## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/ES_Ler_Gim_1_2017-10-14/ES_Ler_Gim_1_2017-10-14.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/ES_Ler_Gim_1_2017-10-14/ES_Ler_Gim_1_2017-10-14.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/ES_Ler_Gim_1_2017-10-14/ES_Ler_Gim_1_2017-10-14.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 04:53:55 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	3974180	19073540	0	0	2031521	5197986	166629	0.295041	28894059

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.006224	9856767	0	9945564
2.0	1.52623	2675527	162339	2635692
3.0	1.794963	690693	1799	660410
4.0	1.933842	169933	52	157174
5.0	2.005613	41015	13	36880
6.0	2.042704	10691	13	9498
7.0	2.061872	3475	7	3077
8.0	2.071777	1490	5	1395
9.0	2.076897	937	4	906
10.0	2.079542	644	1	628
11.0	2.080909	500	2	488
12.0	2.081616	392	2	380
13.0	2.081981	304	2	307
14.0	2.08217	319	1	321
15.0	2.082267	250	0	247
16.0	2.082318	219	0	212
17.0	2.082344	179	1	179
18.0	2.082357	156	0	153
19.0	2.082364	145	2	146
20.0	2.082368	133	0	138
21.0	2.08237	124	0	111
22.0	2.082371	101	0	106
23.0	2.082371	88	0	77
24.0	2.082371	75	0	79
25.0	2.082371	79	1	88
26.0	2.082371	87	0	71
27.0	2.082372	61	0	67
28.0	2.082372	60	1	60
29.0	2.082372	73	0	76
30.0	2.082372	54	0	47
31.0	2.082372	54	0	58
32.0	2.082372	40	0	35
33.0	2.082372	33	0	37
34.0	2.082372	37	0	36
35.0	2.082372	33	0	31
36.0	2.082372	27	1	28
37.0	2.082372	25	0	26
38.0	2.082372	37	0	35
39.0	2.082372	37	0	35
40.0	2.082372	25	0	27
41.0	2.082372	24	0	22
42.0	2.082372	18	0	21
43.0	2.082372	25	0	22
44.0	2.082372	28	0	26
45.0	2.082372	8	0	12
46.0	2.082372	19	0	16
47.0	2.082372	17	0	18
48.0	2.082372	19	0	22
49.0	2.082372	17	0	13
50.0	2.082372	17	0	17
51.0	2.082372	13	0	15
52.0	2.082372	15	0	11
53.0	2.082372	8	0	10
54.0	2.082372	15	0	15
55.0	2.082372	15	0	14
56.0	2.082372	13	0	12
57.0	2.082372	12	0	13
58.0	2.082372	12	0	12
59.0	2.082372	9	0	11
60.0	2.082372	12	0	12
61.0	2.082372	10	0	10
62.0	2.082372	6	0	9
63.0	2.082372	13	0	12
64.0	2.082372	11	0	8
65.0	2.082372	13	0	17
66.0	2.082372	17	0	16
67.0	2.082372	11	0	12
68.0	2.082372	16	0	12
69.0	2.082372	7	0	8
70.0	2.082372	8	0	6
71.0	2.082372	9	0	10
72.0	2.082372	14	0	16
73.0	2.082372	10	0	7
74.0	2.082372	9	0	11
75.0	2.082372	13	0	10
76.0	2.082372	6	0	6
