## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P12-female_nonbleached_44.sorted.bam] OUTPUT=P12-female_nonbleached_44.sorted.dedup.bam METRICS_FILE=P12-female_nonbleached_44-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 18:14:49 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	1034058	24760850	0	2373534	602712	7612541	871291	0.313076	33922256

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.024804	12788593	0	13144891
2.0	1.518702	2902168	665440	2773460
3.0	1.756732	861153	73291	755220
4.0	1.871449	307315	12700	248027
5.0	1.926736	125625	2726	95582
6.0	1.953381	59004	793	44251
7.0	1.966223	31103	306	23561
8.0	1.972412	17908	118	14089
9.0	1.975394	11253	76	9324
10.0	1.976832	7997	52	6809
11.0	1.977525	5756	35	5079
12.0	1.977859	4372	31	3869
13.0	1.978019	3325	18	3099
14.0	1.978097	2754	14	2468
15.0	1.978134	2231	9	1985
16.0	1.978152	1800	12	1688
17.0	1.978161	1580	8	1509
18.0	1.978165	1396	7	1300
19.0	1.978167	1181	3	1054
20.0	1.978168	991	2	943
21.0	1.978169	889	4	863
22.0	1.978169	772	2	733
23.0	1.978169	690	4	632
24.0	1.978169	591	3	535
25.0	1.978169	561	4	507
26.0	1.978169	486	2	455
27.0	1.978169	433	1	420
28.0	1.978169	399	1	360
29.0	1.978169	353	1	343
30.0	1.978169	347	1	314
31.0	1.978169	275	0	281
32.0	1.978169	286	0	261
33.0	1.978169	244	1	219
34.0	1.978169	238	3	236
35.0	1.978169	214	1	226
36.0	1.978169	235	0	177
37.0	1.978169	182	0	168
38.0	1.978169	174	0	161
39.0	1.978169	152	0	155
40.0	1.978169	135	0	143
41.0	1.978169	146	0	146
42.0	1.978169	142	0	126
43.0	1.978169	134	0	103
44.0	1.978169	118	0	107
45.0	1.978169	107	0	96
46.0	1.978169	113	0	95
47.0	1.978169	91	0	71
48.0	1.978169	74	0	88
49.0	1.978169	91	0	82
50.0	1.978169	69	0	53
51.0	1.978169	80	0	76
52.0	1.978169	54	0	68
53.0	1.978169	66	0	56
54.0	1.978169	55	0	54
55.0	1.978169	58	0	51
56.0	1.978169	46	0	46
57.0	1.978169	45	0	45
58.0	1.978169	40	0	32
59.0	1.978169	52	0	49
60.0	1.978169	47	0	42
61.0	1.978169	48	0	43
62.0	1.978169	34	1	35
63.0	1.978169	44	0	46
64.0	1.978169	38	0	28
65.0	1.978169	41	0	44
66.0	1.978169	33	0	29
67.0	1.978169	30	0	23
68.0	1.978169	32	1	29
69.0	1.978169	31	0	22
70.0	1.978169	29	0	38
71.0	1.978169	31	0	31
72.0	1.978169	21	0	29
73.0	1.978169	34	0	27
74.0	1.978169	23	0	37
75.0	1.978169	23	0	24
76.0	1.978169	40	0	20
77.0	1.978169	23	0	24
