## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S59M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S59M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S59M.dup_metrics.txt REMOVE_DUPLICATES=true    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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 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: Wed Mar 09 12:54:05 PST 2022

## 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
Unknown Library	2249228	12856248	10772466	14525070	599942	2366743	50359	0.19074	30986552

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003173	9501558	0	9538191
2.0	1.665677	751323	48512	720503
3.0	2.103199	114854	631	110377
4.0	2.392142	38842	113	38181
5.0	2.582963	19996	30	19722
6.0	2.708982	12323	13	12277
7.0	2.792206	8507	3	8416
8.0	2.847168	6145	2	6101
9.0	2.883465	4621	0	4579
10.0	2.907436	3567	1	3564
11.0	2.923267	2853	2	2810
12.0	2.933722	2347	0	2357
13.0	2.940626	2009	0	1980
14.0	2.945186	1723	0	1713
15.0	2.948197	1400	0	1398
16.0	2.950185	1211	0	1195
17.0	2.951499	1087	0	1092
18.0	2.952366	1001	0	986
19.0	2.952939	851	0	839
20.0	2.953317	771	0	767
21.0	2.953567	706	0	703
22.0	2.953732	597	0	605
23.0	2.953841	567	0	558
24.0	2.953913	517	0	519
25.0	2.95396	480	0	482
26.0	2.953992	435	0	431
27.0	2.954013	404	0	406
28.0	2.954026	380	0	375
29.0	2.954035	338	0	328
30.0	2.954041	334	0	331
31.0	2.954045	276	0	277
32.0	2.954048	306	0	315
33.0	2.954049	265	0	238
34.0	2.954051	222	0	238
35.0	2.954051	205	0	202
36.0	2.954052	256	0	258
37.0	2.954052	211	0	196
38.0	2.954052	180	0	191
39.0	2.954053	182	0	184
40.0	2.954053	174	0	156
41.0	2.954053	149	0	160
42.0	2.954053	138	0	144
43.0	2.954053	146	0	144
44.0	2.954053	154	0	157
45.0	2.954053	134	0	122
46.0	2.954053	140	0	139
47.0	2.954053	113	0	107
48.0	2.954053	110	0	114
49.0	2.954053	106	0	98
50.0	2.954053	97	0	109
51.0	2.954053	107	0	104
52.0	2.954053	99	0	102
53.0	2.954053	91	0	83
54.0	2.954053	94	0	99
55.0	2.954053	87	0	87
56.0	2.954053	93	0	92
57.0	2.954053	111	0	108
58.0	2.954053	74	0	79
59.0	2.954053	81	0	84
60.0	2.954053	81	0	78
61.0	2.954053	68	0	67
62.0	2.954053	65	0	62
63.0	2.954053	66	0	67
64.0	2.954053	69	0	72
65.0	2.954053	70	0	65
66.0	2.954053	58	0	59
67.0	2.954053	63	0	57
68.0	2.954053	39	0	48
69.0	2.954053	55	0	51
70.0	2.954053	45	0	43
71.0	2.954053	45	0	47
72.0	2.954053	59	0	54
73.0	2.954053	43	0	47
74.0	2.954053	47	0	53
75.0	2.954053	62	0	56
76.0	2.954053	46	0	49
77.0	2.954053	53	0	46
78.0	2.954053	34	0	31
79.0	2.954053	36	0	46
80.0	2.954053	50	0	50
81.0	2.954053	42	0	37
82.0	2.954053	40	0	42
83.0	2.954053	39	0	43
84.0	2.954053	41	0	38
85.0	2.954053	39	0	35
86.0	2.954053	32	0	31
87.0	2.954053	33	0	33
88.0	2.954053	31	0	29
89.0	2.954053	24	0	21
90.0	2.954053	25	0	29
91.0	2.954053	42	0	47
92.0	2.954053	26	0	25
93.0	2.954053	28	0	25
94.0	2.954053	20	0	21
95.0	2.954053	33	0	28
96.0	2.954053	25	0	24
97.0	2.954053	22	0	23
98.0	2.954053	21	0	19
99.0	2.954053	22	0	27
100.0	2.954053	25	0	21
101.0	0	23	0	24
102.0	0	17	0	26
103.0	0	23	0	18
104.0	0	29	0	29
105.0	0	25	0	20
106.0	0	21	0	27
107.0	0	23	0	24
108.0	0	20	0	13
109.0	0	18	0	28
110.0	0	24	0	20
111.0	0	22	0	21
112.0	0	19	0	19
113.0	0	19	0	19
114.0	0	17	0	13
115.0	0	15	0	15
116.0	0	12	0	12
117.0	0	20	0	24
118.0	0	18	0	15
119.0	0	17	0	14
120.0	0	8	0	11
121.0	0	12	0	13
122.0	0	17	0	14
123.0	0	14	0	12
124.0	0	19	0	23
125.0	0	16	0	16
126.0	0	15	0	12
127.0	0	10	0	9
128.0	0	11	0	12
129.0	0	12	0	13
130.0	0	8	0	11
131.0	0	14	0	9
132.0	0	18	0	17
133.0	0	8	0	11
134.0	0	11	0	11
135.0	0	12	0	9
136.0	0	7	0	12