77.0	2.082372	6	0	9
78.0	2.082372	10	0	8
79.0	2.082372	7	0	6
80.0	2.082372	8	0	9
81.0	2.082372	4	0	6
82.0	2.082372	13	0	10
83.0	2.082372	6	0	6
84.0	2.082372	10	0	10
85.0	2.082372	10	1	11
86.0	2.082372	7	0	5
87.0	2.082372	7	0	8
88.0	2.082372	2	0	2
89.0	2.082372	4	0	3
90.0	2.082372	3	0	4
91.0	2.082372	3	0	2
92.0	2.082372	5	0	6
93.0	2.082372	4	0	5
94.0	2.082372	3	0	3
95.0	2.082372	3	0	2
96.0	2.082372	3	0	8
97.0	2.082372	9	0	5
98.0	2.082372	4	0	4
99.0	2.082372	6	0	6
100.0	2.082372	5	0	4
101.0	0	3	0	3
102.0	0	2	0	2
103.0	0	5	0	4
104.0	0	2	0	3
105.0	0	6	0	6
106.0	0	7	0	7
107.0	0	2	0	1
108.0	0	7	0	8
109.0	0	2	0	3
110.0	0	4	0	2
111.0	0	0	0	1
112.0	0	6	0	6
113.0	0	3	0	2
114.0	0	4	0	6
115.0	0	5	0	3
116.0	0	3	0	4
117.0	0	5	0	5
118.0	0	2	0	2
119.0	0	5	0	4
120.0	0	2	0	2
121.0	0	1	0	1
122.0	0	1	0	2
123.0	0	3	0	3
124.0	0	5	0	5
125.0	0	2	0	4
126.0	0	4	0	4
127.0	0	4	0	3
128.0	0	4	0	3
129.0	0	2	0	4
130.0	0	4	0	2
131.0	0	4	0	6
132.0	0	4	0	6
133.0	0	7	0	4
134.0	0	4	0	3
135.0	0	1	0	0
136.0	0	3	0	3
137.0	0	3	0	3
138.0	0	1	0	1
139.0	0	2	0	2
140.0	0	2	0	2
141.0	0	2	0	3
142.0	0	4	0	3
143.0	0	1	0	2
144.0	0	2	0	1
147.0	0	0	0	2
148.0	0	4	0	4
149.0	0	4	0	3
150.0	0	5	0	4
151.0	0	1	0	2
152.0	0	1	0	0
153.0	0	1	0	2
154.0	0	1	0	3
155.0	0	4	0	3
156.0	0	1	0	0
157.0	0	2	0	4
158.0	0	3	0	3
159.0	0	3	0	1
160.0	0	2	0	1
161.0	0	4	0	4
162.0	0	1	0	3
163.0	0	3	0	2
164.0	0	3	0	3
166.0	0	2	0	3
167.0	0	1	0	1
168.0	0	2	0	2
169.0	0	3	0	2
170.0	0	4	0	5
171.0	0	3	0	2
172.0	0	2	0	3
173.0	0	2	0	0
174.0	0	0	0	1
175.0	0	1	0	2
176.0	0	4	0	3
177.0	0	2	0	1
180.0	0	2	0	3
181.0	0	1	0	2
182.0	0	2	0	3
183.0	0	3	0	3
184.0	0	4	0	2
185.0	0	1	0	0
186.0	0	0	0	2
187.0	0	2	0	0
188.0	0	1	0	1
190.0	0	1	0	1
191.0	0	0	0	1
192.0	0	2	0	1
193.0	0	0	0	1
194.0	0	1	0	2
195.0	0	2	0	1
197.0	0	2	0	4
198.0	0	2	0	0
199.0	0	3	0	2
200.0	0	1	0	2
201.0	0	1	0	0
202.0	0	3	0	6
203.0	0	3	0	3
204.0	0	3	0	2
205.0	0	4	0	4
207.0	0	2	0	0
208.0	0	1	0	1
209.0	0	0	0	2
210.0	0	3	0	2
211.0	0	3	0	3
212.0	0	1	0	0
213.0	0	1	0	1
214.0	0	1	0	1
215.0	0	1	0	2
216.0	0	1	0	2
217.0	0	2	0	2
218.0	0	2	0	1
219.0	0	1	0	4
220.0	0	3	0	2
221.0	0	1	0	1
222.0	0	2	0	1
223.0	0	1	0	0
224.0	0	2	0	3
225.0	0	2	0	1
227.0	0	1	0	1
228.0	0	1	0	0
229.0	0	0	0	2
230.0	0	1	0	1
231.0	0	1	0	1
232.0	0	3	0	1
233.0	0	1	0	1
234.0	0	0	0	1
235.0	0	2	0	1
236.0	0	1	0	1
