## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S16F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S16F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S16F.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 11:23:16 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	2047705	18157678	12101588	8950279	1103061	5104204	82787	0.294853	26175896

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003174	11229356	0	11280504
2.0	1.504495	1235926	78374	1195488
3.0	1.755022	257938	1571	250612
4.0	1.880218	102314	224	100671
5.0	1.942783	55421	68	54900
6.0	1.974049	34767	24	34508
7.0	1.989674	24054	11	23847
8.0	1.997482	17315	8	17242
9.0	2.001384	13105	4	12917
10.0	2.003334	10187	2	10160
11.0	2.004309	8139	0	8069
12.0	2.004796	6588	1	6574
13.0	2.005039	5536	2	5493
14.0	2.00516	4672	0	4633
15.0	2.005221	3933	0	3919
16.0	2.005252	3466	0	3441
17.0	2.005267	3015	0	3010
18.0	2.005274	2557	0	2500
19.0	2.005278	2295	0	2325
20.0	2.00528	2127	0	2100
21.0	2.005281	1895	0	1871
22.0	2.005281	1714	0	1717
23.0	2.005282	1489	0	1491
24.0	2.005282	1390	0	1414
25.0	2.005282	1299	0	1243
26.0	2.005282	1110	0	1104
27.0	2.005282	1108	0	1082
28.0	2.005282	937	0	959
29.0	2.005282	901	0	886
30.0	2.005282	836	0	817
31.0	2.005282	784	0	789
32.0	2.005282	735	0	721
33.0	2.005282	651	0	645
34.0	2.005282	580	0	599
35.0	2.005282	592	0	585
36.0	2.005282	559	0	536
37.0	2.005282	507	0	530
38.0	2.005282	529	0	511
39.0	2.005282	471	0	475
40.0	2.005282	441	0	434
41.0	2.005282	412	0	430
42.0	2.005282	387	0	366
43.0	2.005282	368	0	364
44.0	2.005282	377	0	371
45.0	2.005282	316	0	330
46.0	2.005282	313	0	305
47.0	2.005282	296	0	281
48.0	2.005282	258	0	282
49.0	2.005282	300	0	296
50.0	2.005282	264	0	257
51.0	2.005282	261	0	241
52.0	2.005282	209	0	225
53.0	2.005282	261	0	255
54.0	2.005282	219	0	208
55.0	2.005282	206	0	216
56.0	2.005282	216	0	224
57.0	2.005282	195	0	180
58.0	2.005282	198	0	183
59.0	2.005282	177	0	190
60.0	2.005282	184	0	178
61.0	2.005282	143	0	151
62.0	2.005282	172	0	169
63.0	2.005282	151	0	151
64.0	2.005282	165	0	152
65.0	2.005282	133	0	137
66.0	2.005282	131	0	149
67.0	2.005282	145	0	129
68.0	2.005282	132	0	130
69.0	2.005282	132	0	126
70.0	2.005282	101	0	104
71.0	2.005282	118	0	111
72.0	2.005282	108	0	106
73.0	2.005282	96	0	108
74.0	2.005282	103	0	89
75.0	2.005282	95	0	111
76.0	2.005282	106	0	90
77.0	2.005282	87	0	100
