## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P13-female_bleached_K5.sorted.bam] OUTPUT=P13-female_bleached_K5.sorted.dedup.bam METRICS_FILE=P13-female_bleached_K5-picard_metrics.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT    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 COMPRESSION_LEVEL=5 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: Thu Jul 18 18:48:47 PDT 2019

## 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	517511	16349603	0	1354249	376263	7725385	453598	0.476478	11526992

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.012988	5779771	0	5890184
2.0	1.258239	1674225	302811	1654451
3.0	1.317616	590850	35760	559058
4.0	1.331992	241282	8024	218235
5.0	1.335472	111504	2863	97066
6.0	1.336315	58577	1413	50571
7.0	1.336519	34592	812	29833
8.0	1.336568	22149	527	19718
9.0	1.33658	15536	366	14121
10.0	1.336583	11586	273	10696
11.0	1.336584	9208	204	8608
12.0	1.336584	7328	150	6979
13.0	1.336584	6107	117	5723
14.0	1.336584	5055	95	4885
15.0	1.336584	4447	82	4220
16.0	1.336584	3733	61	3672
17.0	1.336584	3412	58	3152
18.0	1.336584	2883	60	2815
19.0	1.336584	2641	38	2493
20.0	1.336584	2285	38	2213
21.0	1.336584	2091	24	1996
22.0	1.336584	1880	33	1876
23.0	1.336584	1752	22	1666
24.0	1.336584	1585	22	1533
25.0	1.336584	1502	21	1418
26.0	1.336584	1373	12	1288
27.0	1.336584	1181	15	1137
28.0	1.336584	1123	13	1079
29.0	1.336584	1059	11	1064
30.0	1.336584	984	7	944
31.0	1.336584	872	4	829
32.0	1.336584	870	7	844
33.0	1.336584	846	6	796
34.0	1.336584	748	11	744
35.0	1.336584	723	2	664
36.0	1.336584	683	7	681
37.0	1.336584	612	5	654
38.0	1.336584	624	3	582
39.0	1.336584	572	9	538
40.0	1.336584	523	6	483
41.0	1.336584	488	7	494
42.0	1.336584	504	9	453
43.0	1.336584	444	2	402
44.0	1.336584	411	4	405
45.0	1.336584	402	5	358
46.0	1.336584	394	3	365
47.0	1.336584	337	3	364
48.0	1.336584	336	4	324
49.0	1.336584	330	4	310
50.0	1.336584	321	2	271
51.0	1.336584	321	1	315
52.0	1.336584	299	2	305
53.0	1.336584	261	2	281
54.0	1.336584	280	4	250
55.0	1.336584	265	0	231
56.0	1.336584	247	2	233
57.0	1.336584	213	1	225
58.0	1.336584	238	3	221
59.0	1.336584	220	1	224
60.0	1.336584	202	2	211
61.0	1.336584	220	0	208
62.0	1.336584	197	0	188
63.0	1.336584	185	1	182
64.0	1.336584	198	4	206
65.0	1.336584	199	2	169
66.0	1.336584	181	0	136
67.0	1.336584	149	0	155
68.0	1.336584	143	2	143
69.0	1.336584	162	1	167
70.0	1.336584	150	0	129
