## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S3F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S3F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S3F.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 12:09:06 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	1693801	16950990	8900233	7649415	865971	5274478	63702	0.320682	21385521

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.002473	10271499	0	10309135
2.0	1.456241	1014367	57156	983944
3.0	1.661639	176452	1639	171164
4.0	1.754612	60532	377	59526
5.0	1.796696	30831	166	30467
6.0	1.815746	19417	85	19333
7.0	1.824368	13372	38	13244
8.0	1.828271	10073	28	10033
9.0	1.830038	7824	15	7819
10.0	1.830838	6401	8	6330
11.0	1.8312	5135	9	5124
12.0	1.831364	4347	4	4326
13.0	1.831438	3735	3	3741
14.0	1.831471	3318	4	3297
15.0	1.831487	2847	0	2863
16.0	1.831493	2628	4	2601
17.0	1.831497	2283	2	2283
18.0	1.831498	2082	1	2066
19.0	1.831499	1902	1	1913
20.0	1.831499	1712	2	1689
21.0	1.831499	1567	0	1576
22.0	1.831499	1466	0	1441
23.0	1.831499	1320	1	1310
24.0	1.831499	1213	1	1227
25.0	1.831499	1158	0	1171
26.0	1.831499	1055	0	1054
27.0	1.831499	1008	0	971
28.0	1.831499	953	0	956
29.0	1.831499	910	0	907
30.0	1.831499	893	0	877
31.0	1.831499	698	0	707
32.0	1.831499	686	0	691
33.0	1.831499	695	0	679
34.0	1.831499	684	0	691
35.0	1.831499	622	0	600
36.0	1.831499	576	0	590
37.0	1.831499	550	0	537
38.0	1.831499	476	0	488
39.0	1.831499	480	0	473
40.0	1.831499	472	0	470
41.0	1.831499	459	0	480
42.0	1.831499	491	0	471
43.0	1.831499	383	0	373
44.0	1.831499	410	0	412
45.0	1.831499	395	0	414
46.0	1.831499	387	0	384
47.0	1.831499	324	0	315
48.0	1.831499	351	0	338
49.0	1.831499	344	0	357
50.0	1.831499	323	0	310
51.0	1.831499	304	0	312
52.0	1.831499	315	0	294
53.0	1.831499	273	0	282
54.0	1.831499	264	0	266
55.0	1.831499	253	0	263
56.0	1.831499	256	0	255
57.0	1.831499	253	0	233
58.0	1.831499	248	0	265
59.0	1.831499	233	0	236
60.0	1.831499	237	0	236
61.0	1.831499	220	0	213
62.0	1.831499	207	0	210
63.0	1.831499	213	0	216
64.0	1.831499	204	0	188
65.0	1.831499	179	0	175
66.0	1.831499	183	0	179
67.0	1.831499	163	0	173
68.0	1.831499	177	0	171
69.0	1.831499	147	0	148
70.0	1.831499	162	0	156
71.0	1.831499	158	0	160
72.0	1.831499	146	0	158
73.0	1.831499	145	0	143
74.0	1.831499	178	0	180
75.0	1.831499	148	0	150
76.0	1.831499	169	0	162
77.0	1.831499	162	0	165
78.0	1.831499	149	0	138
