## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Ode_15_Jun_2019/UA_Ode_15_Jun_2019.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Ode_15_Jun_2019/UA_Ode_15_Jun_2019.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Ode_15_Jun_2019/UA_Ode_15_Jun_2019.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 Dec 21 03:22:20 UTC 2022

## 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	2611637	10030983	0	0	1124897	4133796	284251	0.414248	8814248

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.015698	3214243	0	3309449
2.0	1.341174	1335982	234634	1325463
3.0	1.445471	534910	20188	502506
4.0	1.478893	207319	2131	182152
5.0	1.489603	77927	312	63691
6.0	1.493035	28806	60	21667
7.0	1.494134	10935	16	7553
8.0	1.494487	4066	11	2642
9.0	1.4946	1624	12	1081
10.0	1.494636	755	6	523
11.0	1.494647	423	9	343
12.0	1.494651	255	4	218
13.0	1.494652	198	1	181
14.0	1.494653	153	3	147
15.0	1.494653	146	2	145
16.0	1.494653	138	2	133
17.0	1.494653	111	1	116
18.0	1.494653	111	0	115
19.0	1.494653	87	1	79
20.0	1.494653	93	0	90
21.0	1.494653	78	1	78
22.0	1.494653	71	1	69
23.0	1.494653	60	1	57
24.0	1.494653	45	0	49
25.0	1.494653	48	0	48
26.0	1.494653	38	0	37
27.0	1.494653	42	0	39
28.0	1.494653	39	0	42
29.0	1.494653	36	1	35
30.0	1.494653	41	0	43
31.0	1.494653	39	0	39
32.0	1.494653	44	0	44
33.0	1.494653	43	0	45
34.0	1.494653	30	1	27
35.0	1.494653	30	1	34
36.0	1.494653	42	1	38
37.0	1.494653	31	1	30
38.0	1.494653	26	0	25
39.0	1.494653	31	0	28
40.0	1.494653	22	0	25
41.0	1.494653	21	0	19
42.0	1.494653	15	0	12
43.0	1.494653	19	0	20
44.0	1.494653	18	0	20
45.0	1.494653	25	0	29
46.0	1.494653	22	0	19
47.0	1.494653	20	0	21
48.0	1.494653	12	0	11
49.0	1.494653	14	0	13
50.0	1.494653	17	0	16
51.0	1.494653	12	0	12
52.0	1.494653	8	0	11
53.0	1.494653	14	0	11
54.0	1.494653	10	0	12
55.0	1.494653	15	0	12
56.0	1.494653	12	0	9
57.0	1.494653	16	0	19
58.0	1.494653	11	0	11
59.0	1.494653	14	0	13
60.0	1.494653	12	0	13
61.0	1.494653	11	0	11
62.0	1.494653	8	0	7
63.0	1.494653	6	0	3
64.0	1.494653	3	0	5
65.0	1.494653	9	0	14
66.0	1.494653	10	0	6
67.0	1.494653	5	0	7
68.0	1.494653	8	0	9
69.0	1.494653	8	0	6
70.0	1.494653	8	0	6
71.0	1.494653	9	0	9
72.0	1.494653	6	0	10
73.0	1.494653	13	0	8
74.0	1.494653	5	0	7
75.0	1.494653	5	0	6
76.0	1.494653	7	0	7
