## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P15-female_nonbleached_K5.sorted.bam] OUTPUT=P15-female_nonbleached_K5.sorted.dedup.bam METRICS_FILE=P15-female_nonbleached_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 20:30:25 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	1027436	32697079	0	2642852	668774	12332068	855972	0.381396	32758302

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.015696	13805859	0	14067280
2.0	1.390048	4023429	672272	3977937
3.0	1.528022	1406942	67372	1331173
4.0	1.578875	559531	10768	503402
5.0	1.597618	247574	2326	212040
6.0	1.604526	118721	640	98445
7.0	1.607072	62968	216	51557
8.0	1.60801	36627	124	30359
9.0	1.608356	22700	65	19212
10.0	1.608484	15442	46	13328
11.0	1.608531	10956	22	9715
12.0	1.608548	8260	24	7598
13.0	1.608554	6377	7	5780
14.0	1.608557	5083	8	4630
15.0	1.608558	4141	4	3897
16.0	1.608558	3410	9	3241
17.0	1.608558	2964	2	2779
18.0	1.608558	2431	3	2277
19.0	1.608558	2131	1	1996
20.0	1.608558	1796	1	1698
21.0	1.608558	1585	0	1455
22.0	1.608558	1325	0	1323
23.0	1.608558	1248	2	1184
24.0	1.608558	1100	1	982
25.0	1.608558	910	0	882
26.0	1.608558	854	0	788
27.0	1.608558	734	0	712
28.0	1.608558	680	0	635
29.0	1.608558	616	0	573
30.0	1.608558	560	0	524
31.0	1.608558	500	0	467
32.0	1.608558	454	0	431
33.0	1.608558	403	0	404
34.0	1.608558	377	0	334
35.0	1.608558	355	0	350
36.0	1.608558	316	0	285
37.0	1.608558	309	0	296
38.0	1.608558	255	0	277
39.0	1.608558	284	0	270
40.0	1.608558	268	0	232
41.0	1.608558	229	0	203
42.0	1.608558	195	0	187
43.0	1.608558	205	0	192
44.0	1.608558	185	0	181
45.0	1.608558	183	0	162
46.0	1.608558	157	0	151
47.0	1.608558	141	0	130
48.0	1.608558	126	0	122
49.0	1.608558	123	0	130
50.0	1.608558	117	0	117
51.0	1.608558	143	0	124
52.0	1.608558	119	0	110
53.0	1.608558	88	0	101
54.0	1.608558	108	0	104
55.0	1.608558	103	0	87
56.0	1.608558	84	0	65
57.0	1.608558	89	0	86
58.0	1.608558	73	0	76
59.0	1.608558	72	0	58
60.0	1.608558	68	0	71
61.0	1.608558	70	0	62
62.0	1.608558	59	0	66
63.0	1.608558	66	0	57
64.0	1.608558	54	0	56
65.0	1.608558	68	0	51
66.0	1.608558	61	0	62
67.0	1.608558	44	0	48
68.0	1.608558	48	0	43
69.0	1.608558	54	0	42
70.0	1.608558	33	0	31
71.0	1.608558	39	0	42
72.0	1.608558	47	0	49
73.0	1.608558	41	0	30
74.0	1.608558	35	0	38
75.0	1.608558	33	0	27
76.0	1.608558	40	0	32
77.0	1.608558	23	0	37
78.0	1.608558	38	0	31
79.0	1.608558	24	0	23
80.0	1.608558	31	0	17
81.0	1.608558	30	0	23
82.0	1.608558	21	0	26
83.0	1.608558	22	0	25
84.0	1.608558	21	0	24
85.0	1.608558	28	0	22
86.0	1.608558	25	0	23
87.0	1.608558	25	0	22
88.0	1.608558	14	0	20
89.0	1.608558	19	0	25
90.0	1.608558	26	0	19
91.0	1.608558	18	0	18
92.0	1.608558	27	0	19
93.0	1.608558	17	0	18
94.0	1.608558	25	0	17
95.0	1.608558	14	0	20
96.0	1.608558	16	0	14
97.0	1.608558	19	0	10
98.0	1.608558	17	0	15
99.0	1.608558	12	0	11
100.0	1.608558	12	0	11
101.0	0	12	0	17
102.0	0	9	0	10
103.0	0	7	0	14
104.0	0	14	0	12
105.0	0	15	0	13
