## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S35F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S35F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S35F.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 11:55:36 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	1722755	15420453	9392941	7173653	883164	4490973	56297	0.302948	21199949

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.002492	9600983	0	9635133
2.0	1.486869	944528	51633	916942
3.0	1.720906	172756	1267	168128
4.0	1.833987	62048	290	61037
5.0	1.888624	32265	111	31930
6.0	1.915023	20204	47	20057
7.0	1.927779	13748	29	13705
8.0	1.933942	10168	12	10069
9.0	1.936919	7707	5	7691
10.0	1.938358	6293	4	6205
11.0	1.939053	5147	7	5160
12.0	1.939389	4256	3	4251
13.0	1.939552	3731	1	3728
14.0	1.93963	3157	2	3108
15.0	1.939668	2655	0	2669
16.0	1.939686	2491	1	2469
17.0	1.939695	2207	1	2206
18.0	1.939699	1834	2	1826
19.0	1.939701	1712	0	1709
20.0	1.939702	1526	1	1503
21.0	1.939703	1468	0	1477
22.0	1.939703	1287	0	1289
23.0	1.939703	1179	1	1179
24.0	1.939703	1121	0	1091
25.0	1.939703	999	0	1008
26.0	1.939703	975	0	985
27.0	1.939703	922	0	907
28.0	1.939703	874	0	866
29.0	1.939703	784	0	777
30.0	1.939703	702	0	695
31.0	1.939703	639	0	652
32.0	1.939703	617	0	606
33.0	1.939703	585	0	592
34.0	1.939703	585	0	575
35.0	1.939703	538	0	539
36.0	1.939703	503	0	488
37.0	1.939703	422	0	435
38.0	1.939703	447	0	447
39.0	1.939703	420	0	420
40.0	1.939703	424	0	443
41.0	1.939703	396	0	371
42.0	1.939703	374	0	379
43.0	1.939703	375	0	360
44.0	1.939703	315	0	319
45.0	1.939703	319	0	327
46.0	1.939703	340	0	329
47.0	1.939703	315	0	311
48.0	1.939703	282	0	285
49.0	1.939703	282	0	281
50.0	1.939703	280	0	275
51.0	1.939703	230	0	223
52.0	1.939703	244	0	256
53.0	1.939703	239	0	238
54.0	1.939703	237	0	229
55.0	1.939703	222	0	220
56.0	1.939703	207	0	215
57.0	1.939703	207	0	199
58.0	1.939703	195	0	200
59.0	1.939703	181	0	172
60.0	1.939703	178	0	178
61.0	1.939703	154	0	175
62.0	1.939703	175	0	160
63.0	1.939703	169	0	170
64.0	1.939703	157	0	146
65.0	1.939703	158	0	167
66.0	1.939703	146	0	146
67.0	1.939703	136	0	132
68.0	1.939703	141	0	137
69.0	1.939703	145	0	146
70.0	1.939703	153	0	163
71.0	1.939703	151	0	145
72.0	1.939703	137	0	133
73.0	1.939703	108	0	115
74.0	1.939703	131	0	126
75.0	1.939703	123	0	115
76.0	1.939703	118	0	115
77.0	1.939703	112	0	120
