## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/GR_Kri_Ira_1_2018-10-11/GR_Kri_Ira_1_2018-10-11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/GR_Kri_Ira_1_2018-10-11/GR_Kri_Ira_1_2018-10-11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/GR_Kri_Ira_1_2018-10-11/GR_Kri_Ira_1_2018-10-11.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 04:15:39 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	3857549	26799064	0	0	2124566	10092902	231425	0.388306	26238275

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.00501	9896661	0	9979782
2.0	1.366915	3923249	225306	3911958
3.0	1.497237	1488467	2686	1458458
4.0	1.544166	530707	58	508831
5.0	1.561065	179107	19	167621
6.0	1.56715	58427	9	53171
7.0	1.569342	18551	8	16459
8.0	1.570131	5950	6	5275
9.0	1.570415	2084	7	1805
10.0	1.570517	889	2	789
11.0	1.570554	461	1	439
12.0	1.570567	309	1	297
13.0	1.570572	250	2	245
14.0	1.570574	198	0	191
15.0	1.570574	171	2	173
16.0	1.570575	147	0	152
17.0	1.570575	133	0	126
18.0	1.570575	107	0	102
19.0	1.570575	103	0	106
20.0	1.570575	102	1	106
21.0	1.570575	104	0	98
22.0	1.570575	80	0	83
23.0	1.570575	79	0	80
24.0	1.570575	73	0	71
25.0	1.570575	50	1	44
26.0	1.570575	55	0	58
27.0	1.570575	64	0	66
28.0	1.570575	53	0	51
29.0	1.570575	43	0	40
30.0	1.570575	49	0	52
31.0	1.570575	49	1	54
32.0	1.570575	48	0	42
33.0	1.570575	36	0	36
34.0	1.570575	33	0	31
35.0	1.570575	35	0	34
36.0	1.570575	28	0	29
37.0	1.570575	17	0	19
38.0	1.570575	29	0	28
39.0	1.570575	28	0	27
40.0	1.570575	28	0	31
41.0	1.570575	32	0	29
42.0	1.570575	18	0	16
43.0	1.570575	30	0	31
44.0	1.570575	28	0	29
45.0	1.570575	20	0	24
46.0	1.570575	24	0	17
47.0	1.570575	14	0	18
48.0	1.570575	18	0	18
49.0	1.570575	19	0	19
50.0	1.570575	14	0	17
51.0	1.570575	23	0	17
52.0	1.570575	12	0	13
53.0	1.570575	18	0	21
54.0	1.570575	13	0	11
55.0	1.570575	11	0	9
56.0	1.570575	9	0	12
57.0	1.570575	20	0	22
58.0	1.570575	14	0	10
59.0	1.570575	18	0	20
60.0	1.570575	16	1	13
61.0	1.570575	10	0	9
62.0	1.570575	3	0	5
63.0	1.570575	17	0	16
64.0	1.570575	12	0	13
65.0	1.570575	8	0	8
66.0	1.570575	13	0	14
67.0	1.570575	12	0	10
68.0	1.570575	8	0	8
69.0	1.570575	10	0	10
70.0	1.570575	8	0	7
71.0	1.570575	7	0	8
72.0	1.570575	8	0	8
73.0	1.570575	3	0	2
74.0	1.570575	7	0	9
