## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/ES_Ler_Gim_1_2020-10-26/ES_Ler_Gim_1_2020-10-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/ES_Ler_Gim_1_2020-10-26/ES_Ler_Gim_1_2020-10-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/ES_Ler_Gim_1_2020-10-26/ES_Ler_Gim_1_2020-10-26.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 08:55:30 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	4396134	23219508	0	0	2286993	5211986	180759	0.250043	44751645

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.005987	13698373	0	13808465
2.0	1.604753	3049916	176647	2988651
3.0	1.961141	645373	1748	611909
4.0	2.173264	130381	52	119102
5.0	2.29952	26368	15	23270
6.0	2.374668	5712	12	4954
7.0	2.419396	1599	3	1462
8.0	2.446019	699	6	650
9.0	2.461865	503	3	473
10.0	2.471296	369	1	372
11.0	2.47691	258	2	261
12.0	2.480251	188	2	192
13.0	2.48224	175	2	161
14.0	2.483424	136	2	141
15.0	2.484128	152	0	154
16.0	2.484547	127	0	119
17.0	2.484797	103	0	101
18.0	2.484946	91	1	94
19.0	2.485034	83	0	80
20.0	2.485087	71	0	70
21.0	2.485118	80	0	81
22.0	2.485137	63	0	62
23.0	2.485148	72	0	77
24.0	2.485154	52	0	47
25.0	2.485158	58	0	58
26.0	2.485161	45	0	45
27.0	2.485162	38	0	37
28.0	2.485163	51	0	50
29.0	2.485163	31	0	33
30.0	2.485164	31	0	32
31.0	2.485164	32	0	30
32.0	2.485164	36	0	36
33.0	2.485164	21	0	22
34.0	2.485164	21	0	20
35.0	2.485164	21	0	24
36.0	2.485164	24	0	21
37.0	2.485164	26	0	28
38.0	2.485164	27	0	28
39.0	2.485164	26	0	25
40.0	2.485164	17	0	14
41.0	2.485164	19	1	19
42.0	2.485164	17	0	19
43.0	2.485164	22	0	21
44.0	2.485164	13	0	12
45.0	2.485164	18	0	17
46.0	2.485164	14	0	13
47.0	2.485164	9	0	13
48.0	2.485164	18	0	16
49.0	2.485164	14	0	13
50.0	2.485164	11	0	12
51.0	2.485164	17	0	17
52.0	2.485164	8	0	10
53.0	2.485164	10	0	10
54.0	2.485164	13	0	12
55.0	2.485164	9	0	10
56.0	2.485164	16	0	15
57.0	2.485164	9	0	8
58.0	2.485164	9	0	9
59.0	2.485164	7	0	6
60.0	2.485164	9	0	9
61.0	2.485164	14	0	14
62.0	2.485164	8	0	8
63.0	2.485164	4	0	6
64.0	2.485164	13	0	13
65.0	2.485164	11	0	10
66.0	2.485164	10	0	9
67.0	2.485164	6	0	9
68.0	2.485164	10	0	9
69.0	2.485164	8	0	10
