## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2014-08-13/ES_Ler_Gim_1_2014-08-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2014-08-13/ES_Ler_Gim_1_2014-08-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2014-08-13/ES_Ler_Gim_1_2014-08-13.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 08:37:28 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	11694292	17276670	0	0	1827597	527266	0	0.062319	277259475

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	15995785	15995785
2.0	1.939589	377890	377890
3.0	2.822418	7971	7971
4.0	3.651914	760	760
5.0	4.4313	384	384
6.0	5.163602	292	292
7.0	5.851666	199	199
8.0	6.498164	183	183
9.0	7.105606	159	159
10.0	7.676352	131	131
11.0	8.212619	110	110
12.0	8.71649	106	106
13.0	9.189922	84	84
14.0	9.634754	78	78
15.0	10.052713	74	74
16.0	10.445422	63	63
17.0	10.814408	61	61
18.0	11.161104	65	65
19.0	11.486855	78	78
20.0	11.792928	56	56
21.0	12.08051	42	42
22.0	12.35072	37	37
23.0	12.604606	35	35
24.0	12.843154	50	50
25.0	13.067292	23	23
26.0	13.277889	39	39
27.0	13.475764	36	36
28.0	13.661686	30	30
29.0	13.836375	24	24
30.0	14.000512	26	26
31.0	14.154733	25	25
32.0	14.299637	27	27
33.0	14.435788	22	22
34.0	14.563714	16	16
35.0	14.683912	20	20
36.0	14.796848	24	24
37.0	14.902962	21	21
38.0	15.002665	28	28
39.0	15.096346	19	19
40.0	15.184367	11	11
41.0	15.267071	8	8
42.0	15.344778	21	21
43.0	15.417791	13	13
44.0	15.486394	8	8
45.0	15.550852	12	12
46.0	15.611416	14	14
47.0	15.668321	16	16
48.0	15.721789	8	8
49.0	15.772027	20	20
50.0	15.81923	10	10
51.0	15.863581	15	15
52.0	15.905253	8	8
53.0	15.944407	15	15
54.0	15.981197	10	10
55.0	16.015763	11	11
56.0	16.048242	12	12
57.0	16.078758	12	12
58.0	16.107431	9	9
59.0	16.134372	12	12
60.0	16.159685	10	10
61.0	16.18347	13	13
62.0	16.205817	8	8
63.0	16.226814	8	8
64.0	16.246543	5	5
65.0	16.26508	8	8
66.0	16.282497	11	11
67.0	16.298862	7	7
68.0	16.314239	4	4
69.0	16.328686	11	11
70.0	16.342261	6	6
71.0	16.355015	6	6
72.0	16.367	6	6
73.0	16.37826	12	12
74.0	16.38884	2	2
75.0	16.39878	3	3
76.0	16.408121	6	6
77.0	16.416897	6	6
78.0	16.425143	3	3
79.0	16.43289	6	6
80.0	16.44017	10	10
81.0	16.44701	4	4
82.0	16.453437	7	7
83.0	16.459475	5	5
84.0	16.465149	4	4
85.0	16.47048	7	7
86.0	16.475488	5	5
87.0	16.480195	3	3
88.0	16.484617	6	6
89.0	16.488772	5	5
90.0	16.492675	3	3
91.0	16.496343	5	5
92.0	16.49979	1	1
93.0	16.503028	3	3
94.0	16.506071	3	3
95.0	16.508929	1	1
96.0	16.511616	3	3
97.0	16.514139	6	6
98.0	16.516511	6	6
99.0	16.518739	3	3
100.0	16.520832	4	4
101.0	0	4	4
102.0	0	5	5
103.0	0	6	6
104.0	0	1	1
105.0	0	5	5
106.0	0	4	4
107.0	0	6	6
108.0	0	3	3
109.0	0	2	2
110.0	0	8	8
111.0	0	4	4
112.0	0	4	4
113.0	0	5	5
114.0	0	1	1
115.0	0	5	5
116.0	0	5	5
117.0	0	5	5
118.0	0	2	2
119.0	0	1	1
120.0	0	2	2
121.0	0	3	3
122.0	0	3	3
123.0	0	2	2
124.0	0	2	2
125.0	0	1	1
126.0	0	1	1
127.0	0	2	2
128.0	0	2	2
129.0	0	2	2
130.0	0	1	1
131.0	0	2	2
132.0	0	4	4
133.0	0	5	5
134.0	0	3	3
135.0	0	2	2
137.0	0	3	3
138.0	0	2	2
139.0	0	1	1
140.0	0	3	3
141.0	0	2	2
142.0	0	5	5
143.0	0	2	2
144.0	0	2	2
145.0	0	2	2
146.0	0	3	3
147.0	0	3	3
150.0	0	1	1
151.0	0	1	1
152.0	0	3	3
153.0	0	2	2
154.0	0	3	3
157.0	0	2	2
158.0	0	1	1
160.0	0	3	3
161.0	0	5	5
163.0	0	3	3
165.0	0	2	2
166.0	0	2	2
167.0	0	2	2
168.0	0	2	2
169.0	0	1	1
171.0	0	2	2
172.0	0	2	2
173.0	0	2	2
175.0	0	1	1
177.0	0	2	2
178.0	0	2	2
179.0	0	2	2
180.0	0	2	2
182.0	0	1	1
183.0	0	3	3
187.0	0	1	1
188.0	0	3	3
189.0	0	1	1
190.0	0	1	1
193.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	1	1
198.0	0	2	2
199.0	0	1	1
201.0	0	1	1
203.0	0	2	2
207.0	0	2	2
208.0	0	2	2
209.0	0	2	2
210.0	0	3	3
214.0	0	1	1
215.0	0	2	2
216.0	0	2	2
217.0	0	2	2
220.0	0	1	1
224.0	0	3	3
225.0	0	2	2
226.0	0	1	1
227.0	0	1	1
228.0	0	2	2
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
234.0	0	1	1
235.0	0	3	3
237.0	0	1	1
238.0	0	4	4
240.0	0	1	1
241.0	0	1	1
246.0	0	1	1
247.0	0	1	1
250.0	0	2	2
255.0	0	4	4
256.0	0	1	1
257.0	0	1	1
258.0	0	2	2
259.0	0	1	1
260.0	0	3	3
261.0	0	3	3
263.0	0	1	1
267.0	0	1	1
268.0	0	1	1
270.0	0	2	2
271.0	0	1	1
272.0	0	4	4
274.0	0	1	1
275.0	0	1	1
276.0	0	1	1
278.0	0	1	1
281.0	0	3	3
284.0	0	1	1
286.0	0	1	1
288.0	0	2	2
289.0	0	2	2
290.0	0	1	1
292.0	0	1	1
295.0	0	1	1
297.0	0	1	1
299.0	0	1	1
300.0	0	1	1
301.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
307.0	0	2	2
309.0	0	1	1
316.0	0	1	1
322.0	0	1	1
325.0	0	1	1
337.0	0	1	1
339.0	0	1	1
344.0	0	1	1
362.0	0	1	1
367.0	0	2	2
371.0	0	1	1
373.0	0	1	1
378.0	0	1	1
396.0	0	1	1
399.0	0	1	1
401.0	0	1	1
403.0	0	1	1
408.0	0	2	2
418.0	0	1	1
424.0	0	1	1
435.0	0	1	1
451.0	0	1	1
464.0	0	1	1
468.0	0	1	1
470.0	0	1	1
477.0	0	1	1
497.0	0	1	1
527.0	0	2	2
575.0	0	1	1
586.0	0	1	1
631.0	0	1	1
661.0	0	1	1
841.0	0	1	1