## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S50F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S50F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S50F.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 12:35:06 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	1546962	15745597	9191522	6787400	789033	4550957	61374	0.29938	21871357

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.002673	9827181	0	9864640
2.0	1.490765	960621	56446	930361
3.0	1.728365	179156	1367	173928
4.0	1.844027	66708	278	65753
5.0	1.90033	35734	104	35478
6.0	1.927738	22300	40	22057
7.0	1.94108	15462	27	15407
8.0	1.947574	11294	19	11196
9.0	1.950736	8710	11	8669
10.0	1.952275	6938	6	6892
11.0	1.953024	5572	1	5546
12.0	1.953389	4600	3	4592
13.0	1.953566	4025	2	4003
14.0	1.953653	3379	3	3342
15.0	1.953695	3015	5	3025
16.0	1.953715	2632	2	2634
17.0	1.953725	2317	0	2310
18.0	1.95373	2021	2	1974
19.0	1.953732	1785	1	1786
20.0	1.953734	1621	0	1610
21.0	1.953734	1508	1	1490
22.0	1.953734	1324	0	1340
23.0	1.953735	1240	0	1248
24.0	1.953735	1156	0	1146
25.0	1.953735	1041	0	1017
26.0	1.953735	949	0	938
27.0	1.953735	863	0	877
28.0	1.953735	846	0	828
29.0	1.953735	708	0	716
30.0	1.953735	723	1	728
31.0	1.953735	730	0	730
32.0	1.953735	620	0	606
33.0	1.953735	547	0	551
34.0	1.953735	565	0	566
35.0	1.953735	534	0	532
36.0	1.953735	499	0	480
37.0	1.953735	460	0	473
38.0	1.953735	465	0	465
39.0	1.953735	442	0	430
40.0	1.953735	444	0	439
41.0	1.953735	388	0	375
42.0	1.953735	381	0	378
43.0	1.953735	319	0	332
44.0	1.953735	349	0	351
45.0	1.953735	315	0	324
46.0	1.953735	309	0	306
47.0	1.953735	291	0	281
48.0	1.953735	289	0	296
49.0	1.953735	286	0	263
50.0	1.953735	264	0	267
51.0	1.953735	260	0	259
52.0	1.953735	224	0	230
53.0	1.953735	263	0	250
54.0	1.953735	209	0	215
55.0	1.953735	188	0	191
56.0	1.953735	214	0	209
57.0	1.953735	192	0	189
58.0	1.953735	191	0	194
59.0	1.953735	185	0	191
60.0	1.953735	195	0	197
61.0	1.953735	182	0	182
62.0	1.953735	185	0	170
63.0	1.953735	158	0	173
64.0	1.953735	165	0	147
65.0	1.953735	162	0	171
66.0	1.953735	145	0	141
67.0	1.953735	138	0	136
68.0	1.953735	133	0	129
69.0	1.953735	135	0	139
70.0	1.953735	125	0	122
71.0	1.953735	105	0	111
72.0	1.953735	121	0	127
73.0	1.953735	124	0	113
74.0	1.953735	120	0	121
75.0	1.953735	104	0	106
76.0	1.953735	119	0	117
77.0	1.953735	97	0	87
