## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_4_2014-09-13/UA_Kie_Cho_4_2014-09-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_4_2014-09-13/UA_Kie_Cho_4_2014-09-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_4_2014-09-13/UA_Kie_Cho_4_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 15:55:28 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	7562874	18892035	0	0	1559941	563103	0	0.059235	310583566

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	17626801	17626801
2.0	1.940986	387566	387566
3.0	2.826439	6995	6995
4.0	3.659638	655	655
5.0	4.443667	344	344
6.0	5.181426	248	248
7.0	5.875647	202	202
8.0	6.528898	148	148
9.0	7.143599	153	153
10.0	7.722023	128	128
11.0	8.266312	100	100
12.0	8.778479	82	82
13.0	9.260422	94	94
14.0	9.713923	86	86
15.0	10.140661	60	60
16.0	10.542215	52	52
17.0	10.920071	65	65
18.0	11.275629	55	55
19.0	11.610203	38	38
20.0	11.925033	41	41
21.0	12.221283	52	52
22.0	12.50005	41	41
23.0	12.762366	41	41
24.0	13.009202	37	37
25.0	13.24147	37	37
26.0	13.460031	24	24
27.0	13.665694	31	31
28.0	13.85922	29	29
29.0	14.041326	22	22
30.0	14.212684	20	20
31.0	14.373929	22	22
32.0	14.525659	19	19
33.0	14.668435	22	22
34.0	14.802785	20	20
35.0	14.929206	20	20
36.0	15.048166	16	16
37.0	15.160106	17	17
38.0	15.26544	15	15
39.0	15.364558	19	19
40.0	15.457826	19	19
41.0	15.545591	18	18
42.0	15.628175	13	13
43.0	15.705887	17	17
44.0	15.779012	18	18
45.0	15.847821	18	18
46.0	15.91257	17	17
47.0	15.973498	12	12
48.0	16.03083	10	10
49.0	16.084779	14	14
50.0	16.135544	8	8
51.0	16.183313	11	11
52.0	16.228263	12	12
53.0	16.27056	6	6
54.0	16.310361	16	16
55.0	16.347813	8	8
56.0	16.383055	13	13
57.0	16.416218	4	4
58.0	16.447423	12	12
59.0	16.476787	7	7
60.0	16.504417	7	7
61.0	16.530418	11	11
62.0	16.554883	10	10
63.0	16.577905	8	8
64.0	16.599569	9	9
65.0	16.619953	7	7
66.0	16.639135	5	5
67.0	16.657185	8	8
68.0	16.67417	8	8
69.0	16.690152	3	3
70.0	16.705191	5	5
71.0	16.719343	10	10
72.0	16.732659	8	8
73.0	16.74519	6	6
74.0	16.756981	5	5
75.0	16.768076	2	2
76.0	16.778517	6	6
77.0	16.788341	10	10
78.0	16.797586	5	5
79.0	16.806284	9	9
80.0	16.81447	6	6
81.0	16.822173	9	9
82.0	16.829421	8	8
83.0	16.836241	5	5
84.0	16.842659	1	1
85.0	16.848698	7	7
86.0	16.85438	6	6
87.0	16.859728	4	4
88.0	16.864759	6	6
89.0	16.869494	5	5
90.0	16.873949	5	5
91.0	16.878142	4	4
92.0	16.882087	8	8
93.0	16.885799	5	5
94.0	16.889292	4	4
95.0	16.892579	3	3
96.0	16.895672	1	1
97.0	16.898583	3	3
98.0	16.901321	2	2
99.0	16.903898	3	3
100.0	16.906323	4	4
101.0	0	3	3
102.0	0	3	3
103.0	0	3	3
104.0	0	1	1
105.0	0	2	2
106.0	0	4	4
108.0	0	3	3
109.0	0	4	4
110.0	0	3	3
111.0	0	1	1
112.0	0	2	2
113.0	0	4	4
114.0	0	4	4
115.0	0	2	2
116.0	0	4	4
117.0	0	6	6
118.0	0	1	1
119.0	0	2	2
120.0	0	3	3
121.0	0	4	4
