## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S29F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S29F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S29F.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 11:46:25 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	2152847	15718628	11086528	10654381	847156	3660008	62603	0.243142	28620216

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003001	10778104	0	10820421
2.0	1.582137	928792	59239	893583
3.0	1.916532	158317	1025	153081
4.0	2.109613	57507	184	56551
5.0	2.221099	30720	61	30442
6.0	2.285471	19476	32	19302
7.0	2.322639	13452	22	13399
8.0	2.344101	9794	11	9702
9.0	2.356493	7384	4	7347
10.0	2.363648	5956	3	5930
11.0	2.367779	4876	2	4850
12.0	2.370165	3996	3	3978
13.0	2.371542	3391	2	3372
14.0	2.372337	2826	1	2808
15.0	2.372796	2477	0	2469
16.0	2.373062	2158	0	2118
17.0	2.373215	1910	0	1938
18.0	2.373303	1688	0	1655
19.0	2.373354	1474	0	1475
20.0	2.373384	1342	0	1345
21.0	2.373401	1196	0	1177
22.0	2.37341	1128	0	1105
23.0	2.373416	1019	0	1040
24.0	2.373419	902	0	902
25.0	2.373421	854	0	843
26.0	2.373422	821	0	799
27.0	2.373423	723	0	737
28.0	2.373423	668	0	664
29.0	2.373424	647	0	652
30.0	2.373424	578	0	567
31.0	2.373424	563	0	558
32.0	2.373424	494	0	506
33.0	2.373424	492	0	479
34.0	2.373424	452	0	446
35.0	2.373424	416	0	430
36.0	2.373424	397	0	371
37.0	2.373424	393	0	397
38.0	2.373424	372	0	370
39.0	2.373424	326	0	327
40.0	2.373424	316	0	322
41.0	2.373424	290	0	269
42.0	2.373424	263	0	266
43.0	2.373424	259	0	266
44.0	2.373424	259	0	264
45.0	2.373424	269	0	280
46.0	2.373424	275	0	261
47.0	2.373424	239	0	240
48.0	2.373424	206	0	204
49.0	2.373424	230	0	235
50.0	2.373424	232	0	220
51.0	2.373424	175	0	171
52.0	2.373424	183	0	178
53.0	2.373424	172	0	181
54.0	2.373424	165	0	155
55.0	2.373424	151	0	146
56.0	2.373424	168	0	180
57.0	2.373424	157	0	156
58.0	2.373424	156	0	146
59.0	2.373424	135	0	132
60.0	2.373424	134	0	142
61.0	2.373424	117	0	122
62.0	2.373424	130	0	126
63.0	2.373424	126	0	133
