## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S76F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S76F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S76F.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 13:12:23 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	2011473	20154476	11558662	8779727	1086662	7190551	86330	0.365492	21161909

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.002574	11189198	0	11235468
2.0	1.389384	1258070	74480	1222118
3.0	1.538621	235036	2646	227628
4.0	1.5962	81783	726	80225
5.0	1.618414	41754	296	41349
6.0	1.626985	25871	161	25600
7.0	1.630292	17849	85	17692
8.0	1.631568	13034	55	12972
9.0	1.63206	9895	39	9822
10.0	1.63225	7972	31	7951
11.0	1.632323	6559	20	6534
12.0	1.632351	5597	5	5535
13.0	1.632362	4587	13	4584
14.0	1.632366	3996	6	4002
15.0	1.632368	3663	4	3629
16.0	1.632369	3181	6	3192
17.0	1.632369	2812	2	2783
18.0	1.632369	2435	3	2427
19.0	1.632369	2357	1	2347
20.0	1.632369	2094	2	2061
21.0	1.632369	1899	2	1917
22.0	1.632369	1732	0	1721
23.0	1.632369	1638	2	1610
24.0	1.632369	1473	1	1481
25.0	1.632369	1360	1	1355
26.0	1.632369	1298	0	1287
27.0	1.632369	1240	0	1246
28.0	1.632369	1123	0	1127
29.0	1.632369	1095	0	1110
30.0	1.632369	1026	0	970
31.0	1.632369	945	0	972
32.0	1.632369	879	0	883
33.0	1.632369	842	0	808
34.0	1.632369	764	0	776
35.0	1.632369	758	0	762
36.0	1.632369	709	0	704
37.0	1.632369	686	0	683
38.0	1.632369	696	0	693
39.0	1.632369	658	0	659
40.0	1.632369	579	0	575
41.0	1.632369	586	0	579
42.0	1.632369	566	0	553
43.0	1.632369	536	0	552
44.0	1.632369	519	0	513
45.0	1.632369	470	0	471
46.0	1.632369	439	0	438
47.0	1.632369	466	0	476
48.0	1.632369	435	0	432
49.0	1.632369	443	0	426
50.0	1.632369	378	0	360
51.0	1.632369	343	0	360
52.0	1.632369	369	0	367
53.0	1.632369	368	0	374
54.0	1.632369	350	0	332
55.0	1.632369	297	0	289
56.0	1.632369	336	0	342
57.0	1.632369	340	0	348
58.0	1.632369	331	0	315
59.0	1.632369	256	0	275
60.0	1.632369	264	0	248
61.0	1.632369	260	0	277
62.0	1.632369	260	0	264
63.0	1.632369	296	0	269
64.0	1.632369	243	0	259
65.0	1.632369	244	0	244
66.0	1.632369	238	0	230
67.0	1.632369	230	0	225
68.0	1.632369	222	0	224
69.0	1.632369	220	0	226
70.0	1.632369	222	0	220
71.0	1.632369	198	0	195
72.0	1.632369	181	0	187
73.0	1.632369	194	0	184
74.0	1.632369	183	0	181
75.0	1.632369	188	0	187
76.0	1.632369	205	0	216
77.0	1.632369	186	0	200
78.0	1.632369	195	0	169
79.0	1.632369	173	0	166
80.0	1.632369	180	0	186
81.0	1.632369	163	0	163
82.0	1.632369	158	0	161
83.0	1.632369	145	0	153
84.0	1.632369	149	0	147
85.0	1.632369	144	0	151
