## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S22F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S22F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S22F.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 11:33:12 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	2412537	21779737	12621048	9985615	1357370	6741744	112708	0.322824	27742761

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003425	12823888	0	12888775
2.0	1.46108	1563618	101725	1514351
3.0	1.669812	310602	2703	299711
4.0	1.765014	110290	591	107837
5.0	1.808434	55709	231	54886
6.0	1.828238	34056	106	33696
7.0	1.837271	22639	50	22367
8.0	1.84139	16324	50	16223
9.0	1.843269	12244	25	12104
10.0	1.844126	9546	18	9477
11.0	1.844517	7826	13	7787
12.0	1.844695	6397	12	6357
13.0	1.844776	5436	6	5351
14.0	1.844814	4538	6	4595
15.0	1.84483	3917	2	3805
16.0	1.844838	3300	4	3304
17.0	1.844842	2980	2	2979
18.0	1.844843	2576	1	2545
19.0	1.844844	2432	5	2413
20.0	1.844844	2050	1	2069
21.0	1.844845	1886	3	1837
22.0	1.844845	1719	1	1716
23.0	1.844845	1555	0	1546
24.0	1.844845	1494	0	1492
25.0	1.844845	1319	0	1303
26.0	1.844845	1170	2	1162
27.0	1.844845	1092	1	1089
28.0	1.844845	1084	3	1086
29.0	1.844845	966	1	963
30.0	1.844845	866	2	856
31.0	1.844845	895	2	883
32.0	1.844845	784	0	761
33.0	1.844845	761	1	770
34.0	1.844845	743	2	745
35.0	1.844845	679	0	645
36.0	1.844845	606	2	613
37.0	1.844845	549	0	567
38.0	1.844845	573	0	591
39.0	1.844845	562	0	537
40.0	1.844845	512	0	512
41.0	1.844845	509	0	501
42.0	1.844845	488	1	480
43.0	1.844845	431	1	438
44.0	1.844845	437	0	435
45.0	1.844845	368	0	349
46.0	1.844845	370	1	375
47.0	1.844845	378	0	377
48.0	1.844845	351	0	351
49.0	1.844845	315	0	305
50.0	1.844845	313	0	301
51.0	1.844845	280	0	295
52.0	1.844845	306	0	305
53.0	1.844845	273	0	278
54.0	1.844845	281	0	272
55.0	1.844845	249	0	267
56.0	1.844845	288	0	273
57.0	1.844845	273	0	281
58.0	1.844845	221	0	213
59.0	1.844845	223	0	215
60.0	1.844845	218	0	217
61.0	1.844845	216	0	206
62.0	1.844845	199	0	201
63.0	1.844845	166	0	175
64.0	1.844845	192	0	182
65.0	1.844845	194	0	196
66.0	1.844845	180	0	184
67.0	1.844845	201	0	188
68.0	1.844845	157	0	147
69.0	1.844845	163	0	176
70.0	1.844845	154	0	152
71.0	1.844845	155	0	149
72.0	1.844845	142	0	149
73.0	1.844845	129	0	144
74.0	1.844845	149	0	134
75.0	1.844845	147	0	152
76.0	1.844845	132	0	128
77.0	1.844845	144	0	130