78.0	2.005282	99	0	96
79.0	2.005282	123	0	117
80.0	2.005282	85	0	81
81.0	2.005282	81	0	87
82.0	2.005282	81	0	84
83.0	2.005282	80	0	69
84.0	2.005282	85	0	90
85.0	2.005282	68	0	78
86.0	2.005282	81	0	78
87.0	2.005282	73	0	68
88.0	2.005282	74	0	71
89.0	2.005282	67	0	57
90.0	2.005282	57	0	66
91.0	2.005282	63	0	61
92.0	2.005282	64	0	56
93.0	2.005282	54	0	57
94.0	2.005282	52	0	68
95.0	2.005282	59	0	50
96.0	2.005282	56	0	62
97.0	2.005282	57	0	52
98.0	2.005282	52	0	45
99.0	2.005282	53	0	44
100.0	2.005282	47	0	50
101.0	0	36	0	52
102.0	0	52	0	39
103.0	0	45	0	49
104.0	0	45	0	47
105.0	0	48	0	49
106.0	0	47	0	46
107.0	0	42	0	39
108.0	0	42	0	43
109.0	0	47	0	46
110.0	0	35	0	35
111.0	0	35	0	35
112.0	0	39	0	47
113.0	0	46	0	39
114.0	0	47	0	42
115.0	0	41	0	43
116.0	0	37	0	37
117.0	0	32	0	31
118.0	0	36	0	35
119.0	0	28	0	34
120.0	0	37	0	24
121.0	0	34	0	35
122.0	0	25	0	31
123.0	0	30	0	25
124.0	0	28	0	25
125.0	0	19	0	21
126.0	0	22	0	28
127.0	0	32	0	34
128.0	0	29	0	27
129.0	0	26	0	27
130.0	0	41	0	47
131.0	0	27	0	22
132.0	0	31	0	24
133.0	0	26	0	23
134.0	0	28	0	26
135.0	0	24	0	31
136.0	0	25	0	18
137.0	0	24	0	32
138.0	0	25	0	25
139.0	0	24	0	21
140.0	0	21	0	25
141.0	0	17	0	16
142.0	0	17	0	16
143.0	0	20	0	24
144.0	0	18	0	20
145.0	0	27	0	27
146.0	0	27	0	18
147.0	0	15	0	20
148.0	0	20	0	24
149.0	0	29	0	24
150.0	0	17	0	15
151.0	0	21	0	22
152.0	0	22	0	21
153.0	0	16	0	11
154.0	0	14	0	19
155.0	0	25	0	27
156.0	0	26	0	21
157.0	0	20	0	21
158.0	0	11	0	16
159.0	0	17	0	8
160.0	0	18	0	20
161.0	0	21	0	18
162.0	0	14	0	19
163.0	0	15	0	17
164.0	0	16	0	13
165.0	0	17	0	15
166.0	0	14	0	22
167.0	0	27	0	22
168.0	0	17	0	14
169.0	0	11	0	10
170.0	0	16	0	16
171.0	0	17	0	13
172.0	0	12	0	14
173.0	0	9	0	9
174.0	0	12	0	12
175.0	0	14	0	17
176.0	0	12	0	8
177.0	0	11	0	14
178.0	0	19	0	20
179.0	0	15	0	15
180.0	0	13	0	17
181.0	0	13	0	12
182.0	0	10	0	8
183.0	0	12	0	9
184.0	0	11	0	11
185.0	0	16	0	12
186.0	0	5	0	9
187.0	0	8	0	11
188.0	0	8	0	5
189.0	0	8	0	12
190.0	0	15	0	16
191.0	0	10	0	10
192.0	0	13	0	9
193.0	0	11	0	13
194.0	0	9	0	9
195.0	0	15	0	11
196.0	0	9	0	8
197.0	0	10	0	9
198.0	0	6	0	8
199.0	0	8	0	9
200.0	0	10	0	7
201.0	0	7	0	7
202.0	0	9	0	8
203.0	0	7	0	8
204.0	0	12	0	10
205.0	0	5	0	9
206.0	0	13	0	8
207.0	0	7	0	10
208.0	0	9	0	11
209.0	0	9	0	5
210.0	0	5	0	9
211.0	0	6	0	9
212.0	0	11	0	6
213.0	0	9	0	5
214.0	0	3	0	5
215.0	0	5	0	3
216.0	0	4	0	6
217.0	0	6	0	6