78.0	1.953735	93	0	98
79.0	1.953735	105	0	105
80.0	1.953735	94	0	89
81.0	1.953735	98	0	107
82.0	1.953735	95	0	87
83.0	1.953735	95	0	98
84.0	1.953735	85	0	85
85.0	1.953735	82	0	77
86.0	1.953735	79	0	87
87.0	1.953735	80	0	82
88.0	1.953735	83	0	71
89.0	1.953735	81	0	77
90.0	1.953735	66	0	75
91.0	1.953735	76	0	79
92.0	1.953735	71	0	59
93.0	1.953735	61	0	64
94.0	1.953735	61	0	78
95.0	1.953735	86	0	77
96.0	1.953735	65	0	65
97.0	1.953735	65	0	67
98.0	1.953735	77	0	68
99.0	1.953735	62	0	64
100.0	1.953735	66	0	65
101.0	0	59	0	60
102.0	0	55	0	53
103.0	0	59	0	57
104.0	0	48	0	47
105.0	0	45	0	45
106.0	0	47	0	57
107.0	0	56	0	59
108.0	0	40	0	39
109.0	0	65	0	58
110.0	0	56	0	59
111.0	0	58	0	48
112.0	0	45	0	49
113.0	0	39	0	34
114.0	0	56	0	57
115.0	0	43	0	43
116.0	0	38	0	40
117.0	0	41	0	44
118.0	0	48	0	45
119.0	0	36	0	41
120.0	0	40	0	29
121.0	0	36	0	38
122.0	0	54	0	60
123.0	0	32	0	28
124.0	0	31	0	29
125.0	0	33	0	41
126.0	0	46	0	39
127.0	0	38	0	40
128.0	0	33	0	28
129.0	0	29	0	32
130.0	0	33	0	34
131.0	0	38	0	42
132.0	0	35	0	37
133.0	0	37	0	35
134.0	0	30	0	29
135.0	0	38	0	31
136.0	0	31	0	34
137.0	0	36	0	37
138.0	0	24	0	25
139.0	0	32	0	36
140.0	0	40	0	26
141.0	0	23	0	35
142.0	0	34	0	26
143.0	0	24	0	27
144.0	0	36	0	37
145.0	0	33	0	30
146.0	0	23	0	20
147.0	0	21	0	25
148.0	0	27	0	26
149.0	0	28	0	30
150.0	0	30	0	26
151.0	0	24	0	28
152.0	0	16	0	12
153.0	0	25	0	27
154.0	0	24	0	22
155.0	0	19	0	19
156.0	0	16	0	20
157.0	0	27	0	21
158.0	0	23	0	20
159.0	0	14	0	18
160.0	0	19	0	23
161.0	0	28	0	27
162.0	0	21	0	19
163.0	0	20	0	21
164.0	0	30	0	29
165.0	0	29	0	31
166.0	0	19	0	17
167.0	0	17	0	11
168.0	0	13	0	23
169.0	0	25	0	14
170.0	0	11	0	14
171.0	0	17	0	25
172.0	0	19	0	16
173.0	0	30	0	27
174.0	0	15	0	19
175.0	0	13	0	12
176.0	0	11	0	9
177.0	0	21	0	16
178.0	0	9	0	12
179.0	0	21	0	18
180.0	0	12	0	17
181.0	0	13	0	16
182.0	0	13	0	11
183.0	0	12	0	14
184.0	0	19	0	17
185.0	0	19	0	23
186.0	0	17	0	16
187.0	0	20	0	15
188.0	0	20	0	21
189.0	0	20	0	16
190.0	0	10	0	11
191.0	0	10	0	15
192.0	0	20	0	16
193.0	0	13	0	17
194.0	0	15	0	12
195.0	0	14	0	15
196.0	0	15	0	14
197.0	0	20	0	17
198.0	0	13	0	12
199.0	0	13	0	10
200.0	0	9	0	14
201.0	0	12	0	14
202.0	0	13	0	8
203.0	0	13	0	14
204.0	0	11	0	9
205.0	0	12	0	14
206.0	0	9	0	11
207.0	0	9	0	11
208.0	0	15	0	19
209.0	0	17	0	14
210.0	0	17	0	14
211.0	0	7	0	7
212.0	0	14	0	13
213.0	0	10	0	11
214.0	0	14	0	12
215.0	0	9	0	9
216.0	0	9	0	8
