## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S44F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S44F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S44F.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 12:18:13 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	2154276	18199301	13600747	10434294	1065127	5172885	86865	0.29598	25878803

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003306	11275017	0	11328144
2.0	1.499916	1212514	80920	1170291
3.0	1.745725	240203	1891	232635
4.0	1.867394	91685	310	90065
5.0	1.927616	48696	123	48149
6.0	1.957425	30638	42	30340
7.0	1.97218	21089	26	20900
8.0	1.979483	15093	25	14973
9.0	1.983097	11488	3	11442
10.0	1.984887	9049	1	8999
11.0	1.985772	7229	3	7185
12.0	1.986211	5995	3	5948
13.0	1.986428	5104	2	5045
14.0	1.986535	4201	2	4157
15.0	1.986588	3683	1	3677
16.0	1.986615	3049	0	3030
17.0	1.986628	2682	0	2675
18.0	1.986634	2431	0	2436
19.0	1.986637	2212	0	2187
20.0	1.986639	1849	0	1833
21.0	1.98664	1801	2	1792
22.0	1.98664	1640	0	1645
23.0	1.98664	1445	0	1431
24.0	1.98664	1315	0	1307
25.0	1.98664	1265	0	1258
26.0	1.98664	1147	0	1111
27.0	1.98664	1009	0	1037
28.0	1.98664	999	0	972
29.0	1.98664	897	0	912
30.0	1.98664	821	0	821
31.0	1.98664	780	0	769
32.0	1.98664	763	0	740
33.0	1.98664	679	0	673
34.0	1.98664	623	0	637
35.0	1.98664	616	0	628
36.0	1.98664	578	0	542
37.0	1.98664	522	0	527
38.0	1.98664	514	0	514
39.0	1.98664	499	0	478
40.0	1.98664	436	0	446
41.0	1.98664	411	0	431
42.0	1.98664	406	0	385
43.0	1.98664	382	0	393
44.0	1.98664	400	0	391
45.0	1.98664	383	0	376
46.0	1.98664	326	0	327
47.0	1.98664	337	0	329
48.0	1.98664	316	0	314
49.0	1.98664	320	0	318
50.0	1.98664	307	0	304
51.0	1.98664	259	0	256
52.0	1.98664	249	0	237
53.0	1.98664	232	0	230
54.0	1.98664	222	0	252
55.0	1.98664	258	0	240
56.0	1.98664	219	0	219
57.0	1.98664	223	0	223
58.0	1.98664	218	0	219
59.0	1.98664	204	0	183
60.0	1.98664	195	0	213
61.0	1.98664	178	0	173
62.0	1.98664	180	0	183
63.0	1.98664	196	0	198
64.0	1.98664	174	0	159
65.0	1.98664	178	0	176
66.0	1.98664	171	0	173
67.0	1.98664	150	0	151
68.0	1.98664	123	0	118
69.0	1.98664	121	0	126
70.0	1.98664	132	0	138
71.0	1.98664	143	0	130
72.0	1.98664	134	0	136
73.0	1.98664	142	0	145
74.0	1.98664	117	0	120
75.0	1.98664	118	0	109
76.0	1.98664	106	0	103
77.0	1.98664	95	0	100
78.0	1.98664	115	0	118
79.0	1.98664	94	0	87
80.0	1.98664	100	0	103
81.0	1.98664	114	0	107
82.0	1.98664	93	0	96