79.0	1.831499	122	0	117
80.0	1.831499	127	0	123
81.0	1.831499	127	0	151
82.0	1.831499	130	0	114
83.0	1.831499	124	0	124
84.0	1.831499	118	0	116
85.0	1.831499	99	0	110
86.0	1.831499	110	0	90
87.0	1.831499	83	0	75
88.0	1.831499	103	0	125
89.0	1.831499	114	0	110
90.0	1.831499	112	0	108
91.0	1.831499	106	0	99
92.0	1.831499	80	0	79
93.0	1.831499	98	0	102
94.0	1.831499	79	0	92
95.0	1.831499	95	0	82
96.0	1.831499	71	0	75
97.0	1.831499	78	0	83
98.0	1.831499	83	0	86
99.0	1.831499	96	0	82
100.0	1.831499	80	0	75
101.0	0	70	0	76
102.0	0	69	0	71
103.0	0	73	0	65
104.0	0	71	0	74
105.0	0	72	0	67
106.0	0	61	0	67
107.0	0	66	0	71
108.0	0	75	0	73
109.0	0	69	0	65
110.0	0	67	0	68
111.0	0	43	0	38
112.0	0	76	0	76
113.0	0	52	0	71
114.0	0	71	0	55
115.0	0	59	0	54
116.0	0	59	0	59
117.0	0	55	0	64
118.0	0	64	0	59
119.0	0	52	0	54
120.0	0	65	0	65
121.0	0	52	0	51
122.0	0	50	0	41
123.0	0	40	0	41
124.0	0	40	0	56
125.0	0	60	0	51
126.0	0	49	0	45
127.0	0	42	0	49
128.0	0	45	0	36
129.0	0	42	0	46
130.0	0	44	0	50
131.0	0	46	0	46
132.0	0	55	0	48
133.0	0	42	0	42
134.0	0	44	0	44
135.0	0	45	0	45
136.0	0	37	0	40
137.0	0	43	0	45
138.0	0	47	0	41
139.0	0	41	0	43
140.0	0	40	0	39
141.0	0	40	0	30
142.0	0	30	0	38
143.0	0	39	0	39
144.0	0	39	0	44
145.0	0	44	0	46
146.0	0	36	0	30
147.0	0	30	0	20
148.0	0	30	0	34
149.0	0	27	0	34
150.0	0	34	0	28
151.0	0	34	0	44
152.0	0	42	0	35
153.0	0	30	0	32
154.0	0	33	0	35
155.0	0	39	0	37
156.0	0	36	0	31
157.0	0	24	0	28
158.0	0	34	0	29
159.0	0	28	0	26
160.0	0	23	0	33
161.0	0	32	0	29
162.0	0	27	0	22
163.0	0	28	0	29
164.0	0	24	0	27
165.0	0	30	0	20
166.0	0	23	0	29
167.0	0	27	0	31
168.0	0	33	0	28
169.0	0	25	0	35
170.0	0	37	0	37
171.0	0	34	0	26
172.0	0	33	0	29
173.0	0	21	0	25
174.0	0	20	0	21
175.0	0	27	0	27
176.0	0	20	0	19
177.0	0	24	0	28
178.0	0	21	0	10
179.0	0	15	0	23
180.0	0	23	0	18
181.0	0	22	0	19
182.0	0	27	0	31
183.0	0	22	0	22
184.0	0	16	0	15
185.0	0	22	0	20
186.0	0	20	0	20
187.0	0	15	0	13
188.0	0	20	0	25
189.0	0	20	0	16
190.0	0	13	0	22
191.0	0	25	0	25
192.0	0	23	0	18
193.0	0	20	0	18
194.0	0	22	0	26
195.0	0	26	0	20
196.0	0	21	0	30
197.0	0	22	0	21
198.0	0	25	0	25
199.0	0	19	0	16
200.0	0	23	0	23
201.0	0	15	0	12
202.0	0	18	0	28
203.0	0	22	0	20
204.0	0	23	0	18
205.0	0	17	0	22
206.0	0	19	0	26
207.0	0	28	0	17
208.0	0	27	0	28
209.0	0	22	0	19
210.0	0	14	0	13
211.0	0	12	0	17
212.0	0	16	0	11
213.0	0	20	0	17
214.0	0	15	0	15
215.0	0	18	0	23
216.0	0	17	0	8
217.0	0	14	0	15
