## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S53F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S53F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S53F.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 12:44:18 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	1926638	17501338	10600958	8394504	1006620	5224936	73402	0.310228	23327808

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.002828	10666947	0	10710314
2.0	1.476419	1120226	67251	1085922
3.0	1.700075	218209	1617	211888
4.0	1.805698	81915	340	80580
5.0	1.855579	43582	130	43110
6.0	1.879136	26865	47	26662
7.0	1.89026	18315	41	18142
8.0	1.895514	13254	18	13183
9.0	1.897995	10437	18	10363
10.0	1.899167	8025	9	7986
11.0	1.89972	6750	8	6717
12.0	1.899982	5474	5	5457
13.0	1.900105	4639	4	4569
14.0	1.900163	3905	6	3934
15.0	1.900191	3503	1	3464
16.0	1.900204	2937	3	2923
17.0	1.90021	2584	2	2556
18.0	1.900213	2284	0	2256
19.0	1.900214	2058	0	2057
20.0	1.900215	1853	3	1854
21.0	1.900215	1643	1	1632
22.0	1.900215	1493	1	1497
23.0	1.900215	1431	0	1410
24.0	1.900215	1274	1	1281
25.0	1.900215	1155	3	1137
26.0	1.900215	1074	0	1041
27.0	1.900215	982	0	981
28.0	1.900215	836	0	869
29.0	1.900215	878	0	866
30.0	1.900215	827	0	800
31.0	1.900215	728	0	742
32.0	1.900215	672	0	663
33.0	1.900215	678	0	677
34.0	1.900215	641	0	649
35.0	1.900215	597	0	613
36.0	1.900215	614	0	572
37.0	1.900215	512	0	509
38.0	1.900215	488	0	507
39.0	1.900215	493	0	488
40.0	1.900215	435	0	405
41.0	1.900215	388	0	405
42.0	1.900215	417	0	432
43.0	1.900215	391	0	395
44.0	1.900215	430	0	413
45.0	1.900215	387	0	381
46.0	1.900215	373	0	359
47.0	1.900215	301	0	307
48.0	1.900215	311	0	320
49.0	1.900215	298	0	286
50.0	1.900215	289	0	280
51.0	1.900215	246	0	253
52.0	1.900215	261	0	274
53.0	1.900215	254	0	244
54.0	1.900215	248	0	241
55.0	1.900215	237	0	231
56.0	1.900215	229	0	234
57.0	1.900215	214	0	223
58.0	1.900215	204	0	203
59.0	1.900215	222	0	208
60.0	1.900215	186	0	179
61.0	1.900215	190	0	205
62.0	1.900215	190	0	183
63.0	1.900215	162	0	152
64.0	1.900215	143	0	148
65.0	1.900215	146	0	154
66.0	1.900215	168	0	166
67.0	1.900215	155	0	157
68.0	1.900215	166	0	159
69.0	1.900215	159	0	156
70.0	1.900215	146	0	136
71.0	1.900215	115	0	131
72.0	1.900215	154	0	140
73.0	1.900215	115	0	120
74.0	1.900215	116	0	120
75.0	1.900215	119	0	126
76.0	1.900215	133	0	117
77.0	1.900215	97	0	85