71.0	1.336584	173	1	150
72.0	1.336584	123	0	127
73.0	1.336584	127	0	126
74.0	1.336584	132	0	113
75.0	1.336584	143	1	128
76.0	1.336584	113	2	118
77.0	1.336584	124	2	121
78.0	1.336584	119	0	116
79.0	1.336584	106	0	132
80.0	1.336584	110	0	108
81.0	1.336584	117	1	100
82.0	1.336584	128	2	95
83.0	1.336584	93	0	94
84.0	1.336584	102	0	93
85.0	1.336584	83	0	94
86.0	1.336584	92	1	103
87.0	1.336584	93	0	81
88.0	1.336584	104	0	85
89.0	1.336584	83	0	93
90.0	1.336584	85	1	83
91.0	1.336584	95	0	72
92.0	1.336584	72	0	69
93.0	1.336584	75	0	59
94.0	1.336584	78	0	74
95.0	1.336584	61	0	71
96.0	1.336584	77	0	72
97.0	1.336584	70	0	72
98.0	1.336584	60	0	63
99.0	1.336584	68	0	66
100.0	1.336584	55	1	61
101.0	0	57	0	42
102.0	0	61	0	62
103.0	0	69	0	50
104.0	0	56	0	53
105.0	0	53	0	58
106.0	0	61	0	60
107.0	0	53	0	50
108.0	0	53	0	50
109.0	0	50	0	55
110.0	0	47	0	54
111.0	0	51	0	56
112.0	0	46	0	48
113.0	0	54	0	44
114.0	0	59	0	52
115.0	0	61	1	46
116.0	0	51	0	47
117.0	0	38	0	37
118.0	0	47	0	35
119.0	0	37	0	36
120.0	0	39	1	35
121.0	0	41	0	51
122.0	0	36	0	31
123.0	0	34	0	32
124.0	0	43	0	32
125.0	0	32	0	34
126.0	0	28	0	26
127.0	0	37	0	24
128.0	0	38	0	34
129.0	0	34	0	35
130.0	0	35	0	31
131.0	0	25	0	28
132.0	0	32	0	25
133.0	0	24	0	28
134.0	0	21	0	31
135.0	0	36	0	30
136.0	0	39	0	34
137.0	0	17	0	29
138.0	0	32	0	32
139.0	0	30	0	44
140.0	0	31	0	28
141.0	0	38	0	30
142.0	0	31	0	27
143.0	0	28	0	27
144.0	0	28	0	22
145.0	0	26	0	19
146.0	0	26	0	26
147.0	0	23	0	31
148.0	0	20	0	21
149.0	0	28	0	22
150.0	0	30	0	22
151.0	0	16	0	21
152.0	0	32	0	16
153.0	0	25	0	24
154.0	0	18	0	18
155.0	0	20	0	15
156.0	0	22	0	14
157.0	0	31	0	20
158.0	0	17	0	18
159.0	0	18	0	17
160.0	0	11	0	22
161.0	0	15	0	16
162.0	0	15	0	21
163.0	0	19	0	19
164.0	0	19	0	22
165.0	0	24	0	14
166.0	0	13	0	13
167.0	0	15	0	18
168.0	0	16	0	16
169.0	0	16	0	23
170.0	0	26	0	22
171.0	0	12	0	26
172.0	0	12	0	18
173.0	0	14	0	26
174.0	0	24	0	11
175.0	0	17	0	17
176.0	0	24	0	23
177.0	0	21	0	16
178.0	0	24	0	14
179.0	0	18	0	13
180.0	0	20	0	15
181.0	0	16	0	22
182.0	0	25	0	15
183.0	0	11	0	16
184.0	0	16	0	17
185.0	0	8	0	12
186.0	0	20	0	17
187.0	0	15	0	14
188.0	0	19	0	15
189.0	0	13	0	11
190.0	0	11	0	10
191.0	0	15	0	13
192.0	0	14	0	10
193.0	0	7	0	12
194.0	0	15	0	15
195.0	0	14	0	13
196.0	0	17	0	6
197.0	0	9	0	5
198.0	0	17	0	16
199.0	0	8	0	9
200.0	0	5	0	12
201.0	0	7	0	13
202.0	0	17	0	14
203.0	0	11	0	11
204.0	0	9	0	15
205.0	0	14	0	13
206.0	0	17	0	8
207.0	0	8	0	12