64.0	2.373424	114	0	109
65.0	2.373424	131	0	128
66.0	2.373424	115	0	113
67.0	2.373424	119	0	121
68.0	2.373424	111	0	112
69.0	2.373424	113	0	108
70.0	2.373424	102	0	105
71.0	2.373424	85	0	86
72.0	2.373424	104	0	93
73.0	2.373424	90	0	92
74.0	2.373424	84	0	92
75.0	2.373424	93	0	86
76.0	2.373424	75	0	73
77.0	2.373424	84	0	94
78.0	2.373424	73	0	63
79.0	2.373424	77	0	84
80.0	2.373424	80	0	75
81.0	2.373424	74	0	76
82.0	2.373424	90	0	82
83.0	2.373424	67	0	63
84.0	2.373424	74	0	80
85.0	2.373424	63	0	60
86.0	2.373424	60	0	52
87.0	2.373424	33	0	37
88.0	2.373424	58	0	60
89.0	2.373424	52	0	62
90.0	2.373424	59	0	60
91.0	2.373424	69	0	65
92.0	2.373424	57	0	50
93.0	2.373424	47	0	49
94.0	2.373424	56	0	58
95.0	2.373424	57	0	56
96.0	2.373424	47	0	51
97.0	2.373424	61	0	60
98.0	2.373424	59	0	55
99.0	2.373424	43	0	49
100.0	2.373424	48	0	42
101.0	0	48	0	41
102.0	0	38	0	42
103.0	0	34	0	34
104.0	0	45	0	53
105.0	0	53	0	47
106.0	0	44	0	35
107.0	0	32	0	39
108.0	0	30	0	32
109.0	0	40	0	43
110.0	0	38	0	31
111.0	0	31	0	40
112.0	0	47	0	43
113.0	0	44	0	41
114.0	0	19	0	19
115.0	0	30	0	37
116.0	0	34	0	30
117.0	0	29	0	39
118.0	0	37	0	26
119.0	0	38	0	31
120.0	0	29	0	37
121.0	0	30	0	22
122.0	0	21	0	28
123.0	0	28	0	30
124.0	0	30	0	23
125.0	0	26	0	32
126.0	0	33	0	31
127.0	0	26	0	15
128.0	0	26	0	33
129.0	0	24	0	24
130.0	0	30	0	31
131.0	0	24	0	23
132.0	0	22	0	25
133.0	0	21	0	17
134.0	0	22	0	23
135.0	0	22	0	23
136.0	0	17	0	21
137.0	0	21	0	14
138.0	0	26	0	21
139.0	0	16	0	19
140.0	0	21	0	24
141.0	0	18	0	22
142.0	0	28	0	22
143.0	0	23	0	20
144.0	0	11	0	14
145.0	0	13	0	17
146.0	0	15	0	15
147.0	0	28	0	27
148.0	0	19	0	20
149.0	0	19	0	22
150.0	0	25	0	16
151.0	0	11	0	16
152.0	0	18	0	17
153.0	0	15	0	15
154.0	0	23	0	24
155.0	0	17	0	17
156.0	0	17	0	18
157.0	0	16	0	9
158.0	0	21	0	24
159.0	0	13	0	15
160.0	0	12	0	10
161.0	0	17	0	24
162.0	0	18	0	13
163.0	0	16	0	14
164.0	0	12	0	8
165.0	0	9	0	13
166.0	0	13	0	7
167.0	0	9	0	13
168.0	0	11	0	10
169.0	0	10	0	13
170.0	0	16	0	14
171.0	0	7	0	9
172.0	0	13	0	13
