## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_3_2014-09-13/UA_Kie_Cho_3_2014-09-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_3_2014-09-13/UA_Kie_Cho_3_2014-09-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_3_2014-09-13/UA_Kie_Cho_3_2014-09-13.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 16:36:56 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	4865387	22202502	0	0	1148606	698702	0	0.051674	345321730

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20590404	20590404
2.0	1.937728	485691	485691
3.0	2.817062	10427	10427
4.0	3.641639	891	891
5.0	4.414868	455	455
6.0	5.139946	331	331
7.0	5.819872	259	259
8.0	6.457458	191	191
9.0	7.055341	166	166
10.0	7.615992	133	133
11.0	8.141731	117	117
12.0	8.634731	95	95
13.0	9.097031	97	97
14.0	9.530542	106	106
15.0	9.937059	60	60
16.0	10.31826	89	89
17.0	10.675724	74	74
18.0	11.010927	74	74
19.0	11.325257	57	57
20.0	11.620013	63	63
21.0	11.896414	48	48
22.0	12.155603	52	52
23.0	12.398652	45	45
24.0	12.626566	48	48
25.0	12.840287	55	55
26.0	13.0407	40	40
27.0	13.228632	37	37
28.0	13.404862	32	32
29.0	13.570117	29	29
30.0	13.725082	32	32
31.0	13.870396	27	27
32.0	14.006662	27	27
33.0	14.134442	25	25
34.0	14.254265	19	19
35.0	14.366627	20	20
36.0	14.471991	30	30
37.0	14.570795	21	21
38.0	14.663445	29	29
39.0	14.750326	15	15
40.0	14.831797	20	20
41.0	14.908195	11	11
42.0	14.979835	23	23
43.0	15.047014	14	14
44.0	15.110009	15	15
45.0	15.169082	19	19
46.0	15.224476	24	24
47.0	15.276421	15	15
48.0	15.325131	14	14
49.0	15.370808	12	12
50.0	15.41364	15	15
51.0	15.453805	17	17
52.0	15.491469	21	21
53.0	15.526788	14	14
54.0	15.559907	11	11
55.0	15.590964	13	13
56.0	15.620087	24	24
57.0	15.647396	6	6
58.0	15.673005	15	15
59.0	15.697019	6	6
60.0	15.719538	13	13
61.0	15.740654	12	12
62.0	15.760455	9	9
63.0	15.779024	9	9
64.0	15.796436	9	9
65.0	15.812764	7	7
66.0	15.828075	11	11
67.0	15.842432	9	9
68.0	15.855896	2	2
69.0	15.868521	4	4
70.0	15.88036	7	7
71.0	15.891461	12	12
72.0	15.901872	11	11
73.0	15.911634	10	10
74.0	15.920788	5	5
75.0	15.929372	10	10
76.0	15.937422	11	11
77.0	15.94497	4	4
78.0	15.952048	6	6
79.0	15.958686	8	8
80.0	15.96491	4	4
81.0	15.970747	3	3
82.0	15.97622	4	4
83.0	15.981352	6	6
84.0	15.986165	9	9
85.0	15.990678	7	7
86.0	15.99491	5	5
87.0	15.998878	7	7
88.0	16.002599	9	9
89.0	16.006089	6	6
90.0	16.009361	5	5
91.0	16.01243	5	5
92.0	16.015307	5	5
93.0	16.018006	8	8
94.0	16.020536	4	4
95.0	16.022908	6	6
96.0	16.025133	5	5
97.0	16.02722	1	1
98.0	16.029176	7	7
99.0	16.031011	6	6
100.0	16.032731	7	7
101.0	0	7	7
102.0	0	7	7
103.0	0	4	4
104.0	0	5	5
105.0	0	2	2
106.0	0	3	3
107.0	0	4	4
108.0	0	9	9
109.0	0	1	1
110.0	0	3	3
111.0	0	4	4
112.0	0	5	5
113.0	0	6	6
114.0	0	3	3
115.0	0	4	4
116.0	0	5	5
117.0	0	3	3
118.0	0	4	4
119.0	0	2	2
120.0	0	3	3