78.0	1.900215	95	0	108
79.0	1.900215	108	0	115
80.0	1.900215	110	0	105
81.0	1.900215	112	0	112
82.0	1.900215	89	0	86
83.0	1.900215	96	0	95
84.0	1.900215	84	0	87
85.0	1.900215	96	0	92
86.0	1.900215	92	0	85
87.0	1.900215	85	0	94
88.0	1.900215	99	0	94
89.0	1.900215	75	0	79
90.0	1.900215	88	0	74
91.0	1.900215	66	0	88
92.0	1.900215	81	0	73
93.0	1.900215	81	0	85
94.0	1.900215	87	0	80
95.0	1.900215	72	0	66
96.0	1.900215	66	0	64
97.0	1.900215	62	0	62
98.0	1.900215	61	0	68
99.0	1.900215	70	0	78
100.0	1.900215	75	0	69
101.0	0	64	0	59
102.0	0	68	0	72
103.0	0	59	0	48
104.0	0	56	0	60
105.0	0	50	0	53
106.0	0	60	0	58
107.0	0	56	0	61
108.0	0	65	0	67
109.0	0	50	0	65
110.0	0	78	0	63
111.0	0	61	0	54
112.0	0	47	0	54
113.0	0	56	0	50
114.0	0	58	0	52
115.0	0	48	0	50
116.0	0	41	0	33
117.0	0	41	0	54
118.0	0	45	0	46
119.0	0	52	0	48
120.0	0	52	0	45
121.0	0	31	0	34
122.0	0	41	0	37
123.0	0	37	0	47
124.0	0	43	0	37
125.0	0	45	0	45
126.0	0	40	0	45
127.0	0	40	0	33
128.0	0	47	0	45
129.0	0	36	0	35
130.0	0	29	0	42
131.0	0	50	0	47
132.0	0	33	0	35
133.0	0	46	0	41
134.0	0	39	0	35
135.0	0	35	0	31
136.0	0	36	0	40
137.0	0	32	0	39
138.0	0	40	0	28
139.0	0	33	0	34
140.0	0	27	0	32
141.0	0	34	0	29
142.0	0	30	0	29
143.0	0	33	0	32
144.0	0	19	0	23
145.0	0	32	0	36
146.0	0	31	0	24
147.0	0	25	0	25
148.0	0	25	0	33
149.0	0	32	0	38
150.0	0	43	0	39
151.0	0	34	0	27
152.0	0	27	0	29
153.0	0	24	0	21
154.0	0	23	0	27
155.0	0	37	0	33
156.0	0	29	0	27
157.0	0	26	0	21
158.0	0	23	0	25
159.0	0	19	0	27
160.0	0	23	0	23
161.0	0	24	0	23
162.0	0	25	0	30
163.0	0	21	0	14
164.0	0	17	0	19
165.0	0	21	0	18
166.0	0	23	0	23
167.0	0	23	0	26
168.0	0	22	0	23
169.0	0	32	0	21
170.0	0	19	0	21
171.0	0	23	0	21
172.0	0	13	0	15
173.0	0	19	0	26
174.0	0	13	0	15
175.0	0	20	0	16
176.0	0	18	0	26
177.0	0	26	0	17
178.0	0	18	0	12
179.0	0	15	0	18
180.0	0	18	0	21
181.0	0	21	0	20
182.0	0	18	0	27
183.0	0	21	0	20
184.0	0	21	0	16
185.0	0	21	0	18
186.0	0	18	0	20
187.0	0	19	0	16
188.0	0	17	0	14
189.0	0	15	0	20
190.0	0	22	0	22
191.0	0	11	0	7
192.0	0	16	0	12
193.0	0	9	0	16
194.0	0	16	0	15
195.0	0	13	0	7
196.0	0	11	0	14
197.0	0	12	0	16
198.0	0	14	0	11
199.0	0	16	0	15
200.0	0	13	0	16
201.0	0	16	0	17
202.0	0	15	0	20
203.0	0	18	0	7
204.0	0	12	0	11
205.0	0	8	0	18
206.0	0	17	0	16
207.0	0	18	0	15
208.0	0	12	0	15
209.0	0	22	0	22
210.0	0	12	0	10
211.0	0	16	0	17
212.0	0	13	0	6
213.0	0	14	0	22
214.0	0	14	0	12
215.0	0	13	0	16