173.0	0	11	0	13
174.0	0	15	0	14
175.0	0	13	0	10
176.0	0	12	0	15
177.0	0	16	0	10
178.0	0	9	0	12
179.0	0	9	0	10
180.0	0	14	0	18
181.0	0	13	0	9
182.0	0	9	0	10
183.0	0	13	0	9
184.0	0	11	0	11
185.0	0	9	0	10
186.0	0	9	0	7
187.0	0	9	0	14
188.0	0	15	0	9
189.0	0	9	0	11
190.0	0	9	0	9
191.0	0	5	0	5
192.0	0	4	0	6
193.0	0	9	0	6
194.0	0	13	0	12
195.0	0	7	0	6
196.0	0	5	0	11
197.0	0	7	0	7
198.0	0	10	0	12
199.0	0	13	0	5
200.0	0	7	0	9
201.0	0	8	0	5
202.0	0	8	0	9
203.0	0	5	0	6
204.0	0	3	0	4
205.0	0	11	0	10
206.0	0	6	0	7
207.0	0	6	0	8
208.0	0	8	0	8
209.0	0	11	0	8
210.0	0	11	0	12
211.0	0	4	0	9
212.0	0	13	0	4
213.0	0	3	0	6
214.0	0	6	0	8
215.0	0	5	0	4
216.0	0	12	0	9
217.0	0	4	0	4
218.0	0	3	0	5
219.0	0	5	0	6
220.0	0	6	0	8
221.0	0	6	0	8
222.0	0	8	0	8
223.0	0	6	0	5
224.0	0	12	0	5
225.0	0	4	0	5
226.0	0	4	0	4
227.0	0	6	0	7
228.0	0	4	0	3
229.0	0	5	0	7
230.0	0	5	0	6
231.0	0	6	0	8
232.0	0	6	0	4
233.0	0	5	0	6
234.0	0	5	0	6
235.0	0	5	0	1
236.0	0	3	0	3
237.0	0	3	0	5
238.0	0	3	0	5
239.0	0	6	0	3
240.0	0	4	0	7
241.0	0	5	0	3
242.0	0	5	0	5
243.0	0	8	0	7
244.0	0	4	0	3
245.0	0	4	0	5
246.0	0	6	0	5
247.0	0	4	0	2
248.0	0	3	0	4
249.0	0	3	0	3
250.0	0	3	0	3
251.0	0	3	0	5
252.0	0	3	0	3
253.0	0	4	0	7
254.0	0	7	0	3
255.0	0	5	0	7
256.0	0	5	0	5
257.0	0	4	0	4
258.0	0	5	0	5
259.0	0	5	0	6
260.0	0	4	0	5
261.0	0	7	0	2
262.0	0	2	0	4
263.0	0	3	0	1
264.0	0	3	0	4
265.0	0	7	0	9
266.0	0	2	0	3
267.0	0	2	0	2
268.0	0	9	0	7
269.0	0	2	0	3
270.0	0	7	0	4
271.0	0	2	0	2
272.0	0	2	0	3
273.0	0	4	0	7
274.0	0	6	0	4
275.0	0	3	0	0
276.0	0	3	0	5
277.0	0	3	0	2
278.0	0	1	0	2
279.0	0	3	0	0
280.0	0	1	0	1
281.0	0	0	0	4
282.0	0	3	0	2
283.0	0	2	0	4
284.0	0	2	0	1
285.0	0	3	0	7
286.0	0	6	0	3
287.0	0	4	0	5
288.0	0	4	0	2
289.0	0	4	0	2
290.0	0	4	0	5
291.0	0	2	0	4
292.0	0	6	0	4
293.0	0	2	0	3
294.0	0	1	0	1
295.0	0	4	0	2
296.0	0	4	0	2
298.0	0	1	0	3
299.0	0	4	0	3
300.0	0	2	0	4
301.0	0	2	0	2
302.0	0	3	0	4
303.0	0	5	0	3
304.0	0	1	0	1
305.0	0	2	0	3
306.0	0	1	0	2
307.0	0	2	0	3
308.0	0	4	0	3
309.0	0	5	0	1
310.0	0	1	0	0
312.0	0	3	0	8
313.0	0	3	0	1
314.0	0	4	0	4
