## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Myk_Ryb_1_2021-07-22/UA_Myk_Ryb_1_2021-07-22.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Myk_Ryb_1_2021-07-22/UA_Myk_Ryb_1_2021-07-22.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Myk_Ryb_1_2021-07-22/UA_Myk_Ryb_1_2021-07-22.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 Jan 19 09:04:47 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	4684253	22868447	0	0	2522983	4632276	197724	0.233782	50116776

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.006884	14306128	0	14433308
2.0	1.644867	2866457	193951	2790037
3.0	2.049107	551894	1678	515513
4.0	2.305242	102784	30	91868
5.0	2.467535	19744	12	17119
6.0	2.570367	4203	5	3554
7.0	2.635524	1332	5	1208
8.0	2.676809	651	6	616
9.0	2.702967	420	3	406
10.0	2.719542	314	2	312
11.0	2.730045	255	2	254
12.0	2.736699	207	2	209
13.0	2.740915	174	1	168
14.0	2.743587	154	0	154
15.0	2.74528	131	0	127
16.0	2.746352	88	0	88
17.0	2.747032	86	0	91
18.0	2.747462	83	1	78
19.0	2.747735	70	0	76
20.0	2.747908	80	0	79
21.0	2.748018	71	0	66
22.0	2.748087	68	1	64
23.0	2.748131	53	0	58
24.0	2.748159	47	0	47
25.0	2.748177	41	0	40
26.0	2.748188	35	0	32
27.0	2.748195	43	0	41
28.0	2.748199	24	0	28
29.0	2.748202	32	0	30
30.0	2.748204	30	0	30
31.0	2.748205	29	0	34
32.0	2.748206	32	0	31
33.0	2.748206	25	0	26
34.0	2.748207	23	0	19
35.0	2.748207	26	0	27
36.0	2.748207	21	0	22
37.0	2.748207	22	0	20
38.0	2.748207	19	0	22
39.0	2.748207	19	0	14
40.0	2.748207	13	0	15
41.0	2.748207	12	0	11
42.0	2.748207	19	0	21
43.0	2.748207	19	0	17
44.0	2.748207	19	0	22
45.0	2.748207	19	0	17
46.0	2.748207	15	0	12
47.0	2.748207	10	0	14
48.0	2.748207	10	0	9
49.0	2.748207	17	1	17
50.0	2.748207	10	0	8
51.0	2.748207	7	0	8
52.0	2.748207	10	0	9
53.0	2.748207	13	0	13
54.0	2.748207	8	0	9
55.0	2.748207	7	0	6
56.0	2.748207	9	0	10
57.0	2.748207	11	0	12
58.0	2.748207	10	0	9
59.0	2.748207	11	0	11
60.0	2.748207	9	0	8
61.0	2.748207	7	0	7
62.0	2.748207	10	0	11
63.0	2.748207	11	0	10
64.0	2.748207	8	0	7
65.0	2.748207	8	0	12
66.0	2.748207	9	0	6
67.0	2.748207	7	0	8
68.0	2.748207	9	0	9
69.0	2.748207	10	0	9
70.0	2.748207	7	0	8
71.0	2.748207	4	0	4
72.0	2.748207	7	0	6
73.0	2.748207	6	0	7
74.0	2.748207	8	0	6
75.0	2.748207	1	0	2
76.0	2.748207	5	0	7
77.0	2.748207	8	0	5
78.0	2.748207	5	0	6
79.0	2.748207	5	0	4
80.0	2.748207	8	0	9
81.0	2.748207	0	0	1
82.0	2.748207	4	0	6
83.0	2.748207	3	0	1
84.0	2.748207	7	0	5
85.0	2.748207	6	0	6
86.0	2.748207	2	0	2
87.0	2.748207	3	0	3
88.0	2.748207	4	0	5
89.0	2.748207	2	0	4
90.0	2.748207	11	0	9
91.0	2.748207	5	0	7
92.0	2.748207	4	0	2