216.0	0	13	0	9
217.0	0	11	0	11
218.0	0	13	0	11
219.0	0	12	0	11
220.0	0	12	0	15
221.0	0	15	0	11
222.0	0	12	0	16
223.0	0	11	0	8
224.0	0	5	0	6
225.0	0	15	0	15
226.0	0	7	0	5
227.0	0	10	0	7
228.0	0	10	0	10
229.0	0	5	0	7
230.0	0	11	0	11
231.0	0	10	0	11
232.0	0	11	0	10
233.0	0	12	0	12
234.0	0	9	0	10
235.0	0	8	0	11
236.0	0	17	0	14
237.0	0	9	0	8
238.0	0	9	0	8
239.0	0	6	0	8
240.0	0	8	0	5
241.0	0	6	0	7
242.0	0	9	0	5
243.0	0	5	0	6
244.0	0	6	0	11
245.0	0	11	0	10
246.0	0	8	0	7
247.0	0	9	0	8
248.0	0	3	0	3
249.0	0	6	0	9
250.0	0	6	0	7
251.0	0	5	0	9
252.0	0	16	0	15
253.0	0	9	0	4
254.0	0	11	0	8
255.0	0	6	0	7
256.0	0	6	0	9
257.0	0	12	0	10
258.0	0	5	0	3
259.0	0	6	0	2
260.0	0	3	0	4
261.0	0	5	0	11
262.0	0	6	0	3
263.0	0	5	0	5
264.0	0	6	0	8
265.0	0	8	0	12
266.0	0	7	0	5
267.0	0	11	0	9
268.0	0	1	0	2
269.0	0	7	0	7
270.0	0	8	0	5
271.0	0	1	0	2
272.0	0	5	0	3
273.0	0	1	0	4
274.0	0	6	0	12
275.0	0	10	0	8
276.0	0	9	0	9
277.0	0	10	0	4
278.0	0	4	0	7
279.0	0	4	0	5
280.0	0	5	0	1
281.0	0	6	0	10
282.0	0	10	0	5
283.0	0	7	0	7
284.0	0	4	0	6
285.0	0	6	0	6
286.0	0	5	0	7
287.0	0	5	0	5
288.0	0	9	0	5
289.0	0	7	0	7
290.0	0	3	0	5
291.0	0	7	0	8
292.0	0	4	0	3
293.0	0	6	0	10
294.0	0	12	0	8
295.0	0	6	0	9
296.0	0	6	0	5
297.0	0	9	0	7
298.0	0	4	0	2
299.0	0	9	0	11
300.0	0	4	0	7
301.0	0	8	0	7
302.0	0	6	0	4
303.0	0	6	0	3
304.0	0	3	0	1
305.0	0	3	0	7
306.0	0	6	0	8
307.0	0	4	0	7
308.0	0	7	0	4
309.0	0	5	0	5
310.0	0	6	0	5
311.0	0	1	0	4
312.0	0	7	0	1
313.0	0	3	0	3
314.0	0	1	0	1
315.0	0	2	0	5
316.0	0	4	0	3
317.0	0	5	0	1
318.0	0	1	0	5
319.0	0	2	0	3
320.0	0	3	0	2
321.0	0	3	0	2
322.0	0	4	0	6
323.0	0	5	0	1
324.0	0	2	0	2
325.0	0	1	0	4
326.0	0	3	0	2
327.0	0	2	0	4
328.0	0	5	0	2
329.0	0	2	0	3
330.0	0	2	0	4
331.0	0	3	0	3
332.0	0	4	0	2
333.0	0	2	0	1
334.0	0	4	0	7
335.0	0	1	0	2
336.0	0	5	0	1
337.0	0	2	0	3
338.0	0	3	0	2
339.0	0	5	0	6
340.0	0	3	0	3
341.0	0	4	0	2
342.0	0	2	0	5
343.0	0	4	0	6
344.0	0	3	0	4
345.0	0	6	0	4
346.0	0	3	0	3
347.0	0	8	0	5
348.0	0	3	0	0
349.0	0	2	0	3
350.0	0	1	0	2
351.0	0	5	0	9
352.0	0	3	0	2
353.0	0	4	0	3
354.0	0	6	0	2
355.0	0	1	0	4
356.0	0	1	0	5
357.0	0	6	0	1
358.0	0	2	0	1
359.0	0	3	0	4
360.0	0	1	0	3
361.0	0	4	0	1
362.0	0	0	0	3
363.0	0	3	0	3
364.0	0	1	0	3
365.0	0	3	0	5
366.0	0	5	0	1
367.0	0	2	0	5
368.0	0	4	0	1
369.0	0	5	0	1
370.0	0	2	0	5
371.0	0	2	0	3
372.0	0	2	0	1
373.0	0	3	0	4
374.0	0	3	0	1
375.0	0	3	0	7
376.0	0	4	0	2
377.0	0	4	0	3
378.0	0	2	0	3
379.0	0	1	0	5