137.0	0	11	0	10
138.0	0	13	0	6
139.0	0	7	0	13
140.0	0	11	0	15
141.0	0	15	0	13
142.0	0	12	0	11
143.0	0	8	0	12
144.0	0	12	0	9
145.0	0	10	0	8
146.0	0	15	0	9
147.0	0	5	0	9
148.0	0	9	0	11
149.0	0	9	0	10
150.0	0	17	0	13
151.0	0	8	0	8
152.0	0	5	0	5
153.0	0	7	0	5
154.0	0	5	0	7
155.0	0	7	0	7
156.0	0	13	0	15
157.0	0	5	0	10
158.0	0	9	0	7
159.0	0	13	0	7
160.0	0	11	0	17
161.0	0	12	0	10
162.0	0	7	0	4
163.0	0	4	0	4
164.0	0	7	0	7
165.0	0	5	0	8
166.0	0	10	0	5
167.0	0	6	0	5
168.0	0	4	0	5
169.0	0	4	0	7
170.0	0	9	0	12
171.0	0	10	0	6
172.0	0	5	0	6
173.0	0	3	0	5
174.0	0	8	0	5
175.0	0	5	0	6
176.0	0	3	0	2
177.0	0	4	0	5
178.0	0	6	0	6
179.0	0	4	0	4
180.0	0	8	0	7
181.0	0	2	0	2
182.0	0	5	0	8
183.0	0	8	0	8
184.0	0	7	0	5
185.0	0	7	0	9
186.0	0	8	0	5
187.0	0	6	0	4
188.0	0	4	0	4
189.0	0	5	0	5
190.0	0	4	0	6
191.0	0	3	0	5
192.0	0	8	0	8
193.0	0	5	0	4
194.0	0	4	0	3
195.0	0	7	0	4
196.0	0	3	0	6
197.0	0	4	0	3
198.0	0	5	0	4
199.0	0	3	0	3
200.0	0	4	0	3
201.0	0	2	0	4
202.0	0	5	0	5
203.0	0	4	0	6
204.0	0	8	0	7
205.0	0	5	0	3
206.0	0	3	0	3
207.0	0	3	0	2
208.0	0	2	0	7
209.0	0	9	0	7
210.0	0	4	0	4
211.0	0	6	0	4
212.0	0	6	0	7
213.0	0	2	0	1
214.0	0	2	0	5
215.0	0	5	0	2
216.0	0	5	0	6
217.0	0	2	0	3
218.0	0	4	0	6
219.0	0	5	0	5
220.0	0	2	0	2
221.0	0	4	0	2
222.0	0	6	0	8
223.0	0	3	0	0
224.0	0	5	0	5
225.0	0	3	0	1
226.0	0	3	0	3
227.0	0	3	0	4
228.0	0	3	0	3
229.0	0	2	0	5
230.0	0	4	0	3
231.0	0	3	0	2
232.0	0	3	0	5
233.0	0	5	0	4
234.0	0	5	0	3
235.0	0	4	0	3
236.0	0	2	0	2
237.0	0	1	0	3
238.0	0	4	0	3
239.0	0	3	0	5
240.0	0	3	0	2
241.0	0	4	0	2
242.0	0	2	0	4
243.0	0	5	0	6
244.0	0	3	0	2
245.0	0	3	0	6
246.0	0	7	0	5
247.0	0	3	0	4
248.0	0	2	0	1
249.0	0	1	0	2
250.0	0	5	0	2
251.0	0	0	0	3
252.0	0	7	0	5
253.0	0	2	0	2
254.0	0	1	0	2
255.0	0	2	0	1
256.0	0	1	0	0
257.0	0	1	0	0
258.0	0	1	0	1
259.0	0	2	0	3
260.0	0	2	0	1
261.0	0	3	0	3
262.0	0	3	0	4
263.0	0	2	0	2
264.0	0	1	0	0
265.0	0	1	0	0
266.0	0	1	0	2
267.0	0	2	0	2
268.0	0	1	0	3
269.0	0	2	0	2
270.0	0	2	0	2
271.0	0	3	0	1
272.0	0	2	0	3
273.0	0	1	0	1
274.0	0	2	0	1
275.0	0	1	0	5
276.0	0	4	0	3
277.0	0	2	0	3
278.0	0	6	0	3
279.0	0	1	0	3
280.0	0	3	0	1
281.0	0	1	0	4
282.0	0	1	0	3
283.0	0	5	0	3
284.0	0	3	0	0
285.0	0	1	0	0
286.0	0	2	0	2
287.0	0	1	0	3
288.0	0	3	0	1
289.0	0	2	0	1
290.0	0	0	0	3
291.0	0	3	0	2
292.0	0	1	0	3
293.0	0	3	0	2
294.0	0	2	0	0
295.0	0	1	0	3
296.0	0	2	0	2
297.0	0	4	0	3
298.0	0	2	0	1
299.0	0	1	0	2
300.0	0	1	0	1
301.0	0	2	0	1
302.0	0	1	0	1
303.0	0	3	0	4
304.0	0	1	0	0
305.0	0	2	0	2
306.0	0	0	0	2
307.0	0	1	0	0
308.0	0	4	0	2
309.0	0	0	0	2
310.0	0	1	0	3
311.0	0	3	0	0
312.0	0	1	0	2
313.0	0	2	0	1
314.0	0	2	0	1
315.0	0	0	0	2
316.0	0	1	0	0
317.0	0	1	0	4
318.0	0	4	0	2
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321.0	0	3	0	4
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346.0	0	1	0	2
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350.0	0	1	0	0
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353.0	0	1	0	1
354.0	0	3	0	2
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356.0	0	0	0	1
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358.0	0	3	0	2
359.0	0	3	0	0
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368.0	0	0	0	2
370.0	0	0	0	1
371.0	0	2	0	0
372.0	0	1	0	0
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375.0	0	2	0	1
376.0	0	0	0	1
377.0	0	0	0	1
378.0	0	1	0	0
379.0	0	1	0	2
381.0	0	2	0	1
382.0	0	0	0	4
383.0	0	3	0	1
384.0	0	0	0	2
385.0	0	2	0	0
386.0	0	2	0	0
387.0	0	1	0	0
388.0	0	0	0	2
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392.0	0	0	0	1
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400.0	0	1	0	1
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