78.0	1.978169	23	0	23
79.0	1.978169	23	0	27
80.0	1.978169	24	0	23
81.0	1.978169	27	0	22
82.0	1.978169	21	0	16
83.0	1.978169	21	0	13
84.0	1.978169	25	0	18
85.0	1.978169	19	0	21
86.0	1.978169	13	0	17
87.0	1.978169	17	0	14
88.0	1.978169	12	0	14
89.0	1.978169	15	0	10
90.0	1.978169	14	0	17
91.0	1.978169	14	0	10
92.0	1.978169	12	0	13
93.0	1.978169	13	0	20
94.0	1.978169	6	0	12
95.0	1.978169	15	0	12
96.0	1.978169	24	0	14
97.0	1.978169	12	0	10
98.0	1.978169	13	0	12
99.0	1.978169	11	0	10
100.0	1.978169	13	0	7
101.0	0	9	0	11
102.0	0	12	0	10
103.0	0	12	0	6
104.0	0	7	0	13
105.0	0	9	0	12
106.0	0	9	0	8
107.0	0	6	0	7
108.0	0	8	0	2
109.0	0	13	0	7
110.0	0	10	0	1
111.0	0	6	0	6
112.0	0	5	0	8
113.0	0	2	0	5
114.0	0	4	0	7
115.0	0	10	0	4
116.0	0	3	0	11
117.0	0	5	0	7
118.0	0	5	0	7
119.0	0	7	0	11
120.0	0	6	0	4
121.0	0	7	0	8
122.0	0	9	0	12
123.0	0	5	0	5
124.0	0	6	0	7
125.0	0	8	0	8
126.0	0	14	0	4
127.0	0	5	0	6
128.0	0	6	0	1
129.0	0	7	0	6
130.0	0	6	0	4
131.0	0	7	0	10
132.0	0	5	0	8
133.0	0	2	0	8
134.0	0	8	0	1
135.0	0	7	0	7
136.0	0	4	0	4
137.0	0	3	0	2
138.0	0	3	0	5
139.0	0	4	0	4
140.0	0	6	0	5
141.0	0	4	0	0
142.0	0	7	0	3
143.0	0	3	0	4
144.0	0	3	0	3
145.0	0	3	0	4
146.0	0	4	0	2
147.0	0	4	0	1
148.0	0	3	0	4
149.0	0	2	0	5
150.0	0	4	0	2
151.0	0	3	0	2
152.0	0	4	0	2
153.0	0	2	0	1
154.0	0	0	0	2
155.0	0	4	0	2
156.0	0	4	0	4
157.0	0	4	0	0
158.0	0	3	0	2
159.0	0	2	0	3
160.0	0	1	0	0
161.0	0	3	0	1
162.0	0	0	0	3
163.0	0	0	0	3
164.0	0	1	0	1
165.0	0	1	0	4
166.0	0	1	0	4
167.0	0	3	0	1
168.0	0	1	0	2
169.0	0	3	0	2
170.0	0	0	0	5
171.0	0	3	0	3
172.0	0	5	0	2
173.0	0	2	0	4
174.0	0	3	0	4
175.0	0	2	0	3
176.0	0	6	0	3
177.0	0	6	0	3
178.0	0	2	0	1
179.0	0	3	0	1
180.0	0	5	0	4
181.0	0	2	0	3
182.0	0	2	0	0
183.0	0	1	0	2
184.0	0	2	0	5
185.0	0	0	0	1
186.0	0	6	0	2
187.0	0	1	0	3
188.0	0	3	0	1
189.0	0	3	0	2
190.0	0	1	0	2
191.0	0	1	0	3
192.0	0	2	0	1
193.0	0	4	0	2
194.0	0	1	0	0
195.0	0	3	0	1
196.0	0	3	0	2
197.0	0	0	0	1
198.0	0	3	0	1
199.0	0	2	0	2
200.0	0	1	0	4
201.0	0	2	0	2
202.0	0	1	0	3
203.0	0	1	0	1
204.0	0	4	0	4
205.0	0	4	0	5
206.0	0	2	0	0
207.0	0	1	0	2
208.0	0	1	0	0
209.0	0	4	0	2
210.0	0	1	0	0
211.0	0	0	0	1
212.0	0	1	0	3
213.0	0	2	0	1
214.0	0	1	0	2
215.0	0	0	0	1
216.0	0	1	0	2
217.0	0	3	0	1
218.0	0	2	0	0
219.0	0	3	0	2
220.0	0	1	0	0
222.0	0	0	0	1
223.0	0	0	0	1
225.0	0	0	0	1
226.0	0	2	0	1
227.0	0	0	0	2