315.0	0	1	0	0
317.0	0	2	0	4
318.0	0	3	0	1
319.0	0	1	0	0
320.0	0	3	0	3
321.0	0	4	0	5
322.0	0	1	0	7
323.0	0	7	0	1
324.0	0	2	0	1
325.0	0	2	0	2
326.0	0	0	0	1
327.0	0	3	0	2
328.0	0	3	0	3
329.0	0	0	0	2
330.0	0	1	0	2
331.0	0	3	0	3
332.0	0	3	0	2
333.0	0	2	0	3
334.0	0	5	0	3
335.0	0	1	0	1
336.0	0	1	0	1
338.0	0	2	0	2
339.0	0	2	0	4
340.0	0	1	0	2
341.0	0	4	0	2
342.0	0	1	0	0
343.0	0	1	0	0
344.0	0	0	0	3
345.0	0	2	0	2
346.0	0	2	0	2
347.0	0	1	0	2
348.0	0	3	0	0
349.0	0	0	0	1
350.0	0	2	0	3
351.0	0	4	0	2
352.0	0	2	0	4
353.0	0	3	0	0
354.0	0	1	0	2
355.0	0	1	0	4
356.0	0	2	0	0
357.0	0	3	0	2
358.0	0	2	0	1
359.0	0	1	0	1
360.0	0	1	0	1
361.0	0	1	0	3
362.0	0	1	0	2
363.0	0	2	0	1
364.0	0	2	0	2
365.0	0	1	0	1
366.0	0	2	0	0
367.0	0	1	0	2
368.0	0	2	0	2
369.0	0	0	0	1
371.0	0	3	0	1
372.0	0	0	0	1
373.0	0	1	0	0
374.0	0	1	0	2
375.0	0	1	0	0
376.0	0	2	0	4
377.0	0	1	0	1
378.0	0	1	0	2
379.0	0	2	0	2
380.0	0	3	0	1
381.0	0	2	0	0
382.0	0	0	0	1
383.0	0	1	0	1
384.0	0	0	0	4
385.0	0	3	0	2
386.0	0	1	0	0
387.0	0	1	0	1
388.0	0	4	0	2
390.0	0	1	0	1
391.0	0	1	0	1
392.0	0	1	0	1
396.0	0	2	0	2
397.0	0	0	0	1
398.0	0	1	0	2
399.0	0	2	0	0
400.0	0	1	0	1
401.0	0	1	0	0
406.0	0	0	0	1
408.0	0	2	0	1
409.0	0	1	0	2
410.0	0	1	0	1
411.0	0	1	0	1
413.0	0	1	0	0
414.0	0	0	0	3
415.0	0	2	0	0
416.0	0	1	0	1
417.0	0	1	0	2
418.0	0	2	0	2
420.0	0	1	0	1
421.0	0	2	0	1
422.0	0	0	0	2
423.0	0	0	0	2
424.0	0	3	0	2
425.0	0	3	0	1
426.0	0	1	0	1
427.0	0	0	0	1
428.0	0	1	0	1
429.0	0	1	0	2
431.0	0	4	0	0
432.0	0	0	0	1
433.0	0	1	0	2
434.0	0	2	0	1
435.0	0	1	0	0
436.0	0	0	0	1
439.0	0	0	0	2
440.0	0	1	0	1
441.0	0	1	0	0
442.0	0	0	0	1
443.0	0	2	0	0
444.0	0	1	0	0
446.0	0	0	0	1
448.0	0	0	0	2
449.0	0	1	0	0
450.0	0	1	0	1
451.0	0	1	0	0
452.0	0	1	0	0
454.0	0	0	0	1
455.0	0	1	0	0
457.0	0	0	0	2
458.0	0	1	0	1
459.0	0	1	0	4
460.0	0	0	0	1
461.0	0	3	0	2
462.0	0	1	0	1
463.0	0	4	0	0
464.0	0	1	0	1
465.0	0	0	0	1
466.0	0	1	0	2
469.0	0	2	0	0
470.0	0	1	0	0
471.0	0	0	0	1
472.0	0	1	0	1
473.0	0	0	0	1
475.0	0	0	0	1
476.0	0	2	0	1
478.0	0	2	0	0
480.0	0	1	0	3
481.0	0	2	0	0
483.0	0	0	0	1