217.0	0	7	0	9
218.0	0	10	0	9
219.0	0	7	0	8
220.0	0	11	0	9
221.0	0	10	0	15
222.0	0	11	0	12
223.0	0	14	0	11
224.0	0	14	0	10
225.0	0	7	0	10
226.0	0	10	0	11
227.0	0	12	0	8
228.0	0	4	0	12
229.0	0	10	0	14
230.0	0	15	0	8
231.0	0	10	0	7
232.0	0	13	0	12
233.0	0	7	0	15
234.0	0	17	0	10
235.0	0	10	0	9
236.0	0	8	0	5
237.0	0	5	0	13
238.0	0	8	0	7
239.0	0	7	0	8
240.0	0	13	0	7
241.0	0	5	0	9
242.0	0	7	0	9
243.0	0	11	0	8
244.0	0	7	0	9
245.0	0	9	0	7
246.0	0	10	0	10
247.0	0	7	0	3
248.0	0	6	0	4
249.0	0	5	0	7
250.0	0	4	0	2
251.0	0	6	0	6
252.0	0	3	0	7
253.0	0	7	0	5
254.0	0	2	0	6
255.0	0	5	0	3
256.0	0	8	0	4
257.0	0	8	0	12
258.0	0	7	0	6
259.0	0	7	0	9
260.0	0	11	0	10
261.0	0	8	0	6
262.0	0	6	0	5
263.0	0	3	0	5
264.0	0	9	0	12
265.0	0	9	0	9
266.0	0	9	0	9
267.0	0	5	0	4
268.0	0	5	0	4
269.0	0	4	0	3
270.0	0	5	0	6
271.0	0	8	0	5
272.0	0	7	0	8
273.0	0	6	0	4
274.0	0	3	0	5
275.0	0	3	0	4
276.0	0	2	0	9
277.0	0	7	0	1
278.0	0	5	0	3
279.0	0	6	0	7
280.0	0	10	0	10
281.0	0	5	0	4
282.0	0	3	0	7
283.0	0	2	0	5
284.0	0	8	0	2
285.0	0	2	0	4
286.0	0	7	0	10
287.0	0	8	0	6
288.0	0	5	0	6
289.0	0	8	0	1
290.0	0	2	0	5
291.0	0	6	0	1
292.0	0	1	0	5
293.0	0	7	0	6
294.0	0	3	0	6
295.0	0	4	0	4
296.0	0	5	0	6
297.0	0	4	0	12
298.0	0	7	0	2
299.0	0	9	0	6
300.0	0	7	0	6
301.0	0	6	0	6
302.0	0	6	0	6
303.0	0	4	0	2
304.0	0	4	0	7
305.0	0	4	0	7
306.0	0	2	0	2
307.0	0	7	0	3
308.0	0	6	0	3
309.0	0	5	0	6
310.0	0	6	0	6
311.0	0	4	0	4
312.0	0	2	0	4
313.0	0	5	0	1
314.0	0	2	0	3
315.0	0	2	0	4
316.0	0	5	0	3
317.0	0	4	0	4
318.0	0	3	0	2
319.0	0	2	0	4
320.0	0	6	0	6
321.0	0	3	0	3
322.0	0	2	0	4
323.0	0	4	0	2
324.0	0	5	0	5
325.0	0	5	0	7
326.0	0	5	0	3
327.0	0	5	0	5
328.0	0	4	0	4
329.0	0	3	0	3
330.0	0	4	0	1
331.0	0	2	0	3
332.0	0	3	0	9
333.0	0	3	0	6
334.0	0	8	0	4
335.0	0	7	0	4
336.0	0	4	0	1
337.0	0	3	0	9
338.0	0	6	0	6
339.0	0	2	0	2
340.0	0	4	0	1
341.0	0	3	0	2
342.0	0	2	0	5
343.0	0	6	0	4
344.0	0	3	0	2
345.0	0	3	0	2
346.0	0	3	0	3
347.0	0	2	0	4
348.0	0	4	0	1
349.0	0	1	0	2
350.0	0	0	0	1
351.0	0	1	0	3
352.0	0	4	0	7
353.0	0	7	0	5
354.0	0	6	0	3
355.0	0	4	0	4
356.0	0	2	0	1
357.0	0	1	0	3
358.0	0	5	0	2
359.0	0	4	0	6
360.0	0	2	0	0
361.0	0	1	0	3
362.0	0	3	0	4
363.0	0	1	0	2
364.0	0	4	0	2
365.0	0	4	0	2
366.0	0	1	0	7
367.0	0	1	0	4
368.0	0	6	0	1
369.0	0	6	0	5
370.0	0	2	0	2
371.0	0	3	0	1
372.0	0	2	0	2
373.0	0	0	0	2
374.0	0	4	0	2
375.0	0	3	0	0
376.0	0	2	0	7
377.0	0	0	0	1
378.0	0	3	0	2
379.0	0	2	0	3
380.0	0	1	0	1