237.0	0	1	0	2
238.0	0	3	0	2
240.0	0	0	0	1
241.0	0	1	0	0
242.0	0	0	0	1
243.0	0	2	0	1
247.0	0	3	0	3
248.0	0	0	0	1
249.0	0	1	0	0
250.0	0	1	0	1
251.0	0	4	0	5
252.0	0	1	0	1
253.0	0	1	0	1
254.0	0	1	0	1
255.0	0	2	0	1
256.0	0	0	0	1
257.0	0	1	0	1
259.0	0	2	0	2
260.0	0	1	0	1
262.0	0	2	0	2
263.0	0	2	0	2
264.0	0	1	0	0
265.0	0	1	0	2
266.0	0	1	0	1
267.0	0	2	0	2
270.0	0	0	0	1
271.0	0	2	0	0
273.0	0	2	0	2
274.0	0	1	0	1
275.0	0	1	0	1
279.0	0	0	0	1
280.0	0	1	0	0
281.0	0	0	0	1
283.0	0	1	0	1
284.0	0	1	0	1
285.0	0	1	0	1
286.0	0	1	0	0
287.0	0	1	0	1
288.0	0	1	0	1
290.0	0	1	0	1
291.0	0	1	0	1
296.0	0	3	0	3
298.0	0	1	0	1
299.0	0	0	0	3
300.0	0	2	0	1
302.0	0	2	0	1
303.0	0	1	0	0
305.0	0	1	0	2
308.0	0	1	0	2
309.0	0	0	0	1
310.0	0	1	0	0
311.0	0	2	0	0
313.0	0	1	0	1
315.0	0	1	0	2
317.0	0	1	0	0
318.0	0	1	0	3
319.0	0	1	0	0
320.0	0	1	0	1
321.0	0	1	0	0
325.0	0	0	0	2
327.0	0	0	0	1
328.0	0	3	0	1
329.0	0	1	0	0
330.0	0	0	0	1
331.0	0	1	0	2
332.0	0	1	0	0
333.0	0	0	0	1
334.0	0	1	0	0
336.0	0	1	0	0
338.0	0	0	0	2
339.0	0	1	0	0
340.0	0	2	0	1
353.0	0	0	0	1
355.0	0	1	0	1
358.0	0	1	0	0
360.0	0	1	0	1
362.0	0	1	0	1
365.0	0	1	0	1
367.0	0	1	0	1
369.0	0	0	0	1
371.0	0	1	0	0
374.0	0	1	0	1
375.0	0	0	0	1
376.0	0	1	0	0
381.0	0	0	0	1
382.0	0	1	0	0
386.0	0	1	0	1
393.0	0	0	0	1
395.0	0	1	0	1
397.0	0	1	0	1
399.0	0	1	0	1
400.0	0	1	0	0
401.0	0	1	0	1
402.0	0	1	0	1
407.0	0	0	0	1
408.0	0	2	0	1
411.0	0	1	0	1
415.0	0	1	0	1
417.0	0	1	0	2
420.0	0	1	0	0
421.0	0	0	0	1
422.0	0	1	0	1
423.0	0	2	0	1
425.0	0	0	0	1
426.0	0	1	0	0
428.0	0	0	0	1
430.0	0	1	0	0
434.0	0	0	0	1
435.0	0	2	0	1
438.0	0	0	0	1
440.0	0	1	0	0
441.0	0	0	0	2
443.0	0	0	0	1
444.0	0	1	0	0
445.0	0	2	0	0
446.0	0	0	0	1
447.0	0	1	0	0
448.0	0	1	0	1
455.0	0	0	0	1
456.0	0	1	0	0
458.0	0	1	0	1
460.0	0	0	0	1
461.0	0	1	0	0
462.0	0	0	0	1
464.0	0	1	0	0
465.0	0	0	0	1
466.0	0	1	0	0
469.0	0	0	0	1
471.0	0	1	0	0
473.0	0	1	0	1
481.0	0	0	0	1
483.0	0	2	0	3
484.0	0	2	0	0
487.0	0	0	0	1
488.0	0	1	0	0
490.0	0	0	0	1
491.0	0	0	0	1
493.0	0	1	0	0
494.0	0	1	0	0
499.0	0	1	0	1
501.0	0	0	0	1
503.0	0	2	0	1
507.0	0	1	0	2
508.0	0	1	0	0
510.0	0	0	0	1
512.0	0	1	0	1
513.0	0	1	0	0
525.0	0	1	0	1
532.0	0	0	0	1
537.0	0	1	0	0
539.0	0	0	0	1
540.0	0	1	0	0
554.0	0	0	0	1
556.0	0	1	0	1
557.0	0	1	0	0
558.0	0	1	0	2
559.0	0	1	0	2
560.0	0	1	0	0
561.0	0	1	0	0
565.0	0	0	0	1
568.0	0	1	0	0
569.0	0	1	0	1
