## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S77F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S77F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S77F.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 13:17:42 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	2140152	22027438	12440154	8558962	1252671	7787280	115344	0.364265	23456911

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003175	12147315	0	12209853
2.0	1.395412	1491259	99824	1443379
3.0	1.548774	283227	3432	272822
4.0	1.608738	95592	937	93237
5.0	1.632184	47963	395	47298
6.0	1.641351	29315	215	29031
7.0	1.644935	19868	108	19650
8.0	1.646337	14365	67	14278
9.0	1.646885	11155	40	11025
10.0	1.647099	8902	30	8877
11.0	1.647183	7406	30	7369
12.0	1.647216	6077	13	6059
13.0	1.647228	5337	9	5269
14.0	1.647233	4554	3	4517
15.0	1.647235	3854	9	3829
16.0	1.647236	3504	5	3511
17.0	1.647237	3072	9	3056
18.0	1.647237	2905	2	2884
19.0	1.647237	2589	6	2594
20.0	1.647237	2287	2	2252
21.0	1.647237	2083	1	2097
22.0	1.647237	1907	0	1917
23.0	1.647237	1792	2	1755
24.0	1.647237	1644	1	1641
25.0	1.647237	1531	1	1520
26.0	1.647237	1394	1	1366
27.0	1.647237	1320	0	1323
28.0	1.647237	1207	0	1207
29.0	1.647237	1137	0	1125
30.0	1.647237	1102	2	1130
31.0	1.647237	1105	1	1072
32.0	1.647237	962	1	950
33.0	1.647237	899	0	897
34.0	1.647237	834	0	845
35.0	1.647237	832	0	805
36.0	1.647237	751	0	749
37.0	1.647237	804	2	814
38.0	1.647237	657	0	663
39.0	1.647237	661	0	672
40.0	1.647237	695	0	676
41.0	1.647237	625	0	642
42.0	1.647237	686	1	672
43.0	1.647237	615	0	623
44.0	1.647237	622	0	596
45.0	1.647237	525	0	509
46.0	1.647237	478	0	475
47.0	1.647237	462	0	485
48.0	1.647237	511	0	498
49.0	1.647237	425	0	444
50.0	1.647237	438	0	414
51.0	1.647237	435	0	430
52.0	1.647237	395	0	401
53.0	1.647237	384	0	372
54.0	1.647237	371	0	377
55.0	1.647237	347	0	351
56.0	1.647237	351	0	329
57.0	1.647237	323	0	333
58.0	1.647237	354	0	359
59.0	1.647237	326	0	318
60.0	1.647237	298	0	301
61.0	1.647237	308	0	311
62.0	1.647237	331	0	321
63.0	1.647237	278	0	282
64.0	1.647237	280	0	283
65.0	1.647237	293	0	296
66.0	1.647237	260	0	234
67.0	1.647237	231	0	236
68.0	1.647237	245	0	241
69.0	1.647237	229	0	254
70.0	1.647237	275	0	252
71.0	1.647237	235	0	230
72.0	1.647237	217	0	213
73.0	1.647237	187	0	195
74.0	1.647237	227	0	218
75.0	1.647237	180	0	196
76.0	1.647237	219	0	205
77.0	1.647237	176	0	183
78.0	1.647237	179	0	181
79.0	1.647237	179	0	169
80.0	1.647237	168	0	173
