## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S19F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S19F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S19F.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 11:28:23 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	2043899	18537661	10352640	8555273	1134613	5952041	86944	0.333307	22474905

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003034	10939637	0	10989594
2.0	1.442679	1188591	76628	1149246
3.0	1.635383	211873	2450	204106
4.0	1.719848	71571	647	70071
5.0	1.75687	36244	233	35789
6.0	1.773097	22531	130	22292
7.0	1.78021	15424	54	15324
8.0	1.783328	11364	43	11256
9.0	1.784694	8765	22	8681
10.0	1.785293	7084	14	7084
11.0	1.785556	5897	9	5840
12.0	1.785671	5008	8	4992
13.0	1.785721	4257	6	4242
14.0	1.785743	3629	6	3619
15.0	1.785753	3158	3	3122
16.0	1.785757	2859	3	2848
17.0	1.785759	2529	5	2525
18.0	1.78576	2243	2	2212
19.0	1.78576	2096	2	2129
20.0	1.785761	1921	1	1883
21.0	1.785761	1694	5	1700
22.0	1.785761	1585	2	1580
23.0	1.785761	1470	3	1455
24.0	1.785761	1315	1	1331
25.0	1.785761	1274	1	1268
26.0	1.785761	1193	3	1177
27.0	1.785761	1161	2	1144
28.0	1.785761	1014	0	1017
29.0	1.785761	953	0	954
30.0	1.785761	941	0	928
31.0	1.785761	815	0	827
32.0	1.785761	796	0	779
33.0	1.785761	745	0	750
34.0	1.785761	662	0	664
35.0	1.785761	671	0	662
36.0	1.785761	641	0	643
37.0	1.785761	604	0	601
38.0	1.785761	546	0	544
39.0	1.785761	573	0	579
40.0	1.785761	517	0	500
41.0	1.785761	514	0	530
42.0	1.785761	494	0	507
43.0	1.785761	466	0	434
44.0	1.785761	432	0	422
45.0	1.785761	386	0	399
46.0	1.785761	416	0	408
47.0	1.785761	394	0	389
48.0	1.785761	379	0	384
49.0	1.785761	377	0	364
50.0	1.785761	343	0	349
51.0	1.785761	356	0	347
52.0	1.785761	299	0	281
53.0	1.785761	253	0	267
54.0	1.785761	304	0	319
55.0	1.785761	263	0	265
56.0	1.785761	272	0	255
57.0	1.785761	247	0	225
58.0	1.785761	225	0	247
59.0	1.785761	247	0	250
60.0	1.785761	265	0	250
61.0	1.785761	202	0	228
62.0	1.785761	228	0	199
63.0	1.785761	228	0	226
64.0	1.785761	216	0	229
65.0	1.785761	206	0	205
66.0	1.785761	227	0	215
67.0	1.785761	187	0	203
68.0	1.785761	185	0	165
69.0	1.785761	161	0	183
70.0	1.785761	211	0	188
71.0	1.785761	159	0	169
72.0	1.785761	170	0	162
73.0	1.785761	170	0	188
74.0	1.785761	166	0	152
75.0	1.785761	140	0	140
76.0	1.785761	170	0	172
77.0	1.785761	164	0	163
78.0	1.785761	134	0	134
79.0	1.785761	147	0	142