83.0	1.98664	91	0	89
84.0	1.98664	98	0	101
85.0	1.98664	91	0	93
86.0	1.98664	89	0	80
87.0	1.98664	81	0	91
88.0	1.98664	96	0	83
89.0	1.98664	71	0	87
90.0	1.98664	96	0	77
91.0	1.98664	67	0	77
92.0	1.98664	71	0	59
93.0	1.98664	58	0	62
94.0	1.98664	72	0	68
95.0	1.98664	63	0	57
96.0	1.98664	56	0	69
97.0	1.98664	62	0	61
98.0	1.98664	58	0	58
99.0	1.98664	70	0	71
100.0	1.98664	65	0	64
101.0	0	58	0	52
102.0	0	63	0	63
103.0	0	60	0	64
104.0	0	62	0	51
105.0	0	57	0	59
106.0	0	45	0	46
107.0	0	42	0	47
108.0	0	42	0	45
109.0	0	51	0	53
110.0	0	46	0	43
111.0	0	45	0	38
112.0	0	39	0	45
113.0	0	47	0	51
114.0	0	47	0	44
115.0	0	48	0	47
116.0	0	48	0	43
117.0	0	38	0	39
118.0	0	43	0	35
119.0	0	29	0	36
120.0	0	47	0	46
121.0	0	40	0	29
122.0	0	25	0	35
123.0	0	37	0	46
124.0	0	38	0	31
125.0	0	38	0	38
126.0	0	37	0	42
127.0	0	45	0	40
128.0	0	37	0	27
129.0	0	31	0	33
130.0	0	30	0	35
131.0	0	29	0	31
132.0	0	37	0	34
133.0	0	30	0	35
134.0	0	26	0	29
135.0	0	36	0	27
136.0	0	27	0	25
137.0	0	31	0	35
138.0	0	38	0	32
139.0	0	24	0	29
140.0	0	25	0	27
141.0	0	27	0	28
142.0	0	31	0	32
143.0	0	29	0	27
144.0	0	33	0	24
145.0	0	23	0	21
146.0	0	19	0	29
147.0	0	21	0	26
148.0	0	30	0	15
149.0	0	17	0	22
150.0	0	20	0	25
151.0	0	20	0	22
152.0	0	21	0	15
153.0	0	19	0	25
154.0	0	32	0	30
155.0	0	26	0	25
156.0	0	25	0	22
157.0	0	19	0	18
158.0	0	26	0	25
159.0	0	18	0	18
160.0	0	26	0	25
161.0	0	16	0	18
162.0	0	17	0	16
163.0	0	17	0	15
164.0	0	22	0	23
165.0	0	20	0	16
166.0	0	19	0	29
167.0	0	25	0	17
168.0	0	18	0	18
169.0	0	17	0	8
170.0	0	13	0	23
171.0	0	18	0	17
172.0	0	13	0	15
173.0	0	19	0	14
174.0	0	17	0	13
175.0	0	8	0	13
176.0	0	13	0	17
177.0	0	12	0	8
178.0	0	11	0	13
179.0	0	21	0	18
180.0	0	12	0	11
181.0	0	13	0	20
182.0	0	14	0	18
183.0	0	15	0	11
184.0	0	12	0	15
185.0	0	18	0	15
186.0	0	19	0	17
187.0	0	17	0	18
188.0	0	15	0	18
189.0	0	16	0	11
190.0	0	15	0	13
191.0	0	11	0	11
192.0	0	13	0	10
193.0	0	8	0	8
194.0	0	8	0	8
195.0	0	10	0	15
196.0	0	14	0	12
197.0	0	9	0	11
198.0	0	14	0	12
199.0	0	13	0	13
200.0	0	10	0	10
201.0	0	8	0	7
202.0	0	12	0	11
203.0	0	7	0	10
204.0	0	12	0	8
205.0	0	10	0	12
206.0	0	7	0	5
207.0	0	9	0	9
208.0	0	6	0	8
209.0	0	11	0	12
210.0	0	11	0	4
211.0	0	7	0	16
212.0	0	8	0	7
213.0	0	16	0	7
214.0	0	2	0	5
215.0	0	7	0	11
216.0	0	9	0	10
217.0	0	7	0	13
218.0	0	14	0	8
219.0	0	12	0	11
220.0	0	15	0	10
221.0	0	4	0	9
222.0	0	8	0	8
223.0	0	5	0	7
224.0	0	13	0	15
225.0	0	9	0	7
226.0	0	11	0	7
227.0	0	4	0	3
228.0	0	9	0	10