485.0	0	1	0	0
488.0	0	1	0	2
489.0	0	0	0	1
491.0	0	1	0	0
492.0	0	1	0	2
493.0	0	0	0	1
495.0	0	2	0	0
496.0	0	0	0	1
497.0	0	1	0	1
498.0	0	1	0	1
499.0	0	1	0	1
502.0	0	1	0	1
504.0	0	2	0	0
506.0	0	0	0	1
508.0	0	0	0	1
509.0	0	1	0	1
510.0	0	1	0	2
511.0	0	1	0	1
512.0	0	1	0	1
513.0	0	0	0	1
514.0	0	1	0	1
515.0	0	2	0	0
516.0	0	1	0	0
517.0	0	0	0	1
518.0	0	1	0	2
519.0	0	2	0	0
520.0	0	0	0	1
521.0	0	1	0	0
522.0	0	1	0	0
528.0	0	0	0	1
529.0	0	1	0	0
531.0	0	0	0	1
532.0	0	1	0	1
533.0	0	0	0	2
534.0	0	1	0	0
536.0	0	1	0	0
537.0	0	0	0	1
538.0	0	1	0	1
542.0	0	1	0	1
543.0	0	3	0	1
544.0	0	1	0	1
546.0	0	0	0	1
548.0	0	0	0	2
549.0	0	0	0	1
552.0	0	2	0	0
553.0	0	2	0	2
554.0	0	1	0	0
556.0	0	1	0	0
558.0	0	0	0	1
560.0	0	1	0	0
562.0	0	0	0	3
564.0	0	1	0	0
565.0	0	1	0	1
566.0	0	1	0	2
567.0	0	1	0	0
568.0	0	1	0	1
569.0	0	0	0	2
570.0	0	1	0	0
571.0	0	2	0	1
572.0	0	1	0	0
576.0	0	1	0	0
577.0	0	0	0	2
578.0	0	0	0	1
579.0	0	2	0	1
582.0	0	1	0	0
584.0	0	1	0	0
591.0	0	0	0	1
592.0	0	0	0	1
593.0	0	1	0	1
594.0	0	2	0	1
595.0	0	1	0	1
597.0	0	0	0	2
599.0	0	2	0	0
600.0	0	1	0	0
605.0	0	0	0	1
606.0	0	1	0	0
609.0	0	0	0	1
612.0	0	0	0	1
613.0	0	0	0	1
615.0	0	2	0	0
619.0	0	1	0	1
623.0	0	1	0	0
624.0	0	0	0	1
627.0	0	1	0	0
629.0	0	0	0	1
630.0	0	1	0	1
632.0	0	0	0	1
633.0	0	1	0	0
634.0	0	0	0	1
637.0	0	2	0	0
639.0	0	0	0	1
641.0	0	0	0	1
642.0	0	0	0	1
643.0	0	2	0	0
644.0	0	1	0	0
648.0	0	0	0	2
650.0	0	1	0	0
651.0	0	0	0	1
654.0	0	1	0	0
655.0	0	1	0	0
657.0	0	0	0	1
658.0	0	1	0	1
659.0	0	1	0	0
660.0	0	0	0	2
662.0	0	1	0	0
664.0	0	1	0	0
666.0	0	0	0	1
672.0	0	1	0	1
673.0	0	0	0	1
674.0	0	2	0	0
678.0	0	0	0	1
681.0	0	1	0	1
683.0	0	1	0	1
685.0	0	1	0	0
687.0	0	0	0	1
689.0	0	0	0	1
692.0	0	1	0	0
694.0	0	1	0	0
696.0	0	0	0	1
698.0	0	1	0	0
699.0	0	0	0	1
700.0	0	1	0	1
702.0	0	0	0	1
703.0	0	1	0	0
704.0	0	1	0	0
718.0	0	0	0	1
725.0	0	1	0	0
732.0	0	0	0	1
733.0	0	0	0	1
735.0	0	0	0	1
736.0	0	1	0	0
737.0	0	2	0	0
740.0	0	1	0	1
741.0	0	0	0	1
742.0	0	1	0	0
743.0	0	0	0	2
747.0	0	1	0	0
749.0	0	0	0	1
751.0	0	2	0	1
753.0	0	0	0	1
757.0	0	1	0	0
758.0	0	0	0	1
