## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S36F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S36F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S36F.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 11:59:43 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	1862994	16217598	10609467	8253998	932156	4592095	72808	0.294953	23158983

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003114	10173195	0	10217419
2.0	1.50111	1039799	66673	1004793
3.0	1.74834	189397	1677	182636
4.0	1.871078	66936	347	65693
5.0	1.932011	34911	148	34465
6.0	1.962261	21349	57	21224
7.0	1.977278	15111	36	14963
8.0	1.984734	10951	21	10885
9.0	1.988435	8389	13	8329
10.0	1.990273	6556	3	6485
11.0	1.991185	5289	4	5260
12.0	1.991638	4488	4	4486
13.0	1.991863	3873	2	3823
14.0	1.991974	3181	5	3193
15.0	1.99203	2763	3	2776
16.0	1.992057	2507	6	2501
17.0	1.992071	2226	0	2172
18.0	1.992078	1982	0	1980
19.0	1.992081	1777	0	1759
20.0	1.992083	1674	1	1664
21.0	1.992084	1495	1	1498
22.0	1.992084	1355	0	1349
23.0	1.992084	1202	0	1204
24.0	1.992084	1082	0	1085
25.0	1.992084	999	0	976
26.0	1.992084	940	1	934
27.0	1.992084	874	0	867
28.0	1.992084	838	0	835
29.0	1.992084	778	0	777
30.0	1.992084	742	0	728
31.0	1.992084	666	0	688
32.0	1.992084	627	0	616
33.0	1.992084	590	0	572
34.0	1.992084	525	0	511
35.0	1.992084	504	0	516
36.0	1.992084	497	0	496
37.0	1.992084	483	0	470
38.0	1.992084	414	0	408
39.0	1.992084	392	0	389
40.0	1.992084	396	0	415
41.0	1.992084	370	0	362
42.0	1.992084	362	0	353
43.0	1.992084	337	0	335
44.0	1.992084	333	0	340
45.0	1.992084	316	0	315
46.0	1.992084	322	0	321
47.0	1.992084	297	0	296
48.0	1.992084	301	0	300
49.0	1.992084	258	0	270
50.0	1.992084	262	0	243
51.0	1.992084	240	0	238
52.0	1.992084	239	0	235
53.0	1.992084	243	0	245
54.0	1.992084	216	0	217
55.0	1.992084	199	0	202
56.0	1.992084	213	0	196
57.0	1.992084	175	0	186
58.0	1.992084	202	0	208
59.0	1.992084	204	0	201
60.0	1.992084	185	0	170
61.0	1.992084	166	0	170
62.0	1.992084	163	0	171
63.0	1.992084	163	0	152
64.0	1.992084	135	0	130
65.0	1.992084	142	0	144
66.0	1.992084	139	0	141
67.0	1.992084	133	0	134
68.0	1.992084	127	0	119
69.0	1.992084	137	0	142
70.0	1.992084	115	0	117
71.0	1.992084	124	0	123
72.0	1.992084	126	0	122
73.0	1.992084	111	0	107
74.0	1.992084	122	0	112
75.0	1.992084	93	0	101
76.0	1.992084	90	0	89
77.0	1.992084	97	0	108