80.0	1.785761	145	0	140
81.0	1.785761	117	0	115
82.0	1.785761	129	0	124
83.0	1.785761	119	0	138
84.0	1.785761	116	0	117
85.0	1.785761	130	0	119
86.0	1.785761	123	0	126
87.0	1.785761	104	0	103
88.0	1.785761	106	0	105
89.0	1.785761	125	0	116
90.0	1.785761	111	0	116
91.0	1.785761	117	0	105
92.0	1.785761	97	0	108
93.0	1.785761	101	0	103
94.0	1.785761	101	0	87
95.0	1.785761	84	0	83
96.0	1.785761	103	0	126
97.0	1.785761	108	0	105
98.0	1.785761	93	0	84
99.0	1.785761	106	0	103
100.0	1.785761	79	0	75
101.0	0	78	0	72
102.0	0	71	0	90
103.0	0	102	0	102
104.0	0	108	0	95
105.0	0	92	0	84
106.0	0	71	0	80
107.0	0	69	0	82
108.0	0	80	0	69
109.0	0	83	0	82
110.0	0	66	0	70
111.0	0	71	0	63
112.0	0	73	0	68
113.0	0	70	0	71
114.0	0	60	0	63
115.0	0	85	0	70
116.0	0	51	0	63
117.0	0	48	0	52
118.0	0	66	0	75
119.0	0	78	0	79
120.0	0	70	0	62
121.0	0	59	0	61
122.0	0	57	0	46
123.0	0	56	0	59
124.0	0	55	0	63
125.0	0	64	0	46
126.0	0	44	0	51
127.0	0	50	0	44
128.0	0	42	0	45
129.0	0	54	0	49
130.0	0	46	0	58
131.0	0	48	0	52
132.0	0	42	0	35
133.0	0	41	0	41
134.0	0	52	0	50
135.0	0	43	0	41
136.0	0	41	0	43
137.0	0	43	0	46
138.0	0	45	0	41
139.0	0	41	0	44
140.0	0	42	0	45
141.0	0	47	0	46
142.0	0	53	0	46
143.0	0	37	0	40
144.0	0	42	0	37
145.0	0	34	0	35
146.0	0	40	0	42
147.0	0	41	0	37
148.0	0	37	0	37
149.0	0	36	0	30
150.0	0	29	0	39
151.0	0	39	0	43
152.0	0	49	0	40
153.0	0	35	0	42
154.0	0	39	0	39
155.0	0	33	0	26
156.0	0	26	0	24
157.0	0	31	0	36
158.0	0	28	0	26
159.0	0	42	0	39
160.0	0	25	0	25
161.0	0	29	0	25
162.0	0	23	0	31
163.0	0	39	0	39
164.0	0	31	0	35
165.0	0	32	0	31
166.0	0	35	0	30
167.0	0	30	0	26
168.0	0	25	0	33
169.0	0	29	0	31
170.0	0	23	0	23
171.0	0	28	0	24
172.0	0	36	0	27
173.0	0	27	0	28
174.0	0	21	0	22
175.0	0	20	0	21
176.0	0	26	0	37
177.0	0	29	0	22
178.0	0	23	0	24
179.0	0	30	0	21
180.0	0	26	0	27
181.0	0	24	0	26
182.0	0	26	0	39
183.0	0	37	0	22
184.0	0	27	0	30
185.0	0	25	0	33
186.0	0	27	0	18
187.0	0	19	0	26
188.0	0	24	0	28
189.0	0	27	0	30
190.0	0	25	0	22
191.0	0	32	0	22
192.0	0	21	0	25
193.0	0	20	0	20
194.0	0	19	0	16
195.0	0	24	0	19
196.0	0	20	0	18
197.0	0	19	0	14
198.0	0	13	0	16
199.0	0	15	0	26
200.0	0	19	0	19
201.0	0	29	0	26
202.0	0	18	0	22
203.0	0	18	0	19
204.0	0	28	0	18
205.0	0	20	0	22
206.0	0	13	0	11
207.0	0	18	0	20
208.0	0	13	0	21
209.0	0	20	0	21
210.0	0	19	0	12
211.0	0	17	0	14
212.0	0	15	0	13
213.0	0	15	0	25
214.0	0	19	0	14
215.0	0	24	0	23
216.0	0	20	0	18
217.0	0	21	0	25
218.0	0	14	0	22
219.0	0	23	0	19