218.0	0	9	0	24
219.0	0	17	0	12
220.0	0	15	0	13
221.0	0	20	0	17
222.0	0	13	0	13
223.0	0	14	0	16
224.0	0	16	0	19
225.0	0	18	0	17
226.0	0	22	0	22
227.0	0	14	0	16
228.0	0	23	0	22
229.0	0	19	0	11
230.0	0	14	0	15
231.0	0	10	0	17
232.0	0	14	0	18
233.0	0	14	0	11
234.0	0	18	0	20
235.0	0	19	0	13
236.0	0	13	0	7
237.0	0	13	0	14
238.0	0	8	0	6
239.0	0	14	0	16
240.0	0	15	0	19
241.0	0	10	0	14
242.0	0	19	0	15
243.0	0	13	0	12
244.0	0	14	0	15
245.0	0	17	0	17
246.0	0	11	0	15
247.0	0	10	0	16
248.0	0	23	0	13
249.0	0	17	0	14
250.0	0	14	0	20
251.0	0	12	0	9
252.0	0	12	0	13
253.0	0	11	0	11
254.0	0	14	0	15
255.0	0	17	0	12
256.0	0	6	0	7
257.0	0	12	0	10
258.0	0	14	0	14
259.0	0	9	0	9
260.0	0	6	0	9
261.0	0	16	0	11
262.0	0	8	0	7
263.0	0	7	0	9
264.0	0	6	0	8
265.0	0	10	0	8
266.0	0	5	0	5
267.0	0	12	0	13
268.0	0	6	0	8
269.0	0	11	0	13
270.0	0	16	0	11
271.0	0	10	0	6
272.0	0	11	0	15
273.0	0	9	0	15
274.0	0	11	0	10
275.0	0	14	0	6
276.0	0	4	0	6
277.0	0	5	0	9
278.0	0	11	0	4
279.0	0	6	0	12
280.0	0	5	0	7
281.0	0	10	0	8
282.0	0	12	0	11
283.0	0	9	0	9
284.0	0	11	0	10
285.0	0	11	0	12
286.0	0	8	0	15
287.0	0	12	0	8
288.0	0	12	0	9
289.0	0	10	0	9
290.0	0	7	0	7
291.0	0	6	0	6
292.0	0	6	0	11
293.0	0	7	0	10
294.0	0	15	0	5
295.0	0	7	0	4
296.0	0	4	0	5
297.0	0	1	0	4
298.0	0	9	0	8
299.0	0	7	0	8
300.0	0	3	0	10
301.0	0	8	0	4
302.0	0	10	0	9
303.0	0	4	0	8
304.0	0	8	0	5
305.0	0	11	0	6
306.0	0	3	0	2
307.0	0	7	0	9
308.0	0	6	0	9
309.0	0	7	0	6
310.0	0	8	0	8
311.0	0	10	0	10
312.0	0	9	0	4
313.0	0	3	0	6
314.0	0	8	0	10
315.0	0	8	0	9
316.0	0	7	0	3
317.0	0	4	0	5
318.0	0	3	0	7
319.0	0	7	0	9
320.0	0	8	0	4
321.0	0	5	0	2
322.0	0	5	0	6
323.0	0	4	0	4
324.0	0	7	0	6
325.0	0	6	0	6
326.0	0	5	0	6
327.0	0	5	0	9
328.0	0	8	0	6
329.0	0	7	0	6
330.0	0	4	0	3
331.0	0	7	0	12
332.0	0	9	0	7
333.0	0	6	0	3
334.0	0	6	0	5
335.0	0	4	0	5
336.0	0	3	0	2
337.0	0	7	0	8
338.0	0	8	0	9
339.0	0	7	0	4
340.0	0	7	0	3
341.0	0	2	0	6
342.0	0	8	0	8
343.0	0	5	0	4
344.0	0	2	0	7
345.0	0	4	0	6
346.0	0	8	0	6
347.0	0	6	0	6
348.0	0	3	0	3
349.0	0	7	0	5
350.0	0	7	0	4
351.0	0	5	0	8
352.0	0	5	0	6
353.0	0	8	0	7
354.0	0	3	0	3
355.0	0	2	0	5
356.0	0	6	0	10
357.0	0	7	0	5
358.0	0	7	0	4
359.0	0	6	0	5
360.0	0	6	0	4
361.0	0	4	0	2
362.0	0	7	0	6
363.0	0	1	0	7
364.0	0	6	0	3
365.0	0	4	0	3
366.0	0	2	0	4
367.0	0	5	0	4
368.0	0	3	0	5
369.0	0	8	0	5
370.0	0	4	0	2
371.0	0	3	0	2
372.0	0	2	0	4
373.0	0	3	0	3
374.0	0	3	0	2
375.0	0	3	0	4
376.0	0	0	0	8
377.0	0	7	0	4
378.0	0	4	0	5
