## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2016-10-21/ES_Ler_Gim_1_2016-10-21.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2016-10-21/ES_Ler_Gim_1_2016-10-21.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2016-10-21/ES_Ler_Gim_1_2016-10-21.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 08:51:50 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	24794489	10355434	0	0	5460630	832354	0	0.156582	60916562

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8659277	8659277
2.0	1.84367	546800	546800
3.0	2.555449	40689	40689
4.0	3.155956	4961	4961
5.0	3.662586	1637	1637
6.0	4.090014	1032	1032
7.0	4.450623	726	726
8.0	4.754857	532	532
9.0	5.011531	346	346
10.0	5.228079	313	313
11.0	5.410774	271	271
12.0	5.564908	218	218
13.0	5.694947	205	205
14.0	5.804656	176	176
15.0	5.897215	159	159
16.0	5.975304	151	151
17.0	6.041185	114	114
18.0	6.096767	132	132
19.0	6.14366	125	125
20.0	6.183222	103	103
21.0	6.2166	94	94
22.0	6.24476	106	106
23.0	6.268517	66	66
24.0	6.28856	93	93
25.0	6.30547	83	83
26.0	6.319737	79	79
27.0	6.331773	76	76
28.0	6.341928	67	67
29.0	6.350495	54	54
30.0	6.357722	54	54
31.0	6.36382	58	58
32.0	6.368965	49	49
33.0	6.373305	51	51
34.0	6.376967	45	45
35.0	6.380056	41	41
36.0	6.382663	42	42
37.0	6.384862	27	27
38.0	6.386717	37	37
39.0	6.388282	20	20
40.0	6.389603	29	29
41.0	6.390717	35	35
42.0	6.391657	22	22
43.0	6.39245	23	23
44.0	6.393119	25	25
45.0	6.393683	21	21
46.0	6.394159	27	27
47.0	6.394561	14	14
48.0	6.3949	21	21
49.0	6.395186	31	31
50.0	6.395427	15	15
51.0	6.395631	22	22
52.0	6.395802	13	13
53.0	6.395947	17	17
54.0	6.396069	14	14
55.0	6.396173	17	17
56.0	6.39626	23	23
57.0	6.396333	11	11
58.0	6.396395	17	17
59.0	6.396447	9	9
60.0	6.396491	15	15
61.0	6.396528	17	17
62.0	6.39656	12	12
63.0	6.396586	13	13
64.0	6.396608	9	9
65.0	6.396627	9	9
66.0	6.396643	13	13
67.0	6.396657	18	18
68.0	6.396668	10	10
69.0	6.396677	11	11
70.0	6.396686	5	5
71.0	6.396692	9	9
72.0	6.396698	15	15
73.0	6.396703	10	10
74.0	6.396707	13	13
75.0	6.39671	10	10
76.0	6.396713	14	14
77.0	6.396716	9	9
78.0	6.396718	13	13
79.0	6.39672	9	9
80.0	6.396721	11	11
81.0	6.396722	15	15
82.0	6.396723	9	9
83.0	6.396724	14	14
84.0	6.396725	14	14
85.0	6.396726	4	4
86.0	6.396726	2	2
87.0	6.396727	7	7
88.0	6.396727	7	7
89.0	6.396727	6	6
90.0	6.396728	9	9
91.0	6.396728	8	8
92.0	6.396728	10	10
93.0	6.396728	10	10
94.0	6.396728	6	6
95.0	6.396728	8	8
96.0	6.396728	2	2
97.0	6.396729	9	9
98.0	6.396729	9	9
99.0	6.396729	10	10
100.0	6.396729	6	6
101.0	0	9	9
102.0	0	8	8
103.0	0	1	1
104.0	0	5	5
105.0	0	6	6
106.0	0	7	7
107.0	0	5	5
108.0	0	8	8
109.0	0	6	6
110.0	0	6	6
111.0	0	3	3
112.0	0	3	3
113.0	0	4	4
114.0	0	6	6
115.0	0	8	8
116.0	0	5	5
117.0	0	4	4
118.0	0	3	3
119.0	0	5	5
120.0	0	2	2
121.0	0	3	3
122.0	0	8	8
123.0	0	3	3
124.0	0	3	3
125.0	0	2	2
126.0	0	4	4
127.0	0	6	6
128.0	0	2	2
129.0	0	3	3
130.0	0	2	2
131.0	0	2	2
132.0	0	2	2
134.0	0	4	4
135.0	0	2	2
136.0	0	1	1
137.0	0	2	2
138.0	0	1	1
139.0	0	1	1
140.0	0	1	1
142.0	0	1	1
143.0	0	1	1
144.0	0	1	1
145.0	0	1	1
147.0	0	5	5
149.0	0	1	1
150.0	0	3	3
151.0	0	3	3
152.0	0	1	1
153.0	0	2	2
154.0	0	4	4
155.0	0	2	2
156.0	0	3	3
157.0	0	2	2
158.0	0	2	2
161.0	0	2	2
162.0	0	1	1
163.0	0	2	2
165.0	0	2	2
167.0	0	2	2
168.0	0	3	3
169.0	0	3	3
171.0	0	1	1
173.0	0	1	1
174.0	0	3	3
178.0	0	1	1
182.0	0	1	1
183.0	0	3	3
184.0	0	3	3
185.0	0	2	2
186.0	0	1	1
188.0	0	2	2
189.0	0	2	2
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
196.0	0	4	4
197.0	0	1	1
198.0	0	1	1
202.0	0	1	1
204.0	0	1	1
208.0	0	1	1
209.0	0	2	2
212.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	1	1
222.0	0	1	1
225.0	0	1	1
226.0	0	2	2
228.0	0	2	2
230.0	0	1	1
233.0	0	1	1
235.0	0	1	1
236.0	0	1	1
240.0	0	1	1
241.0	0	1	1
251.0	0	1	1
253.0	0	1	1
257.0	0	1	1
259.0	0	1	1
263.0	0	1	1
265.0	0	1	1
266.0	0	2	2
270.0	0	1	1
272.0	0	1	1
273.0	0	2	2
278.0	0	2	2
279.0	0	1	1
281.0	0	2	2
283.0	0	1	1
287.0	0	1	1
289.0	0	1	1
299.0	0	1	1
305.0	0	1	1
313.0	0	1	1
315.0	0	1	1
316.0	0	1	1
317.0	0	1	1
319.0	0	1	1
320.0	0	1	1
334.0	0	1	1
335.0	0	1	1
337.0	0	1	1
339.0	0	2	2
342.0	0	2	2
347.0	0	1	1
361.0	0	1	1
369.0	0	1	1
375.0	0	1	1
376.0	0	1	1
382.0	0	1	1
395.0	0	1	1
409.0	0	1	1
417.0	0	2	2
425.0	0	1	1
440.0	0	1	1
445.0	0	1	1
486.0	0	1	1
611.0	0	1	1
624.0	0	1	1
675.0	0	1	1
765.0	0	1	1
789.0	0	1	1
842.0	0	1	1
844.0	0	1	1
1354.0	0	1	1
2061.0	0	1	1