77.0	1.494653	7	0	9
78.0	1.494653	8	0	7
79.0	1.494653	8	0	5
80.0	1.494653	7	0	8
81.0	1.494653	2	0	1
82.0	1.494653	6	0	4
83.0	1.494653	4	0	7
84.0	1.494653	10	0	10
85.0	1.494653	6	0	9
86.0	1.494653	8	0	6
87.0	1.494653	6	0	3
88.0	1.494653	3	0	4
89.0	1.494653	2	0	1
90.0	1.494653	2	0	3
91.0	1.494653	4	0	3
92.0	1.494653	4	0	7
93.0	1.494653	8	0	7
94.0	1.494653	4	0	6
95.0	1.494653	9	0	7
96.0	1.494653	5	0	5
97.0	1.494653	6	0	6
98.0	1.494653	5	0	3
99.0	1.494653	5	0	4
100.0	1.494653	5	0	5
101.0	0	2	0	6
102.0	0	5	0	5
103.0	0	3	0	1
104.0	0	6	0	5
105.0	0	1	0	3
106.0	0	4	0	3
107.0	0	2	0	4
108.0	0	6	0	6
109.0	0	9	0	9
110.0	0	5	0	6
111.0	0	4	0	1
112.0	0	4	0	5
113.0	0	1	0	0
114.0	0	3	0	4
115.0	0	4	0	3
116.0	0	4	0	8
117.0	0	2	0	3
118.0	0	4	0	3
119.0	0	5	0	7
120.0	0	6	0	3
121.0	0	6	0	5
122.0	0	1	0	0
123.0	0	3	0	4
124.0	0	4	0	3
125.0	0	3	0	3
126.0	0	2	0	2
127.0	0	2	0	2
128.0	0	1	0	2
129.0	0	7	0	5
130.0	0	3	0	6
131.0	0	5	0	3
132.0	0	1	0	0
133.0	0	1	0	0
134.0	0	2	0	3
135.0	0	3	0	1
136.0	0	1	0	2
137.0	0	3	0	4
138.0	0	4	0	2
139.0	0	1	0	3
140.0	0	5	0	4
141.0	0	0	0	1
142.0	0	4	0	7
143.0	0	4	0	3
144.0	0	2	0	3
145.0	0	6	0	3
146.0	0	2	0	2
147.0	0	2	0	2
148.0	0	4	0	3
149.0	0	1	0	2
150.0	0	5	0	4
151.0	0	0	1	0
153.0	0	0	0	1
154.0	0	4	0	8
155.0	0	3	0	1
156.0	0	3	0	1
157.0	0	4	0	7
158.0	0	6	0	5
159.0	0	3	0	3
160.0	0	3	0	2
161.0	0	1	0	2
162.0	0	6	0	2
164.0	0	3	0	5
165.0	0	1	0	1
166.0	0	3	0	2
167.0	0	2	0	1
168.0	0	0	0	2
169.0	0	1	0	3
170.0	0	2	0	3
171.0	0	3	0	3
172.0	0	4	0	2
173.0	0	1	0	1
174.0	0	3	0	4
175.0	0	3	0	1
176.0	0	1	0	0
177.0	0	2	0	3
178.0	0	1	0	1
179.0	0	2	0	2
180.0	0	2	0	2
181.0	0	3	0	2
182.0	0	0	0	3
183.0	0	4	0	4
184.0	0	5	0	2
185.0	0	1	0	3
186.0	0	1	0	1
187.0	0	4	0	3
188.0	0	1	0	0
189.0	0	0	0	1
190.0	0	2	0	2
191.0	0	2	0	4
192.0	0	3	0	3
194.0	0	2	0	0
195.0	0	1	0	1
196.0	0	2	0	1
197.0	0	1	0	0
198.0	0	1	0	2
199.0	0	3	0	3
200.0	0	2	0	2
201.0	0	1	0	1
202.0	0	2	0	2
203.0	0	1	0	2
204.0	0	2	0	2
205.0	0	4	0	2
206.0	0	2	0	3
207.0	0	1	0	0
208.0	0	0	0	3
209.0	0	1	0	1
210.0	0	4	0	3
211.0	0	1	0	0
212.0	0	1	0	2
213.0	0	4	0	3
214.0	0	0	0	2
215.0	0	2	0	1
216.0	0	1	0	0
217.0	0	1	0	2
218.0	0	2	0	3
219.0	0	2	0	2
220.0	0	1	0	2
221.0	0	2	0	1
222.0	0	2	0	1
223.0	0	3	0	3
225.0	0	1	0	0
226.0	0	1	0	1
227.0	0	1	0	0
230.0	0	0	0	1
233.0	0	2	0	2
234.0	0	0	0	2
235.0	0	1	0	1