81.0	1.647237	185	0	197
82.0	1.647237	194	0	171
83.0	1.647237	159	0	167
84.0	1.647237	169	0	170
85.0	1.647237	159	0	154
86.0	1.647237	176	0	162
87.0	1.647237	134	0	142
88.0	1.647237	143	0	136
89.0	1.647237	140	0	145
90.0	1.647237	139	0	136
91.0	1.647237	131	0	133
92.0	1.647237	126	0	128
93.0	1.647237	132	0	145
94.0	1.647237	144	0	153
95.0	1.647237	142	0	123
96.0	1.647237	125	0	125
97.0	1.647237	136	0	134
98.0	1.647237	115	0	101
99.0	1.647237	112	0	114
100.0	1.647237	116	0	118
101.0	0	98	0	97
102.0	0	103	0	108
103.0	0	106	0	121
104.0	0	126	0	112
105.0	0	102	0	95
106.0	0	111	0	119
107.0	0	116	0	106
108.0	0	103	0	105
109.0	0	110	0	115
110.0	0	94	0	85
111.0	0	91	0	98
112.0	0	111	0	108
113.0	0	95	0	98
114.0	0	94	0	84
115.0	0	93	0	88
116.0	0	85	0	80
117.0	0	67	0	81
118.0	0	90	0	75
119.0	0	71	0	80
120.0	0	78	0	94
121.0	0	90	0	72
122.0	0	70	0	75
123.0	0	60	0	70
124.0	0	91	0	89
125.0	0	81	0	64
126.0	0	60	0	66
127.0	0	68	0	78
128.0	0	83	0	78
129.0	0	73	0	57
130.0	0	54	0	60
131.0	0	66	0	65
132.0	0	56	0	58
133.0	0	62	0	65
134.0	0	70	0	67
135.0	0	57	0	70
136.0	0	65	0	57
137.0	0	60	0	65
138.0	0	69	0	60
139.0	0	58	0	66
140.0	0	77	0	72
141.0	0	63	0	60
142.0	0	53	0	58
143.0	0	67	0	64
144.0	0	67	0	69
145.0	0	51	0	61
146.0	0	56	0	58
147.0	0	64	0	56
148.0	0	62	0	48
149.0	0	47	0	54
150.0	0	61	0	64
151.0	0	59	0	57
152.0	0	66	0	71
153.0	0	61	0	54
154.0	0	52	0	32
155.0	0	32	0	48
156.0	0	54	0	53
157.0	0	51	0	58
158.0	0	43	0	47
159.0	0	59	0	52
160.0	0	46	0	49
161.0	0	48	0	43
162.0	0	47	0	35
163.0	0	42	0	33
164.0	0	39	0	43
165.0	0	36	0	38
166.0	0	35	0	38
167.0	0	42	0	47
168.0	0	31	0	34
169.0	0	50	0	52
170.0	0	53	0	50
171.0	0	37	0	43
172.0	0	47	0	33
173.0	0	33	0	34
174.0	0	31	0	39
175.0	0	35	0	36
176.0	0	40	0	40
177.0	0	43	0	39
178.0	0	28	0	23
179.0	0	34	0	41
180.0	0	38	0	31
181.0	0	35	0	36
182.0	0	36	0	24
183.0	0	27	0	42
184.0	0	33	0	31
185.0	0	37	0	31
186.0	0	31	0	35
187.0	0	33	0	29
188.0	0	29	0	34
189.0	0	34	0	34
190.0	0	36	0	32
191.0	0	27	0	32
192.0	0	33	0	41
193.0	0	38	0	26
194.0	0	28	0	32
195.0	0	35	0	31
196.0	0	26	0	26
197.0	0	28	0	29
198.0	0	29	0	34
199.0	0	32	0	27
200.0	0	35	0	36
201.0	0	28	0	26
202.0	0	31	0	28
203.0	0	23	0	29
204.0	0	27	0	28
205.0	0	26	0	21
206.0	0	27	0	25
207.0	0	27	0	23
208.0	0	17	0	17
209.0	0	19	0	26
210.0	0	15	0	18
211.0	0	27	0	13
212.0	0	19	0	28
213.0	0	20	0	18
214.0	0	25	0	21
215.0	0	18	0	26
216.0	0	20	0	24
217.0	0	26	0	24
218.0	0	29	0	23
219.0	0	15	0	13
220.0	0	17	0	21