379.0	0	4	0	1
380.0	0	5	0	1
381.0	0	1	0	4
382.0	0	6	0	4
383.0	0	6	0	2
384.0	0	0	0	3
385.0	0	2	0	3
386.0	0	2	0	4
387.0	0	5	0	5
388.0	0	3	0	4
389.0	0	5	0	5
390.0	0	7	0	2
391.0	0	1	0	8
392.0	0	6	0	3
393.0	0	3	0	5
394.0	0	4	0	4
395.0	0	6	0	3
396.0	0	2	0	2
397.0	0	3	0	4
398.0	0	6	0	3
399.0	0	1	0	2
400.0	0	2	0	2
401.0	0	4	0	3
402.0	0	1	0	2
403.0	0	2	0	4
404.0	0	6	0	10
405.0	0	4	0	6
406.0	0	7	0	5
407.0	0	5	0	1
408.0	0	4	0	1
409.0	0	2	0	4
410.0	0	2	0	3
411.0	0	2	0	1
412.0	0	3	0	1
413.0	0	3	0	5
414.0	0	4	0	6
415.0	0	4	0	3
416.0	0	4	0	5
417.0	0	3	0	3
418.0	0	6	0	4
419.0	0	2	0	4
420.0	0	7	0	6
421.0	0	2	0	3
422.0	0	4	0	1
423.0	0	5	0	2
424.0	0	1	0	3
425.0	0	1	0	2
426.0	0	2	0	1
427.0	0	1	0	1
428.0	0	0	0	1
429.0	0	2	0	5
430.0	0	4	0	1
431.0	0	2	0	4
432.0	0	4	0	5
433.0	0	4	0	6
434.0	0	7	0	5
435.0	0	3	0	3
436.0	0	3	0	2
437.0	0	4	0	1
438.0	0	2	0	4
439.0	0	2	0	0
440.0	0	2	0	2
441.0	0	1	0	2
442.0	0	1	0	2
443.0	0	1	0	0
444.0	0	2	0	2
445.0	0	1	0	3
446.0	0	3	0	3
447.0	0	2	0	2
448.0	0	3	0	2
449.0	0	2	0	3
450.0	0	7	0	5
451.0	0	1	0	7
452.0	0	5	0	3
453.0	0	8	0	4
454.0	0	1	0	6
455.0	0	3	0	3
456.0	0	4	0	3
457.0	0	5	0	0
458.0	0	1	0	1
459.0	0	3	0	2
460.0	0	1	0	1
461.0	0	2	0	2
462.0	0	1	0	0
463.0	0	0	0	1
464.0	0	1	0	3
465.0	0	1	0	2
466.0	0	3	0	7
467.0	0	5	0	3
468.0	0	6	0	0
469.0	0	1	0	1
470.0	0	2	0	4
471.0	0	2	0	3
472.0	0	2	0	1
473.0	0	1	0	4
474.0	0	1	0	5
475.0	0	4	0	3
476.0	0	7	0	3
477.0	0	1	0	2
478.0	0	6	0	2
479.0	0	0	0	3
480.0	0	4	0	4
481.0	0	2	0	2
482.0	0	3	0	0
483.0	0	1	0	0
484.0	0	2	0	2
485.0	0	1	0	0
487.0	0	1	0	2
488.0	0	1	0	1
489.0	0	0	0	1
490.0	0	2	0	3
491.0	0	0	0	1
492.0	0	2	0	5
493.0	0	3	0	4
494.0	0	4	0	3
495.0	0	6	0	1
496.0	0	1	0	3
497.0	0	3	0	5
498.0	0	3	0	3
499.0	0	2	0	1
500.0	0	4	0	3
501.0	0	2	0	0
502.0	0	0	0	2
503.0	0	4	0	5
504.0	0	2	0	1
505.0	0	2	0	1
506.0	0	2	0	1
507.0	0	1	0	0
508.0	0	0	0	1
509.0	0	2	0	1
510.0	0	1	0	3
511.0	0	2	0	3
512.0	0	1	0	2
513.0	0	1	0	1
514.0	0	3	0	1
515.0	0	2	0	1
516.0	0	2	0	4
518.0	0	2	0	0
519.0	0	1	0	0
520.0	0	2	0	2
521.0	0	0	0	1
522.0	0	2	0	2
523.0	0	1	0	2
524.0	0	4	0	4
525.0	0	0	0	1
526.0	0	2	0	2
527.0	0	1	0	2
528.0	0	2	0	3
529.0	0	2	0	2
530.0	0	2	0	3
531.0	0	5	0	3
532.0	0	1	0	6
533.0	0	3	0	2
534.0	0	5	0	0
535.0	0	0	0	2
536.0	0	3	0	0
537.0	0	1	0	2
538.0	0	3	0	3
539.0	0	1	0	0
540.0	0	1	0	3
541.0	0	3	0	3
542.0	0	2	0	3
543.0	0	1	0	1
544.0	0	3	0	2
545.0	0	2	0	0
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