121.0	0	1	1
122.0	0	2	2
123.0	0	7	7
125.0	0	6	6
126.0	0	5	5
127.0	0	5	5
129.0	0	6	6
130.0	0	3	3
131.0	0	4	4
132.0	0	6	6
133.0	0	5	5
134.0	0	3	3
135.0	0	4	4
136.0	0	7	7
137.0	0	1	1
138.0	0	3	3
139.0	0	3	3
140.0	0	4	4
141.0	0	1	1
142.0	0	3	3
143.0	0	1	1
144.0	0	8	8
145.0	0	2	2
146.0	0	6	6
147.0	0	3	3
148.0	0	3	3
149.0	0	1	1
151.0	0	6	6
152.0	0	1	1
154.0	0	5	5
155.0	0	1	1
156.0	0	3	3
158.0	0	2	2
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	1	1
163.0	0	4	4
164.0	0	3	3
165.0	0	1	1
166.0	0	3	3
167.0	0	2	2
168.0	0	6	6
169.0	0	3	3
170.0	0	1	1
171.0	0	2	2
172.0	0	1	1
173.0	0	2	2
174.0	0	1	1
175.0	0	4	4
176.0	0	4	4
177.0	0	1	1
178.0	0	3	3
180.0	0	3	3
181.0	0	1	1
182.0	0	1	1
183.0	0	5	5
185.0	0	2	2
186.0	0	2	2
187.0	0	5	5
189.0	0	2	2
193.0	0	2	2
194.0	0	4	4
195.0	0	2	2
196.0	0	3	3
197.0	0	1	1
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
203.0	0	3	3
204.0	0	1	1
205.0	0	1	1
206.0	0	3	3
207.0	0	2	2
208.0	0	1	1
210.0	0	1	1
211.0	0	1	1
212.0	0	2	2
215.0	0	3	3
216.0	0	2	2
217.0	0	1	1
218.0	0	3	3
219.0	0	2	2
220.0	0	2	2
223.0	0	1	1
224.0	0	2	2
225.0	0	2	2
226.0	0	1	1
231.0	0	1	1
232.0	0	2	2
235.0	0	3	3
236.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	2	2
240.0	0	1	1
241.0	0	2	2
242.0	0	1	1
244.0	0	1	1
245.0	0	2	2
246.0	0	1	1
248.0	0	2	2
251.0	0	1	1
253.0	0	2	2
255.0	0	1	1
258.0	0	1	1
259.0	0	1	1
260.0	0	1	1
262.0	0	2	2
266.0	0	1	1
268.0	0	1	1
269.0	0	1	1
271.0	0	2	2
274.0	0	1	1
277.0	0	1	1
279.0	0	1	1
281.0	0	1	1
282.0	0	2	2
283.0	0	1	1
286.0	0	2	2
287.0	0	3	3
288.0	0	1	1
293.0	0	1	1
294.0	0	3	3
297.0	0	1	1
298.0	0	1	1
300.0	0	1	1
301.0	0	1	1
302.0	0	1	1
307.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
315.0	0	2	2
316.0	0	1	1
319.0	0	1	1
320.0	0	2	2
321.0	0	1	1
322.0	0	1	1
323.0	0	1	1
324.0	0	1	1
325.0	0	1	1
327.0	0	1	1
329.0	0	1	1
331.0	0	1	1
333.0	0	1	1
335.0	0	2	2
336.0	0	1	1
337.0	0	1	1
338.0	0	1	1
340.0	0	2	2
342.0	0	2	2
344.0	0	1	1
349.0	0	1	1
350.0	0	2	2
352.0	0	2	2
355.0	0	2	2
356.0	0	1	1
357.0	0	2	2
362.0	0	1	1
364.0	0	1	1
365.0	0	1	1
369.0	0	2	2
370.0	0	2	2
380.0	0	1	1
385.0	0	1	1
389.0	0	1	1
394.0	0	1	1
395.0	0	1	1
398.0	0	1	1
399.0	0	1	1
400.0	0	1	1
402.0	0	1	1
408.0	0	1	1
413.0	0	1	1
422.0	0	2	2
433.0	0	1	1
434.0	0	1	1
436.0	0	1	1
437.0	0	1	1
440.0	0	1	1
442.0	0	1	1
448.0	0	1	1
452.0	0	1	1
454.0	0	1	1
459.0	0	1	1
462.0	0	1	1
469.0	0	2	2
470.0	0	1	1
478.0	0	1	1
486.0	0	1	1
489.0	0	1	1
492.0	0	1	1
505.0	0	1	1
507.0	0	1	1
513.0	0	1	1
528.0	0	1	1
530.0	0	1	1
536.0	0	1	1
538.0	0	1	1
554.0	0	1	1
559.0	0	2	2
568.0	0	1	1
584.0	0	1	1
586.0	0	1	1
599.0	0	1	1
611.0	0	1	1
620.0	0	1	1
622.0	0	2	2
635.0	0	1	1
652.0	0	1	1
654.0	0	1	1
662.0	0	1	1
674.0	0	1	1
683.0	0	2	2
696.0	0	1	1
702.0	0	1	1
717.0	0	1	1
723.0	0	1	1
724.0	0	1	1
764.0	0	1	1
821.0	0	1	1
925.0	0	1	1
948.0	0	1	1
1005.0	0	1	1
1006.0	0	1	1