70.0	2.485164	7	0	4
71.0	2.485164	11	0	12
72.0	2.485164	10	0	8
73.0	2.485164	2	0	1
74.0	2.485164	5	0	5
75.0	2.485164	4	0	5
76.0	2.485164	3	0	4
77.0	2.485164	7	0	7
78.0	2.485164	7	0	6
79.0	2.485164	4	0	3
80.0	2.485164	1	0	2
81.0	2.485164	4	0	4
82.0	2.485164	4	0	5
83.0	2.485164	4	0	3
84.0	2.485164	2	0	2
85.0	2.485164	6	0	8
86.0	2.485164	6	0	6
87.0	2.485164	7	0	7
88.0	2.485164	7	0	6
89.0	2.485164	2	0	1
90.0	2.485164	3	0	2
91.0	2.485164	2	0	5
92.0	2.485164	6	0	4
93.0	2.485164	4	0	3
94.0	2.485164	6	0	7
95.0	2.485164	2	0	3
96.0	2.485164	9	0	8
97.0	2.485164	5	0	5
98.0	2.485164	6	0	5
99.0	2.485164	6	1	7
100.0	2.485164	3	0	3
101.0	0	2	0	1
102.0	0	3	0	3
103.0	0	7	0	9
104.0	0	1	0	0
105.0	0	8	0	8
106.0	0	5	0	4
107.0	0	2	0	3
108.0	0	5	0	5
109.0	0	1	0	3
110.0	0	5	0	2
111.0	0	2	0	2
112.0	0	2	0	2
113.0	0	5	0	7
114.0	0	4	0	3
115.0	0	3	0	3
116.0	0	2	0	1
117.0	0	4	0	6
118.0	0	2	0	4
119.0	0	6	0	3
120.0	0	6	0	6
121.0	0	5	0	5
122.0	0	2	0	2
123.0	0	5	0	4
124.0	0	4	0	4
125.0	0	5	0	5
126.0	0	3	0	3
127.0	0	2	0	3
128.0	0	3	0	2
129.0	0	5	0	6
130.0	0	2	0	3
131.0	0	5	0	3
132.0	0	2	0	4
133.0	0	3	0	3
134.0	0	6	0	4
135.0	0	1	0	1
136.0	0	2	0	3
137.0	0	2	0	4
138.0	0	3	0	0
140.0	0	0	0	1
141.0	0	4	0	3
142.0	0	2	0	3
143.0	0	2	0	2
144.0	0	5	0	5
145.0	0	3	0	3
146.0	0	3	0	3
147.0	0	2	0	4
148.0	0	3	0	3
149.0	0	2	0	1
150.0	0	4	0	3
151.0	0	1	0	0
152.0	0	0	0	1
153.0	0	2	0	1
154.0	0	1	0	2
155.0	0	2	0	3
156.0	0	5	0	3
157.0	0	1	0	2
158.0	0	4	0	4
159.0	0	1	0	0
160.0	0	4	0	4
161.0	0	1	0	1
162.0	0	1	0	2
163.0	0	1	0	2
164.0	0	2	0	0
165.0	0	2	0	2
166.0	0	3	0	6
167.0	0	5	0	2
168.0	0	0	0	2
169.0	0	3	0	2
170.0	0	2	0	2
171.0	0	2	0	3
172.0	0	2	0	1
174.0	0	2	0	1
175.0	0	1	0	2
176.0	0	3	0	3
178.0	0	1	0	1
179.0	0	1	0	2
180.0	0	3	0	3
181.0	0	2	0	1
182.0	0	1	0	0
183.0	0	0	0	1
184.0	0	1	0	0
186.0	0	2	0	2
187.0	0	1	0	1
188.0	0	2	0	2
189.0	0	1	0	2
190.0	0	3	0	2
192.0	0	0	0	2
193.0	0	3	0	2
195.0	0	1	0	2
196.0	0	2	0	2
197.0	0	3	0	2
198.0	0	3	0	2
200.0	0	1	0	1
201.0	0	1	0	1
202.0	0	0	0	2
203.0	0	3	0	1
204.0	0	2	0	2
205.0	0	0	0	1
207.0	0	1	0	1
209.0	0	2	0	1
210.0	0	0	0	2
211.0	0	0	0	1
212.0	0	1	0	0
213.0	0	2	0	1
214.0	0	2	0	2