228.0	0	1	0	0
229.0	0	3	0	1
230.0	0	2	0	1
231.0	0	0	0	1
232.0	0	1	0	0
233.0	0	3	0	1
235.0	0	1	0	0
236.0	0	2	0	2
237.0	0	0	0	1
238.0	0	1	0	2
239.0	0	0	0	1
240.0	0	1	0	0
241.0	0	1	0	0
243.0	0	1	0	0
244.0	0	0	0	1
245.0	0	1	0	2
246.0	0	2	0	0
247.0	0	3	0	2
248.0	0	0	0	1
251.0	0	2	0	1
253.0	0	0	0	2
255.0	0	0	0	1
256.0	0	1	0	0
257.0	0	1	0	1
259.0	0	1	0	0
260.0	0	0	0	1
261.0	0	0	0	1
263.0	0	1	0	0
264.0	0	2	0	0
265.0	0	1	0	0
270.0	0	1	0	1
272.0	0	1	0	0
273.0	0	0	0	1
274.0	0	1	0	1
276.0	0	1	0	0
282.0	0	1	0	1
283.0	0	0	0	1
285.0	0	0	0	1
286.0	0	1	0	0
288.0	0	1	0	1
289.0	0	0	0	1
292.0	0	0	0	1
294.0	0	1	0	1
295.0	0	1	0	1
296.0	0	0	0	1
297.0	0	1	0	0
300.0	0	1	0	0
301.0	0	1	0	0
305.0	0	0	0	1
306.0	0	0	0	1
307.0	0	1	0	1
309.0	0	1	0	0
311.0	0	1	0	0
312.0	0	1	0	0
313.0	0	1	0	2
315.0	0	0	0	1
316.0	0	0	0	1
321.0	0	2	0	1
322.0	0	0	0	1
323.0	0	1	0	1
326.0	0	1	0	0
327.0	0	1	0	0
332.0	0	1	0	1
335.0	0	2	0	1
336.0	0	1	0	0
337.0	0	0	0	1
338.0	0	0	0	1
344.0	0	0	0	1
345.0	0	1	0	0
346.0	0	0	0	1
347.0	0	2	0	0
348.0	0	0	0	1
350.0	0	0	0	2
353.0	0	1	0	0
355.0	0	0	0	1
356.0	0	0	0	2
357.0	0	1	0	0
359.0	0	0	0	1
360.0	0	2	0	0
361.0	0	1	0	1
364.0	0	1	0	0
365.0	0	1	0	1
368.0	0	1	0	0
373.0	0	0	0	1
374.0	0	2	0	0
376.0	0	1	0	0
385.0	0	1	0	0
390.0	0	0	0	1
397.0	0	0	0	1
400.0	0	1	0	1
401.0	0	0	0	1
405.0	0	0	0	1
406.0	0	1	0	0
409.0	0	1	0	0
410.0	0	0	0	1
414.0	0	1	0	3
418.0	0	1	0	0
421.0	0	1	0	0
425.0	0	1	0	0
429.0	0	1	0	0
433.0	0	0	0	1
438.0	0	1	0	0
450.0	0	1	0	0
454.0	0	0	0	1
455.0	0	0	0	1
457.0	0	0	0	1
470.0	0	2	0	0
480.0	0	1	0	1
492.0	0	0	0	1
497.0	0	0	0	1
501.0	0	0	0	1
502.0	0	1	0	0
504.0	0	1	0	0
508.0	0	0	0	1
512.0	0	0	0	1
514.0	0	1	0	0
515.0	0	1	0	0
516.0	0	1	0	0
527.0	0	1	0	0
528.0	0	0	0	2
532.0	0	0	0	1
535.0	0	1	0	0
540.0	0	0	0	1
543.0	0	0	0	1
548.0	0	1	0	0
550.0	0	1	0	0
551.0	0	1	0	0
560.0	0	0	0	1
571.0	0	1	0	0
573.0	0	0	0	1
577.0	0	1	0	1
580.0	0	0	0	2
584.0	0	0	0	1
589.0	0	1	0	0
595.0	0	1	0	0
600.0	0	1	0	0
602.0	0	1	0	0
604.0	0	1	0	0
617.0	0	0	0	1
631.0	0	0	0	1
643.0	0	1	0	0
646.0	0	1	0	0
651.0	0	0	0	1
660.0	0	1	0	0
716.0	0	0	0	2
727.0	0	0	0	1
738.0	0	1	0	0
748.0	0	1	0	0
756.0	0	1	0	0
771.0	0	0	0	1
804.0	0	1	0	0
852.0	0	0	0	1
867.0	0	1	0	0
936.0	0	0	0	1
963.0	0	1	0	0
1505.0	0	0	0	1
1510.0	0	0	0	1
1538.0	0	1	0	0
1543.0	0	1	0	0
1870.0	0	0	0	1
1931.0	0	1	0	0
2301.0	0	0	0	1
2368.0	0	1	0	0