## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S54F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S54F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S54F.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 12:49:11 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	1996289	16663684	11374203	10107863	878111	4428609	72799	0.275604	25783040

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003122	10768577	0	10814483
2.0	1.528737	1074126	66854	1037275
3.0	1.804148	186342	1507	179566
4.0	1.948457	63257	344	62093
5.0	2.024072	32339	122	31972
6.0	2.063693	19827	48	19612
7.0	2.084453	13622	28	13525
8.0	2.095331	9662	17	9569
9.0	2.101031	7608	15	7572
10.0	2.104018	6040	8	6012
11.0	2.105583	4851	10	4817
12.0	2.106403	4081	7	4077
13.0	2.106832	3441	3	3401
14.0	2.107058	2810	2	2809
15.0	2.107176	2622	3	2609
16.0	2.107237	2306	4	2310
17.0	2.10727	1944	2	1921
18.0	2.107287	1780	1	1763
19.0	2.107296	1589	1	1577
20.0	2.1073	1459	1	1438
21.0	2.107303	1297	0	1311
22.0	2.107304	1102	2	1111
23.0	2.107305	1062	2	1046
24.0	2.107305	1051	1	1038
25.0	2.107305	903	2	906
26.0	2.107305	911	1	910
27.0	2.107305	788	1	781
28.0	2.107305	721	1	709
29.0	2.107305	684	0	681
30.0	2.107305	657	0	656
31.0	2.107305	602	1	615
32.0	2.107305	604	0	595
33.0	2.107305	544	0	546
34.0	2.107305	524	0	520
35.0	2.107305	469	0	458
36.0	2.107305	444	0	438
37.0	2.107305	418	0	401
38.0	2.107305	409	0	429
39.0	2.107305	390	0	387
40.0	2.107305	373	0	376
41.0	2.107305	352	0	345
42.0	2.107305	344	0	351
43.0	2.107305	320	0	308
44.0	2.107305	307	0	306
45.0	2.107305	295	0	308
46.0	2.107305	309	0	286
47.0	2.107305	270	0	284
48.0	2.107305	272	0	258
49.0	2.107305	211	0	228
50.0	2.107305	255	0	240
51.0	2.107305	234	0	228
52.0	2.107305	194	0	203
53.0	2.107305	224	0	214
54.0	2.107305	188	0	186
55.0	2.107305	195	0	201
56.0	2.107305	157	0	158
57.0	2.107305	167	0	165
58.0	2.107305	189	0	189
59.0	2.107305	191	0	194
60.0	2.107305	200	0	197
61.0	2.107305	179	0	171
62.0	2.107305	160	0	156
63.0	2.107305	134	0	142
64.0	2.107305	153	0	151
65.0	2.107305	129	0	137
66.0	2.107305	133	0	117
67.0	2.107305	117	0	125
68.0	2.107305	124	0	115
69.0	2.107305	118	0	129
70.0	2.107305	129	0	126
71.0	2.107305	120	0	118
72.0	2.107305	135	0	133
73.0	2.107305	118	0	131
74.0	2.107305	114	0	106
75.0	2.107305	107	0	87
76.0	2.107305	102	0	112
77.0	2.107305	107	0	100
78.0	2.107305	85	0	84
79.0	2.107305	85	0	93