215.0	0	1	0	0
216.0	0	2	0	2
217.0	0	1	0	1
219.0	0	1	0	2
220.0	0	1	0	1
221.0	0	3	0	4
222.0	0	2	0	0
223.0	0	2	0	3
224.0	0	0	0	1
225.0	0	2	0	2
226.0	0	3	0	1
228.0	0	2	0	3
229.0	0	2	0	1
230.0	0	1	0	1
232.0	0	1	0	1
234.0	0	1	0	2
235.0	0	1	0	3
236.0	0	3	0	1
237.0	0	1	0	0
238.0	0	1	0	1
239.0	0	2	0	2
240.0	0	2	0	2
241.0	0	1	0	1
244.0	0	0	0	1
245.0	0	1	0	1
247.0	0	1	0	0
248.0	0	2	0	3
249.0	0	1	0	1
250.0	0	2	0	2
252.0	0	1	0	1
253.0	0	1	0	0
256.0	0	0	0	1
257.0	0	1	0	0
261.0	0	1	0	2
262.0	0	1	0	2
263.0	0	3	0	2
264.0	0	1	0	0
267.0	0	0	0	1
268.0	0	1	0	0
270.0	0	0	0	2
271.0	0	2	0	0
275.0	0	1	0	2
276.0	0	1	0	2
277.0	0	1	0	0
278.0	0	1	0	2
279.0	0	1	0	0
280.0	0	1	0	0
281.0	0	1	0	1
282.0	0	1	0	1
283.0	0	1	0	1
284.0	0	1	0	1
286.0	0	0	0	2
287.0	0	1	0	0
288.0	0	0	0	1
289.0	0	2	0	1
290.0	0	2	0	1
291.0	0	1	0	1
292.0	0	1	0	1
300.0	0	0	0	1
301.0	0	1	0	3
303.0	0	2	0	1
304.0	0	1	0	0
305.0	0	0	0	2
306.0	0	1	0	1
309.0	0	1	0	1
310.0	0	3	0	1
311.0	0	1	0	0
319.0	0	1	0	1
320.0	0	0	0	1
321.0	0	1	0	1
324.0	0	2	0	2
326.0	0	1	0	0
327.0	0	0	0	3
328.0	0	1	0	0
329.0	0	2	0	0
331.0	0	3	0	3
334.0	0	1	0	1
335.0	0	1	0	1
339.0	0	0	0	1
340.0	0	2	0	1
343.0	0	1	0	1
346.0	0	1	0	1
348.0	0	1	0	1
354.0	0	0	0	1
357.0	0	1	0	0
358.0	0	0	0	1
359.0	0	1	0	1
360.0	0	1	0	0
365.0	0	0	0	1
368.0	0	1	0	0
369.0	0	0	0	1
371.0	0	2	0	2
372.0	0	1	0	0
373.0	0	0	0	1
374.0	0	0	0	2
375.0	0	1	0	0
377.0	0	2	0	0
379.0	0	2	0	2
384.0	0	0	0	1
389.0	0	1	0	0
391.0	0	0	0	1
392.0	0	0	0	1
393.0	0	1	0	0
394.0	0	1	0	1
397.0	0	1	0	0
398.0	0	0	0	1
399.0	0	1	0	0
401.0	0	0	0	2
402.0	0	2	0	0
413.0	0	1	0	1
414.0	0	1	0	1
416.0	0	0	0	1
417.0	0	1	0	0
418.0	0	1	0	1
420.0	0	1	0	1
430.0	0	0	0	1
432.0	0	1	0	1
434.0	0	2	0	1
441.0	0	1	0	1
444.0	0	0	0	1
446.0	0	1	0	1
450.0	0	1	0	0
452.0	0	0	0	1
453.0	0	1	0	0
460.0	0	1	0	1
462.0	0	0	0	1
464.0	0	1	0	0
476.0	0	0	0	1
477.0	0	1	0	1
480.0	0	1	0	0
482.0	0	1	0	1
483.0	0	1	0	1
484.0	0	0	0	1
487.0	0	1	0	0
488.0	0	1	0	1
493.0	0	0	0	1
494.0	0	1	0	1
496.0	0	1	0	0
499.0	0	0	0	1
503.0	0	2	0	1
513.0	0	0	0	1
515.0	0	1	0	0
521.0	0	1	0	1
524.0	0	1	0	1
525.0	0	1	0	1
532.0	0	1	0	1
533.0	0	1	0	2
535.0	0	1	0	0
536.0	0	1	0	1
540.0	0	1	0	1