75.0	1.570575	7	0	8
76.0	1.570575	9	0	10
77.0	1.570575	6	0	3
78.0	1.570575	3	0	3
79.0	1.570575	5	0	5
80.0	1.570575	5	0	4
81.0	1.570575	5	0	5
82.0	1.570575	4	0	6
83.0	1.570575	10	0	10
84.0	1.570575	4	1	5
85.0	1.570575	6	0	4
86.0	1.570575	8	0	10
87.0	1.570575	9	0	8
88.0	1.570575	4	0	4
89.0	1.570575	5	0	3
90.0	1.570575	4	0	6
91.0	1.570575	5	0	5
92.0	1.570575	6	0	5
93.0	1.570575	4	0	4
94.0	1.570575	8	0	7
95.0	1.570575	4	0	4
96.0	1.570575	6	0	8
97.0	1.570575	5	0	3
98.0	1.570575	3	0	4
99.0	1.570575	3	0	2
100.0	1.570575	1	0	1
101.0	0	2	0	3
102.0	0	2	0	2
103.0	0	3	0	6
104.0	0	8	0	5
105.0	0	2	0	2
106.0	0	4	0	3
107.0	0	4	0	4
108.0	0	2	0	3
109.0	0	6	0	6
110.0	0	5	0	5
111.0	0	3	0	2
112.0	0	4	0	5
113.0	0	7	0	6
115.0	0	1	0	1
116.0	0	2	0	2
117.0	0	1	0	2
118.0	0	1	0	2
119.0	0	5	0	4
120.0	0	6	0	5
121.0	0	3	0	5
122.0	0	3	0	3
123.0	0	4	0	3
124.0	0	2	0	3
125.0	0	2	0	2
126.0	0	3	0	2
127.0	0	6	0	5
128.0	0	3	0	5
129.0	0	3	0	3
130.0	0	3	0	1
131.0	0	4	0	4
132.0	0	4	0	4
133.0	0	2	0	4
134.0	0	2	0	2
135.0	0	6	0	5
136.0	0	4	0	3
137.0	0	2	0	5
138.0	0	3	0	4
139.0	0	7	0	4
140.0	0	3	0	6
141.0	0	4	0	4
142.0	0	3	0	1
143.0	0	2	0	0
144.0	0	4	0	4
145.0	0	4	0	5
146.0	0	1	0	2
147.0	0	3	0	3
148.0	0	4	0	2
149.0	0	2	0	2
150.0	0	2	0	2
151.0	0	5	0	6
152.0	0	3	0	3
153.0	0	4	0	4
154.0	0	3	0	3
155.0	0	1	0	1
156.0	0	2	0	1
157.0	0	3	0	3
158.0	0	1	0	1
160.0	0	1	0	1
161.0	0	4	0	5
162.0	0	3	0	3
163.0	0	1	0	0
164.0	0	1	0	1
165.0	0	3	0	4
167.0	0	4	0	4
168.0	0	7	0	6
169.0	0	1	0	3
170.0	0	3	0	2
171.0	0	1	0	2
172.0	0	2	0	1
173.0	0	3	0	2
174.0	0	4	0	6
175.0	0	4	0	2
176.0	0	1	0	2
178.0	0	2	0	2
179.0	0	2	0	3
180.0	0	4	0	2
181.0	0	1	0	2
182.0	0	2	0	4
183.0	0	3	0	2
184.0	0	2	0	1
185.0	0	2	0	2
186.0	0	2	0	3
187.0	0	1	0	1
188.0	0	2	0	1
189.0	0	3	0	2
191.0	0	1	0	1
192.0	0	1	0	2
193.0	0	2	0	2
195.0	0	1	0	0
196.0	0	2	0	2
197.0	0	1	0	1
198.0	0	3	0	4
199.0	0	2	0	2
201.0	0	0	0	1
202.0	0	1	0	1
203.0	0	1	0	1
204.0	0	2	0	1
205.0	0	3	0	2
206.0	0	1	0	2
207.0	0	2	0	2
208.0	0	1	0	0
209.0	0	2	0	4
210.0	0	3	0	5
211.0	0	2	0	1
212.0	0	2	0	0
213.0	0	3	0	4
214.0	0	0	0	1
215.0	0	2	0	0
216.0	0	3	0	3
217.0	0	1	0	2
218.0	0	2	0	2
219.0	0	1	0	0
220.0	0	3	0	3
221.0	0	1	0	1
222.0	0	2	0	3
223.0	0	2	0	1
224.0	0	2	0	1
226.0	0	3	0	3
229.0	0	0	0	1
230.0	0	1	0	0
231.0	0	0	0	1
234.0	0	2	0	1