78.0	1.992084	98	0	97
79.0	1.992084	95	0	90
80.0	1.992084	100	0	104
81.0	1.992084	98	0	91
82.0	1.992084	65	0	73
83.0	1.992084	108	0	107
84.0	1.992084	85	0	72
85.0	1.992084	74	0	84
86.0	1.992084	81	0	78
87.0	1.992084	81	0	86
88.0	1.992084	82	0	76
89.0	1.992084	76	0	77
90.0	1.992084	79	0	76
91.0	1.992084	76	0	87
92.0	1.992084	79	0	66
93.0	1.992084	66	0	71
94.0	1.992084	78	0	67
95.0	1.992084	54	0	54
96.0	1.992084	59	0	63
97.0	1.992084	62	0	65
98.0	1.992084	63	0	64
99.0	1.992084	56	0	57
100.0	1.992084	62	0	58
101.0	0	56	0	56
102.0	0	62	0	67
103.0	0	61	0	55
104.0	0	48	0	47
105.0	0	50	0	55
106.0	0	56	0	46
107.0	0	47	0	52
108.0	0	48	0	53
109.0	0	64	0	53
110.0	0	43	0	47
111.0	0	51	0	45
112.0	0	48	0	45
113.0	0	42	0	51
114.0	0	45	0	45
115.0	0	45	0	41
116.0	0	42	0	40
117.0	0	39	0	33
118.0	0	36	0	49
119.0	0	41	0	45
120.0	0	42	0	34
121.0	0	41	0	53
122.0	0	47	0	47
123.0	0	42	0	28
124.0	0	31	0	33
125.0	0	41	0	35
126.0	0	40	0	45
127.0	0	33	0	35
128.0	0	44	0	53
129.0	0	46	0	33
130.0	0	32	0	39
131.0	0	34	0	37
132.0	0	43	0	32
133.0	0	35	0	49
134.0	0	38	0	31
135.0	0	37	0	33
136.0	0	29	0	27
137.0	0	22	0	35
138.0	0	46	0	34
139.0	0	32	0	30
140.0	0	22	0	23
141.0	0	27	0	32
142.0	0	31	0	23
143.0	0	26	0	23
144.0	0	27	0	28
145.0	0	21	0	23
146.0	0	24	0	25
147.0	0	22	0	24
148.0	0	28	0	25
149.0	0	29	0	29
150.0	0	20	0	29
151.0	0	30	0	27
152.0	0	33	0	24
153.0	0	17	0	28
154.0	0	24	0	22
155.0	0	31	0	25
156.0	0	22	0	23
157.0	0	32	0	32
158.0	0	14	0	17
159.0	0	29	0	30
160.0	0	27	0	25
161.0	0	29	0	25
162.0	0	20	0	20
163.0	0	24	0	21
164.0	0	16	0	14
165.0	0	16	0	23
166.0	0	21	0	13
167.0	0	16	0	23
168.0	0	20	0	21
169.0	0	22	0	20
170.0	0	17	0	23
171.0	0	25	0	19
172.0	0	18	0	19
173.0	0	14	0	21
174.0	0	22	0	14
175.0	0	24	0	30
176.0	0	14	0	14
177.0	0	20	0	12
178.0	0	24	0	24
179.0	0	19	0	15
180.0	0	16	0	25
181.0	0	17	0	15
182.0	0	22	0	19
183.0	0	17	0	17
184.0	0	14	0	13
185.0	0	14	0	11
186.0	0	13	0	22
187.0	0	18	0	8
188.0	0	10	0	15
189.0	0	16	0	14
190.0	0	12	0	17
191.0	0	12	0	13
192.0	0	15	0	9
193.0	0	15	0	21
194.0	0	17	0	14
195.0	0	15	0	14
196.0	0	13	0	11
197.0	0	12	0	13
198.0	0	11	0	15
199.0	0	14	0	9
200.0	0	15	0	11
201.0	0	8	0	9
202.0	0	10	0	15
203.0	0	11	0	5
204.0	0	6	0	15
205.0	0	13	0	9
206.0	0	13	0	10
207.0	0	9	0	10
208.0	0	8	0	11
209.0	0	13	0	13
210.0	0	11	0	9
211.0	0	15	0	11
212.0	0	8	0	14
213.0	0	10	0	8
214.0	0	13	0	18
215.0	0	17	0	11
216.0	0	11	0	10