543.0	0	0	0	1
544.0	0	0	0	1
545.0	0	1	0	0
548.0	0	1	0	0
550.0	0	1	0	1
557.0	0	0	0	1
558.0	0	1	0	1
559.0	0	1	0	0
562.0	0	0	0	1
564.0	0	1	0	0
565.0	0	1	0	1
573.0	0	1	0	1
578.0	0	0	0	1
580.0	0	2	0	1
582.0	0	1	0	1
593.0	0	0	0	1
595.0	0	1	0	0
597.0	0	0	0	1
599.0	0	1	0	0
603.0	0	0	0	1
604.0	0	0	0	1
605.0	0	1	0	0
611.0	0	1	0	0
621.0	0	0	0	1
624.0	0	1	0	0
627.0	0	0	0	1
628.0	0	1	0	0
643.0	0	1	0	1
656.0	0	1	0	1
667.0	0	0	0	1
668.0	0	0	0	1
669.0	0	0	0	1
672.0	0	2	0	0
673.0	0	1	0	1
676.0	0	2	0	1
677.0	0	1	0	2
678.0	0	1	0	1
682.0	0	1	0	0
689.0	0	0	0	1
691.0	0	1	0	0
692.0	0	0	0	1
694.0	0	1	0	0
698.0	0	1	0	1
705.0	0	1	0	1
735.0	0	0	0	1
737.0	0	1	0	0
753.0	0	0	0	1
754.0	0	1	0	0
764.0	0	0	0	1
767.0	0	1	0	0
777.0	0	1	0	1
779.0	0	1	0	1
785.0	0	1	0	1
792.0	0	0	0	1
795.0	0	1	0	0
799.0	0	0	0	1
806.0	0	1	0	0
813.0	0	1	0	1
815.0	0	0	0	1
816.0	0	0	0	1
817.0	0	1	0	1
819.0	0	2	0	0
858.0	0	0	0	1
860.0	0	1	0	0
871.0	0	0	0	1
877.0	0	0	0	1
878.0	0	1	0	0
880.0	0	1	0	0
921.0	0	0	0	1
923.0	0	1	0	1
927.0	0	1	0	0
931.0	0	0	0	1
935.0	0	1	0	0
964.0	0	0	0	1
974.0	0	1	0	0
991.0	0	0	0	1
997.0	0	1	0	0
1010.0	0	1	0	1
1024.0	0	0	0	1
1034.0	0	1	0	0
1055.0	0	0	0	1
1059.0	0	1	0	0
1141.0	0	0	0	1
1145.0	0	1	0	0
1164.0	0	0	0	1
1168.0	0	1	0	1
1172.0	0	1	0	0
1247.0	0	0	0	1
1253.0	0	1	0	0
1291.0	0	0	0	1
1300.0	0	0	0	1
1302.0	0	1	0	1
1308.0	0	1	0	0
1309.0	0	1	0	0
1326.0	0	0	0	1
1327.0	0	0	0	1
1330.0	0	1	0	0
1331.0	0	1	0	0
1372.0	0	0	0	1
1377.0	0	1	0	0
1412.0	0	0	0	1
1417.0	0	1	0	1
1422.0	0	1	0	0
1448.0	0	0	0	1
1452.0	0	1	0	0
1486.0	0	0	0	1
1490.0	0	1	0	0
1538.0	0	1	0	1
1587.0	0	0	0	1
1592.0	0	0	0	1
1595.0	0	1	0	0
1599.0	0	1	0	0
1628.0	0	0	0	1
1631.0	0	1	0	0
1637.0	0	0	0	1
1640.0	0	1	0	0
1644.0	0	1	0	1
1773.0	0	0	0	1
1784.0	0	1	0	0
1840.0	0	0	0	1
1844.0	0	1	0	0
1887.0	0	1	0	1
1951.0	0	0	0	1
1963.0	0	1	0	0
1990.0	0	1	0	1
2055.0	0	0	0	1
2068.0	0	1	0	0
2226.0	0	0	0	1
2235.0	0	1	0	0
2575.0	0	0	0	1
2592.0	0	1	0	0
2884.0	0	0	0	1
2897.0	0	1	0	0
3375.0	0	0	0	1
3376.0	0	1	0	0
4159.0	0	0	0	1
4163.0	0	1	0	0
8252.0	0	0	0	1
8259.0	0	1	0	0
9893.0	0	0	0	1
9905.0	0	1	0	0
16350.0	0	0	0	1
16390.0	0	1	0	0
38090.0	0	0	0	1
38188.0	0	1	0	0