229.0	0	7	0	10
230.0	0	12	0	14
231.0	0	12	0	11
232.0	0	9	0	6
233.0	0	8	0	7
234.0	0	7	0	9
235.0	0	9	0	11
236.0	0	14	0	12
237.0	0	6	0	8
238.0	0	10	0	4
239.0	0	7	0	8
240.0	0	5	0	4
241.0	0	4	0	7
242.0	0	9	0	5
243.0	0	4	0	2
244.0	0	2	0	6
245.0	0	2	0	4
246.0	0	9	0	7
247.0	0	6	0	5
248.0	0	4	0	8
249.0	0	9	0	10
250.0	0	10	0	17
251.0	0	10	0	4
252.0	0	7	0	7
253.0	0	10	0	6
254.0	0	6	0	7
255.0	0	7	0	3
256.0	0	7	0	6
257.0	0	3	0	6
258.0	0	4	0	2
259.0	0	6	0	4
260.0	0	5	0	7
261.0	0	3	0	4
262.0	0	7	0	9
263.0	0	5	0	5
264.0	0	5	0	3
265.0	0	5	0	4
266.0	0	4	0	6
267.0	0	5	0	4
268.0	0	8	0	6
269.0	0	2	0	5
270.0	0	7	0	4
271.0	0	4	0	2
272.0	0	6	0	8
273.0	0	2	0	6
274.0	0	6	0	2
275.0	0	2	0	2
276.0	0	5	0	7
277.0	0	6	0	9
278.0	0	6	0	5
279.0	0	5	0	5
280.0	0	5	0	7
281.0	0	10	0	7
282.0	0	6	0	5
283.0	0	4	0	7
284.0	0	4	0	3
285.0	0	9	0	12
286.0	0	9	0	3
287.0	0	3	0	3
288.0	0	4	0	6
289.0	0	5	0	4
290.0	0	5	0	8
291.0	0	5	0	3
292.0	0	5	0	2
293.0	0	3	0	5
294.0	0	1	0	2
295.0	0	5	0	6
296.0	0	9	0	3
297.0	0	1	0	1
298.0	0	2	0	5
299.0	0	3	0	3
300.0	0	3	0	5
301.0	0	5	0	2
302.0	0	6	0	3
303.0	0	2	0	2
304.0	0	2	0	4
305.0	0	1	0	2
306.0	0	3	0	2
307.0	0	1	0	1
308.0	0	4	0	4
309.0	0	4	0	2
310.0	0	2	0	6
311.0	0	2	0	2
312.0	0	4	0	5
313.0	0	3	0	6
314.0	0	5	0	6
315.0	0	7	0	3
316.0	0	3	0	4
317.0	0	5	0	6
318.0	0	1	0	4
319.0	0	3	0	5
320.0	0	8	0	3
321.0	0	2	0	3
322.0	0	5	0	2
323.0	0	3	0	6
324.0	0	6	0	3
325.0	0	5	0	6
326.0	0	5	0	1
327.0	0	4	0	5
328.0	0	4	0	3
329.0	0	3	0	2
330.0	0	3	0	6
331.0	0	1	0	1
332.0	0	5	0	4
333.0	0	3	0	2
334.0	0	3	0	3
335.0	0	2	0	7
336.0	0	6	0	1
337.0	0	1	0	1
338.0	0	3	0	2
339.0	0	1	0	1
340.0	0	2	0	3
341.0	0	1	0	3
342.0	0	3	0	3
343.0	0	3	0	5
344.0	0	4	0	2
345.0	0	3	0	5
346.0	0	3	0	3
347.0	0	6	0	1
348.0	0	0	0	4
349.0	0	1	0	2
350.0	0	4	0	3
351.0	0	4	0	2
352.0	0	2	0	4
353.0	0	4	0	3
354.0	0	3	0	3
355.0	0	3	0	3
356.0	0	4	0	2
357.0	0	1	0	1
358.0	0	6	0	5
359.0	0	1	0	1
360.0	0	0	0	2
361.0	0	2	0	1
362.0	0	2	0	2
363.0	0	1	0	1
364.0	0	2	0	2
365.0	0	1	0	3
366.0	0	1	0	4
367.0	0	2	0	0
368.0	0	4	0	4
369.0	0	4	0	2
370.0	0	3	0	1
371.0	0	2	0	3
372.0	0	3	0	3
373.0	0	1	0	5
374.0	0	2	0	1
375.0	0	5	0	3
376.0	0	1	0	1
377.0	0	2	0	2
378.0	0	3	0	2
379.0	0	2	0	4
380.0	0	2	0	1
381.0	0	2	0	3
382.0	0	3	0	3
383.0	0	4	0	1
384.0	0	1	0	3
385.0	0	2	0	3
386.0	0	5	0	1
387.0	0	0	0	2
388.0	0	2	0	0
389.0	0	0	0	2
390.0	0	1	0	3
391.0	0	2	0	3
392.0	0	4	0	0
393.0	0	2	0	1
394.0	0	1	0	1
395.0	0	1	0	1
396.0	0	0	0	3
397.0	0	1	0	1