217.0	0	8	0	7
218.0	0	15	0	14
219.0	0	7	0	5
220.0	0	8	0	16
221.0	0	12	0	6
222.0	0	12	0	16
223.0	0	12	0	18
224.0	0	15	0	13
225.0	0	11	0	8
226.0	0	7	0	6
227.0	0	13	0	14
228.0	0	13	0	7
229.0	0	4	0	6
230.0	0	12	0	15
231.0	0	14	0	9
232.0	0	9	0	10
233.0	0	8	0	10
234.0	0	9	0	6
235.0	0	4	0	7
236.0	0	13	0	6
237.0	0	4	0	6
238.0	0	7	0	11
239.0	0	11	0	10
240.0	0	9	0	11
241.0	0	12	0	15
242.0	0	9	0	7
243.0	0	8	0	10
244.0	0	10	0	6
245.0	0	8	0	9
246.0	0	10	0	5
247.0	0	7	0	8
248.0	0	6	0	8
249.0	0	7	0	11
250.0	0	10	0	5
251.0	0	5	0	4
252.0	0	4	0	4
253.0	0	9	0	6
254.0	0	5	0	7
255.0	0	4	0	4
256.0	0	6	0	12
257.0	0	12	0	10
258.0	0	6	0	8
259.0	0	10	0	9
260.0	0	5	0	5
261.0	0	6	0	10
262.0	0	11	0	8
263.0	0	12	0	6
264.0	0	5	0	4
265.0	0	4	0	4
266.0	0	7	0	9
267.0	0	6	0	6
268.0	0	8	0	9
269.0	0	5	0	12
270.0	0	9	0	7
271.0	0	7	0	3
272.0	0	4	0	3
273.0	0	9	0	5
274.0	0	4	0	6
275.0	0	3	0	7
276.0	0	3	0	3
277.0	0	4	0	4
278.0	0	7	0	7
279.0	0	7	0	2
280.0	0	4	0	10
281.0	0	6	0	5
282.0	0	4	0	5
283.0	0	8	0	4
284.0	0	3	0	7
285.0	0	7	0	10
286.0	0	12	0	6
287.0	0	5	0	9
288.0	0	7	0	7
289.0	0	5	0	3
290.0	0	7	0	5
291.0	0	4	0	5
292.0	0	6	0	7
293.0	0	6	0	4
294.0	0	8	0	6
295.0	0	5	0	8
296.0	0	4	0	8
297.0	0	9	0	2
298.0	0	5	0	5
299.0	0	4	0	5
300.0	0	5	0	7
301.0	0	4	0	6
302.0	0	8	0	6
303.0	0	4	0	3
304.0	0	3	0	1
305.0	0	4	0	4
306.0	0	4	0	3
307.0	0	4	0	7
308.0	0	2	0	4
309.0	0	6	0	3
310.0	0	6	0	6
311.0	0	5	0	2
312.0	0	2	0	5
313.0	0	8	0	3
314.0	0	2	0	6
315.0	0	4	0	2
316.0	0	0	0	4
317.0	0	4	0	3
318.0	0	8	0	4
319.0	0	2	0	9
320.0	0	6	0	2
321.0	0	2	0	5
322.0	0	6	0	4
323.0	0	2	0	2
324.0	0	1	0	1
325.0	0	5	0	3
326.0	0	0	0	1
327.0	0	6	0	5
328.0	0	1	0	2
329.0	0	4	0	7
330.0	0	6	0	7
331.0	0	6	0	5
332.0	0	8	0	5
333.0	0	4	0	8
334.0	0	6	0	3
335.0	0	2	0	2
336.0	0	4	0	4
337.0	0	7	0	3
338.0	0	6	0	6
339.0	0	4	0	5
340.0	0	1	0	1
341.0	0	1	0	1
342.0	0	0	0	6
343.0	0	6	0	3
344.0	0	4	0	4
345.0	0	6	0	4
346.0	0	4	0	2
347.0	0	2	0	5
348.0	0	3	0	2
349.0	0	6	0	4
351.0	0	2	0	4
352.0	0	4	0	0
353.0	0	0	0	1
354.0	0	1	0	3
355.0	0	3	0	3
356.0	0	1	0	2
357.0	0	1	0	0
358.0	0	3	0	4
359.0	0	3	0	1
360.0	0	5	0	4
361.0	0	1	0	3
362.0	0	2	0	2
363.0	0	3	0	9
364.0	0	10	0	3
365.0	0	2	0	2
366.0	0	1	0	7
367.0	0	4	0	3
368.0	0	6	0	5
369.0	0	3	0	1
370.0	0	2	0	1
371.0	0	3	0	1
372.0	0	2	0	3
373.0	0	0	0	3
374.0	0	3	0	3
375.0	0	2	0	3
376.0	0	2	0	5
377.0	0	6	0	2
378.0	0	3	0	5
379.0	0	2	0	3
380.0	0	3	0	0
381.0	0	4	0	0