86.0	1.632369	174	0	165
87.0	1.632369	154	0	136
88.0	1.632369	135	0	126
89.0	1.632369	134	0	141
90.0	1.632369	128	0	141
91.0	1.632369	137	0	111
92.0	1.632369	120	0	130
93.0	1.632369	133	0	123
94.0	1.632369	89	0	106
95.0	1.632369	130	0	136
96.0	1.632369	129	0	126
97.0	1.632369	122	0	122
98.0	1.632369	114	0	120
99.0	1.632369	125	0	128
100.0	1.632369	135	0	113
101.0	0	105	0	113
102.0	0	104	0	96
103.0	0	105	0	109
104.0	0	102	0	94
105.0	0	88	0	93
106.0	0	103	0	107
107.0	0	102	0	104
108.0	0	83	0	92
109.0	0	103	0	96
110.0	0	85	0	74
111.0	0	86	0	101
112.0	0	101	0	94
113.0	0	78	0	75
114.0	0	107	0	100
115.0	0	90	0	98
116.0	0	88	0	80
117.0	0	79	0	80
118.0	0	84	0	71
119.0	0	68	0	76
120.0	0	81	0	79
121.0	0	73	0	83
122.0	0	65	0	60
123.0	0	78	0	79
124.0	0	77	0	85
125.0	0	73	0	64
126.0	0	78	0	67
127.0	0	51	0	54
128.0	0	70	0	72
129.0	0	70	0	74
130.0	0	72	0	81
131.0	0	68	0	71
132.0	0	59	0	66
133.0	0	69	0	58
134.0	0	66	0	64
135.0	0	73	0	60
136.0	0	50	0	65
137.0	0	55	0	57
138.0	0	68	0	66
139.0	0	53	0	54
140.0	0	64	0	56
141.0	0	57	0	52
142.0	0	48	0	47
143.0	0	46	0	57
144.0	0	57	0	49
145.0	0	60	0	65
146.0	0	62	0	62
147.0	0	51	0	54
148.0	0	54	0	51
149.0	0	46	0	56
150.0	0	54	0	46
151.0	0	50	0	54
152.0	0	57	0	47
153.0	0	52	0	52
154.0	0	52	0	56
155.0	0	49	0	39
156.0	0	41	0	53
157.0	0	54	0	42
158.0	0	64	0	68
159.0	0	51	0	49
160.0	0	41	0	48
161.0	0	50	0	44
162.0	0	42	0	41
163.0	0	43	0	48
164.0	0	33	0	36
165.0	0	56	0	48
166.0	0	34	0	38
167.0	0	48	0	54
168.0	0	42	0	31
169.0	0	50	0	46
170.0	0	32	0	39
171.0	0	38	0	46
172.0	0	50	0	40
173.0	0	39	0	33
174.0	0	31	0	39
175.0	0	41	0	37
176.0	0	29	0	34
177.0	0	39	0	34
178.0	0	36	0	29
179.0	0	35	0	35
180.0	0	29	0	35
181.0	0	31	0	34
182.0	0	34	0	29
183.0	0	35	0	36
184.0	0	33	0	32
185.0	0	32	0	33
186.0	0	49	0	49
187.0	0	33	0	36
188.0	0	36	0	29
189.0	0	22	0	23
190.0	0	31	0	33
191.0	0	28	0	27
192.0	0	28	0	33
193.0	0	33	0	31
194.0	0	30	0	44
195.0	0	43	0	27
196.0	0	24	0	30
197.0	0	36	0	25
198.0	0	26	0	20
199.0	0	19	0	29
200.0	0	35	0	33
201.0	0	30	0	32
202.0	0	28	0	26
203.0	0	19	0	24
204.0	0	32	0	20
205.0	0	21	0	23
206.0	0	16	0	24
207.0	0	27	0	36
208.0	0	31	0	18
209.0	0	24	0	18
210.0	0	25	0	30
211.0	0	25	0	27
212.0	0	25	0	24
213.0	0	25	0	23
214.0	0	27	0	25
215.0	0	20	0	23
216.0	0	18	0	22
217.0	0	22	0	21
218.0	0	27	0	21
219.0	0	19	0	23
220.0	0	19	0	19
221.0	0	23	0	21
222.0	0	23	0	14
223.0	0	12	0	23
224.0	0	23	0	20
225.0	0	19	0	21
226.0	0	22	0	26
227.0	0	17	0	19
228.0	0	17	0	19
229.0	0	29	0	11
230.0	0	20	0	26
231.0	0	17	0	29
232.0	0	30	0	24
233.0	0	20	0	12
234.0	0	17	0	18
235.0	0	17	0	22
