## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-09-08/UA_Kie_Kyi_1_2014-09-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-09-08/UA_Kie_Kyi_1_2014-09-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2014-09-08/UA_Kie_Kyi_1_2014-09-08.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 16:23:14 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	7372998	14466915	0	0	1363070	542935	0	0.067451	187887875

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	13354388	13354388
2.0	1.925892	247884	247884
3.0	2.783168	4641	4641
4.0	3.576913	790	790
5.0	4.311836	476	476
6.0	4.992295	331	331
7.0	5.622326	255	255
8.0	6.205667	214	214
9.0	6.745778	165	165
10.0	7.245862	127	127
11.0	7.708887	110	110
12.0	8.137597	125	125
13.0	8.534537	86	86
14.0	8.90206	87	87
15.0	9.242347	73	73
16.0	9.557416	78	78
17.0	9.849135	58	58
18.0	10.119236	67	67
19.0	10.369321	58	58
20.0	10.600872	54	54
21.0	10.815263	47	47
22.0	11.013767	51	51
23.0	11.197559	34	34
24.0	11.367732	44	44
25.0	11.525293	40	40
26.0	11.671177	40	40
27.0	11.80625	32	32
28.0	11.931314	33	33
29.0	12.047109	31	31
30.0	12.154323	38	38
31.0	12.253591	25	25
32.0	12.345503	35	35
33.0	12.430603	22	22
34.0	12.509397	28	28
35.0	12.582352	18	18
36.0	12.6499	18	18
37.0	12.712442	23	23
38.0	12.770349	12	12
39.0	12.823965	22	22
40.0	12.873608	22	22
41.0	12.919572	11	11
42.0	12.962129	14	14
43.0	13.001532	20	20
44.0	13.038016	24	24
45.0	13.071796	14	14
46.0	13.103072	11	11
47.0	13.132031	16	16
48.0	13.158843	15	15
49.0	13.183669	17	17
50.0	13.206654	9	9
51.0	13.227937	20	20
52.0	13.247642	12	12
53.0	13.265886	11	11
54.0	13.282779	13	13
55.0	13.29842	7	7
56.0	13.312902	12	12
57.0	13.32631	17	17
58.0	13.338725	11	11
59.0	13.35022	7	7
60.0	13.360863	13	13
61.0	13.370717	4	4
62.0	13.379841	10	10
63.0	13.388289	11	11
64.0	13.396111	9	9
65.0	13.403353	12	12
66.0	13.410058	9	9
67.0	13.416266	11	11
68.0	13.422015	4	4
69.0	13.427337	11	11
70.0	13.432265	5	5
71.0	13.436828	5	5
72.0	13.441053	13	13
73.0	13.444964	13	13
74.0	13.448586	10	10
75.0	13.451939	9	9
76.0	13.455044	7	7
77.0	13.457918	10	10
78.0	13.46058	5	5
79.0	13.463044	1	1
80.0	13.465326	11	11
81.0	13.467439	6	6
82.0	13.469395	7	7
83.0	13.471206	8	8
84.0	13.472883	5	5
85.0	13.474436	4	4
86.0	13.475873	7	7
87.0	13.477204	8	8
88.0	13.478437	9	9
89.0	13.479578	6	6