221.0	0	17	0	19
222.0	0	29	0	33
223.0	0	23	0	21
224.0	0	29	0	22
225.0	0	23	0	23
226.0	0	20	0	19
227.0	0	18	0	18
228.0	0	21	0	25
229.0	0	18	0	19
230.0	0	26	0	30
231.0	0	20	0	12
232.0	0	20	0	20
233.0	0	23	0	25
234.0	0	19	0	20
235.0	0	26	0	24
236.0	0	13	0	20
237.0	0	20	0	15
238.0	0	20	0	29
239.0	0	24	0	16
240.0	0	21	0	18
241.0	0	19	0	21
242.0	0	22	0	18
243.0	0	20	0	23
244.0	0	20	0	17
245.0	0	21	0	21
246.0	0	16	0	21
247.0	0	18	0	21
248.0	0	21	0	18
249.0	0	16	0	15
250.0	0	19	0	18
251.0	0	18	0	19
252.0	0	20	0	15
253.0	0	11	0	15
254.0	0	22	0	16
255.0	0	16	0	14
256.0	0	12	0	15
257.0	0	15	0	16
258.0	0	14	0	16
259.0	0	12	0	16
260.0	0	21	0	12
261.0	0	14	0	11
262.0	0	8	0	12
263.0	0	11	0	9
264.0	0	13	0	11
265.0	0	14	0	16
266.0	0	16	0	15
267.0	0	15	0	13
268.0	0	15	0	22
269.0	0	13	0	22
270.0	0	17	0	15
271.0	0	22	0	14
272.0	0	17	0	15
273.0	0	11	0	12
274.0	0	20	0	18
275.0	0	13	0	16
276.0	0	17	0	19
277.0	0	19	0	16
278.0	0	11	0	16
279.0	0	15	0	9
280.0	0	18	0	17
281.0	0	15	0	15
282.0	0	11	0	18
283.0	0	17	0	14
284.0	0	14	0	12
285.0	0	13	0	8
286.0	0	8	0	14
287.0	0	17	0	17
288.0	0	16	0	13
289.0	0	12	0	7
290.0	0	9	0	16
291.0	0	10	0	10
292.0	0	10	0	8
293.0	0	9	0	13
294.0	0	12	0	7
295.0	0	9	0	8
296.0	0	15	0	8
297.0	0	7	0	8
298.0	0	7	0	9
299.0	0	8	0	5
300.0	0	6	0	12
301.0	0	13	0	9
302.0	0	8	0	12
303.0	0	10	0	13
304.0	0	8	0	6
305.0	0	11	0	9
306.0	0	13	0	18
307.0	0	15	0	9
308.0	0	6	0	12
309.0	0	13	0	16
310.0	0	14	0	6
311.0	0	12	0	4
312.0	0	4	0	11
313.0	0	9	0	8
314.0	0	8	0	8
315.0	0	9	0	11
316.0	0	9	0	17
317.0	0	8	0	11
318.0	0	18	0	9
319.0	0	11	0	10
320.0	0	9	0	13
321.0	0	9	0	8
322.0	0	10	0	13
323.0	0	11	0	11
324.0	0	9	0	4
325.0	0	11	0	12
326.0	0	13	0	9
327.0	0	10	0	11
328.0	0	9	0	7
329.0	0	9	0	13
330.0	0	10	0	9
331.0	0	12	0	11
332.0	0	6	0	9
333.0	0	9	0	9
334.0	0	6	0	8
335.0	0	13	0	5
336.0	0	7	0	6
337.0	0	4	0	9
338.0	0	11	0	9
339.0	0	4	0	5
340.0	0	6	0	8
341.0	0	12	0	6
342.0	0	5	0	11
343.0	0	4	0	6
344.0	0	11	0	5
345.0	0	3	0	9
346.0	0	11	0	11
347.0	0	7	0	8
348.0	0	9	0	15
349.0	0	20	0	9
350.0	0	9	0	10
351.0	0	11	0	6
352.0	0	8	0	12
353.0	0	11	0	13
354.0	0	7	0	4
355.0	0	6	0	8
356.0	0	9	0	10
357.0	0	6	0	8
358.0	0	9	0	10
359.0	0	11	0	5
360.0	0	8	0	16
361.0	0	8	0	5
362.0	0	6	0	6
363.0	0	11	0	12
364.0	0	11	0	6
365.0	0	13	0	11
366.0	0	7	0	4
367.0	0	10	0	8
368.0	0	4	0	4
369.0	0	5	0	2
370.0	0	5	0	8
371.0	0	4	0	7
372.0	0	4	0	4
373.0	0	6	0	6
374.0	0	6	0	6
375.0	0	11	0	8
376.0	0	6	0	8
377.0	0	3	0	9
378.0	0	7	0	6
379.0	0	6	0	8