218.0	0	7	0	8
219.0	0	7	0	7
220.0	0	7	0	9
221.0	0	6	0	7
222.0	0	9	0	6
223.0	0	4	0	2
224.0	0	3	0	5
225.0	0	5	0	9
226.0	0	7	0	5
227.0	0	12	0	7
228.0	0	4	0	3
229.0	0	4	0	6
230.0	0	3	0	5
231.0	0	5	0	9
232.0	0	5	0	7
233.0	0	10	0	12
234.0	0	9	0	4
235.0	0	11	0	10
236.0	0	9	0	6
237.0	0	6	0	6
238.0	0	6	0	6
239.0	0	6	0	5
240.0	0	3	0	4
241.0	0	2	0	7
242.0	0	5	0	3
243.0	0	6	0	2
244.0	0	2	0	4
245.0	0	6	0	1
246.0	0	2	0	4
247.0	0	2	0	6
248.0	0	5	0	3
249.0	0	3	0	2
250.0	0	3	0	1
251.0	0	3	0	3
252.0	0	1	0	5
253.0	0	7	0	9
254.0	0	6	0	2
255.0	0	5	0	8
256.0	0	6	0	7
257.0	0	5	0	3
258.0	0	3	0	2
259.0	0	2	0	6
260.0	0	6	0	4
261.0	0	8	0	3
262.0	0	5	0	5
263.0	0	5	0	7
264.0	0	4	0	9
265.0	0	6	0	4
266.0	0	6	0	7
267.0	0	4	0	3
268.0	0	5	0	3
269.0	0	4	0	3
270.0	0	1	0	2
271.0	0	4	0	2
272.0	0	4	0	4
273.0	0	3	0	1
274.0	0	3	0	3
275.0	0	0	0	3
276.0	0	2	0	1
277.0	0	2	0	3
278.0	0	4	0	4
279.0	0	4	0	5
280.0	0	4	0	7
281.0	0	5	0	7
282.0	0	7	0	3
283.0	0	4	0	0
284.0	0	1	0	4
285.0	0	3	0	2
286.0	0	3	0	3
287.0	0	0	0	3
288.0	0	8	0	4
289.0	0	3	0	1
290.0	0	2	0	2
291.0	0	1	0	3
292.0	0	3	0	2
293.0	0	1	0	5
294.0	0	6	0	4
295.0	0	1	0	1
296.0	0	1	0	1
297.0	0	2	0	1
298.0	0	4	0	2
299.0	0	2	0	2
300.0	0	1	0	0
301.0	0	2	0	2
302.0	0	0	0	1
303.0	0	0	0	2
304.0	0	0	0	1
305.0	0	3	0	1
306.0	0	2	0	0
307.0	0	0	0	1
308.0	0	1	0	1
309.0	0	2	0	3
310.0	0	3	0	3
311.0	0	2	0	0
312.0	0	0	0	1
313.0	0	2	0	3
314.0	0	1	0	1
315.0	0	1	0	3
316.0	0	3	0	4
317.0	0	2	0	3
318.0	0	5	0	3
319.0	0	3	0	3
320.0	0	2	0	2
321.0	0	2	0	2
322.0	0	3	0	2
323.0	0	4	0	3
324.0	0	1	0	1
325.0	0	1	0	2
326.0	0	1	0	0
327.0	0	2	0	2
328.0	0	1	0	3
329.0	0	1	0	3
330.0	0	3	0	0
331.0	0	4	0	4
332.0	0	1	0	2
333.0	0	2	0	0
334.0	0	2	0	0
335.0	0	0	0	1
337.0	0	0	0	2
338.0	0	0	0	2
339.0	0	3	0	3
340.0	0	3	0	4
341.0	0	6	0	3
342.0	0	1	0	2
343.0	0	1	0	0
344.0	0	1	0	0
345.0	0	0	0	2
346.0	0	3	0	2
347.0	0	2	0	1
348.0	0	1	0	2
349.0	0	1	0	3
350.0	0	3	0	2
351.0	0	1	0	1
352.0	0	3	0	1
353.0	0	1	0	3
354.0	0	2	0	0
355.0	0	0	0	2
356.0	0	0	0	1
357.0	0	1	0	1
358.0	0	3	0	1
359.0	0	3	0	1
360.0	0	0	0	2
361.0	0	3	0	3
362.0	0	1	0	5
363.0	0	4	0	0
364.0	0	2	0	1
365.0	0	2	0	1
366.0	0	1	0	1
367.0	0	0	0	4
368.0	0	3	0	2
369.0	0	2	0	2
370.0	0	2	0	1
371.0	0	2	0	1
372.0	0	0	0	1
373.0	0	3	0	3
374.0	0	2	0	3
375.0	0	3	0	2
376.0	0	1	0	1
377.0	0	1	0	0
378.0	0	1	0	2
379.0	0	2	0	3
380.0	0	1	0	2
381.0	0	1	0	2
382.0	0	3	0	0
383.0	0	1	0	2
385.0	0	1	0	1
386.0	0	3	0	3