759.0	0	1	0	0
762.0	0	0	0	1
764.0	0	1	0	1
765.0	0	1	0	0
766.0	0	1	0	0
790.0	0	0	0	1
793.0	0	1	0	0
795.0	0	0	0	1
796.0	0	0	0	1
797.0	0	1	0	0
799.0	0	1	0	0
800.0	0	0	0	1
804.0	0	1	0	0
805.0	0	0	0	1
806.0	0	0	0	1
808.0	0	2	0	0
811.0	0	0	0	1
813.0	0	1	0	0
814.0	0	0	0	1
816.0	0	1	0	0
820.0	0	0	0	1
823.0	0	1	0	0
826.0	0	0	0	1
831.0	0	0	0	1
832.0	0	1	0	0
833.0	0	1	0	0
845.0	0	0	0	1
848.0	0	0	0	1
849.0	0	1	0	0
850.0	0	1	0	0
852.0	0	0	0	1
857.0	0	1	0	1
859.0	0	0	0	1
862.0	0	2	0	0
873.0	0	0	0	1
876.0	0	1	0	0
878.0	0	0	0	1
882.0	0	0	0	2
884.0	0	1	0	0
886.0	0	1	0	1
887.0	0	1	0	0
891.0	0	0	0	2
893.0	0	1	0	0
894.0	0	2	0	0
895.0	0	0	0	1
900.0	0	1	0	0
906.0	0	0	0	1
913.0	0	1	0	0
914.0	0	0	0	1
915.0	0	0	0	1
916.0	0	0	0	1
921.0	0	1	0	0
922.0	0	1	0	0
924.0	0	0	0	1
925.0	0	1	0	0
929.0	0	1	0	0
960.0	0	0	0	1
964.0	0	1	0	0
973.0	0	0	0	1
980.0	0	1	0	0
981.0	0	0	0	1
985.0	0	1	0	0
997.0	0	0	0	1
1000.0	0	1	0	0
1005.0	0	0	0	1
1008.0	0	0	0	1
1011.0	0	2	0	0
1019.0	0	0	0	1
1020.0	0	0	0	1
1023.0	0	1	0	0
1027.0	0	1	0	0
1040.0	0	0	0	1
1043.0	0	0	0	1
1046.0	0	2	0	0
1052.0	0	0	0	1
1057.0	0	0	0	1
1061.0	0	1	0	0
1062.0	0	1	0	0
1069.0	0	0	0	1
1075.0	0	1	0	0
1079.0	0	0	0	1
1082.0	0	0	0	1
1088.0	0	1	0	0
1090.0	0	1	0	0
1094.0	0	0	0	1
1097.0	0	1	0	0
1118.0	0	0	0	1
1122.0	0	0	0	1
1123.0	0	1	0	0
1126.0	0	1	0	0
1180.0	0	0	0	1
1184.0	0	1	0	0
1238.0	0	0	0	1
1244.0	0	1	0	2
1248.0	0	1	0	0
1249.0	0	1	0	0
1257.0	0	0	0	1
1260.0	0	1	0	0
1272.0	0	0	0	1
1279.0	0	1	0	0
1319.0	0	0	0	1
1325.0	0	1	0	0
1354.0	0	0	0	1
1360.0	0	1	0	0
1391.0	0	0	0	1
1392.0	0	1	0	0
1413.0	0	0	0	1
1420.0	0	1	0	0
1484.0	0	0	0	1
1489.0	0	1	0	0
1546.0	0	0	0	1
1547.0	0	0	0	1
1553.0	0	0	0	1
1556.0	0	1	0	0
1558.0	0	1	0	0
1561.0	0	1	0	0
1593.0	0	0	0	1
1598.0	0	0	0	1
1603.0	0	1	0	1
1606.0	0	1	0	0
1609.0	0	1	0	0
1633.0	0	0	0	1
1635.0	0	0	0	1
1640.0	0	1	0	0
1641.0	0	1	0	0
1922.0	0	0	0	1
1929.0	0	1	0	0
1967.0	0	0	0	1
1978.0	0	1	0	0
1997.0	0	0	0	1
2009.0	0	1	0	0
2078.0	0	0	0	1
2087.0	0	1	0	0
2217.0	0	0	0	1
2227.0	0	1	0	0
2276.0	0	0	0	1
2287.0	0	1	0	0