80.0	2.107305	92	0	90
81.0	2.107305	89	0	85
82.0	2.107305	79	0	79
83.0	2.107305	77	0	82
84.0	2.107305	78	0	85
85.0	2.107305	99	0	91
86.0	2.107305	69	0	64
87.0	2.107305	82	0	78
88.0	2.107305	81	0	87
89.0	2.107305	80	0	78
90.0	2.107305	71	0	70
91.0	2.107305	65	0	71
92.0	2.107305	68	0	69
93.0	2.107305	71	0	73
94.0	2.107305	62	0	65
95.0	2.107305	69	0	56
96.0	2.107305	62	0	71
97.0	2.107305	69	0	63
98.0	2.107305	59	0	65
99.0	2.107305	63	0	54
100.0	2.107305	54	0	58
101.0	0	69	0	60
102.0	0	48	0	53
103.0	0	47	0	50
104.0	0	61	0	55
105.0	0	49	0	49
106.0	0	51	0	55
107.0	0	54	0	54
108.0	0	56	0	56
109.0	0	50	0	47
110.0	0	43	0	40
111.0	0	46	0	37
112.0	0	38	0	47
113.0	0	43	0	43
114.0	0	44	0	49
115.0	0	46	0	46
116.0	0	55	0	44
117.0	0	33	0	39
118.0	0	40	0	39
119.0	0	34	0	35
120.0	0	43	0	34
121.0	0	30	0	35
122.0	0	25	0	29
123.0	0	30	0	22
124.0	0	32	0	34
125.0	0	37	0	37
126.0	0	27	0	26
127.0	0	32	0	39
128.0	0	28	0	32
129.0	0	38	0	34
130.0	0	43	0	34
131.0	0	23	0	25
132.0	0	28	0	32
133.0	0	24	0	21
134.0	0	31	0	43
135.0	0	36	0	37
136.0	0	40	0	31
137.0	0	29	0	29
138.0	0	29	0	26
139.0	0	26	0	26
140.0	0	26	0	34
141.0	0	34	0	34
142.0	0	31	0	28
143.0	0	37	0	31
144.0	0	22	0	25
145.0	0	24	0	23
146.0	0	31	0	22
147.0	0	19	0	19
148.0	0	22	0	22
149.0	0	20	0	25
150.0	0	20	0	22
151.0	0	27	0	27
152.0	0	20	0	34
153.0	0	31	0	24
154.0	0	25	0	26
155.0	0	32	0	18
156.0	0	18	0	18
157.0	0	13	0	11
158.0	0	16	0	18
159.0	0	16	0	23
160.0	0	24	0	17
161.0	0	19	0	16
162.0	0	12	0	11
163.0	0	12	0	15
164.0	0	12	0	14
165.0	0	18	0	22
166.0	0	18	0	21
167.0	0	23	0	24
168.0	0	16	0	17
169.0	0	25	0	15
170.0	0	19	0	16
171.0	0	16	0	18
172.0	0	11	0	15
173.0	0	15	0	19
174.0	0	15	0	17
175.0	0	24	0	25
176.0	0	25	0	21
177.0	0	12	0	9
178.0	0	12	0	12
179.0	0	10	0	14
180.0	0	15	0	16
181.0	0	16	0	14
182.0	0	17	0	18
183.0	0	21	0	15
184.0	0	16	0	14
185.0	0	9	0	10
186.0	0	12	0	10
187.0	0	22	0	19
188.0	0	9	0	10
189.0	0	12	0	15
190.0	0	14	0	15
191.0	0	13	0	13
192.0	0	10	0	11
193.0	0	18	0	19
194.0	0	14	0	9
195.0	0	11	0	12
196.0	0	12	0	11
197.0	0	13	0	12
198.0	0	11	0	14
199.0	0	14	0	12
200.0	0	10	0	16
201.0	0	21	0	17
202.0	0	7	0	10
203.0	0	10	0	8
204.0	0	8	0	6
205.0	0	16	0	16
206.0	0	16	0	20
207.0	0	14	0	12
208.0	0	8	0	5
209.0	0	11	0	14
210.0	0	8	0	6
211.0	0	7	0	10
212.0	0	10	0	7
213.0	0	10	0	12
214.0	0	8	0	8
215.0	0	13	0	5
216.0	0	4	0	8
217.0	0	9	0	10
218.0	0	7	0	13
219.0	0	18	0	11
220.0	0	6	0	10
221.0	0	13	0	8
