## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2014-10-15/DE_Bad_Bro_1_2014-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2014-10-15/DE_Bad_Bro_1_2014-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2014-10-15/DE_Bad_Bro_1_2014-10-15.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: Fri Jan 20 08:26:59 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	2106971	25944046	0	0	549931	797808	0	0.039736	413146211

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	24090612	24090612
2.0	1.939135	557548	557548
3.0	2.821109	10881	10881
4.0	3.649401	966	966
5.0	4.42728	503	503
6.0	5.157812	323	323
7.0	5.843881	264	264
8.0	6.488192	194	194
9.0	7.093287	165	165
10.0	7.661552	152	152
11.0	8.19523	115	115
12.0	8.696425	129	129
13.0	9.167116	130	130
14.0	9.609157	124	124
15.0	10.024293	98	98
16.0	10.414163	103	103
17.0	10.780302	92	92
18.0	11.124157	81	81
19.0	11.447082	85	85
20.0	11.750353	85	85
21.0	12.035165	59	59
22.0	12.302642	69	69
23.0	12.553839	57	57
24.0	12.789747	72	72
25.0	13.011296	50	50
26.0	13.21936	61	61
27.0	13.414761	39	39
28.0	13.598269	35	35
29.0	13.770607	54	54
30.0	13.932456	39	39
31.0	14.084454	43	43
32.0	14.2272	34	34
33.0	14.361258	29	29
34.0	14.487157	31	31
35.0	14.605393	33	33
36.0	14.716432	30	30
37.0	14.820713	31	31
38.0	14.918647	21	21
39.0	15.010621	26	26
40.0	15.096996	29	29
41.0	15.178114	22	22
42.0	15.254294	28	28
43.0	15.325838	18	18
44.0	15.393028	28	28
45.0	15.456127	21	21
46.0	15.515387	17	17
47.0	15.571039	21	21
48.0	15.623304	22	22
49.0	15.672388	20	20
50.0	15.718485	17	17
51.0	15.761776	23	23
52.0	15.802432	22	22
53.0	15.840613	18	18
54.0	15.876471	22	22
55.0	15.910146	11	11
56.0	15.941771	14	14
57.0	15.971471	20	20
58.0	15.999364	12	12
59.0	16.025559	14	14
60.0	16.05016	17	17
61.0	16.073263	8	8
62.0	16.094961	15	15
63.0	16.115337	10	10
64.0	16.134473	9	9
65.0	16.152445	11	11
66.0	16.169323	7	7
67.0	16.185173	10	10
68.0	16.200059	9	9
69.0	16.214039	12	12
70.0	16.227168	10	10
71.0	16.239497	13	13
72.0	16.251077	10	10
73.0	16.261951	5	5
74.0	16.272164	11	11
75.0	16.281755	6	6
76.0	16.290762	7	7
77.0	16.299221	11	11
78.0	16.307165	5	5
79.0	16.314626	6	6
80.0	16.321633	5	5
81.0	16.328213	7	7
82.0	16.334392	6	6
83.0	16.340196	8	8
84.0	16.345646	4	4
85.0	16.350765	6	6
86.0	16.355572	13	13
87.0	16.360086	5	5
88.0	16.364326	5	5
89.0	16.368307	4	4
90.0	16.372047	8	8
91.0	16.375558	5	5
92.0	16.378856	3	3
93.0	16.381953	5	5
94.0	16.384862	3	3
95.0	16.387594	8	8
96.0	16.390159	6	6
97.0	16.392568	9	9
98.0	16.394831	6	6
99.0	16.396956	8	8
100.0	16.398951	7	7
101.0	0	3	3
102.0	0	6	6
103.0	0	6	6
104.0	0	4	4
105.0	0	5	5
106.0	0	4	4
107.0	0	5	5
108.0	0	7	7
109.0	0	10	10
110.0	0	7	7
111.0	0	6	6
112.0	0	2	2
113.0	0	5	5
114.0	0	3	3
115.0	0	6	6
116.0	0	4	4
117.0	0	2	2
118.0	0	5	5