208.0	0	11	0	5
209.0	0	23	0	13
210.0	0	13	0	15
211.0	0	10	0	9
212.0	0	9	0	7
213.0	0	6	0	9
214.0	0	6	0	9
215.0	0	10	0	12
216.0	0	8	0	5
217.0	0	14	0	12
218.0	0	11	0	3
219.0	0	14	0	4
220.0	0	9	0	8
221.0	0	8	0	11
222.0	0	7	0	12
223.0	0	6	0	10
224.0	0	10	0	12
225.0	0	4	0	4
226.0	0	14	0	9
227.0	0	7	0	9
228.0	0	7	0	6
229.0	0	10	0	7
230.0	0	9	0	6
231.0	0	7	0	12
232.0	0	11	0	12
233.0	0	12	0	10
234.0	0	10	0	6
235.0	0	3	0	8
236.0	0	9	0	9
237.0	0	7	0	5
238.0	0	9	0	8
239.0	0	6	0	9
240.0	0	5	0	6
241.0	0	8	0	3
242.0	0	5	0	5
243.0	0	9	0	8
244.0	0	11	0	8
245.0	0	9	0	5
246.0	0	12	0	4
247.0	0	8	0	3
248.0	0	4	0	12
249.0	0	2	0	10
250.0	0	8	0	4
251.0	0	3	0	4
252.0	0	4	0	5
253.0	0	4	0	3
254.0	0	7	0	5
255.0	0	9	0	3
256.0	0	6	0	2
257.0	0	5	0	11
258.0	0	7	0	10
259.0	0	2	0	8
260.0	0	8	0	5
261.0	0	6	0	3
262.0	0	4	0	5
263.0	0	8	0	4
264.0	0	6	0	3
265.0	0	6	0	7
266.0	0	4	0	5
267.0	0	5	0	5
268.0	0	8	0	5
269.0	0	4	0	7
270.0	0	6	0	4
271.0	0	5	0	5
272.0	0	2	0	9
273.0	0	5	0	6
274.0	0	4	0	4
275.0	0	8	0	8
276.0	0	5	0	4
277.0	0	3	0	3
278.0	0	5	0	8
279.0	0	3	0	4
280.0	0	5	0	2
281.0	0	2	0	4
282.0	0	3	0	5
283.0	0	6	0	6
284.0	0	2	0	5
285.0	0	10	0	5
286.0	0	3	0	6
287.0	0	8	0	5
288.0	0	5	0	4
289.0	0	4	0	7
290.0	0	5	0	2
291.0	0	4	0	4
292.0	0	3	0	7
293.0	0	5	0	1
294.0	0	8	0	5
295.0	0	5	0	2
296.0	0	6	0	5
297.0	0	10	0	4
298.0	0	4	0	6
299.0	0	4	0	2
300.0	0	3	0	2
301.0	0	4	0	4
302.0	0	3	0	1
303.0	0	5	0	3
304.0	0	5	0	4
305.0	0	7	0	1
306.0	0	2	0	0
307.0	0	4	0	3
308.0	0	4	0	1
309.0	0	2	0	7
310.0	0	1	0	4
311.0	0	2	0	4
312.0	0	2	0	5
313.0	0	4	0	5
314.0	0	1	0	5
315.0	0	2	0	2
316.0	0	1	0	1
317.0	0	3	0	2
318.0	0	2	0	5
319.0	0	4	0	3
320.0	0	2	0	4
321.0	0	4	0	2
322.0	0	1	0	2
323.0	0	4	0	1
324.0	0	6	0	8
325.0	0	1	0	1
326.0	0	1	0	3
327.0	0	4	0	0
328.0	0	8	0	1
329.0	0	3	0	2
330.0	0	7	0	1
331.0	0	2	0	1
332.0	0	2	0	4
333.0	0	2	0	7
334.0	0	1	0	4
335.0	0	5	0	2
336.0	0	1	0	6
337.0	0	1	0	2
338.0	0	5	0	4
339.0	0	4	0	1
340.0	0	1	0	1
341.0	0	5	0	3
342.0	0	1	0	2
343.0	0	4	0	2
344.0	0	3	0	3
345.0	0	1	0	4
346.0	0	4	0	0
347.0	0	1	0	1
348.0	0	2	0	4
349.0	0	1	0	1
350.0	0	7	0	5
351.0	0	4	0	6
352.0	0	0	0	1
353.0	0	6	0	3
354.0	0	2	0	0
355.0	0	4	0	1
356.0	0	1	0	3
357.0	0	1	0	1
358.0	0	1	0	1
359.0	0	2	0	4
360.0	0	0	0	2
361.0	0	1	0	1
362.0	0	2	0	1
363.0	0	1	0	4
364.0	0	2	0	0
365.0	0	0	0	5
366.0	0	3	0	1
367.0	0	1	0	1
368.0	0	2	0	1
369.0	0	2	0	3
370.0	0	4	0	1
371.0	0	2	0	3
372.0	0	4	0	0
373.0	0	2	0	2
374.0	0	3	0	4
375.0	0	2	0	2