236.0	0	20	0	20
237.0	0	21	0	19
238.0	0	20	0	17
239.0	0	17	0	21
240.0	0	19	0	17
241.0	0	14	0	17
242.0	0	21	0	16
243.0	0	20	0	20
244.0	0	19	0	19
245.0	0	15	0	18
246.0	0	26	0	24
247.0	0	12	0	15
248.0	0	18	0	12
249.0	0	16	0	17
250.0	0	14	0	17
251.0	0	18	0	23
252.0	0	20	0	19
253.0	0	21	0	14
254.0	0	9	0	11
255.0	0	9	0	20
256.0	0	19	0	11
257.0	0	18	0	8
258.0	0	6	0	17
259.0	0	14	0	14
260.0	0	20	0	15
261.0	0	13	0	19
262.0	0	27	0	26
263.0	0	21	0	16
264.0	0	11	0	15
265.0	0	20	0	17
266.0	0	12	0	18
267.0	0	16	0	16
268.0	0	18	0	16
269.0	0	17	0	13
270.0	0	19	0	15
271.0	0	19	0	16
272.0	0	4	0	10
273.0	0	15	0	13
274.0	0	11	0	14
275.0	0	17	0	14
276.0	0	14	0	13
277.0	0	15	0	18
278.0	0	14	0	24
279.0	0	18	0	17
280.0	0	16	0	10
281.0	0	16	0	13
282.0	0	16	0	17
283.0	0	15	0	9
284.0	0	11	0	15
285.0	0	9	0	6
286.0	0	13	0	18
287.0	0	11	0	11
288.0	0	13	0	13
289.0	0	10	0	8
290.0	0	13	0	20
291.0	0	13	0	12
292.0	0	16	0	19
293.0	0	16	0	7
294.0	0	12	0	8
295.0	0	12	0	16
296.0	0	12	0	10
297.0	0	16	0	11
298.0	0	8	0	13
299.0	0	11	0	11
300.0	0	12	0	13
301.0	0	12	0	12
302.0	0	10	0	12
303.0	0	16	0	10
304.0	0	9	0	10
305.0	0	8	0	6
306.0	0	9	0	11
307.0	0	10	0	15
308.0	0	15	0	15
309.0	0	6	0	6
310.0	0	10	0	8
311.0	0	11	0	4
312.0	0	7	0	14
313.0	0	11	0	9
314.0	0	8	0	13
315.0	0	9	0	10
316.0	0	19	0	9
317.0	0	5	0	4
318.0	0	9	0	11
319.0	0	14	0	16
320.0	0	9	0	7
321.0	0	7	0	7
322.0	0	6	0	7
323.0	0	8	0	7
324.0	0	4	0	5
325.0	0	12	0	8
326.0	0	5	0	12
327.0	0	9	0	12
328.0	0	14	0	15
329.0	0	17	0	9
330.0	0	6	0	5
331.0	0	9	0	10
332.0	0	9	0	15
333.0	0	17	0	10
334.0	0	6	0	5
335.0	0	5	0	5
336.0	0	5	0	5
337.0	0	5	0	12
338.0	0	10	0	8
339.0	0	6	0	4
340.0	0	8	0	6
341.0	0	7	0	9
342.0	0	10	0	9
343.0	0	8	0	9
344.0	0	9	0	7
345.0	0	7	0	9
346.0	0	7	0	11
347.0	0	10	0	4
348.0	0	9	0	12
349.0	0	9	0	6
350.0	0	6	0	9
351.0	0	5	0	9
352.0	0	13	0	11
353.0	0	9	0	9
354.0	0	7	0	6
355.0	0	8	0	6
356.0	0	7	0	7
357.0	0	8	0	3
358.0	0	2	0	8
359.0	0	8	0	7
360.0	0	8	0	6
361.0	0	8	0	9
362.0	0	6	0	8
363.0	0	9	0	6
364.0	0	9	0	9
365.0	0	5	0	6
366.0	0	8	0	10
367.0	0	12	0	8
368.0	0	4	0	5
369.0	0	6	0	7
370.0	0	11	0	8
371.0	0	5	0	12
372.0	0	8	0	7
373.0	0	10	0	3
374.0	0	3	0	7
375.0	0	6	0	3
376.0	0	3	0	7
377.0	0	6	0	11
378.0	0	6	0	8
379.0	0	11	0	10
380.0	0	11	0	11
381.0	0	9	0	9
382.0	0	10	0	2
383.0	0	6	0	6
384.0	0	4	0	9
385.0	0	6	0	8
386.0	0	9	0	9
387.0	0	9	0	4
388.0	0	4	0	7
389.0	0	8	0	5
390.0	0	3	0	5
391.0	0	9	0	3
392.0	0	5	0	5
393.0	0	6	0	12
394.0	0	7	0	10
395.0	0	7	0	8
396.0	0	10	0	4
397.0	0	6	0	5
398.0	0	7	0	7
399.0	0	4	0	6
400.0	0	7	0	3
401.0	0	1	0	7
402.0	0	7	0	5
403.0	0	8	0	3
404.0	0	7	0	7
405.0	0	3	0	8