236.0	0	1	0	0
237.0	0	1	0	1
239.0	0	2	0	0
240.0	0	2	0	2
241.0	0	1	0	1
242.0	0	2	0	2
244.0	0	1	0	4
245.0	0	1	0	1
246.0	0	3	0	2
247.0	0	0	0	1
249.0	0	1	0	0
250.0	0	1	0	1
251.0	0	2	0	2
252.0	0	3	0	1
253.0	0	2	0	3
254.0	0	1	0	0
258.0	0	0	0	1
259.0	0	3	0	2
260.0	0	0	0	1
261.0	0	1	0	1
262.0	0	2	0	1
263.0	0	3	0	4
265.0	0	1	0	0
266.0	0	1	0	2
267.0	0	1	0	0
268.0	0	2	0	2
270.0	0	0	0	1
271.0	0	0	0	1
272.0	0	1	0	0
274.0	0	1	0	1
275.0	0	1	0	1
276.0	0	0	0	1
278.0	0	1	0	1
280.0	0	2	0	0
282.0	0	2	0	2
284.0	0	1	0	1
285.0	0	1	0	1
286.0	0	2	0	2
287.0	0	0	0	1
289.0	0	1	0	0
292.0	0	1	0	2
294.0	0	0	0	1
295.0	0	1	0	0
296.0	0	1	0	0
297.0	0	0	0	1
298.0	0	0	0	1
299.0	0	1	0	1
301.0	0	1	0	5
302.0	0	2	0	0
303.0	0	1	0	0
305.0	0	3	0	2
306.0	0	1	0	0
308.0	0	1	0	1
309.0	0	1	0	0
310.0	0	1	0	1
311.0	0	0	0	1
313.0	0	1	0	1
315.0	0	1	0	1
318.0	0	1	0	0
322.0	0	0	1	0
324.0	0	1	0	1
325.0	0	1	0	1
326.0	0	2	0	2
327.0	0	1	0	2
329.0	0	1	0	0
332.0	0	0	0	1
333.0	0	2	0	2
335.0	0	0	0	1
336.0	0	1	0	0
337.0	0	1	0	0
338.0	0	1	0	2
342.0	0	0	0	1
343.0	0	1	0	2
344.0	0	1	0	1
346.0	0	2	0	2
348.0	0	2	0	0
349.0	0	2	0	1
351.0	0	1	0	3
352.0	0	1	0	1
354.0	0	1	0	0
355.0	0	1	0	1
358.0	0	2	0	1
360.0	0	1	0	2
361.0	0	1	0	0
363.0	0	1	0	1
366.0	0	1	0	1
374.0	0	2	0	2
375.0	0	1	0	1
377.0	0	0	0	1
380.0	0	2	0	1
381.0	0	1	0	1
383.0	0	1	0	2
386.0	0	0	0	2
389.0	0	1	0	0
392.0	0	1	0	0
394.0	0	1	0	0
395.0	0	1	0	1
400.0	0	2	0	2
402.0	0	1	0	1
405.0	0	0	0	1
406.0	0	0	0	1
407.0	0	1	0	0
415.0	0	1	0	0
417.0	0	0	0	1
418.0	0	1	0	1
419.0	0	0	0	1
420.0	0	1	0	0
421.0	0	1	0	0
425.0	0	1	0	1
426.0	0	2	0	2
427.0	0	1	0	2
428.0	0	2	0	2
431.0	0	1	0	1
432.0	0	1	0	0
434.0	0	1	0	1
439.0	0	1	0	1
440.0	0	0	0	1
441.0	0	1	0	1
442.0	0	0	0	1
444.0	0	0	0	1
450.0	0	1	0	0
451.0	0	1	0	0
452.0	0	1	0	0
457.0	0	1	0	1
458.0	0	1	0	1
459.0	0	1	0	1
467.0	0	1	0	1
468.0	0	1	0	1
472.0	0	1	0	1
477.0	0	0	0	1
478.0	0	1	0	0
489.0	0	0	0	1
496.0	0	1	0	1
497.0	0	1	0	0
502.0	0	1	0	1
503.0	0	1	0	1
509.0	0	0	0	1
510.0	0	1	0	0
513.0	0	0	0	1
514.0	0	0	0	1
516.0	0	1	0	1
518.0	0	1	0	0
520.0	0	2	0	2
526.0	0	1	0	0
528.0	0	1	0	1
532.0	0	0	0	1
533.0	0	1	0	1
535.0	0	0	0	1
536.0	0	1	0	0
539.0	0	1	0	1
541.0	0	1	0	1
542.0	0	1	0	1
544.0	0	1	0	0
547.0	0	1	0	1
551.0	0	0	0	1
553.0	0	1	0	1
556.0	0	1	0	0
557.0	0	0	0	1
559.0	0	0	0	1
567.0	0	1	0	0
568.0	0	1	0	0
