889	320	0	282
20.0	1.1889	246	0	229
21.0	1.1889	183	0	172
22.0	1.1889	185	1	195
23.0	1.1889	161	1	162
24.0	1.1889	140	0	131
25.0	1.1889	133	0	125
26.0	1.1889	101	1	107
27.0	1.1889	105	0	98
28.0	1.1889	109	0	106
29.0	1.1889	103	0	108
30.0	1.1889	97	0	90
31.0	1.1889	80	2	75
32.0	1.1889	73	0	76
33.0	1.1889	71	0	69
34.0	1.1889	69	0	72
35.0	1.1889	64	0	69
36.0	1.1889	61	1	54
37.0	1.1889	65	0	61
38.0	1.1889	45	0	50
39.0	1.1889	58	0	59
40.0	1.1889	52	0	50
41.0	1.1889	44	0	42
42.0	1.1889	41	0	39
43.0	1.1889	47	0	47
44.0	1.1889	37	0	37
45.0	1.1889	34	0	34
46.0	1.1889	28	0	29
47.0	1.1889	33	0	32
48.0	1.1889	26	0	24
49.0	1.1889	37	0	31
50.0	1.1889	29	0	31
51.0	1.1889	24	0	27
52.0	1.1889	24	0	28
53.0	1.1889	31	0	25
54.0	1.1889	25	1	26
55.0	1.1889	23	0	24
56.0	1.1889	20	0	20
57.0	1.1889	30	0	30
58.0	1.1889	24	0	23
59.0	1.1889	17	0	15
60.0	1.1889	27	1	28
61.0	1.1889	24	0	25
62.0	1.1889	11	0	12
63.0	1.1889	15	0	14
64.0	1.1889	13	0	16
65.0	1.1889	14	0	16
66.0	1.1889	25	0	19
67.0	1.1889	15	0	14
68.0	1.1889	19	0	18
69.0	1.1889	15	0	18
70.0	1.1889	18	0	18
71.0	1.1889	13	0	16
72.0	1.1889	15	0	12
73.0	1.1889	11	0	12
74.0	1.1889	16	0	17
75.0	1.1889	11	0	11
76.0	1.1889	14	0	10
77.0	1.1889	11	0	10
78.0	1.1889	9	1	9
79.0	1.1889	10	0	12
80.0	1.1889	16	0	14
81.0	1.1889	7	0	9
82.0	1.1889	12	0	11
83.0	1.1889	13	0	13
84.0	1.1889	9	0	9
85.0	1.1889	7	0	6
86.0	1.1889	19	0	17
87.0	1.1889	6	0	6
88.0	1.1889	8	0	9
89.0	1.1889	9	0	7
90.0	1.1889	8	0	9
91.0	1.1889	9	0	10
92.0	1.1889	3	0	3
93.0	1.1889	14	0	13
94.0	1.1889	7	0	7
95.0	1.1889	3	0	4
96.0	1.1889	10	0	12
97.0	1.1889	10	0	8
98.0	1.1889	5	0	5
99.0	1.1889	5	1	8
100.0	1.1889	6	0	5
101.0	0	8	0	7
102.0	0	6	0	6
103.0	0	8	0	9
104.0	0	9	0	6
105.0	0	5	0	7
106.0	0	9	0	7
107.0	0	4	0	4
108.0	0	5	0	6
109.0	0	3	0	4
110.0	0	5	0	6
111.0	0	6	0	7
112.0	0	10	0	7
113.0	0	5	0	6
114.0	0	4	0	6
115.0	0	10	0	7
116.0	0	6	0	6
117.0	0	2	0	5
118.0	0	8	0	5
119.0	0	4	0	4
120.0	0	6	0	6
121.0	0	6	0	5
122.0	0	5	0	4
123.0	0	4	0	6
124.0	0	5	0	5