406.0	0	5	0	7
407.0	0	8	0	3
408.0	0	7	0	6
409.0	0	4	0	1
410.0	0	4	0	8
411.0	0	6	0	5
412.0	0	5	0	5
413.0	0	6	0	7
414.0	0	7	0	8
415.0	0	4	0	4
416.0	0	6	0	5
417.0	0	5	0	5
418.0	0	4	0	5
419.0	0	5	0	7
420.0	0	12	0	6
421.0	0	2	0	6
422.0	0	5	0	4
423.0	0	6	0	4
424.0	0	4	0	6
425.0	0	5	0	7
426.0	0	7	0	8
427.0	0	4	0	4
428.0	0	8	0	5
429.0	0	7	0	5
430.0	0	4	0	4
431.0	0	4	0	3
432.0	0	3	0	4
433.0	0	3	0	6
434.0	0	7	0	6
435.0	0	6	0	6
436.0	0	4	0	5
437.0	0	5	0	5
438.0	0	3	0	7
439.0	0	5	0	5
440.0	0	10	0	7
441.0	0	8	0	3
442.0	0	3	0	5
443.0	0	4	0	3
444.0	0	6	0	7
445.0	0	4	0	8
446.0	0	5	0	4
447.0	0	5	0	2
448.0	0	5	0	5
449.0	0	4	0	7
450.0	0	4	0	2
451.0	0	3	0	2
452.0	0	2	0	8
453.0	0	4	0	4
454.0	0	4	0	4
455.0	0	7	0	3
456.0	0	3	0	4
457.0	0	7	0	5
458.0	0	2	0	4
459.0	0	6	0	8
460.0	0	8	0	4
461.0	0	4	0	2
462.0	0	4	0	2
463.0	0	2	0	3
464.0	0	3	0	4
465.0	0	3	0	4
466.0	0	5	0	7
467.0	0	3	0	4
468.0	0	4	0	5
469.0	0	8	0	1
470.0	0	5	0	2
471.0	0	4	0	2
472.0	0	0	0	5
473.0	0	2	0	6
474.0	0	4	0	6
475.0	0	5	0	5
476.0	0	6	0	6
477.0	0	8	0	8
478.0	0	6	0	6
479.0	0	3	0	4
480.0	0	7	0	7
481.0	0	9	0	5
482.0	0	3	0	4
483.0	0	3	0	6
484.0	0	7	0	5
485.0	0	6	0	8
486.0	0	5	0	2
487.0	0	1	0	2
488.0	0	4	0	3
489.0	0	6	0	3
490.0	0	3	0	2
491.0	0	4	0	1
492.0	0	3	0	4
493.0	0	1	0	6
494.0	0	4	0	4
495.0	0	4	0	0
496.0	0	4	0	7
497.0	0	2	0	5
498.0	0	6	0	6
499.0	0	5	0	4
500.0	0	5	0	7
501.0	0	9	0	2
502.0	0	3	0	2
503.0	0	1	0	4
504.0	0	3	0	3
505.0	0	5	0	4
506.0	0	1	0	6
507.0	0	2	0	5
508.0	0	8	0	5
509.0	0	2	0	1
510.0	0	8	0	5
511.0	0	2	0	0
512.0	0	1	0	1
513.0	0	4	0	2
514.0	0	1	0	1
515.0	0	0	0	1
516.0	0	3	0	6
517.0	0	3	0	3
518.0	0	2	0	6
519.0	0	0	0	1
520.0	0	4	0	4
521.0	0	7	0	4
522.0	0	6	0	0
523.0	0	0	0	4
524.0	0	1	0	3
525.0	0	0	0	3
526.0	0	5	0	0
527.0	0	4	0	1
528.0	0	0	0	1
529.0	0	3	0	3
530.0	0	0	0	4
531.0	0	3	0	5
532.0	0	3	0	2
533.0	0	3	0	3
534.0	0	5	0	1
535.0	0	4	0	0
536.0	0	2	0	2
537.0	0	1	0	3
538.0	0	1	0	5
539.0	0	3	0	5
540.0	0	3	0	2
541.0	0	4	0	4
542.0	0	4	0	7
543.0	0	8	0	3
544.0	0	1	0	1
545.0	0	4	0	4
546.0	0	2	0	4
547.0	0	4	0	0
548.0	0	1	0	2
549.0	0	4	0	4
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1743.0	0	2	0	0
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1751.0	0	1	0	0
1757.0	0	0	0	2
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1763.0	0	1	0	0
1765.0	0	0	0	1
1767.0	0	2	0	0
1769.0	0	1	0	0
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1777.0	0	1	0	0
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1818.0	0	2	0	0
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1935.0	0	0	0	1
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