78.0	1.939703	111	0	112
79.0	1.939703	114	0	108
80.0	1.939703	106	0	104
81.0	1.939703	105	0	121
82.0	1.939703	108	0	94
83.0	1.939703	80	0	92
84.0	1.939703	102	0	92
85.0	1.939703	80	0	81
86.0	1.939703	96	0	98
87.0	1.939703	89	0	86
88.0	1.939703	81	0	85
89.0	1.939703	98	0	84
90.0	1.939703	63	0	63
91.0	1.939703	72	0	78
92.0	1.939703	85	0	80
93.0	1.939703	76	0	85
94.0	1.939703	80	0	76
95.0	1.939703	82	0	86
96.0	1.939703	73	0	63
97.0	1.939703	60	0	60
98.0	1.939703	65	0	70
99.0	1.939703	70	0	77
100.0	1.939703	61	0	67
101.0	0	69	0	54
102.0	0	53	0	55
103.0	0	54	0	51
104.0	0	62	0	63
105.0	0	55	0	50
106.0	0	63	0	72
107.0	0	60	0	53
108.0	0	68	0	69
109.0	0	58	0	64
110.0	0	61	0	57
111.0	0	54	0	52
112.0	0	54	0	58
113.0	0	47	0	45
114.0	0	43	0	41
115.0	0	52	0	55
116.0	0	55	0	46
117.0	0	44	0	44
118.0	0	45	0	40
119.0	0	30	0	39
120.0	0	45	0	49
121.0	0	45	0	44
122.0	0	48	0	42
123.0	0	34	0	31
124.0	0	36	0	45
125.0	0	31	0	29
126.0	0	35	0	42
127.0	0	49	0	43
128.0	0	45	0	53
129.0	0	36	0	26
130.0	0	46	0	42
131.0	0	31	0	33
132.0	0	31	0	33
133.0	0	39	0	43
134.0	0	36	0	29
135.0	0	36	0	30
136.0	0	27	0	38
137.0	0	38	0	32
138.0	0	42	0	38
139.0	0	29	0	41
140.0	0	39	0	35
141.0	0	36	0	36
142.0	0	35	0	27
143.0	0	26	0	30
144.0	0	36	0	36
145.0	0	27	0	26
146.0	0	33	0	26
147.0	0	24	0	27
148.0	0	22	0	28
149.0	0	34	0	30
150.0	0	31	0	37
151.0	0	30	0	23
152.0	0	23	0	22
153.0	0	17	0	19
154.0	0	24	0	26
155.0	0	28	0	26
156.0	0	30	0	31
157.0	0	22	0	27
158.0	0	23	0	14
159.0	0	20	0	21
160.0	0	21	0	22
161.0	0	23	0	21
162.0	0	22	0	18
163.0	0	17	0	18
164.0	0	20	0	23
165.0	0	17	0	24
166.0	0	30	0	23
167.0	0	16	0	21
168.0	0	19	0	20
169.0	0	23	0	27
170.0	0	30	0	19
171.0	0	13	0	17
172.0	0	25	0	23
173.0	0	22	0	18
174.0	0	13	0	14
175.0	0	19	0	22
176.0	0	16	0	21
177.0	0	21	0	18
178.0	0	18	0	15
179.0	0	18	0	19
180.0	0	16	0	16
181.0	0	24	0	23
182.0	0	13	0	8
183.0	0	12	0	15
184.0	0	13	0	14
185.0	0	15	0	21
186.0	0	20	0	15
187.0	0	16	0	14
188.0	0	15	0	24
189.0	0	19	0	14
190.0	0	15	0	13
191.0	0	8	0	13
192.0	0	17	0	17
193.0	0	26	0	25
194.0	0	15	0	13
195.0	0	18	0	13
196.0	0	10	0	13
197.0	0	12	0	20
198.0	0	23	0	15
199.0	0	13	0	14
200.0	0	16	0	12
201.0	0	14	0	22
202.0	0	15	0	10
203.0	0	14	0	16
204.0	0	16	0	17
205.0	0	19	0	20
206.0	0	19	0	13
207.0	0	14	0	16
208.0	0	6	0	12
209.0	0	18	0	6
210.0	0	7	0	8
211.0	0	11	0	13
212.0	0	12	0	14
213.0	0	9	0	8
214.0	0	14	0	15
215.0	0	13	0	16