382.0	0	2	0	3
383.0	0	0	0	2
384.0	0	2	0	3
385.0	0	3	0	3
386.0	0	5	0	1
387.0	0	1	0	3
388.0	0	2	0	3
389.0	0	0	0	2
390.0	0	3	0	0
391.0	0	2	0	2
392.0	0	2	0	4
393.0	0	5	0	1
394.0	0	1	0	4
395.0	0	1	0	0
396.0	0	2	0	2
397.0	0	1	0	2
398.0	0	1	0	4
399.0	0	2	0	1
400.0	0	5	0	2
401.0	0	2	0	2
402.0	0	2	0	2
403.0	0	2	0	2
404.0	0	2	0	2
405.0	0	2	0	3
406.0	0	2	0	2
407.0	0	2	0	3
408.0	0	4	0	1
409.0	0	2	0	0
411.0	0	1	0	3
412.0	0	0	0	2
413.0	0	3	0	0
414.0	0	1	0	3
415.0	0	1	0	3
416.0	0	3	0	2
417.0	0	2	0	0
418.0	0	3	0	2
419.0	0	1	0	1
420.0	0	0	0	2
421.0	0	2	0	2
422.0	0	2	0	2
423.0	0	3	0	0
424.0	0	0	0	1
425.0	0	0	0	4
426.0	0	2	0	2
427.0	0	3	0	1
428.0	0	1	0	4
429.0	0	4	0	4
430.0	0	3	0	4
431.0	0	1	0	2
432.0	0	5	0	0
433.0	0	3	0	1
434.0	0	3	0	7
435.0	0	4	0	4
436.0	0	2	0	0
437.0	0	1	0	2
438.0	0	1	0	2
439.0	0	2	0	1
440.0	0	2	0	1
441.0	0	2	0	0
442.0	0	1	0	3
443.0	0	2	0	2
444.0	0	1	0	1
445.0	0	4	0	1
446.0	0	0	0	1
447.0	0	1	0	0
449.0	0	1	0	1
450.0	0	0	0	1
451.0	0	0	0	2
452.0	0	2	0	1
453.0	0	1	0	2
454.0	0	0	0	2
455.0	0	2	0	4
456.0	0	5	0	7
457.0	0	4	0	2
458.0	0	4	0	0
459.0	0	2	0	6
460.0	0	2	0	1
461.0	0	4	0	1
462.0	0	3	0	2
464.0	0	1	0	1
465.0	0	1	0	0
466.0	0	0	0	1
467.0	0	2	0	1
468.0	0	0	0	2
469.0	0	2	0	2
470.0	0	3	0	2
471.0	0	2	0	1
472.0	0	0	0	2
473.0	0	2	0	3
474.0	0	4	0	0
475.0	0	0	0	1
476.0	0	1	0	1
477.0	0	0	0	2
479.0	0	2	0	1
480.0	0	1	0	1
481.0	0	2	0	1
482.0	0	0	0	2
483.0	0	0	0	1
484.0	0	1	0	2
485.0	0	4	0	2
486.0	0	0	0	2
487.0	0	3	0	1
489.0	0	1	0	0
490.0	0	2	0	2
491.0	0	0	0	2
492.0	0	1	0	2
493.0	0	2	0	3
494.0	0	3	0	4
495.0	0	3	0	0
496.0	0	2	0	0
497.0	0	2	0	1
500.0	0	2	0	1
501.0	0	0	0	1
502.0	0	0	0	2
503.0	0	2	0	1
504.0	0	3	0	1
505.0	0	1	0	3
506.0	0	2	0	3
507.0	0	1	0	3
508.0	0	2	0	1
509.0	0	1	0	1
510.0	0	2	0	1
511.0	0	2	0	1
512.0	0	0	0	1
513.0	0	2	0	1
514.0	0	0	0	1
515.0	0	1	0	2
516.0	0	2	0	0
517.0	0	2	0	1
518.0	0	1	0	0
519.0	0	0	0	1
520.0	0	1	0	1
521.0	0	1	0	0
522.0	0	1	0	0
523.0	0	0	0	1
524.0	0	1	0	1
525.0	0	1	0	1
527.0	0	1	0	0
529.0	0	0	0	1
530.0	0	1	0	1
531.0	0	1	0	2
532.0	0	0	0	2
534.0	0	0	0	1
535.0	0	3	0	1
537.0	0	2	0	0
538.0	0	1	0	3
539.0	0	0	0	1
540.0	0	0	0	1
541.0	0	3	0	3
542.0	0	2	0	0
543.0	0	2	0	1
544.0	0	1	0	0
545.0	0	0	0	1
546.0	0	2	0	1
547.0	0	0	0	1
548.0	0	1	0	0
549.0	0	1	0	1
550.0	0	1	0	2
551.0	0	0	0	1
552.0	0	2	0	1
554.0	0	0	0	1
555.0	0	1	0	3
556.0	0	1	0	0
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