119.0	0	3	3
120.0	0	3	3
121.0	0	2	2
122.0	0	5	5
123.0	0	6	6
124.0	0	4	4
125.0	0	6	6
126.0	0	2	2
127.0	0	2	2
128.0	0	3	3
129.0	0	4	4
130.0	0	4	4
131.0	0	2	2
132.0	0	3	3
133.0	0	3	3
134.0	0	3	3
135.0	0	4	4
136.0	0	2	2
137.0	0	3	3
138.0	0	9	9
140.0	0	2	2
141.0	0	4	4
142.0	0	5	5
143.0	0	6	6
145.0	0	5	5
146.0	0	1	1
147.0	0	2	2
148.0	0	4	4
149.0	0	7	7
150.0	0	2	2
151.0	0	3	3
152.0	0	3	3
153.0	0	1	1
154.0	0	1	1
155.0	0	2	2
157.0	0	1	1
158.0	0	3	3
159.0	0	2	2
160.0	0	6	6
161.0	0	2	2
162.0	0	5	5
163.0	0	4	4
165.0	0	1	1
166.0	0	3	3
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	3	3
175.0	0	3	3
176.0	0	1	1
177.0	0	2	2
178.0	0	2	2
179.0	0	3	3
180.0	0	2	2
181.0	0	1	1
182.0	0	3	3
183.0	0	3	3
185.0	0	3	3
186.0	0	1	1
187.0	0	2	2
188.0	0	3	3
189.0	0	2	2
190.0	0	1	1
191.0	0	3	3
192.0	0	2	2
193.0	0	2	2
194.0	0	3	3
195.0	0	3	3
197.0	0	3	3
199.0	0	1	1
200.0	0	2	2
202.0	0	1	1
206.0	0	1	1
209.0	0	1	1
211.0	0	1	1
212.0	0	3	3
214.0	0	1	1
215.0	0	2	2
217.0	0	1	1
218.0	0	1	1
220.0	0	1	1
221.0	0	2	2
222.0	0	3	3
223.0	0	1	1
227.0	0	1	1
229.0	0	1	1
230.0	0	2	2
231.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
236.0	0	2	2
237.0	0	2	2
238.0	0	2	2
239.0	0	1	1
241.0	0	3	3
242.0	0	1	1
245.0	0	2	2
247.0	0	1	1
248.0	0	2	2
252.0	0	1	1
253.0	0	2	2
257.0	0	1	1
258.0	0	2	2
262.0	0	1	1
263.0	0	2	2
264.0	0	1	1
267.0	0	2	2
268.0	0	3	3
272.0	0	2	2
274.0	0	2	2
276.0	0	1	1
281.0	0	1	1
283.0	0	1	1
284.0	0	2	2
286.0	0	4	4
290.0	0	2	2
295.0	0	1	1
297.0	0	1	1
298.0	0	1	1
301.0	0	1	1
302.0	0	1	1
303.0	0	2	2
307.0	0	2	2
308.0	0	1	1
312.0	0	3	3
313.0	0	1	1
314.0	0	1	1
316.0	0	2	2
324.0	0	3	3
325.0	0	1	1
326.0	0	2	2
327.0	0	2	2
330.0	0	2	2
333.0	0	1	1
334.0	0	1	1
335.0	0	2	2
339.0	0	2	2
340.0	0	1	1
347.0	0	2	2
349.0	0	1	1
350.0	0	1	1
353.0	0	1	1
354.0	0	1	1
356.0	0	1	1
361.0	0	2	2
364.0	0	2	2
365.0	0	1	1
366.0	0	1	1
371.0	0	1	1
373.0	0	2	2
374.0	0	1	1
376.0	0	1	1
377.0	0	3	3
382.0	0	1	1
384.0	0	2	2
385.0	0	2	2
390.0	0	2	2
396.0	0	1	1
401.0	0	1	1
402.0	0	2	2
405.0	0	1	1
406.0	0	1	1
410.0	0	1	1
414.0	0	1	1
415.0	0	1	1
416.0	0	1	1
418.0	0	1	1
423.0	0	2	2
425.0	0	1	1
429.0	0	1	1
434.0	0	2	2
435.0	0	1	1
436.0	0	3	3
437.0	0	1	1
438.0	0	1	1
444.0	0	1	1
446.0	0	2	2
451.0	0	1	1
455.0	0	1	1
467.0	0	1	1
471.0	0	1	1
481.0	0	1	1
482.0	0	1	1
487.0	0	1	1
490.0	0	1	1
494.0	0	1	1
502.0	0	1	1
506.0	0	1	1
508.0	0	1	1
517.0	0	1	1
520.0	0	1	1
531.0	0	2	2
533.0	0	2	2
550.0	0	1	1
560.0	0	1	1
572.0	0	1	1
584.0	0	1	1
588.0	0	1	1
609.0	0	1	1
610.0	0	1	1
618.0	0	1	1
628.0	0	1	1
645.0	0	1	1
656.0	0	1	1
667.0	0	1	1
684.0	0	1	1
689.0	0	1	1
703.0	0	1	1
719.0	0	2	2
721.0	0	1	1
725.0	0	1	1
743.0	0	1	1
761.0	0	1	1
763.0	0	1	1
773.0	0	1	1
778.0	0	1	1
787.0	0	1	1
800.0	0	1	1
825.0	0	1	1
851.0	0	1	1
854.0	0	1	1
859.0	0	1	1
876.0	0	1	1
949.0	0	1	1
991.0	0	1	1
1004.0	0	1	1
1108.0	0	1	1