216.0	0	15	0	16
217.0	0	16	0	12
218.0	0	8	0	8
219.0	0	13	0	9
220.0	0	9	0	9
221.0	0	12	0	15
222.0	0	14	0	16
223.0	0	10	0	10
224.0	0	15	0	14
225.0	0	12	0	6
226.0	0	8	0	14
227.0	0	11	0	5
228.0	0	10	0	10
229.0	0	7	0	11
230.0	0	11	0	12
231.0	0	13	0	13
232.0	0	7	0	14
233.0	0	16	0	13
234.0	0	14	0	7
235.0	0	6	0	7
236.0	0	8	0	11
237.0	0	12	0	10
238.0	0	13	0	10
239.0	0	6	0	4
240.0	0	5	0	12
241.0	0	9	0	7
242.0	0	9	0	12
243.0	0	12	0	9
244.0	0	8	0	5
245.0	0	4	0	8
246.0	0	13	0	10
247.0	0	8	0	5
248.0	0	5	0	10
249.0	0	10	0	8
250.0	0	7	0	7
251.0	0	5	0	7
252.0	0	8	0	6
253.0	0	8	0	10
254.0	0	9	0	9
255.0	0	7	0	10
256.0	0	6	0	6
257.0	0	8	0	9
258.0	0	9	0	9
259.0	0	10	0	7
260.0	0	7	0	7
261.0	0	12	0	11
262.0	0	8	0	8
263.0	0	12	0	11
264.0	0	12	0	9
265.0	0	8	0	10
266.0	0	6	0	4
267.0	0	5	0	8
268.0	0	5	0	7
269.0	0	9	0	11
270.0	0	9	0	7
271.0	0	12	0	8
272.0	0	6	0	3
273.0	0	2	0	5
274.0	0	6	0	5
275.0	0	4	0	4
276.0	0	6	0	3
277.0	0	6	0	6
278.0	0	3	0	6
279.0	0	4	0	3
280.0	0	4	0	5
281.0	0	4	0	4
282.0	0	5	0	5
283.0	0	7	0	8
284.0	0	4	0	4
285.0	0	7	0	7
286.0	0	7	0	9
287.0	0	7	0	4
288.0	0	6	0	7
289.0	0	5	0	5
290.0	0	2	0	4
291.0	0	4	0	5
292.0	0	8	0	4
293.0	0	4	0	4
294.0	0	3	0	11
295.0	0	8	0	7
296.0	0	6	0	6
297.0	0	10	0	6
298.0	0	5	0	3
299.0	0	2	0	6
300.0	0	5	0	4
301.0	0	5	0	3
302.0	0	6	0	7
303.0	0	6	0	7
304.0	0	4	0	6
305.0	0	7	0	4
306.0	0	3	0	6
307.0	0	6	0	5
308.0	0	10	0	3
309.0	0	3	0	5
310.0	0	3	0	6
311.0	0	2	0	10
312.0	0	12	0	4
313.0	0	2	0	2
314.0	0	7	0	6
315.0	0	4	0	6
316.0	0	3	0	4
317.0	0	5	0	2
318.0	0	5	0	7
319.0	0	5	0	6
320.0	0	7	0	5
321.0	0	7	0	4
322.0	0	5	0	4
323.0	0	2	0	1
324.0	0	4	0	7
325.0	0	1	0	1
326.0	0	2	0	1
327.0	0	2	0	5
328.0	0	3	0	6
329.0	0	7	0	3
330.0	0	4	0	6
331.0	0	8	0	3
332.0	0	2	0	4
333.0	0	5	0	3
334.0	0	2	0	2
335.0	0	3	0	3
336.0	0	5	0	4
337.0	0	2	0	2
338.0	0	3	0	2
339.0	0	3	0	6
340.0	0	2	0	4
341.0	0	3	0	2
342.0	0	7	0	5
343.0	0	4	0	3
344.0	0	4	0	4
345.0	0	2	0	3
346.0	0	1	0	0
347.0	0	2	0	3
348.0	0	5	0	3
349.0	0	1	0	4
350.0	0	1	0	2
351.0	0	5	0	3
352.0	0	2	0	3
353.0	0	4	0	3
354.0	0	3	0	3
355.0	0	4	0	8
356.0	0	6	0	2
357.0	0	2	0	5
358.0	0	4	0	3
359.0	0	5	0	3
360.0	0	6	0	4
361.0	0	2	0	3
362.0	0	2	0	6
363.0	0	2	0	1
364.0	0	3	0	3
365.0	0	4	0	5
366.0	0	3	0	5
367.0	0	5	0	5
368.0	0	7	0	4
369.0	0	2	0	3
370.0	0	5	0	1
371.0	0	1	0	0
372.0	0	5	0	5
373.0	0	3	0	4
374.0	0	3	0	0
375.0	0	0	0	2
376.0	0	2	0	2
377.0	0	2	0	2
378.0	0	1	0	1
379.0	0	2	0	2