78.0	1.844845	118	0	119
79.0	1.844845	121	0	121
80.0	1.844845	130	0	133
81.0	1.844845	112	0	110
82.0	1.844845	108	0	102
83.0	1.844845	109	0	119
84.0	1.844845	112	0	98
85.0	1.844845	104	0	109
86.0	1.844845	98	0	104
87.0	1.844845	116	0	106
88.0	1.844845	92	0	100
89.0	1.844845	98	0	103
90.0	1.844845	90	0	96
91.0	1.844845	109	0	93
92.0	1.844845	99	0	99
93.0	1.844845	80	0	82
94.0	1.844845	91	0	85
95.0	1.844845	88	0	98
96.0	1.844845	81	0	90
97.0	1.844845	96	0	80
98.0	1.844845	77	0	72
99.0	1.844845	80	0	85
100.0	1.844845	86	0	83
101.0	0	68	0	66
102.0	0	62	0	66
103.0	0	70	0	62
104.0	0	76	0	88
105.0	0	62	0	58
106.0	0	66	0	62
107.0	0	66	0	69
108.0	0	75	0	79
109.0	0	55	0	51
110.0	0	75	0	60
111.0	0	47	0	55
112.0	0	71	0	77
113.0	0	71	0	71
114.0	0	65	0	56
115.0	0	51	0	56
116.0	0	57	0	56
117.0	0	49	0	59
118.0	0	69	0	53
119.0	0	51	0	52
120.0	0	56	0	56
121.0	0	46	0	55
122.0	0	60	0	55
123.0	0	54	0	52
124.0	0	55	0	54
125.0	0	43	0	45
126.0	0	61	0	55
127.0	0	41	0	49
128.0	0	51	0	47
129.0	0	41	0	37
130.0	0	43	0	49
131.0	0	41	0	46
132.0	0	55	0	42
133.0	0	40	0	40
134.0	0	45	0	41
135.0	0	34	0	40
136.0	0	34	0	38
137.0	0	33	0	31
138.0	0	34	0	39
139.0	0	49	0	48
140.0	0	33	0	29
141.0	0	43	0	40
142.0	0	32	0	35
143.0	0	42	0	44
144.0	0	41	0	35
145.0	0	37	0	34
146.0	0	23	0	28
147.0	0	40	0	34
148.0	0	32	0	42
149.0	0	40	0	46
150.0	0	44	0	29
151.0	0	28	0	43
152.0	0	39	0	32
153.0	0	42	0	36
154.0	0	31	0	29
155.0	0	33	0	32
156.0	0	26	0	28
157.0	0	25	0	26
158.0	0	29	0	40
159.0	0	48	0	30
160.0	0	30	0	35
161.0	0	37	0	36
162.0	0	29	0	26
163.0	0	25	0	33
164.0	0	31	0	24
165.0	0	25	0	31
166.0	0	30	0	30
167.0	0	31	0	26
168.0	0	19	0	21
169.0	0	36	0	30
170.0	0	27	0	29
171.0	0	22	0	28
172.0	0	27	0	20
173.0	0	27	0	30
174.0	0	22	0	20
175.0	0	28	0	32
176.0	0	24	0	30
177.0	0	34	0	24
178.0	0	18	0	26
179.0	0	25	0	26
180.0	0	26	0	20
181.0	0	24	0	28
182.0	0	27	0	19
183.0	0	15	0	22
184.0	0	25	0	20
185.0	0	29	0	27
186.0	0	16	0	19
187.0	0	23	0	20
188.0	0	16	0	15
189.0	0	19	0	22
190.0	0	20	0	20
191.0	0	22	0	29
192.0	0	26	0	16
193.0	0	20	0	24
194.0	0	16	0	11
195.0	0	16	0	12
196.0	0	15	0	12
197.0	0	15	0	21
198.0	0	15	0	10
199.0	0	19	0	20
200.0	0	11	0	13
201.0	0	16	0	10
202.0	0	13	0	22
203.0	0	11	0	25
204.0	0	21	0	14
205.0	0	22	0	17
206.0	0	15	0	14
207.0	0	16	0	9
208.0	0	14	0	18
209.0	0	14	0	16
210.0	0	17	0	16
211.0	0	13	0	12
212.0	0	13	0	10
213.0	0	7	0	10
214.0	0	18	0	16
215.0	0	16	0	22
216.0	0	17	0	10