90.0	13.480634	14	14
91.0	13.481612	8	8
92.0	13.482518	3	3
93.0	13.483357	5	5
94.0	13.484133	8	8
95.0	13.484852	4	4
96.0	13.485518	7	7
97.0	13.486134	4	4
98.0	13.486705	6	6
99.0	13.487233	4	4
100.0	13.487722	6	6
101.0	0	3	3
102.0	0	6	6
103.0	0	2	2
104.0	0	7	7
105.0	0	2	2
106.0	0	7	7
107.0	0	4	4
108.0	0	1	1
109.0	0	2	2
110.0	0	7	7
111.0	0	8	8
112.0	0	7	7
113.0	0	6	6
114.0	0	3	3
115.0	0	5	5
116.0	0	1	1
117.0	0	5	5
118.0	0	7	7
119.0	0	3	3
120.0	0	5	5
121.0	0	4	4
122.0	0	7	7
123.0	0	3	3
124.0	0	5	5
125.0	0	4	4
126.0	0	1	1
127.0	0	1	1
128.0	0	4	4
129.0	0	3	3
130.0	0	2	2
131.0	0	4	4
132.0	0	2	2
133.0	0	6	6
134.0	0	3	3
135.0	0	2	2
136.0	0	7	7
137.0	0	3	3
138.0	0	3	3
139.0	0	1	1
140.0	0	2	2
141.0	0	3	3
142.0	0	7	7
143.0	0	3	3
144.0	0	1	1
145.0	0	3	3
146.0	0	1	1
147.0	0	4	4
148.0	0	1	1
149.0	0	4	4
150.0	0	2	2
151.0	0	3	3
152.0	0	2	2
153.0	0	6	6
154.0	0	1	1
155.0	0	1	1
156.0	0	5	5
157.0	0	8	8
158.0	0	2	2
159.0	0	2	2
160.0	0	1	1
161.0	0	1	1
162.0	0	4	4
163.0	0	2	2
165.0	0	3	3
166.0	0	3	3
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
170.0	0	3	3
171.0	0	7	7
172.0	0	2	2
173.0	0	1	1
174.0	0	2	2
175.0	0	3	3
176.0	0	1	1
178.0	0	3	3
179.0	0	3	3
181.0	0	3	3
182.0	0	1	1
183.0	0	2	2
184.0	0	2	2
185.0	0	1	1
186.0	0	1	1
187.0	0	2	2
188.0	0	3	3
189.0	0	3	3
190.0	0	7	7
191.0	0	1	1
193.0	0	5	5
196.0	0	2	2
197.0	0	1	1
198.0	0	4	4
199.0	0	1	1
200.0	0	4	4
203.0	0	1	1
204.0	0	1	1
205.0	0	3	3
207.0	0	2	2
209.0	0	3	3
211.0	0	2	2
212.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	2	2
217.0	0	1	1
218.0	0	3	3
220.0	0	3	3
221.0	0	1	1
222.0	0	2	2
223.0	0	2	2
224.0	0	1	1
226.0	0	4	4
227.0	0	1	1
228.0	0	3	3
229.0	0	3	3
230.0	0	2	2
231.0	0	1	1
232.0	0	2	2
233.0	0	2	2
234.0	0	4	4
235.0	0	2	2
237.0	0	2	2
239.0	0	1	1
240.0	0	1	1
242.0	0	4	4
243.0	0	1	1
244.0	0	2	2
245.0	0	1	1
246.0	0	2	2
247.0	0	2	2
249.0	0	1	1
251.0	0	1	1
252.0	0	3	3
253.0	0	1	1
255.0	0	1	1
256.0	0	4	4
257.0	0	1	1
258.0	0	1	1
260.0	0	2	2
261.0	0	1	1
262.0	0	1	1
264.0	0	3	3
270.0	0	2	2
271.0	0	2	2
272.0	0	1	1
274.0	0	1	1
275.0	0	1	1
277.0	0	1	1
278.0	0	1	1
280.0	0	1	1
281.0	0	2	2
283.0	0	1	1
284.0	0	1	1
285.0	0	2	2
287.0	0	2	2
289.0	0	1	1
290.0	0	1	1
291.0	0	1	1
292.0	0	1	1
296.0	0	1	1
297.0	0	2	2
299.0	0	2	2
300.0	0	1	1
303.0	0	1	1
305.0	0	1	1
307.0	0	2	2
308.0	0	2	2
309.0	0	2	2
312.0	0	2	2
314.0	0	1	1
319.0	0	1	1
320.0	0	2	2