222.0	0	8	0	8
223.0	0	2	0	4
224.0	0	10	0	11
225.0	0	7	0	10
226.0	0	8	0	7
227.0	0	10	0	5
228.0	0	7	0	9
229.0	0	5	0	11
230.0	0	9	0	5
231.0	0	7	0	7
232.0	0	9	0	7
233.0	0	7	0	6
234.0	0	6	0	3
235.0	0	3	0	7
236.0	0	8	0	13
237.0	0	17	0	11
238.0	0	8	0	6
239.0	0	5	0	7
240.0	0	4	0	3
241.0	0	5	0	4
242.0	0	5	0	4
243.0	0	6	0	8
244.0	0	5	0	5
245.0	0	3	0	4
246.0	0	10	0	12
247.0	0	5	0	2
248.0	0	5	0	5
249.0	0	5	0	5
250.0	0	6	0	6
251.0	0	6	0	9
252.0	0	5	0	5
253.0	0	8	0	9
254.0	0	11	0	11
255.0	0	9	0	5
256.0	0	8	0	8
257.0	0	9	0	7
258.0	0	4	0	6
259.0	0	7	0	2
260.0	0	2	0	6
261.0	0	7	0	10
262.0	0	4	0	3
263.0	0	7	0	6
264.0	0	6	0	3
265.0	0	4	0	11
266.0	0	8	0	5
267.0	0	6	0	5
268.0	0	3	0	2
269.0	0	4	0	5
270.0	0	6	0	9
271.0	0	3	0	4
272.0	0	8	0	6
273.0	0	8	0	6
274.0	0	4	0	5
275.0	0	6	0	4
276.0	0	3	0	5
277.0	0	4	0	4
278.0	0	5	0	2
279.0	0	4	0	1
280.0	0	2	0	7
281.0	0	6	0	6
282.0	0	4	0	2
283.0	0	4	0	9
284.0	0	9	0	3
285.0	0	5	0	10
286.0	0	6	0	7
287.0	0	4	0	2
288.0	0	8	0	6
289.0	0	3	0	6
290.0	0	3	0	2
291.0	0	5	0	2
292.0	0	4	0	2
293.0	0	5	0	4
294.0	0	2	0	4
295.0	0	2	0	5
296.0	0	7	0	4
297.0	0	3	0	6
298.0	0	5	0	1
299.0	0	0	0	7
300.0	0	2	0	2
301.0	0	9	0	7
302.0	0	6	0	5
303.0	0	5	0	2
304.0	0	2	0	4
305.0	0	3	0	3
306.0	0	6	0	7
307.0	0	4	0	4
308.0	0	3	0	1
309.0	0	2	0	9
310.0	0	6	0	1
311.0	0	5	0	2
312.0	0	4	0	3
313.0	0	1	0	3
314.0	0	4	0	2
315.0	0	3	0	3
316.0	0	3	0	2
317.0	0	0	0	4
318.0	0	4	0	5
319.0	0	3	0	4
320.0	0	5	0	3
321.0	0	5	0	2
322.0	0	1	0	8
323.0	0	4	0	1
324.0	0	6	0	1
325.0	0	0	0	3
326.0	0	3	0	4
327.0	0	3	0	2
328.0	0	1	0	4
329.0	0	5	0	2
330.0	0	6	0	3
331.0	0	2	0	4
332.0	0	3	0	3
333.0	0	3	0	3
334.0	0	1	0	4
335.0	0	1	0	2
336.0	0	5	0	5
337.0	0	5	0	0
338.0	0	2	0	3
339.0	0	1	0	4
340.0	0	3	0	1
341.0	0	1	0	3
342.0	0	2	0	3
343.0	0	6	0	4
344.0	0	5	0	2
345.0	0	5	0	7
346.0	0	3	0	6
347.0	0	4	0	5
348.0	0	6	0	0
349.0	0	2	0	1
350.0	0	0	0	2
351.0	0	3	0	3
352.0	0	1	0	2
353.0	0	2	0	2
354.0	0	1	0	5
355.0	0	4	0	1
356.0	0	3	0	2
357.0	0	3	0	1
358.0	0	1	0	0
359.0	0	0	0	2
360.0	0	4	0	3
361.0	0	2	0	4
362.0	0	3	0	1
363.0	0	0	0	1
364.0	0	5	0	3
365.0	0	1	0	5
366.0	0	2	0	3
367.0	0	4	0	1
368.0	0	2	0	2
369.0	0	2	0	1
370.0	0	2	0	3
371.0	0	1	0	0
372.0	0	0	0	2
373.0	0	4	0	2
374.0	0	1	0	3
375.0	0	3	0	5
376.0	0	3	0	6
377.0	0	3	0	0
378.0	0	3	0	4
379.0	0	5	0	3
380.0	0	1	0	4
381.0	0	6	0	2
382.0	0	1	0	4
383.0	0	3	0	2
384.0	0	2	0	1
385.0	0	3	0	2
386.0	0	3	0	4
387.0	0	4	0	4
388.0	0	2	0	2
389.0	0	6	0	2
390.0	0	0	0	1