217.0	0	16	0	20
218.0	0	12	0	16
219.0	0	21	0	23
220.0	0	19	0	11
221.0	0	13	0	15
222.0	0	8	0	10
223.0	0	19	0	11
224.0	0	10	0	12
225.0	0	9	0	10
226.0	0	17	0	17
227.0	0	10	0	14
228.0	0	12	0	14
229.0	0	20	0	19
230.0	0	15	0	8
231.0	0	12	0	15
232.0	0	13	0	9
233.0	0	8	0	10
234.0	0	8	0	7
235.0	0	12	0	15
236.0	0	11	0	12
237.0	0	8	0	11
238.0	0	19	0	14
239.0	0	8	0	12
240.0	0	14	0	11
241.0	0	10	0	12
242.0	0	11	0	11
243.0	0	10	0	15
244.0	0	14	0	11
245.0	0	16	0	15
246.0	0	11	0	16
247.0	0	18	0	12
248.0	0	11	0	12
249.0	0	10	0	11
250.0	0	20	0	14
251.0	0	14	0	11
252.0	0	4	0	7
253.0	0	8	0	6
254.0	0	5	0	4
255.0	0	11	0	11
256.0	0	6	0	7
257.0	0	10	0	6
258.0	0	9	0	11
259.0	0	8	0	9
260.0	0	9	0	11
261.0	0	9	0	8
262.0	0	9	0	10
263.0	0	8	0	7
264.0	0	6	0	11
265.0	0	8	0	10
266.0	0	8	0	9
267.0	0	15	0	7
268.0	0	12	0	14
269.0	0	10	0	12
270.0	0	11	0	8
271.0	0	6	0	12
272.0	0	10	0	8
273.0	0	8	0	5
274.0	0	11	0	10
275.0	0	8	0	11
276.0	0	9	0	5
277.0	0	9	0	11
278.0	0	6	0	3
279.0	0	10	0	9
280.0	0	5	0	3
281.0	0	5	0	8
282.0	0	5	0	11
283.0	0	9	0	4
284.0	0	14	0	7
285.0	0	5	0	7
286.0	0	7	0	11
287.0	0	4	0	9
288.0	0	11	0	12
289.0	0	8	0	3
290.0	0	9	0	3
291.0	0	5	0	11
292.0	0	5	0	8
293.0	0	9	0	12
294.0	0	6	0	3
295.0	0	10	0	12
296.0	0	9	0	4
297.0	0	8	0	10
298.0	0	8	0	8
299.0	0	5	0	4
300.0	0	7	0	5
301.0	0	9	0	7
302.0	0	2	0	4
303.0	0	5	0	8
304.0	0	9	0	3
305.0	0	6	0	7
306.0	0	2	0	4
307.0	0	5	0	3
308.0	0	5	0	5
309.0	0	7	0	8
310.0	0	2	0	3
311.0	0	9	0	7
312.0	0	5	0	6
313.0	0	6	0	4
314.0	0	3	0	9
315.0	0	10	0	4
316.0	0	7	0	6
317.0	0	6	0	7
318.0	0	1	0	5
319.0	0	5	0	7
320.0	0	3	0	4
321.0	0	13	0	5
322.0	0	3	0	6
323.0	0	5	0	5
324.0	0	4	0	8
325.0	0	6	0	4
326.0	0	7	0	5
327.0	0	8	0	9
328.0	0	5	0	5
329.0	0	4	0	5
330.0	0	10	0	7
331.0	0	5	0	7
332.0	0	7	0	6
333.0	0	2	0	4
334.0	0	8	0	7
335.0	0	6	0	8
336.0	0	4	0	7
337.0	0	11	0	4
338.0	0	6	0	2
339.0	0	1	0	4
340.0	0	2	0	5
341.0	0	4	0	5
342.0	0	6	0	5
343.0	0	6	0	4
344.0	0	4	0	4
345.0	0	4	0	6
346.0	0	3	0	6
347.0	0	7	0	7
348.0	0	5	0	5
349.0	0	6	0	5
350.0	0	9	0	9
351.0	0	5	0	9
352.0	0	8	0	8
353.0	0	8	0	5
354.0	0	10	0	4
355.0	0	3	0	5
356.0	0	3	0	5
357.0	0	6	0	6
358.0	0	6	0	3
359.0	0	4	0	4
360.0	0	7	0	4
361.0	0	3	0	5
362.0	0	5	0	5
363.0	0	5	0	2
364.0	0	1	0	5
365.0	0	4	0	8
366.0	0	5	0	5
367.0	0	7	0	4
368.0	0	7	0	6
369.0	0	5	0	4
370.0	0	4	0	4
371.0	0	1	0	1
372.0	0	5	0	6
373.0	0	4	0	2
374.0	0	1	0	6
375.0	0	5	0	8
376.0	0	8	0	4
377.0	0	3	0	1
378.0	0	5	0	5