380.0	0	1	0	0
381.0	0	3	0	4
382.0	0	0	0	1
383.0	0	0	0	1
384.0	0	4	0	4
385.0	0	1	0	1
386.0	0	2	0	3
387.0	0	5	0	1
388.0	0	1	0	2
389.0	0	3	0	4
390.0	0	1	0	2
391.0	0	0	0	2
392.0	0	4	0	3
393.0	0	1	0	1
394.0	0	1	0	3
395.0	0	7	0	6
396.0	0	2	0	3
397.0	0	6	0	2
398.0	0	3	0	0
400.0	0	1	0	4
401.0	0	1	0	3
402.0	0	3	0	1
403.0	0	1	0	1
404.0	0	2	0	1
405.0	0	0	0	2
406.0	0	2	0	2
407.0	0	2	0	1
408.0	0	1	0	3
409.0	0	2	0	1
410.0	0	1	0	3
411.0	0	4	0	3
412.0	0	4	0	3
413.0	0	1	0	0
414.0	0	2	0	0
415.0	0	0	0	4
416.0	0	4	0	1
418.0	0	0	0	1
419.0	0	3	0	5
420.0	0	3	0	2
421.0	0	2	0	2
422.0	0	0	0	3
423.0	0	7	0	3
424.0	0	2	0	2
425.0	0	3	0	2
427.0	0	0	0	2
428.0	0	3	0	3
429.0	0	2	0	0
430.0	0	2	0	1
431.0	0	0	0	3
432.0	0	2	0	2
433.0	0	2	0	0
434.0	0	1	0	5
435.0	0	3	0	0
436.0	0	2	0	2
437.0	0	2	0	1
438.0	0	0	0	2
439.0	0	4	0	5
440.0	0	2	0	2
441.0	0	1	0	2
442.0	0	3	0	2
443.0	0	4	0	0
444.0	0	1	0	3
445.0	0	1	0	2
446.0	0	0	0	1
447.0	0	2	0	0
448.0	0	2	0	5
449.0	0	4	0	2
450.0	0	1	0	2
451.0	0	3	0	2
452.0	0	2	0	3
453.0	0	2	0	3
454.0	0	4	0	2
455.0	0	0	0	3
456.0	0	2	0	2
457.0	0	4	0	2
458.0	0	2	0	2
459.0	0	5	0	1
460.0	0	2	0	2
461.0	0	0	0	1
463.0	0	0	0	1
464.0	0	2	0	1
466.0	0	2	0	3
467.0	0	1	0	0
468.0	0	0	0	1
469.0	0	2	0	2
470.0	0	3	0	1
471.0	0	0	0	1
472.0	0	0	0	2
473.0	0	1	0	0
474.0	0	0	0	1
475.0	0	1	0	3
476.0	0	2	0	1
477.0	0	6	0	2
478.0	0	0	0	2
479.0	0	1	0	0
480.0	0	2	0	1
481.0	0	1	0	0
482.0	0	0	0	1
483.0	0	0	0	3
484.0	0	1	0	1
485.0	0	3	0	1
486.0	0	1	0	2
487.0	0	1	0	1
489.0	0	3	0	1
490.0	0	1	0	0
491.0	0	0	0	3
492.0	0	0	0	1
493.0	0	2	0	1
494.0	0	2	0	2
495.0	0	2	0	1
496.0	0	0	0	1
497.0	0	2	0	1
498.0	0	1	0	0
499.0	0	0	0	4
500.0	0	1	0	0
501.0	0	3	0	0
502.0	0	0	0	2
503.0	0	1	0	2
504.0	0	2	0	0
505.0	0	1	0	2
506.0	0	1	0	1
507.0	0	1	0	3
508.0	0	1	0	2
509.0	0	3	0	1
510.0	0	1	0	0
511.0	0	3	0	5
513.0	0	1	0	0
514.0	0	3	0	1
516.0	0	2	0	1
517.0	0	1	0	0
519.0	0	1	0	1
520.0	0	1	0	2
521.0	0	1	0	0
522.0	0	0	0	1
523.0	0	0	0	1
524.0	0	1	0	1
525.0	0	1	0	1
526.0	0	0	0	1
527.0	0	2	0	0
529.0	0	0	0	2
530.0	0	1	0	2
531.0	0	2	0	1
532.0	0	2	0	1
533.0	0	1	0	0
534.0	0	1	0	0
535.0	0	0	0	1
536.0	0	1	0	1
537.0	0	0	0	2
538.0	0	3	0	1
539.0	0	0	0	1
540.0	0	2	0	0
541.0	0	0	0	2
543.0	0	2	0	0
544.0	0	1	0	1
546.0	0	0	0	2
547.0	0	0	0	1
549.0	0	1	0	1
550.0	0	1	0	1
551.0	0	2	0	1
552.0	0	2	0	0
554.0	0	0	0	1
556.0	0	0	0	1
557.0	0	0	0	1
558.0	0	1	0	0
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