321.0	0	2	2
324.0	0	3	3
325.0	0	1	1
328.0	0	3	3
330.0	0	1	1
334.0	0	2	2
335.0	0	1	1
336.0	0	1	1
338.0	0	1	1
343.0	0	1	1
346.0	0	2	2
348.0	0	3	3
349.0	0	1	1
351.0	0	1	1
353.0	0	1	1
355.0	0	1	1
357.0	0	2	2
358.0	0	1	1
359.0	0	1	1
362.0	0	3	3
363.0	0	1	1
364.0	0	1	1
368.0	0	1	1
369.0	0	1	1
372.0	0	1	1
374.0	0	2	2
377.0	0	1	1
378.0	0	2	2
379.0	0	1	1
383.0	0	2	2
384.0	0	1	1
385.0	0	1	1
386.0	0	1	1
387.0	0	1	1
388.0	0	1	1
391.0	0	1	1
392.0	0	1	1
394.0	0	1	1
398.0	0	1	1
400.0	0	2	2
404.0	0	1	1
405.0	0	3	3
406.0	0	1	1
411.0	0	1	1
416.0	0	1	1
417.0	0	1	1
418.0	0	1	1
419.0	0	1	1
420.0	0	1	1
421.0	0	2	2
422.0	0	1	1
425.0	0	1	1
428.0	0	1	1
432.0	0	1	1
433.0	0	1	1
435.0	0	1	1
436.0	0	1	1
438.0	0	1	1
444.0	0	1	1
445.0	0	1	1
447.0	0	1	1
449.0	0	1	1
455.0	0	1	1
456.0	0	1	1
459.0	0	2	2
460.0	0	1	1
461.0	0	1	1
462.0	0	1	1
463.0	0	2	2
465.0	0	1	1
466.0	0	1	1
467.0	0	1	1
474.0	0	1	1
475.0	0	2	2
482.0	0	1	1
485.0	0	1	1
486.0	0	1	1
487.0	0	1	1
493.0	0	1	1
495.0	0	1	1
496.0	0	1	1
498.0	0	1	1
499.0	0	1	1
502.0	0	1	1
509.0	0	1	1
512.0	0	1	1
516.0	0	3	3
520.0	0	1	1
523.0	0	1	1
527.0	0	1	1
530.0	0	1	1
532.0	0	1	1
540.0	0	1	1
542.0	0	1	1
548.0	0	1	1
551.0	0	2	2
561.0	0	1	1
562.0	0	1	1
566.0	0	1	1
567.0	0	1	1
568.0	0	1	1
569.0	0	1	1
570.0	0	1	1
572.0	0	1	1
574.0	0	1	1
575.0	0	1	1
577.0	0	1	1
583.0	0	1	1
585.0	0	1	1
591.0	0	1	1
597.0	0	1	1
602.0	0	2	2
603.0	0	1	1
605.0	0	1	1
620.0	0	2	2
622.0	0	1	1
624.0	0	1	1
625.0	0	1	1
633.0	0	1	1
641.0	0	2	2
645.0	0	1	1
650.0	0	1	1
652.0	0	1	1
656.0	0	1	1
657.0	0	1	1
662.0	0	1	1
686.0	0	2	2
687.0	0	1	1
709.0	0	1	1
712.0	0	1	1
714.0	0	1	1
720.0	0	1	1
724.0	0	1	1
732.0	0	1	1
735.0	0	1	1
747.0	0	1	1
761.0	0	1	1
763.0	0	1	1
767.0	0	1	1
770.0	0	1	1
772.0	0	1	1
774.0	0	1	1
780.0	0	1	1
786.0	0	1	1
787.0	0	1	1
789.0	0	1	1
792.0	0	1	1
799.0	0	1	1
806.0	0	1	1
807.0	0	1	1
822.0	0	1	1
830.0	0	1	1
833.0	0	1	1
842.0	0	2	2
863.0	0	1	1
869.0	0	1	1
877.0	0	1	1
881.0	0	1	1
884.0	0	1	1
889.0	0	1	1
891.0	0	1	1
904.0	0	1	1
906.0	0	1	1
926.0	0	1	1
934.0	0	1	1
939.0	0	1	1
967.0	0	1	1
975.0	0	1	1
983.0	0	1	1
991.0	0	1	1
1040.0	0	1	1
1043.0	0	1	1
1076.0	0	1	1
1094.0	0	1	1
1125.0	0	1	1
1128.0	0	1	1
1131.0	0	1	1
1148.0	0	1	1
1167.0	0	1	1
1175.0	0	1	1
1212.0	0	1	1
1268.0	0	1	1
1290.0	0	1	1
1319.0	0	1	1
1399.0	0	1	1
1422.0	0	1	1
1423.0	0	1	1
1511.0	0	1	1
1699.0	0	1	1
1890.0	0	1	1