583.0	0	1	0	1
584.0	0	0	0	1
589.0	0	1	0	0
591.0	0	1	0	1
595.0	0	0	0	1
596.0	0	1	0	0
600.0	0	0	0	1
606.0	0	1	0	0
613.0	0	1	0	2
615.0	0	1	0	1
616.0	0	1	0	0
633.0	0	1	0	1
643.0	0	2	0	2
648.0	0	0	0	1
649.0	0	0	0	1
651.0	0	2	0	0
656.0	0	0	0	1
660.0	0	1	0	0
673.0	0	0	0	1
676.0	0	0	0	1
678.0	0	1	0	0
681.0	0	2	0	1
690.0	0	0	0	1
693.0	0	1	0	0
702.0	0	0	0	1
708.0	0	1	0	0
710.0	0	0	0	1
715.0	0	1	0	1
719.0	0	1	0	0
726.0	0	0	0	1
729.0	0	1	0	0
734.0	0	0	0	1
744.0	0	1	0	0
747.0	0	1	0	1
759.0	0	0	0	1
762.0	0	1	0	0
763.0	0	1	0	1
771.0	0	1	0	1
772.0	0	0	0	1
778.0	0	1	0	0
783.0	0	0	0	1
787.0	0	1	0	0
799.0	0	0	0	1
801.0	0	1	0	0
805.0	0	0	0	1
806.0	0	1	0	1
809.0	0	0	0	1
811.0	0	1	0	0
816.0	0	1	0	0
822.0	0	0	0	1
825.0	0	0	0	1
826.0	0	1	0	0
827.0	0	1	0	0
836.0	0	0	0	1
837.0	0	1	0	1
838.0	0	0	0	1
841.0	0	1	0	0
843.0	0	1	0	0
845.0	0	1	0	1
849.0	0	0	0	1
850.0	0	1	0	0
863.0	0	0	0	1
866.0	0	1	0	0
872.0	0	1	0	1
879.0	0	0	0	1
884.0	0	1	0	0
894.0	0	0	0	1
895.0	0	1	0	0
897.0	0	0	0	1
899.0	0	0	0	1
900.0	0	1	0	0
904.0	0	1	0	0
924.0	0	0	0	1
928.0	0	1	0	0
992.0	0	0	0	1
996.0	0	1	0	0
1008.0	0	0	0	1
1013.0	0	1	0	0
1023.0	0	1	0	1
1029.0	0	0	0	1
1030.0	0	1	0	1
1041.0	0	1	0	0
1048.0	0	0	0	1
1055.0	0	1	0	0
1126.0	0	0	0	1
1127.0	0	1	0	0
1165.0	0	0	0	1
1167.0	0	1	0	0
1195.0	0	0	0	1
1200.0	0	1	0	0
1252.0	0	1	0	1
1253.0	0	0	0	1
1260.0	0	1	0	0
1263.0	0	0	0	1
1274.0	0	1	0	0
1275.0	0	0	0	1
1282.0	0	1	0	0
1312.0	0	0	0	1
1317.0	0	1	0	0
1328.0	0	0	0	1
1336.0	0	1	0	0
1338.0	0	0	0	1
1342.0	0	1	0	0
1366.0	0	0	0	1
1368.0	0	0	0	1
1370.0	0	1	0	0
1374.0	0	1	0	0
1393.0	0	0	0	1
1395.0	0	1	0	0
1430.0	0	0	0	1
1432.0	0	1	0	0
1436.0	0	0	0	1
1446.0	0	1	0	0
1571.0	0	0	0	1
1573.0	0	1	0	0
1579.0	0	0	0	1
1584.0	0	1	0	0
1657.0	0	0	0	1
1663.0	0	1	0	0
1672.0	0	1	0	1
1686.0	0	0	0	1
1688.0	0	1	0	0
1767.0	0	1	0	1
1827.0	0	0	0	1
1830.0	0	1	0	1
1831.0	0	0	0	1
1835.0	0	1	0	0
1837.0	0	1	0	0
1989.0	0	0	0	1
2001.0	0	1	0	0
2024.0	0	0	0	1
2033.0	0	1	0	0
2160.0	0	0	0	1
2176.0	0	1	0	0
2294.0	0	0	0	1
2304.0	0	0	0	1
2307.0	0	1	0	0
2316.0	0	1	0	0
2490.0	0	0	0	1
2508.0	0	1	0	0
2651.0	0	0	0	1
2669.0	0	1	0	0
2844.0	0	0	0	1
2871.0	0	1	0	0
2975.0	0	0	0	1
2977.0	0	1	0	0
3371.0	0	0	0	1
3379.0	0	1	0	0
8110.0	0	0	0	1
8115.0	0	1	0	0
8448.0	0	0	0	1
8472.0	0	1	0	0
13683.0	0	0	0	1
13718.0	0	1	0	0
33247.0	0	0	0	1
33331.0	0	1	0	0