381.0	0	4	0	1
382.0	0	1	0	1
383.0	0	1	0	2
384.0	0	1	0	1
385.0	0	3	0	1
386.0	0	0	0	4
387.0	0	2	0	1
388.0	0	5	0	6
389.0	0	4	0	3
390.0	0	4	0	3
391.0	0	2	0	2
392.0	0	1	0	1
393.0	0	2	0	1
394.0	0	2	0	5
395.0	0	4	0	1
396.0	0	4	0	6
397.0	0	1	0	5
398.0	0	1	0	0
399.0	0	5	0	2
400.0	0	4	0	1
401.0	0	2	0	0
402.0	0	0	0	1
403.0	0	1	0	2
404.0	0	1	0	1
405.0	0	1	0	3
406.0	0	2	0	2
407.0	0	2	0	0
408.0	0	2	0	6
409.0	0	2	0	2
410.0	0	2	0	5
411.0	0	4	0	1
412.0	0	5	0	1
413.0	0	1	0	0
414.0	0	0	0	3
415.0	0	2	0	1
416.0	0	2	0	1
417.0	0	3	0	4
418.0	0	4	0	3
420.0	0	2	0	1
421.0	0	4	0	4
422.0	0	0	0	2
423.0	0	1	0	0
424.0	0	1	0	1
425.0	0	1	0	2
426.0	0	3	0	0
427.0	0	0	0	1
428.0	0	1	0	2
429.0	0	1	0	4
430.0	0	3	0	0
431.0	0	2	0	3
432.0	0	2	0	0
433.0	0	1	0	2
434.0	0	1	0	1
435.0	0	2	0	3
436.0	0	2	0	3
437.0	0	1	0	1
438.0	0	1	0	1
439.0	0	2	0	1
440.0	0	2	0	2
441.0	0	1	0	1
442.0	0	1	0	1
443.0	0	4	0	4
444.0	0	1	0	0
445.0	0	2	0	1
446.0	0	0	0	3
447.0	0	3	0	3
448.0	0	0	0	1
449.0	0	3	0	1
450.0	0	3	0	1
451.0	0	1	0	1
452.0	0	1	0	1
453.0	0	0	0	1
454.0	0	1	0	2
455.0	0	2	0	1
457.0	0	2	0	2
458.0	0	0	0	4
459.0	0	2	0	5
460.0	0	5	0	1
461.0	0	4	0	0
462.0	0	0	0	2
463.0	0	1	0	0
464.0	0	2	0	2
465.0	0	1	0	2
466.0	0	2	0	2
467.0	0	1	0	3
468.0	0	6	0	4
469.0	0	1	0	2
470.0	0	4	0	3
471.0	0	1	0	1
472.0	0	2	0	0
473.0	0	1	0	1
474.0	0	0	0	2
475.0	0	2	0	2
476.0	0	0	0	1
477.0	0	3	0	2
478.0	0	2	0	1
479.0	0	0	0	1
480.0	0	0	0	1
481.0	0	3	0	2
482.0	0	1	0	0
483.0	0	1	0	2
484.0	0	2	0	2
486.0	0	1	0	2
487.0	0	1	0	0
488.0	0	2	0	2
489.0	0	0	0	2
490.0	0	1	0	2
491.0	0	3	0	3
492.0	0	2	0	4
493.0	0	3	0	3
494.0	0	3	0	1
495.0	0	2	0	0
496.0	0	2	0	1
497.0	0	2	0	0
498.0	0	0	0	2
499.0	0	1	0	2
500.0	0	1	0	1
501.0	0	2	0	2
502.0	0	2	0	1
503.0	0	0	0	2
504.0	0	3	0	3
505.0	0	1	0	0
506.0	0	3	0	2
507.0	0	0	0	2
508.0	0	3	0	1
509.0	0	0	0	3
510.0	0	4	0	1
511.0	0	2	0	2
512.0	0	0	0	1
513.0	0	3	0	1
514.0	0	1	0	1
515.0	0	2	0	0
517.0	0	0	0	1
519.0	0	1	0	2
521.0	0	0	0	1
522.0	0	1	0	2
523.0	0	2	0	3
524.0	0	3	0	0
525.0	0	2	0	0
526.0	0	0	0	1
527.0	0	0	0	2
528.0	0	3	0	0
530.0	0	0	0	1
532.0	0	1	0	0
535.0	0	0	0	1
536.0	0	1	0	1
537.0	0	0	0	1
538.0	0	0	0	2
539.0	0	1	0	1
540.0	0	1	0	1
541.0	0	3	0	1
542.0	0	1	0	0
543.0	0	0	0	2
544.0	0	1	0	0
545.0	0	1	0	2
546.0	0	1	0	1
547.0	0	1	0	0
548.0	0	2	0	1
549.0	0	0	0	2
550.0	0	1	0	1
551.0	0	1	0	0
552.0	0	1	0	0
553.0	0	0	0	1
554.0	0	1	0	2
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