125.0	0	5	0	6
126.0	0	5	0	4
127.0	0	3	0	5
128.0	0	3	0	3
129.0	0	7	0	8
130.0	0	7	0	2
131.0	0	3	0	4
132.0	0	2	0	4
133.0	0	4	0	4
134.0	0	5	0	2
135.0	0	2	0	6
136.0	0	7	0	4
137.0	0	3	0	4
138.0	0	4	0	5
139.0	0	5	0	2
140.0	0	1	0	3
141.0	0	8	0	7
142.0	0	3	0	3
143.0	0	1	0	3
144.0	0	8	0	7
145.0	0	6	0	5
146.0	0	5	0	5
147.0	0	2	0	1
148.0	0	2	0	3
149.0	0	4	0	3
150.0	0	1	0	1
151.0	0	3	0	5
152.0	0	5	0	4
153.0	0	4	0	4
154.0	0	1	0	4
155.0	0	5	0	3
156.0	0	6	0	4
157.0	0	1	0	3
158.0	0	4	0	4
159.0	0	2	0	2
160.0	0	4	0	2
161.0	0	3	0	5
162.0	0	2	0	4
163.0	0	4	0	3
164.0	0	1	0	4
165.0	0	8	0	6
166.0	0	3	0	3
167.0	0	4	0	1
168.0	0	2	0	2
169.0	0	4	0	3
170.0	0	1	0	2
171.0	0	3	0	2
173.0	0	3	0	4
174.0	0	2	0	2
175.0	0	2	0	4
176.0	0	3	0	4
177.0	0	4	0	2
178.0	0	3	0	4
179.0	0	4	0	3
180.0	0	4	0	3
182.0	0	2	0	5
183.0	0	4	0	1
184.0	0	3	0	3
185.0	0	2	0	1
186.0	0	3	0	6
187.0	0	4	0	3
188.0	0	5	0	7
189.0	0	4	0	2
190.0	0	3	0	1
191.0	0	2	0	2
192.0	0	1	0	2
193.0	0	1	0	1
194.0	0	2	0	3
195.0	0	5	0	4
196.0	0	2	0	1
197.0	0	1	0	2
198.0	0	1	0	2
199.0	0	4	0	3
200.0	0	0	0	2
201.0	0	5	0	4
202.0	0	2	0	0
203.0	0	1	0	2
204.0	0	5	0	5
205.0	0	1	0	0
207.0	0	2	0	3
208.0	0	1	0	5
209.0	0	2	0	2
210.0	0	2	0	0
211.0	0	4	0	2
212.0	0	1	0	0
214.0	0	1	0	3
215.0	0	0	0	1
216.0	0	4	0	4
217.0	0	3	0	1
218.0	0	3	0	2
219.0	0	0	0	2
220.0	0	1	0	1
221.0	0	2	0	0
222.0	0	3	0	4
223.0	0	2	0	1
224.0	0	2	0	2
225.0	0	1	0	2
226.0	0	2	0	2
227.0	0	3	0	2
228.0	0	3	0	4
230.0	0	1	0	1
231.0	0	2	0	3
232.0	0	2	0	1
233.0	0	2	0	3
234.0	0	2	0	1
235.0	0	1	0	3
236.0	0	2	0	1
237.0	0	2	0	2
238.0	0	2	0	0
239.0	0	0	0	1
240.0	0	2	0	4
241.0	0	4	0	3
242.0	0	3	0	3
243.0	0	2	0	3
244.0	0	2	0	2
245.0	0	3	0	1
246.0	0	1	0	2
247.0	0	1	0	1
249.0	0	2	0	1
251.0	0	0	0	1
252.0	0	3	0	2
253.0	0	2	0	2
254.0	0	2	0	1
256.0	0	1	0	2
257.0	0	1	0	2
258.0	0	1	0	1
261.0	0	2	0	1
262.0	0	1	0	1
263.0	0	2	0	1
264.0	0	2	0	2
265.0	0	0	0	2
266.0	0	1	0	1
267.0	0	0	0	1
268.0	0	1	0	0
269.0	0	2	0	2
270.0	0	2	0	1
272.0	0	2	0	1
273.0	0	0	0	1
274.0	0	2	0	2
275.0	0	1	0	0