93.0	2.748207	4	0	3
94.0	2.748207	2	0	4
95.0	2.748207	6	0	5
96.0	2.748207	1	0	0
97.0	2.748207	2	0	3
98.0	2.748207	3	0	2
99.0	2.748207	4	0	5
100.0	2.748207	2	0	2
101.0	0	5	0	4
102.0	0	3	0	3
103.0	0	1	0	2
104.0	0	5	0	4
105.0	0	4	0	5
106.0	0	2	0	1
107.0	0	2	0	4
108.0	0	2	0	1
109.0	0	7	0	6
110.0	0	1	0	2
111.0	0	1	0	2
112.0	0	4	0	2
113.0	0	2	0	3
114.0	0	4	0	3
115.0	0	6	0	8
116.0	0	2	0	0
117.0	0	2	0	2
118.0	0	3	0	5
119.0	0	8	0	8
120.0	0	1	0	1
121.0	0	5	0	4
122.0	0	2	0	3
123.0	0	5	0	5
124.0	0	3	0	1
125.0	0	1	0	2
126.0	0	3	0	2
127.0	0	0	0	1
128.0	0	2	0	1
129.0	0	1	0	1
130.0	0	2	0	2
131.0	0	7	0	7
132.0	0	0	0	1
133.0	0	0	0	1
134.0	0	3	0	3
135.0	0	5	0	3
136.0	0	2	0	3
137.0	0	3	0	3
138.0	0	2	0	2
139.0	0	4	0	5
140.0	0	2	0	0
141.0	0	1	0	1
142.0	0	1	0	4
143.0	0	5	0	2
144.0	0	3	0	4
145.0	0	1	0	0
146.0	0	0	0	1
147.0	0	2	0	1
148.0	0	2	0	3
149.0	0	4	0	4
150.0	0	1	0	0
151.0	0	1	0	1
152.0	0	1	0	1
156.0	0	5	0	5
158.0	0	2	0	2
159.0	0	1	0	1
160.0	0	0	0	1
161.0	0	6	0	5
162.0	0	2	0	3
163.0	0	5	0	5
164.0	0	2	0	2
165.0	0	2	0	1
167.0	0	1	0	1
169.0	0	2	0	2
170.0	0	2	0	2
171.0	0	1	0	2
172.0	0	1	0	1
173.0	0	2	0	1
174.0	0	2	0	3
175.0	0	2	0	1
177.0	0	1	0	3
178.0	0	2	0	1
179.0	0	1	0	1
180.0	0	2	0	2
181.0	0	2	0	1
182.0	0	0	0	1
183.0	0	1	0	0
184.0	0	1	0	2
185.0	0	2	0	2
186.0	0	1	0	0
187.0	0	0	0	1
188.0	0	1	0	0
189.0	0	2	0	2
190.0	0	1	0	2
192.0	0	1	0	0
193.0	0	2	0	2
194.0	0	1	0	3
195.0	0	0	0	1
196.0	0	3	0	0
197.0	0	0	0	2
198.0	0	1	0	0
199.0	0	1	0	1
200.0	0	2	0	2
201.0	0	2	0	1
202.0	0	1	0	1
203.0	0	1	0	2
204.0	0	1	0	0
206.0	0	0	0	1
207.0	0	3	0	3
208.0	0	1	0	2
209.0	0	2	0	2
210.0	0	3	0	1
212.0	0	0	0	1
214.0	0	1	0	1
217.0	0	1	0	0
218.0	0	0	0	1
219.0	0	1	0	0
220.0	0	0	0	1
223.0	0	1	0	1
225.0	0	1	0	1
226.0	0	0	0	1
227.0	0	1	0	0
228.0	0	1	0	1
229.0	0	2	0	2
230.0	0	2	0	1
232.0	0	1	0	2
233.0	0	1	0	0
235.0	0	1	0	1
239.0	0	1	0	1
240.0	0	1	0	2
241.0	0	2	0	1
242.0	0	0	0	1
243.0	0	1	0	1
244.0	0	1	0	0
245.0	0	0	0	1
246.0	0	1	0	0
249.0	0	1	0	2
250.0	0	1	0	0
252.0	0	1	0	1
256.0	0	0	0	2
257.0	0	1	0	1
258.0	0	1	0	0
261.0	0	1	0	3
262.0	0	2	0	0
263.0	0	1	0	0
265.0	0	2	0	2
266.0	0	1	0	1
267.0	0	0	0	1
268.0	0	1	0	0
271.0	0	0	0	2
272.0	0	1	0	0
273.0	0	2	0	1
274.0	0	1	0	1
276.0	0	0	0	3
278.0	0	4	0	1
279.0	0	1	0	2
280.0	0	1	0	0
284.0	0	0	0	1
286.0	0	1	0	1
287.0	0	2	0	1
288.0	0	1	0	1
293.0	0	1	0	1
299.0	0	1	0	1
301.0	0	0	0	1
302.0	0	0	0	1
303.0	0	0	0	1
304.0	0	3	0	1
305.0	0	0	0	1
306.0	0	3	0	2
308.0	0	2	0	1
312.0	0	1	0	1
313.0	0	1	0	1
317.0	0	0	0	1
318.0	0	0	0	1
320.0	0	1	0	0
321.0	0	1	0	0
322.0	0	1	0	1
324.0	0	0	0	1
326.0	0	2	0	1
334.0	0	1	0	2