387.0	0	1	0	1
388.0	0	2	0	1
389.0	0	2	0	0
390.0	0	1	0	0
391.0	0	0	0	2
392.0	0	0	0	1
393.0	0	2	0	1
394.0	0	1	0	2
395.0	0	2	0	2
396.0	0	1	0	2
397.0	0	2	0	3
398.0	0	1	0	1
399.0	0	1	0	2
400.0	0	1	0	0
401.0	0	4	0	3
402.0	0	3	0	1
403.0	0	2	0	1
405.0	0	0	0	3
407.0	0	3	0	0
408.0	0	1	0	2
409.0	0	0	0	2
410.0	0	2	0	2
411.0	0	2	0	1
412.0	0	1	0	0
414.0	0	1	0	2
415.0	0	1	0	0
417.0	0	1	0	2
418.0	0	1	0	0
419.0	0	1	0	1
420.0	0	0	0	2
421.0	0	2	0	0
422.0	0	2	0	1
423.0	0	0	0	1
424.0	0	1	0	0
425.0	0	1	0	0
426.0	0	0	0	2
427.0	0	1	0	0
428.0	0	1	0	1
429.0	0	0	0	1
430.0	0	2	0	0
432.0	0	1	0	2
433.0	0	1	0	1
434.0	0	1	0	0
435.0	0	0	0	3
437.0	0	0	0	1
438.0	0	2	0	0
439.0	0	2	0	3
440.0	0	1	0	1
441.0	0	1	0	0
442.0	0	1	0	2
443.0	0	1	0	1
444.0	0	2	0	0
445.0	0	0	0	1
447.0	0	1	0	1
448.0	0	0	0	1
449.0	0	1	0	1
450.0	0	2	0	0
451.0	0	1	0	0
452.0	0	0	0	1
453.0	0	0	0	1
455.0	0	1	0	0
456.0	0	0	0	2
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458.0	0	1	0	1
459.0	0	1	0	1
460.0	0	0	0	1
461.0	0	1	0	0
462.0	0	1	0	3
463.0	0	1	0	1
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465.0	0	1	0	0
466.0	0	3	0	1
467.0	0	0	0	1
468.0	0	2	0	0
469.0	0	1	0	0
472.0	0	0	0	2
473.0	0	0	0	2
474.0	0	0	0	1
475.0	0	3	0	1
476.0	0	0	0	1
477.0	0	3	0	0
480.0	0	1	0	1
485.0	0	1	0	0
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490.0	0	1	0	0
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494.0	0	2	0	4
495.0	0	2	0	0
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500.0	0	0	0	1
501.0	0	3	0	1
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505.0	0	1	0	1
506.0	0	2	0	0
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515.0	0	2	0	1
519.0	0	0	0	2
520.0	0	1	0	1
521.0	0	1	0	1
522.0	0	1	0	0
523.0	0	1	0	1
524.0	0	1	0	1
525.0	0	1	0	2
526.0	0	1	0	0
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578.0	0	0	0	1
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581.0	0	1	0	0
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619.0	0	1	0	0
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629.0	0	0	0	1
632.0	0	1	0	0
633.0	0	1	0	0
638.0	0	0	0	1
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641.0	0	2	0	0
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653.0	0	0	0	1
657.0	0	1	0	1
658.0	0	0	0	1
660.0	0	1	0	0
663.0	0	1	0	0
664.0	0	0	0	1
667.0	0	0	0	1
668.0	0	1	0	0
672.0	0	1	0	0
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