122.0	0	5	5
123.0	0	5	5
124.0	0	2	2
125.0	0	2	2
126.0	0	3	3
127.0	0	2	2
128.0	0	6	6
130.0	0	2	2
131.0	0	5	5
132.0	0	1	1
134.0	0	2	2
135.0	0	1	1
136.0	0	1	1
137.0	0	2	2
138.0	0	3	3
139.0	0	4	4
140.0	0	2	2
141.0	0	1	1
142.0	0	3	3
143.0	0	4	4
144.0	0	2	2
145.0	0	2	2
146.0	0	1	1
148.0	0	1	1
150.0	0	2	2
151.0	0	4	4
152.0	0	2	2
153.0	0	4	4
154.0	0	4	4
156.0	0	3	3
159.0	0	1	1
160.0	0	4	4
161.0	0	1	1
162.0	0	5	5
163.0	0	1	1
164.0	0	2	2
165.0	0	2	2
166.0	0	3	3
167.0	0	1	1
170.0	0	3	3
171.0	0	2	2
172.0	0	1	1
173.0	0	2	2
174.0	0	1	1
175.0	0	1	1
176.0	0	1	1
177.0	0	3	3
179.0	0	2	2
182.0	0	2	2
183.0	0	1	1
184.0	0	2	2
185.0	0	1	1
186.0	0	1	1
187.0	0	5	5
188.0	0	1	1
189.0	0	1	1
190.0	0	2	2
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
195.0	0	2	2
196.0	0	2	2
198.0	0	2	2
199.0	0	2	2
200.0	0	2	2
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	1	1
207.0	0	2	2
208.0	0	1	1
210.0	0	2	2
211.0	0	1	1
212.0	0	2	2
213.0	0	1	1
214.0	0	2	2
215.0	0	1	1
216.0	0	2	2
218.0	0	3	3
219.0	0	1	1
221.0	0	3	3
222.0	0	3	3
224.0	0	1	1
225.0	0	2	2
226.0	0	2	2
227.0	0	1	1
228.0	0	1	1
230.0	0	3	3
231.0	0	1	1
232.0	0	2	2
233.0	0	1	1
235.0	0	2	2
236.0	0	2	2
238.0	0	1	1
240.0	0	1	1
241.0	0	2	2
242.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
246.0	0	1	1
247.0	0	1	1
250.0	0	1	1
251.0	0	1	1
252.0	0	1	1
255.0	0	1	1
257.0	0	2	2
259.0	0	3	3
261.0	0	2	2
263.0	0	1	1
264.0	0	1	1
265.0	0	2	2
266.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	0	1	1
272.0	0	3	3
276.0	0	1	1
278.0	0	2	2
279.0	0	1	1
281.0	0	2	2
284.0	0	1	1
286.0	0	1	1
288.0	0	1	1
289.0	0	2	2
291.0	0	1	1
292.0	0	1	1
295.0	0	1	1
298.0	0	1	1
299.0	0	2	2
300.0	0	2	2
301.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
306.0	0	2	2
312.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
317.0	0	1	1
318.0	0	2	2
319.0	0	1	1
320.0	0	1	1
321.0	0	2	2
322.0	0	1	1
327.0	0	1	1
340.0	0	2	2
342.0	0	1	1
345.0	0	1	1
347.0	0	1	1
351.0	0	1	1
353.0	0	2	2
358.0	0	1	1
360.0	0	1	1
373.0	0	1	1
375.0	0	1	1
376.0	0	1	1
378.0	0	1	1
385.0	0	1	1
387.0	0	1	1
389.0	0	1	1
391.0	0	1	1
397.0	0	1	1
398.0	0	1	1
401.0	0	2	2
404.0	0	1	1
407.0	0	1	1
412.0	0	1	1
413.0	0	1	1
414.0	0	2	2
416.0	0	2	2
425.0	0	1	1
426.0	0	1	1
427.0	0	1	1
430.0	0	1	1
433.0	0	1	1
438.0	0	1	1
439.0	0	1	1
442.0	0	1	1
446.0	0	1	1
447.0	0	1	1
451.0	0	1	1
457.0	0	1	1
463.0	0	1	1
469.0	0	1	1
471.0	0	1	1
472.0	0	1	1
473.0	0	1	1
476.0	0	1	1
477.0	0	1	1
482.0	0	1	1
490.0	0	1	1
492.0	0	2	2
493.0	0	1	1
500.0	0	1	1
504.0	0	1	1
505.0	0	1	1
507.0	0	1	1
519.0	0	2	2
521.0	0	1	1
522.0	0	1	1
536.0	0	1	1
543.0	0	1	1
554.0	0	3	3
563.0	0	1	1
580.0	0	1	1
584.0	0	1	1
593.0	0	1	1
595.0	0	1	1
613.0	0	1	1
630.0	0	1	1
705.0	0	1	1
706.0	0	1	1
707.0	0	1	1
717.0	0	1	1
721.0	0	1	1
744.0	0	1	1
770.0	0	1	1
861.0	0	1	1
1026.0	0	1	1