106.0	0	15	0	18
107.0	0	9	0	9
108.0	0	12	0	18
109.0	0	12	0	10
110.0	0	19	0	8
111.0	0	8	0	11
112.0	0	8	0	7
113.0	0	8	0	10
114.0	0	12	0	10
115.0	0	10	0	12
116.0	0	15	0	5
117.0	0	7	0	8
118.0	0	7	0	8
119.0	0	12	0	7
120.0	0	4	0	4
121.0	0	10	0	8
122.0	0	8	0	11
123.0	0	7	0	7
124.0	0	5	0	4
125.0	0	7	0	7
126.0	0	4	0	7
127.0	0	10	0	7
128.0	0	4	0	3
129.0	0	7	0	5
130.0	0	4	0	5
131.0	0	6	0	8
132.0	0	4	0	2
133.0	0	8	0	4
134.0	0	6	0	7
135.0	0	5	0	2
136.0	0	4	0	4
137.0	0	2	0	7
138.0	0	7	0	3
139.0	0	2	0	10
140.0	0	6	0	4
141.0	0	5	0	4
142.0	0	4	0	6
143.0	0	6	0	5
144.0	0	8	0	5
145.0	0	6	0	3
146.0	0	6	0	1
147.0	0	5	0	5
148.0	0	5	0	2
149.0	0	2	0	2
150.0	0	2	0	4
151.0	0	7	0	6
152.0	0	5	0	4
153.0	0	4	0	3
154.0	0	3	0	5
155.0	0	3	0	1
156.0	0	4	0	2
157.0	0	2	0	3
158.0	0	2	0	3
159.0	0	4	0	4
160.0	0	5	0	4
161.0	0	3	0	3
162.0	0	2	0	2
163.0	0	1	0	3
164.0	0	3	0	3
165.0	0	2	0	6
166.0	0	1	0	6
167.0	0	3	0	3
168.0	0	3	0	1
169.0	0	4	0	3
170.0	0	5	0	1
171.0	0	7	0	6
172.0	0	1	0	1
173.0	0	4	0	3
174.0	0	2	0	5
175.0	0	4	0	1
176.0	0	3	0	3
177.0	0	1	0	3
178.0	0	1	0	1
179.0	0	4	0	3
180.0	0	2	0	2
181.0	0	1	0	2
182.0	0	2	0	4
183.0	0	3	0	4
184.0	0	5	0	3
185.0	0	1	0	2
186.0	0	2	0	2
187.0	0	2	0	5
188.0	0	2	0	1
189.0	0	4	0	1
190.0	0	2	0	5
191.0	0	3	0	0
192.0	0	2	0	3
193.0	0	1	0	0
194.0	0	4	0	2
195.0	0	2	0	1
196.0	0	6	0	0
198.0	0	4	0	3
200.0	0	1	0	2
201.0	0	1	0	0
202.0	0	1	0	2
203.0	0	1	0	1
204.0	0	2	0	1
205.0	0	1	0	0
206.0	0	1	0	3
207.0	0	2	0	0
208.0	0	0	0	1
209.0	0	0	0	3
210.0	0	1	0	1
211.0	0	1	0	2
212.0	0	1	0	0
213.0	0	3	0	2
214.0	0	1	0	1
216.0	0	1	0	1
217.0	0	1	0	3
218.0	0	2	0	0
219.0	0	1	0	2
220.0	0	2	0	0
224.0	0	1	0	0
225.0	0	3	0	1
226.0	0	2	0	1
227.0	0	2	0	1
230.0	0	0	0	1
231.0	0	1	0	0
233.0	0	1	0	2
236.0	0	1	0	0
238.0	0	1	0	1
240.0	0	0	0	1
241.0	0	0	0	1
242.0	0	0	0	1
243.0	0	1	0	0
244.0	0	1	0	0
246.0	0	0	0	2
247.0	0	0	0	1
248.0	0	1	0	0
249.0	0	1	0	1
250.0	0	1	0	0
251.0	0	1	0	0
252.0	0	1	0	1
253.0	0	1	0	0
254.0	0	1	0	0
255.0	0	0	0	1
257.0	0	1	0	2
260.0	0	0	0	3
261.0	0	1	0	0
262.0	0	1	0	0
263.0	0	1	0	0
266.0	0	1	0	1
267.0	0	0	0	1
268.0	0	2	0	0
271.0	0	1	0	0
273.0	0	1	0	1
274.0	0	0	0	1
278.0	0	1	0	0
280.0	0	1	0	1
281.0	0	0	0	1
284.0	0	0	0	1
288.0	0	0	0	1
289.0	0	0	0	1
291.0	0	2	0	0
293.0	0	1	0	0
297.0	0	0	0	1
299.0	0	3	0	1
301.0	0	0	0	1
304.0	0	0	0	1
305.0	0	0	0	1
306.0	0	0	0	1
308.0	0	2	0	0
311.0	0	0	0	1
312.0	0	0	0	1
313.0	0	1	0	0
314.0	0	1	0	0
315.0	0	2	0	0
324.0	0	1	0	0
326.0	0	0	0	1
327.0	0	0	0	1
328.0	0	0	0	1
338.0	0	0	0	1
341.0	0	1	0	0
344.0	0	2	0	0
352.0	0	1	0	1
358.0	0	1	0	0
364.0	0	0	0	2
368.0	0	1	0	0
371.0	0	1	0	0
382.0	0	0	0	1
404.0	0	1	0	0
407.0	0	0	0	2
411.0	0	1	0	0
415.0	0	0	0	1
422.0	0	1	0	0
423.0	0	0	0	1
430.0	0	1	0	0
431.0	0	0	0	1
434.0	0	1	0	0
445.0	0	1	0	0
457.0	0	0	0	1
479.0	0	1	0	1
483.0	0	1	0	0
489.0	0	0	0	1
498.0	0	1	0	0
541.0	0	0	0	1
545.0	0	1	0	0
550.0	0	0	0	1
559.0	0	0	0	1
567.0	0	1	0	0
574.0	0	1	0	0
587.0	0	0	0	1
603.0	0	1	0	0
674.0	0	0	0	1
697.0	0	1	0	0
720.0	0	0	0	1
737.0	0	1	0	0