398.0	0	1	0	2
399.0	0	5	0	1
400.0	0	0	0	1
401.0	0	2	0	5
402.0	0	5	0	3
403.0	0	2	0	0
404.0	0	1	0	2
405.0	0	2	0	1
406.0	0	2	0	1
407.0	0	1	0	2
408.0	0	1	0	1
409.0	0	1	0	2
410.0	0	2	0	3
411.0	0	2	0	2
412.0	0	2	0	1
413.0	0	2	0	5
414.0	0	1	0	2
415.0	0	2	0	1
416.0	0	4	0	1
417.0	0	1	0	3
418.0	0	2	0	1
419.0	0	3	0	5
420.0	0	2	0	1
421.0	0	5	0	2
422.0	0	0	0	2
423.0	0	2	0	1
424.0	0	1	0	1
425.0	0	0	0	2
426.0	0	1	0	2
427.0	0	3	0	0
428.0	0	1	0	3
429.0	0	2	0	1
430.0	0	2	0	1
431.0	0	2	0	2
432.0	0	2	0	1
433.0	0	1	0	1
434.0	0	1	0	5
435.0	0	4	0	1
436.0	0	2	0	0
437.0	0	2	0	4
438.0	0	1	0	2
439.0	0	0	0	1
440.0	0	3	0	0
441.0	0	0	0	2
442.0	0	3	0	2
443.0	0	1	0	3
444.0	0	4	0	3
445.0	0	1	0	2
446.0	0	3	0	1
447.0	0	2	0	3
448.0	0	2	0	0
449.0	0	0	0	1
450.0	0	2	0	0
452.0	0	1	0	1
453.0	0	0	0	4
454.0	0	1	0	0
455.0	0	3	0	1
456.0	0	0	0	3
457.0	0	1	0	1
458.0	0	1	0	0
459.0	0	3	0	1
461.0	0	2	0	0
462.0	0	0	0	1
463.0	0	0	0	1
464.0	0	2	0	3
465.0	0	2	0	1
466.0	0	1	0	1
468.0	0	2	0	1
469.0	0	1	0	1
470.0	0	0	0	3
471.0	0	1	0	3
472.0	0	2	0	3
473.0	0	3	0	2
474.0	0	3	0	1
475.0	0	1	0	0
476.0	0	1	0	0
477.0	0	2	0	1
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480.0	0	1	0	0
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482.0	0	1	0	1
484.0	0	0	0	2
486.0	0	0	0	1
487.0	0	1	0	1
488.0	0	1	0	0
489.0	0	1	0	1
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491.0	0	1	0	0
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508.0	0	2	0	2
510.0	0	0	0	1
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512.0	0	0	0	1
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514.0	0	0	0	2
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516.0	0	1	0	1
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520.0	0	1	0	0
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524.0	0	2	0	0
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527.0	0	1	0	1
529.0	0	1	0	1
532.0	0	0	0	2
533.0	0	1	0	1
535.0	0	1	0	1
536.0	0	0	0	1
537.0	0	3	0	1
538.0	0	0	0	1
539.0	0	2	0	2
540.0	0	1	0	0
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543.0	0	0	0	2
544.0	0	1	0	0
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546.0	0	1	0	1
547.0	0	3	0	1
549.0	0	0	0	1
552.0	0	1	0	0
553.0	0	0	0	1
554.0	0	0	0	1
557.0	0	2	0	1
560.0	0	1	0	0
561.0	0	0	0	1
562.0	0	1	0	2
563.0	0	0	0	1
564.0	0	0	0	1
565.0	0	1	0	0
566.0	0	1	0	0
567.0	0	1	0	0
569.0	0	1	0	1
573.0	0	1	0	0
574.0	0	0	0	1
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