335.0	0	1	0	0
339.0	0	0	0	2
340.0	0	1	0	0
341.0	0	1	0	2
343.0	0	2	0	0
346.0	0	1	0	1
348.0	0	1	0	1
351.0	0	1	0	1
352.0	0	1	0	1
354.0	0	1	0	1
356.0	0	1	0	2
357.0	0	0	0	1
358.0	0	1	0	0
360.0	0	2	0	2
361.0	0	1	0	1
362.0	0	1	0	1
363.0	0	1	0	1
368.0	0	1	0	0
375.0	0	0	0	1
377.0	0	1	0	0
381.0	0	1	0	2
384.0	0	1	0	0
387.0	0	1	0	1
390.0	0	0	0	1
391.0	0	1	0	1
392.0	0	1	0	0
395.0	0	1	0	1
397.0	0	0	0	1
398.0	0	1	0	0
405.0	0	1	0	1
407.0	0	0	0	1
408.0	0	1	0	1
409.0	0	1	0	0
410.0	0	0	0	1
411.0	0	2	0	1
412.0	0	0	0	1
413.0	0	1	0	0
419.0	0	0	0	1
421.0	0	1	0	1
422.0	0	1	0	0
424.0	0	0	0	1
425.0	0	0	0	2
426.0	0	3	0	0
439.0	0	1	0	1
440.0	0	0	0	1
443.0	0	1	0	0
454.0	0	0	0	1
455.0	0	0	0	1
456.0	0	1	0	0
458.0	0	1	0	0
463.0	0	0	0	1
467.0	0	1	0	1
468.0	0	1	0	0
471.0	0	0	0	1
473.0	0	1	0	0
484.0	0	1	0	1
487.0	0	1	0	1
489.0	0	1	0	1
503.0	0	0	0	1
504.0	0	0	0	1
505.0	0	2	0	0
512.0	0	0	0	1
514.0	0	1	0	0
535.0	0	0	0	1
536.0	0	1	0	0
549.0	0	0	0	1
550.0	0	1	0	0
587.0	0	0	0	1
588.0	0	1	0	0
594.0	0	0	0	1
595.0	0	1	0	0
601.0	0	0	0	1
605.0	0	1	0	0
606.0	0	1	0	1
613.0	0	0	0	1
617.0	0	1	0	0
618.0	0	0	0	1
620.0	0	1	0	1
623.0	0	1	0	0
642.0	0	1	0	2
643.0	0	1	0	0
648.0	0	0	0	1
649.0	0	0	0	1
650.0	0	1	0	0
655.0	0	1	0	0
685.0	0	0	0	1
692.0	0	1	0	0
726.0	0	0	0	1
727.0	0	0	0	1
730.0	0	2	0	0
738.0	0	0	0	1
740.0	0	1	0	0
766.0	0	0	0	1
768.0	0	0	0	1
772.0	0	1	0	0
775.0	0	1	0	0
780.0	0	0	0	1
782.0	0	1	0	0
783.0	0	0	0	1
786.0	0	1	0	0
827.0	0	0	0	1
829.0	0	1	0	0
842.0	0	0	0	1
844.0	0	1	0	0
845.0	0	1	0	1
867.0	0	0	0	1
869.0	0	0	0	1
871.0	0	1	0	0
875.0	0	1	0	1
876.0	0	1	0	0
912.0	0	0	0	2
913.0	0	1	0	0
915.0	0	1	0	0
916.0	0	0	0	1
917.0	0	1	0	0
926.0	0	0	0	1
929.0	0	1	0	0
930.0	0	0	0	1
934.0	0	1	0	0
963.0	0	0	0	1
973.0	0	1	0	0
990.0	0	0	0	1
991.0	0	1	0	0
1024.0	0	0	0	1
1025.0	0	1	0	0
1049.0	0	0	0	1
1051.0	0	1	0	0
1076.0	0	0	0	1
1083.0	0	0	0	1
1084.0	0	1	0	0
1089.0	0	1	0	0
1115.0	0	0	0	1
1122.0	0	1	0	0
1128.0	0	0	0	1
1135.0	0	1	0	0
1136.0	0	0	0	1
1137.0	0	1	0	0
1159.0	0	0	0	1
1163.0	0	0	0	1
1164.0	0	1	0	0
1167.0	0	1	0	0
1210.0	0	0	0	1
1212.0	0	1	0	1
1217.0	0	1	0	0
1228.0	0	1	0	1
1273.0	0	0	0	1
1277.0	0	1	0	0
1341.0	0	0	0	1
1352.0	0	1	0	0
1354.0	0	0	0	1
1365.0	0	1	0	0
1372.0	0	0	0	1
1373.0	0	1	0	0
1409.0	0	0	0	1
1419.0	0	1	0	0
1814.0	0	0	0	1
1820.0	0	1	0	0
1896.0	0	0	0	1
1897.0	0	1	0	0
1899.0	0	0	0	1
1902.0	0	1	0	0
1961.0	0	0	0	1
1970.0	0	1	0	0
2039.0	0	0	0	1
2048.0	0	1	0	0
2078.0	0	0	0	1
2084.0	0	1	0	0
2497.0	0	0	0	1
2505.0	0	1	0	0
2555.0	0	0	0	1
2572.0	0	1	0	0
5144.0	0	0	0	1
5156.0	0	1	0	0
5696.0	0	1	0	1
7669.0	0	0	0	1
7690.0	0	1	0	0
20151.0	0	0	0	1
20199.0	0	1	0	0