380.0	0	7	0	5
381.0	0	6	0	6
382.0	0	9	0	6
383.0	0	5	0	2
384.0	0	3	0	4
385.0	0	5	0	8
386.0	0	5	0	6
387.0	0	5	0	8
388.0	0	8	0	7
389.0	0	9	0	5
390.0	0	4	0	1
391.0	0	2	0	5
392.0	0	8	0	13
393.0	0	8	0	7
394.0	0	5	0	7
395.0	0	8	0	6
396.0	0	7	0	4
397.0	0	7	0	9
398.0	0	3	0	6
399.0	0	7	0	5
400.0	0	10	0	4
401.0	0	7	0	6
402.0	0	2	0	4
403.0	0	6	0	2
404.0	0	4	0	10
405.0	0	5	0	3
406.0	0	4	0	9
407.0	0	8	0	7
408.0	0	8	0	8
409.0	0	6	0	4
410.0	0	9	0	6
411.0	0	4	0	4
412.0	0	1	0	3
413.0	0	8	0	9
414.0	0	5	0	4
415.0	0	5	0	3
416.0	0	4	0	5
417.0	0	4	0	3
418.0	0	6	0	4
419.0	0	3	0	5
420.0	0	4	0	3
421.0	0	6	0	8
422.0	0	3	0	7
423.0	0	6	0	7
424.0	0	7	0	4
425.0	0	4	0	7
426.0	0	8	0	7
427.0	0	5	0	5
428.0	0	8	0	3
429.0	0	8	0	3
430.0	0	4	0	6
431.0	0	3	0	5
432.0	0	5	0	5
433.0	0	4	0	5
434.0	0	5	0	5
435.0	0	2	0	5
436.0	0	5	0	4
437.0	0	7	0	5
438.0	0	1	0	4
439.0	0	8	0	2
440.0	0	4	0	4
441.0	0	4	0	3
442.0	0	1	0	4
443.0	0	5	0	4
444.0	0	6	0	1
445.0	0	1	0	3
446.0	0	2	0	6
447.0	0	5	0	4
448.0	0	3	0	2
449.0	0	2	0	6
450.0	0	6	0	5
451.0	0	5	0	5
452.0	0	4	0	1
453.0	0	2	0	1
454.0	0	3	0	7
455.0	0	3	0	6
456.0	0	4	0	3
457.0	0	5	0	7
458.0	0	4	0	2
459.0	0	8	0	0
460.0	0	3	0	0
461.0	0	2	0	3
462.0	0	2	0	3
463.0	0	1	0	4
464.0	0	1	0	4
465.0	0	2	0	7
466.0	0	5	0	5
467.0	0	8	0	1
468.0	0	1	0	4
469.0	0	4	0	3
470.0	0	3	0	3
471.0	0	4	0	4
472.0	0	5	0	4
473.0	0	1	0	5
474.0	0	4	0	5
475.0	0	4	0	5
476.0	0	4	0	3
477.0	0	6	0	1
478.0	0	4	0	5
479.0	0	5	0	1
480.0	0	1	0	1
481.0	0	3	0	7
482.0	0	0	0	1
483.0	0	5	0	6
484.0	0	4	0	2
485.0	0	4	0	3
486.0	0	4	0	1
487.0	0	2	0	3
488.0	0	2	0	7
489.0	0	5	0	7
490.0	0	3	0	2
491.0	0	4	0	0
492.0	0	2	0	2
493.0	0	2	0	3
494.0	0	7	0	3
495.0	0	0	0	2
496.0	0	2	0	4
497.0	0	3	0	2
498.0	0	3	0	4
499.0	0	3	0	7
500.0	0	4	0	4
501.0	0	4	0	1
502.0	0	5	0	6
503.0	0	5	0	3
504.0	0	4	0	4
505.0	0	6	0	4
506.0	0	1	0	5
507.0	0	4	0	4
508.0	0	3	0	3
509.0	0	5	0	3
510.0	0	3	0	6
511.0	0	4	0	3
512.0	0	5	0	3
513.0	0	5	0	3
514.0	0	5	0	2
515.0	0	3	0	5
516.0	0	1	0	4
517.0	0	4	0	6
518.0	0	4	0	2
519.0	0	4	0	4
520.0	0	5	0	3
521.0	0	3	0	3
522.0	0	2	0	3
523.0	0	3	0	3
524.0	0	2	0	6
525.0	0	1	0	3
526.0	0	5	0	4
527.0	0	3	0	3
528.0	0	3	0	0
529.0	0	4	0	1
530.0	0	3	0	3
531.0	0	2	0	7
532.0	0	3	0	2
533.0	0	2	0	1
534.0	0	4	0	2
535.0	0	2	0	3
536.0	0	3	0	1
537.0	0	5	0	3
538.0	0	2	0	1
539.0	0	0	0	3
540.0	0	5	0	1
541.0	0	1	0	2
542.0	0	2	0	6
543.0	0	2	0	4
544.0	0	0	0	1
545.0	0	3	0	2
546.0	0	8	0	2
547.0	0	1	0	6
548.0	0	3	0	2
549.0	0	3	0	0
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