379.0	0	3	0	6
380.0	0	6	0	8
381.0	0	3	0	1
382.0	0	5	0	4
383.0	0	4	0	3
384.0	0	7	0	5
385.0	0	3	0	2
386.0	0	2	0	3
387.0	0	1	0	2
388.0	0	3	0	4
389.0	0	5	0	9
390.0	0	5	0	6
391.0	0	9	0	7
392.0	0	5	0	6
393.0	0	5	0	3
394.0	0	6	0	2
395.0	0	2	0	2
396.0	0	3	0	4
397.0	0	5	0	4
398.0	0	1	0	3
399.0	0	6	0	1
400.0	0	2	0	2
401.0	0	3	0	5
402.0	0	1	0	4
403.0	0	6	0	3
404.0	0	4	0	4
405.0	0	4	0	4
406.0	0	1	0	4
407.0	0	4	0	2
408.0	0	3	0	7
409.0	0	3	0	3
410.0	0	6	0	4
411.0	0	2	0	5
412.0	0	5	0	2
413.0	0	2	0	3
414.0	0	4	0	7
415.0	0	4	0	2
416.0	0	4	0	3
417.0	0	7	0	4
418.0	0	4	0	2
419.0	0	3	0	4
420.0	0	2	0	3
421.0	0	3	0	2
422.0	0	4	0	4
423.0	0	2	0	3
424.0	0	2	0	3
425.0	0	3	0	2
426.0	0	4	0	4
427.0	0	2	0	4
428.0	0	4	0	1
429.0	0	4	0	2
430.0	0	1	0	2
431.0	0	1	0	2
432.0	0	2	0	2
433.0	0	1	0	2
434.0	0	4	0	1
435.0	0	4	0	3
436.0	0	1	0	3
437.0	0	1	0	3
438.0	0	4	0	1
439.0	0	3	0	2
440.0	0	0	0	1
441.0	0	3	0	4
442.0	0	3	0	1
443.0	0	1	0	3
444.0	0	1	0	1
445.0	0	2	0	4
446.0	0	5	0	3
447.0	0	0	0	2
448.0	0	4	0	4
449.0	0	3	0	5
450.0	0	3	0	2
451.0	0	3	0	1
452.0	0	3	0	6
453.0	0	2	0	1
454.0	0	3	0	1
455.0	0	2	0	0
456.0	0	3	0	1
457.0	0	3	0	2
459.0	0	0	0	1
460.0	0	3	0	1
461.0	0	1	0	6
462.0	0	3	0	5
463.0	0	1	0	4
464.0	0	2	0	3
465.0	0	3	0	0
466.0	0	5	0	0
467.0	0	2	0	0
468.0	0	0	0	2
469.0	0	3	0	4
470.0	0	2	0	3
471.0	0	0	0	2
472.0	0	5	0	1
473.0	0	1	0	4
474.0	0	2	0	1
475.0	0	2	0	2
476.0	0	2	0	1
477.0	0	2	0	2
478.0	0	2	0	3
479.0	0	3	0	2
480.0	0	2	0	3
481.0	0	3	0	1
482.0	0	2	0	1
483.0	0	2	0	2
484.0	0	0	0	2
485.0	0	1	0	2
486.0	0	1	0	1
487.0	0	6	0	2
489.0	0	2	0	0
490.0	0	0	0	2
491.0	0	1	0	2
492.0	0	1	0	2
493.0	0	1	0	3
494.0	0	1	0	1
495.0	0	2	0	1
496.0	0	1	0	1
499.0	0	2	0	2
500.0	0	4	0	1
501.0	0	0	0	1
502.0	0	2	0	3
503.0	0	0	0	3
504.0	0	2	0	2
505.0	0	2	0	1
506.0	0	1	0	1
507.0	0	1	0	1
508.0	0	1	0	2
509.0	0	5	0	6
510.0	0	2	0	3
511.0	0	1	0	0
512.0	0	3	0	0
513.0	0	4	0	3
514.0	0	0	0	1
515.0	0	0	0	2
516.0	0	2	0	2
517.0	0	2	0	2
518.0	0	2	0	0
519.0	0	2	0	4
520.0	0	2	0	2
521.0	0	2	0	2
522.0	0	2	0	2
523.0	0	1	0	0
524.0	0	4	0	2
525.0	0	2	0	2
526.0	0	2	0	0
527.0	0	0	0	1
528.0	0	2	0	3
529.0	0	1	0	1
530.0	0	1	0	2
531.0	0	1	0	1
532.0	0	2	0	0
533.0	0	1	0	0
534.0	0	2	0	2
535.0	0	0	0	1
536.0	0	2	0	1
537.0	0	0	0	2
538.0	0	2	0	1
539.0	0	1	0	1
540.0	0	0	0	2
541.0	0	1	0	2
542.0	0	4	0	1
543.0	0	2	0	0
544.0	0	0	0	3
545.0	0	1	0	3
546.0	0	1	0	3
547.0	0	5	0	0
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