376.0	0	3	0	6
377.0	0	3	0	1
378.0	0	1	0	1
379.0	0	4	0	1
380.0	0	2	0	0
381.0	0	2	0	2
382.0	0	3	0	0
383.0	0	0	0	1
384.0	0	3	0	4
385.0	0	2	0	3
386.0	0	2	0	2
387.0	0	0	0	2
388.0	0	2	0	1
389.0	0	0	0	2
390.0	0	4	0	2
391.0	0	2	0	3
392.0	0	0	0	4
393.0	0	7	0	0
394.0	0	4	0	3
395.0	0	3	0	2
396.0	0	1	0	2
397.0	0	2	0	1
398.0	0	2	0	2
399.0	0	1	0	4
400.0	0	0	0	2
402.0	0	4	0	1
403.0	0	2	0	1
404.0	0	3	0	2
405.0	0	1	0	3
406.0	0	3	0	1
407.0	0	1	0	4
408.0	0	1	0	1
409.0	0	1	0	0
411.0	0	2	0	1
412.0	0	1	0	3
413.0	0	5	0	0
414.0	0	3	0	3
415.0	0	2	0	1
416.0	0	1	0	0
417.0	0	1	0	1
418.0	0	3	0	1
419.0	0	1	0	2
420.0	0	0	0	1
421.0	0	4	0	1
423.0	0	1	0	3
424.0	0	0	0	1
425.0	0	2	0	1
426.0	0	2	0	1
427.0	0	1	0	2
428.0	0	1	0	1
429.0	0	1	0	0
430.0	0	1	0	0
431.0	0	1	0	1
432.0	0	2	0	0
433.0	0	0	0	2
434.0	0	1	0	0
435.0	0	1	0	1
436.0	0	3	0	1
437.0	0	1	0	1
438.0	0	1	0	3
439.0	0	2	0	1
440.0	0	1	0	2
441.0	0	1	0	2
442.0	0	1	0	2
443.0	0	0	0	3
444.0	0	0	0	1
445.0	0	1	0	2
446.0	0	1	0	0
447.0	0	2	0	1
448.0	0	2	0	1
449.0	0	2	0	2
450.0	0	2	0	1
451.0	0	1	0	2
452.0	0	0	0	2
453.0	0	1	0	1
454.0	0	0	0	2
455.0	0	1	0	1
456.0	0	1	0	2
457.0	0	1	0	1
458.0	0	3	0	0
459.0	0	2	0	1
460.0	0	1	0	1
461.0	0	2	0	0
462.0	0	2	0	1
463.0	0	2	0	2
464.0	0	1	0	3
465.0	0	3	0	1
466.0	0	1	0	3
467.0	0	0	0	2
468.0	0	2	0	1
469.0	0	1	0	0
470.0	0	1	0	1
471.0	0	0	0	1
472.0	0	2	0	2
474.0	0	1	0	0
475.0	0	0	0	1
476.0	0	2	0	1
477.0	0	3	0	3
478.0	0	3	0	0
479.0	0	1	0	1
480.0	0	3	0	0
481.0	0	1	0	2
482.0	0	3	0	0
483.0	0	1	0	2
484.0	0	1	0	0
485.0	0	0	0	1
486.0	0	0	0	2
487.0	0	2	0	0
489.0	0	0	0	1
490.0	0	3	0	2
491.0	0	1	0	0
493.0	0	1	0	2
494.0	0	1	0	0
497.0	0	2	0	0
498.0	0	1	0	1
499.0	0	1	0	0
501.0	0	0	0	1
502.0	0	1	0	1
503.0	0	0	0	1
504.0	0	2	0	1
505.0	0	0	0	1
506.0	0	1	0	0
507.0	0	2	0	0
508.0	0	0	0	2
509.0	0	0	0	2
510.0	0	0	0	1
512.0	0	1	0	1
516.0	0	1	0	3
517.0	0	1	0	0
518.0	0	0	0	2
520.0	0	0	0	1
523.0	0	2	0	2
524.0	0	1	0	1
525.0	0	1	0	1
526.0	0	0	0	1
527.0	0	0	0	1
528.0	0	3	0	1
529.0	0	0	0	1
530.0	0	1	0	0
531.0	0	0	0	1
532.0	0	0	0	2
533.0	0	1	0	0
534.0	0	3	0	2
535.0	0	0	0	2
536.0	0	1	0	1
537.0	0	1	0	2
539.0	0	1	0	0
540.0	0	2	0	1
541.0	0	1	0	1
542.0	0	0	0	1
543.0	0	1	0	0
545.0	0	3	0	1
546.0	0	0	0	1
547.0	0	4	0	1
549.0	0	0	0	2
550.0	0	0	0	1
551.0	0	2	0	1
552.0	0	1	0	0
554.0	0	0	0	2
555.0	0	1	0	0
556.0	0	3	0	0
557.0	0	0	0	2
558.0	0	1	0	0
559.0	0	1	0	1
560.0	0	1	0	1
563.0	0	1	0	2
564.0	0	1	0	1
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