220.0	0	25	0	21
221.0	0	14	0	11
222.0	0	15	0	16
223.0	0	19	0	19
224.0	0	18	0	11
225.0	0	14	0	23
226.0	0	16	0	6
227.0	0	11	0	16
228.0	0	16	0	14
229.0	0	13	0	15
230.0	0	13	0	19
231.0	0	14	0	22
232.0	0	24	0	12
233.0	0	16	0	13
234.0	0	15	0	15
235.0	0	12	0	17
236.0	0	17	0	15
237.0	0	19	0	15
238.0	0	13	0	16
239.0	0	13	0	19
240.0	0	17	0	10
241.0	0	14	0	12
242.0	0	9	0	9
243.0	0	13	0	11
244.0	0	12	0	9
245.0	0	8	0	12
246.0	0	15	0	17
247.0	0	9	0	15
248.0	0	13	0	14
249.0	0	24	0	10
250.0	0	8	0	6
251.0	0	15	0	19
252.0	0	10	0	12
253.0	0	5	0	10
254.0	0	14	0	15
255.0	0	19	0	14
256.0	0	8	0	10
257.0	0	13	0	12
258.0	0	6	0	10
259.0	0	14	0	15
260.0	0	9	0	7
261.0	0	14	0	11
262.0	0	11	0	12
263.0	0	10	0	14
264.0	0	18	0	17
265.0	0	12	0	9
266.0	0	9	0	8
267.0	0	9	0	8
268.0	0	8	0	7
269.0	0	4	0	11
270.0	0	11	0	10
271.0	0	11	0	14
272.0	0	12	0	13
273.0	0	11	0	5
274.0	0	15	0	9
275.0	0	6	0	5
276.0	0	6	0	8
277.0	0	7	0	13
278.0	0	9	0	8
279.0	0	13	0	9
280.0	0	7	0	7
281.0	0	12	0	12
282.0	0	9	0	11
283.0	0	10	0	7
284.0	0	7	0	9
285.0	0	12	0	9
286.0	0	8	0	9
287.0	0	10	0	7
288.0	0	7	0	14
289.0	0	8	0	3
290.0	0	7	0	15
291.0	0	11	0	6
292.0	0	10	0	16
293.0	0	12	0	7
294.0	0	15	0	12
295.0	0	7	0	8
296.0	0	11	0	11
297.0	0	9	0	9
298.0	0	8	0	7
299.0	0	9	0	15
300.0	0	13	0	7
301.0	0	12	0	10
302.0	0	4	0	11
303.0	0	14	0	9
304.0	0	8	0	6
305.0	0	7	0	7
306.0	0	7	0	6
307.0	0	7	0	7
308.0	0	6	0	9
309.0	0	9	0	10
310.0	0	6	0	5
311.0	0	4	0	6
312.0	0	11	0	4
313.0	0	5	0	5
314.0	0	6	0	11
315.0	0	6	0	7
316.0	0	4	0	8
317.0	0	14	0	8
318.0	0	4	0	6
319.0	0	8	0	9
320.0	0	15	0	12
321.0	0	6	0	10
322.0	0	6	0	8
323.0	0	8	0	6
324.0	0	10	0	8
325.0	0	11	0	9
326.0	0	7	0	8
327.0	0	7	0	5
328.0	0	5	0	9
329.0	0	9	0	7
330.0	0	10	0	10
331.0	0	5	0	3
332.0	0	5	0	5
333.0	0	7	0	8
334.0	0	7	0	2
335.0	0	6	0	13
336.0	0	8	0	9
337.0	0	5	0	3
338.0	0	8	0	9
339.0	0	6	0	4
340.0	0	4	0	5
341.0	0	7	0	4
342.0	0	6	0	5
343.0	0	5	0	5
344.0	0	4	0	8
345.0	0	4	0	4
346.0	0	5	0	4
347.0	0	5	0	5
348.0	0	7	0	5
349.0	0	7	0	8
350.0	0	5	0	5
351.0	0	4	0	4
352.0	0	11	0	9
353.0	0	1	0	2
354.0	0	7	0	4
355.0	0	5	0	8
356.0	0	6	0	6
357.0	0	4	0	6
358.0	0	5	0	5
359.0	0	11	0	7
360.0	0	5	0	11
361.0	0	5	0	6
362.0	0	9	0	5
363.0	0	7	0	5
364.0	0	5	0	8
365.0	0	3	0	5
366.0	0	6	0	3
367.0	0	6	0	6
368.0	0	6	0	4
369.0	0	4	0	5
370.0	0	10	0	7
371.0	0	4	0	3
372.0	0	2	0	3
373.0	0	6	0	6
374.0	0	4	0	4
375.0	0	4	0	6
376.0	0	4	0	6
377.0	0	4	0	5
378.0	0	8	0	2
379.0	0	3	0	3
380.0	0	3	0	4
381.0	0	3	0	4
382.0	0	4	0	5