391.0	0	3	0	2
392.0	0	0	0	3
393.0	0	2	0	2
394.0	0	3	0	1
395.0	0	1	0	1
396.0	0	0	0	1
397.0	0	4	0	3
398.0	0	1	0	1
399.0	0	1	0	4
400.0	0	6	0	2
401.0	0	1	0	1
402.0	0	1	0	2
403.0	0	0	0	4
404.0	0	2	0	2
405.0	0	6	0	2
406.0	0	0	0	2
407.0	0	2	0	1
408.0	0	3	0	0
409.0	0	1	0	2
410.0	0	0	0	1
411.0	0	0	0	2
412.0	0	3	0	4
413.0	0	3	0	3
414.0	0	3	0	3
415.0	0	2	0	3
416.0	0	3	0	2
417.0	0	2	0	2
418.0	0	2	0	0
419.0	0	2	0	2
420.0	0	1	0	1
421.0	0	3	0	4
422.0	0	2	0	1
423.0	0	2	0	1
424.0	0	2	0	0
425.0	0	1	0	3
426.0	0	0	0	2
427.0	0	1	0	1
428.0	0	4	0	2
429.0	0	0	0	1
430.0	0	3	0	0
431.0	0	1	0	1
432.0	0	1	0	1
433.0	0	1	0	6
434.0	0	1	0	1
435.0	0	1	0	2
436.0	0	5	0	0
437.0	0	1	0	1
438.0	0	1	0	1
439.0	0	2	0	2
440.0	0	0	0	4
441.0	0	3	0	2
442.0	0	2	0	0
443.0	0	2	0	3
444.0	0	2	0	2
445.0	0	1	0	0
446.0	0	1	0	1
447.0	0	1	0	3
448.0	0	1	0	1
449.0	0	3	0	0
450.0	0	1	0	5
451.0	0	2	0	2
452.0	0	2	0	2
453.0	0	2	0	0
454.0	0	1	0	0
455.0	0	2	0	2
457.0	0	1	0	0
458.0	0	3	0	1
459.0	0	0	0	1
460.0	0	0	0	2
461.0	0	0	0	2
462.0	0	4	0	3
463.0	0	1	0	2
464.0	0	2	0	5
465.0	0	2	0	1
466.0	0	3	0	1
467.0	0	1	0	0
468.0	0	4	0	0
469.0	0	0	0	2
470.0	0	1	0	1
471.0	0	0	0	3
472.0	0	1	0	0
473.0	0	2	0	1
474.0	0	2	0	0
475.0	0	1	0	3
477.0	0	1	0	3
478.0	0	1	0	2
479.0	0	2	0	1
480.0	0	3	0	1
481.0	0	2	0	2
482.0	0	1	0	3
483.0	0	1	0	0
484.0	0	1	0	1
485.0	0	2	0	1
486.0	0	3	0	2
487.0	0	0	0	2
488.0	0	2	0	1
489.0	0	3	0	0
490.0	0	0	0	3
491.0	0	1	0	1
492.0	0	0	0	1
493.0	0	3	0	1
494.0	0	1	0	2
495.0	0	1	0	2
496.0	0	1	0	3
497.0	0	2	0	0
498.0	0	2	0	1
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500.0	0	1	0	1
501.0	0	2	0	1
502.0	0	3	0	3
503.0	0	2	0	1
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505.0	0	1	0	3
506.0	0	4	0	2
507.0	0	0	0	1
508.0	0	1	0	1
509.0	0	2	0	0
510.0	0	0	0	1
511.0	0	1	0	0
515.0	0	0	0	1
516.0	0	1	0	1
518.0	0	1	0	1
520.0	0	1	0	2
521.0	0	0	0	1
522.0	0	3	0	2
523.0	0	1	0	1
524.0	0	0	0	1
525.0	0	1	0	0
527.0	0	2	0	0
531.0	0	0	0	1
532.0	0	0	0	1
533.0	0	2	0	2
534.0	0	0	0	1
535.0	0	1	0	1
536.0	0	1	0	2
537.0	0	1	0	0
538.0	0	2	0	1
539.0	0	1	0	0
540.0	0	0	0	1
541.0	0	2	0	1
544.0	0	0	0	1
545.0	0	2	0	2
547.0	0	1	0	0
548.0	0	1	0	1
549.0	0	1	0	0
552.0	0	0	0	1
554.0	0	1	0	0
555.0	0	0	0	3
556.0	0	0	0	2
557.0	0	0	0	1
558.0	0	2	0	1
559.0	0	1	0	0
560.0	0	3	0	1
561.0	0	1	0	0
563.0	0	0	0	1
564.0	0	0	0	1
565.0	0	1	0	1
567.0	0	1	0	0
568.0	0	0	0	1
569.0	0	1	0	0
570.0	0	1	0	3
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