276.0	0	1	0	3
277.0	0	2	0	0
279.0	0	0	0	1
280.0	0	1	0	3
281.0	0	5	0	3
282.0	0	2	0	3
283.0	0	2	0	1
285.0	0	2	0	1
286.0	0	1	0	4
287.0	0	0	0	1
288.0	0	3	0	2
289.0	0	2	1	1
290.0	0	1	0	1
291.0	0	1	0	0
292.0	0	2	0	2
293.0	0	1	0	0
295.0	0	1	0	1
296.0	0	0	0	1
297.0	0	0	0	1
298.0	0	2	0	1
299.0	0	1	0	1
300.0	0	1	0	1
301.0	0	1	0	3
302.0	0	1	0	0
303.0	0	1	0	0
304.0	0	1	0	1
305.0	0	1	0	0
308.0	0	1	0	1
309.0	0	2	0	4
310.0	0	1	0	1
311.0	0	1	0	2
312.0	0	0	0	1
313.0	0	2	0	1
314.0	0	3	0	2
315.0	0	2	0	2
316.0	0	0	0	1
317.0	0	2	0	0
318.0	0	1	0	2
319.0	0	2	0	2
320.0	0	2	0	1
321.0	0	4	0	3
323.0	0	1	0	2
325.0	0	1	0	0
326.0	0	1	0	2
327.0	0	1	0	1
328.0	0	1	0	0
330.0	0	2	0	2
333.0	0	2	0	2
335.0	0	1	0	2
336.0	0	3	0	4
337.0	0	1	0	0
338.0	0	1	0	0
339.0	0	0	0	1
342.0	0	1	0	1
343.0	0	2	0	1
344.0	0	0	0	1
346.0	0	3	0	3
347.0	0	1	0	0
348.0	0	1	0	1
349.0	0	1	0	1
350.0	0	1	0	2
351.0	0	2	0	1
352.0	0	1	0	1
353.0	0	1	0	1
355.0	0	0	0	1
356.0	0	1	0	2
357.0	0	3	0	2
358.0	0	3	0	2
359.0	0	0	0	1
361.0	0	0	0	2
362.0	0	2	0	3
364.0	0	2	0	1
365.0	0	2	0	0
366.0	0	1	0	1
367.0	0	1	0	1
368.0	0	0	0	2
371.0	0	2	0	1
372.0	0	2	0	1
373.0	0	1	0	1
375.0	0	0	0	1
376.0	0	2	0	1
378.0	0	1	0	0
379.0	0	0	0	1
380.0	0	1	0	0
382.0	0	1	0	3
383.0	0	2	0	0
384.0	0	1	0	2
385.0	0	0	0	1
388.0	0	2	0	1
389.0	0	1	0	2
390.0	0	1	0	0
391.0	0	1	0	0
392.0	0	1	0	1
393.0	0	1	0	1
394.0	0	0	0	1
395.0	0	0	0	1
398.0	0	2	0	0
399.0	0	1	0	1
402.0	0	1	0	1
406.0	0	1	0	2
407.0	0	1	0	1
408.0	0	1	0	1
409.0	0	1	0	1
411.0	0	0	0	1
413.0	0	1	0	0
414.0	0	0	0	1
415.0	0	1	0	1
416.0	0	1	0	1
419.0	0	0	0	1
420.0	0	2	0	1
423.0	0	2	0	0
428.0	0	1	0	1
435.0	0	1	0	1
436.0	0	1	0	1
439.0	0	2	0	2
440.0	0	1	0	1
447.0	0	2	0	2
449.0	0	1	0	1
450.0	0	0	0	1
451.0	0	2	0	2
453.0	0	3	0	2
454.0	0	2	0	2
455.0	0	1	0	1
459.0	0	1	0	2
461.0	0	1	0	0
463.0	0	1	0	1
467.0	0	3	0	3
469.0	0	1	0	1
471.0	0	1	0	2
473.0	0	1	0	1
474.0	0	1	0	0
475.0	0	1	0	1
476.0	0	1	0	1
479.0	0	2	0	2
482.0	0	0	0	1
483.0	0	2	0	1
486.0	0	0	0	1
491.0	0	1	0	0
493.0	0	1	0	2
494.0	0	2	0	1