383.0	0	4	0	5
384.0	0	2	0	4
385.0	0	5	0	4
386.0	0	4	0	5
387.0	0	3	0	6
388.0	0	8	0	2
389.0	0	6	0	7
390.0	0	2	0	2
391.0	0	3	0	4
392.0	0	4	0	3
393.0	0	5	0	4
394.0	0	4	0	3
395.0	0	3	0	5
396.0	0	6	0	5
397.0	0	7	0	7
398.0	0	5	0	4
399.0	0	6	0	4
400.0	0	2	0	3
401.0	0	4	0	6
402.0	0	5	0	4
403.0	0	4	0	1
404.0	0	3	0	1
405.0	0	1	0	3
406.0	0	2	0	5
407.0	0	3	0	3
408.0	0	1	0	6
409.0	0	6	0	4
410.0	0	2	0	4
411.0	0	4	0	5
412.0	0	3	0	3
413.0	0	5	0	2
414.0	0	5	0	5
415.0	0	4	0	2
416.0	0	3	0	2
417.0	0	2	0	3
418.0	0	3	0	1
419.0	0	4	0	3
420.0	0	3	0	1
421.0	0	1	0	4
422.0	0	2	0	1
423.0	0	3	0	4
424.0	0	2	0	0
425.0	0	1	0	3
426.0	0	3	0	6
427.0	0	3	0	2
428.0	0	4	0	3
429.0	0	2	0	3
430.0	0	2	0	3
431.0	0	3	0	4
432.0	0	5	0	2
433.0	0	4	0	2
434.0	0	3	0	2
435.0	0	1	0	2
436.0	0	4	0	7
437.0	0	3	0	3
438.0	0	6	0	5
439.0	0	2	0	3
440.0	0	3	0	3
441.0	0	6	0	2
442.0	0	2	0	4
443.0	0	3	0	1
444.0	0	1	0	6
445.0	0	5	0	3
446.0	0	6	0	6
447.0	0	2	0	3
448.0	0	2	0	5
449.0	0	6	0	4
450.0	0	3	0	0
451.0	0	2	0	1
452.0	0	4	0	3
453.0	0	1	0	4
454.0	0	4	0	2
455.0	0	2	0	5
456.0	0	3	0	2
457.0	0	1	0	2
458.0	0	5	0	7
459.0	0	4	0	2
460.0	0	3	0	3
461.0	0	3	0	4
462.0	0	1	0	4
463.0	0	5	0	4
464.0	0	2	0	1
465.0	0	6	0	4
466.0	0	4	0	1
467.0	0	1	0	2
468.0	0	2	0	4
469.0	0	1	0	2
470.0	0	3	0	2
471.0	0	4	0	2
472.0	0	2	0	2
473.0	0	2	0	3
474.0	0	4	0	3
475.0	0	1	0	2
476.0	0	4	0	1
477.0	0	2	0	2
478.0	0	0	0	3
479.0	0	1	0	1
480.0	0	2	0	2
481.0	0	3	0	3
482.0	0	2	0	5
483.0	0	4	0	5
484.0	0	3	0	2
485.0	0	3	0	3
486.0	0	3	0	4
487.0	0	3	0	3
488.0	0	6	0	4
489.0	0	3	0	4
490.0	0	4	0	2
491.0	0	2	0	2
492.0	0	3	0	2
493.0	0	2	0	3
494.0	0	3	0	1
495.0	0	2	0	3
496.0	0	3	0	1
497.0	0	3	0	4
498.0	0	2	0	3
499.0	0	3	0	3
500.0	0	2	0	4
501.0	0	5	0	5
502.0	0	3	0	0
503.0	0	2	0	8
504.0	0	1	0	4
505.0	0	4	0	3
506.0	0	6	0	3
507.0	0	7	0	0
508.0	0	4	0	1
509.0	0	1	0	3
510.0	0	1	0	2
511.0	0	2	0	3
512.0	0	3	0	2
513.0	0	3	0	5
514.0	0	1	0	3
515.0	0	3	0	1
516.0	0	1	0	2
517.0	0	4	0	2
518.0	0	2	0	0
519.0	0	2	0	2
520.0	0	2	0	1
521.0	0	1	0	2
522.0	0	1	0	2
523.0	0	2	0	4
524.0	0	2	0	1
525.0	0	2	0	1
526.0	0	1	0	3
527.0	0	2	0	1
528.0	0	2	0	1
529.0	0	1	0	1
530.0	0	2	0	3
531.0	0	3	0	3
532.0	0	0	0	4
533.0	0	3	0	2
534.0	0	1	0	1
535.0	0	4	0	1
536.0	0	3	0	2
537.0	0	1	0	1
538.0	0	2	0	2
539.0	0	1	0	2
540.0	0	1	0	2
541.0	0	1	0	2
542.0	0	3	0	0
543.0	0	1	0	1
544.0	0	2	0	1
545.0	0	2	0	2
546.0	0	1	0	2
547.0	0	1	0	2
548.0	0	2	0	2
549.0	0	1	0	1
550.0	0	2	0	4
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