570.0	0	0	0	1
573.0	0	0	0	1
576.0	0	0	0	1
579.0	0	1	0	0
580.0	0	1	0	0
584.0	0	1	0	0
586.0	0	1	0	2
587.0	0	2	0	2
588.0	0	1	0	1
597.0	0	1	0	0
598.0	0	0	0	1
600.0	0	1	0	0
604.0	0	1	0	2
605.0	0	1	0	1
606.0	0	1	0	1
612.0	0	1	0	1
615.0	0	1	0	1
619.0	0	1	0	1
620.0	0	1	0	1
625.0	0	1	0	0
628.0	0	0	0	1
632.0	0	1	0	1
633.0	0	1	0	1
634.0	0	1	0	0
644.0	0	0	0	1
646.0	0	1	0	0
649.0	0	2	0	2
651.0	0	0	0	1
652.0	0	1	0	1
660.0	0	0	0	1
662.0	0	0	0	1
665.0	0	1	0	0
669.0	0	1	0	0
671.0	0	1	0	1
673.0	0	1	0	2
674.0	0	1	0	0
678.0	0	0	0	1
681.0	0	1	0	0
684.0	0	1	0	1
686.0	0	1	0	0
692.0	0	1	0	1
702.0	0	0	0	1
704.0	0	0	0	1
705.0	0	1	0	1
707.0	0	0	0	1
710.0	0	1	0	1
711.0	0	1	0	2
714.0	0	1	0	0
715.0	0	2	0	0
719.0	0	1	0	0
723.0	0	0	0	1
725.0	0	1	0	0
732.0	0	1	0	1
752.0	0	0	0	1
755.0	0	1	0	1
757.0	0	1	0	0
763.0	0	0	0	1
769.0	0	0	0	1
771.0	0	0	0	1
773.0	0	1	0	0
776.0	0	0	0	2
777.0	0	1	0	0
781.0	0	1	0	0
783.0	0	0	0	1
784.0	0	2	0	0
790.0	0	0	0	1
794.0	0	2	0	1
798.0	0	1	0	0
807.0	0	1	0	1
814.0	0	1	0	1
826.0	0	1	0	2
827.0	0	1	0	0
848.0	0	1	0	2
856.0	0	1	0	0
858.0	0	0	0	1
859.0	0	1	0	1
865.0	0	1	0	0
874.0	0	1	0	1
935.0	0	1	0	1
942.0	0	0	0	1
947.0	0	1	0	1
949.0	0	1	0	0
954.0	0	1	0	1
978.0	0	0	0	1
980.0	0	1	0	0
981.0	0	0	0	1
992.0	0	1	0	0
999.0	0	0	0	1
1000.0	0	1	0	0
1015.0	0	1	0	1
1016.0	0	0	0	1
1018.0	0	1	0	0
1021.0	0	1	0	1
1024.0	0	1	0	1
1025.0	0	0	0	1
1036.0	0	1	0	0
1055.0	0	0	0	1
1056.0	0	2	0	2
1058.0	0	1	0	0
1061.0	0	0	0	1
1065.0	0	0	0	1
1068.0	0	0	0	1
1070.0	0	1	0	0
1074.0	0	1	0	0
1075.0	0	2	0	1
1086.0	0	0	0	1
1092.0	0	0	0	1
1097.0	0	1	0	1
1099.0	0	1	0	0
1101.0	0	1	0	0
1106.0	0	0	0	1
1108.0	0	1	0	0
1114.0	0	1	0	1
1121.0	0	0	0	1
1123.0	0	1	0	0
1124.0	0	1	0	1
1125.0	0	1	0	1
1128.0	0	0	0	1
1135.0	0	1	0	0
1165.0	0	1	0	1
1171.0	0	0	0	1
1173.0	0	0	0	1
1175.0	0	1	0	0
1177.0	0	1	0	0
1225.0	0	0	0	1
1229.0	0	1	0	0
1232.0	0	0	0	1
1233.0	0	1	0	0
1265.0	0	1	0	1
1279.0	0	0	0	1
1282.0	0	1	0	0
1318.0	0	0	0	1
1338.0	0	1	0	0
1346.0	0	1	0	1
1354.0	0	1	0	1
1358.0	0	1	0	1
1359.0	0	0	0	1
1360.0	0	1	0	0
1363.0	0	0	0	1
1364.0	0	1	0	0
1370.0	0	0	0	1
1372.0	0	1	0	0
1411.0	0	1	0	1
1413.0	0	0	0	1
1417.0	0	2	0	1
1459.0	0	1	0	1
1473.0	0	0	0	1
1476.0	0	0	0	1
1477.0	0	1	0	0
1494.0	0	1	0	0
1591.0	0	0	0	1
1609.0	0	1	0	0
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