236.0	0	0	0	1
237.0	0	1	0	1
238.0	0	1	0	1
239.0	0	3	0	3
240.0	0	1	0	1
241.0	0	1	0	2
242.0	0	2	0	1
243.0	0	0	0	2
244.0	0	1	0	0
245.0	0	3	0	2
246.0	0	1	0	1
247.0	0	1	0	1
248.0	0	1	0	1
249.0	0	2	0	3
250.0	0	2	0	3
251.0	0	4	0	2
252.0	0	0	0	1
253.0	0	5	0	3
255.0	0	1	0	1
257.0	0	1	0	2
258.0	0	0	0	1
259.0	0	1	0	0
260.0	0	1	0	0
261.0	0	2	0	2
264.0	0	0	0	1
265.0	0	0	0	1
266.0	0	1	0	0
267.0	0	1	0	0
269.0	0	1	0	1
270.0	0	2	0	3
271.0	0	0	0	1
272.0	0	2	0	4
273.0	0	2	0	1
274.0	0	2	0	2
275.0	0	4	0	2
276.0	0	2	0	2
278.0	0	2	0	1
279.0	0	2	0	2
280.0	0	1	0	1
281.0	0	1	0	1
285.0	0	2	0	2
286.0	0	0	0	1
288.0	0	1	0	1
289.0	0	1	0	2
290.0	0	1	0	1
291.0	0	1	0	1
292.0	0	2	0	4
293.0	0	5	0	2
295.0	0	2	0	1
298.0	0	1	0	1
300.0	0	0	0	1
301.0	0	2	0	1
302.0	0	1	0	1
303.0	0	1	0	2
304.0	0	1	0	1
305.0	0	0	0	1
306.0	0	1	0	1
307.0	0	2	0	1
308.0	0	1	0	0
309.0	0	1	0	1
312.0	0	1	0	2
313.0	0	1	0	0
315.0	0	1	0	2
316.0	0	1	0	1
317.0	0	0	0	2
318.0	0	1	0	2
319.0	0	2	0	1
320.0	0	3	0	0
323.0	0	1	0	1
324.0	0	1	0	1
325.0	0	0	0	1
327.0	0	2	0	1
329.0	0	1	0	1
330.0	0	1	0	2
331.0	0	0	0	1
333.0	0	2	0	0
334.0	0	0	0	1
336.0	0	1	0	0
338.0	0	2	0	2
341.0	0	1	0	1
342.0	0	1	0	2
345.0	0	2	0	4
346.0	0	2	0	1
347.0	0	1	0	0
348.0	0	1	0	0
349.0	0	0	0	1
350.0	0	1	0	0
352.0	0	1	0	1
354.0	0	0	0	1
355.0	0	1	0	0
358.0	0	0	0	1
359.0	0	1	0	1
360.0	0	1	0	0
361.0	0	0	0	1
362.0	0	1	0	1
367.0	0	1	0	1
369.0	0	1	0	0
373.0	0	0	0	1
374.0	0	1	0	1
375.0	0	1	0	0
379.0	0	1	0	1
382.0	0	1	0	1
383.0	0	1	0	1
384.0	0	1	0	1
387.0	0	2	0	4
388.0	0	1	0	1
389.0	0	1	0	1
390.0	0	1	0	0
392.0	0	1	0	0
394.0	0	1	0	1
396.0	0	0	0	1
397.0	0	1	0	0
398.0	0	0	0	1
399.0	0	1	0	1
400.0	0	1	0	1
401.0	0	2	0	2
403.0	0	1	0	0
412.0	0	1	0	2
413.0	0	1	0	0
418.0	0	1	0	1
423.0	0	0	0	1
424.0	0	1	0	1
425.0	0	1	0	0
426.0	0	0	0	1
427.0	0	2	0	1
428.0	0	0	0	1
429.0	0	1	0	1
430.0	0	1	0	0
432.0	0	1	0	1
435.0	0	1	0	1
437.0	0	1	0	1
439.0	0	1	0	2
440.0	0	1	0	0
442.0	0	1	0	1
449.0	0	0	0	1
451.0	0	1	0	0
460.0	0	0	0	1
462.0	0	1	0	0
465.0	0	1	0	1
473.0	0	0	0	1
476.0	0	1	0	0
481.0	0	1	0	2
483.0	0	0	0	1
484.0	0	1	0	0
485.0	0	1	0	0
487.0	0	0	0	1
489.0	0	0	0	1
491.0	0	2	0	1
493.0	0	0	0	1
494.0	0	2	0	1
495.0	0	1	0	0
496.0	0	1	0	1
501.0	0	2	0	2
514.0	0	0	0	1
517.0	0	1	0	0
520.0	0	1	0	1
521.0	0	0	0	1
524.0	0	1	0	1
526.0	0	1	0	0