496.0	0	1	0	1
499.0	0	1	0	1
501.0	0	1	0	1
504.0	0	1	0	1
506.0	0	1	0	1
516.0	0	2	0	2
526.0	0	1	0	1
531.0	0	1	0	1
534.0	0	2	0	2
538.0	0	0	0	1
540.0	0	3	0	3
543.0	0	2	0	1
552.0	0	1	0	1
553.0	0	2	0	2
555.0	0	1	0	1
557.0	0	1	0	1
566.0	0	1	0	1
567.0	0	1	0	1
568.0	0	0	0	1
573.0	0	1	0	2
576.0	0	1	0	0
577.0	0	1	0	2
579.0	0	1	0	0
583.0	0	1	0	1
585.0	0	1	0	0
586.0	0	0	0	2
589.0	0	0	0	1
591.0	0	2	0	0
594.0	0	2	0	1
597.0	0	1	0	1
600.0	0	0	0	1
601.0	0	1	0	1
604.0	0	1	0	1
606.0	0	0	0	1
608.0	0	0	0	1
609.0	0	1	0	0
610.0	0	4	0	3
615.0	0	1	0	0
617.0	0	0	0	1
619.0	0	1	0	0
620.0	0	1	0	1
624.0	0	1	0	1
625.0	0	0	0	1
626.0	0	1	0	1
631.0	0	1	0	0
632.0	0	1	0	1
634.0	0	0	0	1
636.0	0	2	0	2
637.0	0	1	0	1
643.0	0	1	0	0
652.0	0	1	0	1
653.0	0	1	0	2
654.0	0	1	0	0
655.0	0	0	0	1
661.0	0	0	0	1
663.0	0	1	0	0
667.0	0	1	0	0
668.0	0	1	0	1
673.0	0	2	0	2
674.0	0	3	1	3
679.0	0	1	0	1
680.0	0	2	0	2
681.0	0	1	0	2
684.0	0	1	0	1
685.0	0	2	0	2
688.0	0	2	0	1
689.0	0	1	0	1
694.0	0	1	0	1
696.0	0	1	0	1
701.0	0	1	0	1
704.0	0	1	0	2
705.0	0	1	0	1
707.0	0	2	0	1
716.0	0	0	0	1
719.0	0	1	0	1
722.0	0	1	0	0
727.0	0	0	0	1
728.0	0	1	0	1
730.0	0	2	0	2
731.0	0	1	0	1
736.0	0	1	0	0
742.0	0	1	0	1
746.0	0	0	0	1
747.0	0	1	0	0
749.0	0	0	0	1
750.0	0	1	0	1
755.0	0	1	0	0
756.0	0	1	0	1
766.0	0	1	0	1
770.0	0	0	0	1
772.0	0	0	0	1
773.0	0	1	0	1
774.0	0	1	0	0
775.0	0	1	0	0
780.0	0	1	0	1
782.0	0	1	0	1
788.0	0	0	0	1
789.0	0	1	0	1
790.0	0	1	0	0
800.0	0	1	0	1
807.0	0	1	0	1
809.0	0	1	0	1
812.0	0	1	0	1
823.0	0	1	0	1
833.0	0	0	0	1
834.0	0	1	0	0
838.0	0	1	0	2
843.0	0	2	0	1
845.0	0	1	0	1
846.0	0	0	0	1
847.0	0	1	0	1
849.0	0	1	0	1
851.0	0	1	0	0
856.0	0	1	0	1
866.0	0	1	0	1
870.0	0	1	0	1
872.0	0	0	0	1
876.0	0	2	0	1
881.0	0	0	0	1
885.0	0	1	0	1
889.0	0	1	0	0
893.0	0	1	0	1
896.0	0	0	0	1
898.0	0	1	0	1
900.0	0	1	0	1
904.0	0	1	0	0
918.0	0	1	0	1
920.0	0	0	0	1
921.0	0	1	0	0
927.0	0	0	0	1
928.0	0	1	0	0
931.0	0	0	0	1
932.0	0	0	0	1
935.0	0	1	0	1
937.0	0	1	0	1
938.0	0	2	0	0
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