380.0	0	5	0	3
381.0	0	5	0	2
382.0	0	3	0	1
383.0	0	2	0	4
384.0	0	3	0	3
385.0	0	2	0	1
386.0	0	3	0	5
387.0	0	1	0	2
388.0	0	3	0	2
389.0	0	1	0	5
390.0	0	5	0	1
391.0	0	4	0	5
392.0	0	4	0	3
393.0	0	3	0	1
394.0	0	2	0	3
396.0	0	3	0	3
397.0	0	2	0	2
398.0	0	2	0	2
399.0	0	3	0	3
400.0	0	3	0	4
401.0	0	2	0	1
402.0	0	3	0	1
403.0	0	0	0	1
404.0	0	1	0	1
405.0	0	1	0	1
406.0	0	0	0	4
407.0	0	4	0	1
408.0	0	2	0	0
409.0	0	0	0	3
410.0	0	2	0	2
411.0	0	1	0	4
412.0	0	3	0	3
413.0	0	5	0	2
414.0	0	2	0	4
415.0	0	1	0	1
416.0	0	3	0	1
417.0	0	2	0	1
418.0	0	2	0	2
419.0	0	2	0	2
420.0	0	3	0	2
421.0	0	2	0	2
422.0	0	1	0	2
423.0	0	2	0	0
424.0	0	1	0	2
425.0	0	2	0	0
426.0	0	0	0	3
427.0	0	2	0	3
428.0	0	4	0	2
429.0	0	1	0	3
430.0	0	3	0	2
431.0	0	3	0	1
432.0	0	2	0	0
435.0	0	0	0	1
436.0	0	2	0	4
437.0	0	1	0	2
438.0	0	3	0	3
439.0	0	1	0	2
440.0	0	5	0	2
442.0	0	1	0	3
443.0	0	2	0	1
444.0	0	2	0	0
445.0	0	2	0	3
446.0	0	0	0	1
447.0	0	0	0	3
448.0	0	4	0	3
449.0	0	1	0	0
450.0	0	4	0	1
451.0	0	0	0	2
453.0	0	1	0	0
454.0	0	3	0	4
455.0	0	1	0	0
456.0	0	1	0	1
457.0	0	1	0	1
458.0	0	1	0	0
459.0	0	0	0	1
460.0	0	0	0	3
461.0	0	4	0	4
462.0	0	1	0	2
463.0	0	4	0	1
464.0	0	1	0	3
465.0	0	3	0	0
466.0	0	1	0	1
467.0	0	1	0	1
468.0	0	0	0	1
469.0	0	2	0	2
470.0	0	2	0	3
471.0	0	2	0	2
472.0	0	1	0	1
473.0	0	3	0	1
474.0	0	1	0	1
475.0	0	1	0	1
476.0	0	0	0	1
477.0	0	2	0	2
478.0	0	0	0	3
479.0	0	4	0	1
480.0	0	0	0	1
481.0	0	3	0	0
483.0	0	1	0	4
484.0	0	1	0	2
485.0	0	2	0	1
486.0	0	3	0	0
487.0	0	1	0	1
488.0	0	1	0	1
489.0	0	1	0	2
490.0	0	1	0	0
491.0	0	1	0	1
493.0	0	1	0	1
494.0	0	1	0	0
497.0	0	0	0	1
500.0	0	1	0	3
501.0	0	2	0	2
502.0	0	0	0	1
503.0	0	1	0	1
504.0	0	2	0	2
505.0	0	1	0	1
506.0	0	3	0	1
507.0	0	1	0	1
508.0	0	1	0	2
509.0	0	0	0	3
510.0	0	2	0	1
511.0	0	2	0	0
512.0	0	2	0	1
514.0	0	0	0	1
515.0	0	2	0	0
516.0	0	0	0	1
517.0	0	1	0	3
518.0	0	3	0	1
519.0	0	0	0	2
520.0	0	1	0	1
521.0	0	2	0	2
522.0	0	1	0	3
523.0	0	1	0	2
524.0	0	4	0	1
525.0	0	3	0	0
526.0	0	0	0	4
527.0	0	1	0	1
528.0	0	2	0	2
529.0	0	1	0	2
530.0	0	4	0	1
531.0	0	2	0	3
532.0	0	2	0	1
533.0	0	1	0	1
534.0	0	1	0	0
535.0	0	1	0	3
536.0	0	1	0	0
537.0	0	1	0	2
538.0	0	1	0	3
539.0	0	3	0	2
540.0	0	1	0	2
541.0	0	3	0	0
542.0	0	1	0	1
543.0	0	0	0	1
544.0	0	3	0	2
545.0	0	1	0	3
547.0	0	3	0	0
548.0	0	1	0	4
550.0	0	2	0	0
551.0	0	1	0	0
552.0	0	2	0	0
554.0	0	0	0	2
555.0	0	1	0	1
556.0	0	0	0	2
557.0	0	1	0	2
558.0	0	3	0	1
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