529.0	0	1	0	1
545.0	0	0	0	1
548.0	0	0	0	1
549.0	0	1	0	0
552.0	0	1	0	0
564.0	0	0	0	1
567.0	0	1	0	0
573.0	0	0	0	1
574.0	0	1	0	0
575.0	0	1	0	1
576.0	0	0	0	1
578.0	0	1	0	1
580.0	0	1	0	0
581.0	0	1	0	1
585.0	0	1	0	1
599.0	0	1	0	1
600.0	0	0	0	1
601.0	0	1	0	1
602.0	0	1	0	0
604.0	0	0	0	1
605.0	0	1	0	0
606.0	0	1	0	1
607.0	0	0	0	1
610.0	0	1	0	0
614.0	0	0	0	1
618.0	0	1	0	0
619.0	0	1	0	1
627.0	0	1	0	2
631.0	0	1	0	0
639.0	0	1	0	1
643.0	0	1	0	1
657.0	0	0	0	1
659.0	0	1	0	1
660.0	0	1	0	0
678.0	0	1	0	1
681.0	0	1	0	2
682.0	0	1	0	1
684.0	0	1	0	0
690.0	0	1	0	1
702.0	0	0	0	1
705.0	0	1	0	0
715.0	0	1	0	1
722.0	0	0	0	1
726.0	0	1	0	0
728.0	0	1	0	1
729.0	0	0	0	1
730.0	0	1	0	0
738.0	0	0	0	1
740.0	0	1	0	1
744.0	0	1	0	0
745.0	0	1	0	1
749.0	0	1	0	1
753.0	0	0	0	1
755.0	0	1	0	0
758.0	0	1	0	1
772.0	0	1	0	1
773.0	0	0	0	1
776.0	0	1	0	0
792.0	0	0	0	1
794.0	0	1	0	0
802.0	0	1	0	2
805.0	0	1	0	0
817.0	0	0	0	1
822.0	0	1	0	0
825.0	0	0	0	1
826.0	0	1	0	1
827.0	0	1	0	1
832.0	0	1	0	0
833.0	0	0	0	1
834.0	0	0	0	1
837.0	0	1	0	0
838.0	0	1	0	0
839.0	0	1	0	1
842.0	0	0	0	1
850.0	0	2	0	1
854.0	0	0	0	1
857.0	0	1	0	0
870.0	0	0	0	1
872.0	0	1	0	0
873.0	0	1	0	1
876.0	0	0	0	1
879.0	0	0	0	1
887.0	0	1	0	0
888.0	0	1	0	0
925.0	0	0	0	1
928.0	0	1	0	0
934.0	0	0	0	1
941.0	0	1	0	0
944.0	0	1	0	1
952.0	0	0	0	1
957.0	0	1	0	1
958.0	0	1	0	0
966.0	0	0	0	1
972.0	0	1	0	0
975.0	0	0	0	1
977.0	0	1	0	0
981.0	0	0	0	1
984.0	0	0	0	1
989.0	0	2	0	0
993.0	0	0	0	1
995.0	0	1	0	1
1000.0	0	1	0	0
1046.0	0	0	0	1
1058.0	0	1	0	0
1060.0	0	0	0	1
1062.0	0	1	0	0
1084.0	0	0	0	1
1090.0	0	0	0	1
1091.0	0	1	0	0
1093.0	0	0	0	1
1096.0	0	1	0	0
1098.0	0	1	0	0
1102.0	0	0	0	1
1103.0	0	1	0	0
1104.0	0	1	0	1
1112.0	0	0	0	1
1114.0	0	1	0	1
1119.0	0	1	0	0
1123.0	0	0	0	1
1124.0	0	0	0	1
1126.0	0	1	0	0
1129.0	0	1	0	0
1141.0	0	0	0	1
1144.0	0	0	0	1
1146.0	0	1	0	0
1148.0	0	1	0	0
1183.0	0	0	0	1
1192.0	0	1	0	0
1200.0	0	1	0	1
1219.0	0	0	0	1
1220.0	0	1	0	0
1241.0	0	0	0	1
1252.0	0	1	0	0
1260.0	0	0	0	1
1264.0	0	1	0	0
1277.0	0	0	0	1
1279.0	0	0	0	1
1283.0	0	1	0	0
1284.0	0	1	0	0
1315.0	0	1	0	1
1393.0	0	1	0	1
1512.0	0	1	0	1
1724.0	0	0	0	1
1734.0	0	1	0	1
1743.0	0	1	0	0
1794.0	0	0	0	1
1798.0	0	0	0	1
1802.0	0	2	0	0
1804.0	0	0	0	1
1810.0	0	1	0	0
1834.0	0	0	0	1
1837.0	0	1	0	0
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