## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P05-female_nonbleached_44.sorted.bam] OUTPUT=P05-female_nonbleached_44.sorted.dedup.bam METRICS_FILE=P05-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 13:24:57 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	932861	24707343	0	1833935	641149	8578675	740006	0.353513	28118488

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.019309	11228145	0	11473144
2.0	1.442656	3075247	574866	3022901
3.0	1.618484	1048046	61162	977583
4.0	1.691511	409660	10091	359226
5.0	1.72184	176689	2092	146409
6.0	1.734437	83131	523	65488
7.0	1.739669	41444	132	31476
8.0	1.741842	22398	49	16809
9.0	1.742745	12810	18	9513
10.0	1.743119	7749	3	5986
11.0	1.743275	5040	2	3970
12.0	1.74334	3502	0	2801
13.0	1.743367	2505	0	2070
14.0	1.743378	1880	0	1661
15.0	1.743382	1463	1	1284
16.0	1.743384	1106	0	1030
17.0	1.743385	963	2	883
18.0	1.743385	799	0	694
19.0	1.743386	610	0	594
20.0	1.743386	566	0	569
21.0	1.743386	485	0	440
22.0	1.743386	422	0	403
23.0	1.743386	378	1	351
24.0	1.743386	341	1	324
25.0	1.743386	278	1	228
26.0	1.743386	247	0	217
27.0	1.743386	203	0	204
28.0	1.743386	191	0	176
29.0	1.743386	168	0	150
30.0	1.743386	137	0	146
31.0	1.743386	128	0	107
32.0	1.743386	131	0	108
33.0	1.743386	96	0	115
34.0	1.743386	106	0	87
35.0	1.743386	94	0	88
36.0	1.743386	84	0	89
37.0	1.743386	79	0	73
38.0	1.743386	66	0	61
39.0	1.743386	63	0	53
40.0	1.743386	61	0	58
41.0	1.743386	56	0	59
42.0	1.743386	60	0	47
43.0	1.743386	47	0	54
44.0	1.743386	62	0	50
45.0	1.743386	44	0	44
46.0	1.743386	36	0	29
47.0	1.743386	32	0	27
48.0	1.743386	30	1	35
49.0	1.743386	27	0	38
50.0	1.743386	32	0	25
51.0	1.743386	33	0	37
52.0	1.743386	29	0	26
53.0	1.743386	29	0	28
54.0	1.743386	31	0	24
55.0	1.743386	25	0	22
56.0	1.743386	17	0	26
57.0	1.743386	23	0	14
58.0	1.743386	17	0	11
59.0	1.743386	15	0	18
60.0	1.743386	17	0	19
61.0	1.743386	16	0	23
62.0	1.743386	22	0	19
63.0	1.743386	23	0	16
64.0	1.743386	15	0	13
65.0	1.743386	15	0	9
66.0	1.743386	15	0	21
67.0	1.743386	16	0	9
68.0	1.743386	9	0	11
69.0	1.743386	15	0	13
70.0	1.743386	8	0	5
71.0	1.743386	12	0	11
72.0	1.743386	5	0	11
73.0	1.743386	14	1	14
74.0	1.743386	9	0	8
75.0	1.743386	9	0	9
76.0	1.743386	7	0	7
77.0	1.743386	12	0	5
78.0	1.743386	10	0	10
79.0	1.743386	6	0	8
80.0	1.743386	2	0	6
81.0	1.743386	8	0	4
82.0	1.743386	14	0	8
83.0	1.743386	3	0	2
84.0	1.743386	2	0	3
85.0	1.743386	4	0	3
86.0	1.743386	2	0	8
87.0	1.743386	3	0	5
88.0	1.743386	7	0	5
89.0	1.743386	10	0	11
90.0	1.743386	9	0	5
91.0	1.743386	3	0	5
92.0	1.743386	4	0	6
93.0	1.743386	6	0	9
94.0	1.743386	7	0	3
95.0	1.743386	7	0	4
96.0	1.743386	3	0	8
97.0	1.743386	4	0	4
98.0	1.743386	7	0	4
99.0	1.743386	7	0	5
100.0	1.743386	1	0	2
101.0	0	4	0	3
102.0	0	2	0	3
103.0	0	4	0	3
104.0	0	1	0	4
105.0	0	3	0	1
106.0	0	6	0	5
107.0	0	2	0	2
108.0	0	2	0	1
109.0	0	4	0	2
110.0	0	3	0	1
111.0	0	1	0	2
112.0	0	1	0	2
113.0	0	1	0	3
114.0	0	2	0	4
115.0	0	4	0	1
116.0	0	4	0	2
117.0	0	1	0	2
118.0	0	2	0	3
119.0	0	4	0	1
120.0	0	1	0	2
121.0	0	2	0	1
122.0	0	1	0	1
123.0	0	1	0	3
124.0	0	1	0	2
125.0	0	3	0	2
126.0	0	1	0	1
127.0	0	3	0	2
128.0	0	2	0	1
129.0	0	2	0	2
130.0	0	1	0	0
131.0	0	0	0	2
132.0	0	0	0	1
133.0	0	0	0	4
134.0	0	4	0	1
135.0	0	3	0	0
136.0	0	1	0	0
137.0	0	1	0	1
138.0	0	1	0	0
139.0	0	1	0	1
140.0	0	0	0	2
141.0	0	1	0	2
142.0	0	2	0	1
143.0	0	1	0	0
144.0	0	1	0	0
145.0	0	1	0	0
146.0	0	1	0	1
147.0	0	0	0	2
148.0	0	0	0	2
149.0	0	2	0	1
151.0	0	1	0	0
152.0	0	2	0	1
153.0	0	0	0	2
154.0	0	1	0	1
155.0	0	0	0	1
156.0	0	2	0	0
157.0	0	0	0	1
158.0	0	2	0	1
159.0	0	1	0	0
160.0	0	1	0	0
161.0	0	1	0	0
162.0	0	0	0	2
164.0	0	2	0	2
167.0	0	1	0	0
168.0	0	1	0	0
170.0	0	0	0	1
174.0	0	1	0	0
176.0	0	1	0	3
178.0	0	1	0	0
179.0	0	1	0	0
180.0	0	0	0	1
183.0	0	0	0	1
184.0	0	1	0	1
188.0	0	1	0	0
191.0	0	1	0	0
192.0	0	0	0	1
193.0	0	1	0	0
203.0	0	0	0	1
204.0	0	0	0	1
210.0	0	1	0	0
211.0	0	0	0	1
212.0	0	1	0	0
215.0	0	1	0	0
246.0	0	0	0	1
248.0	0	1	0	1
252.0	0	0	0	1
254.0	0	1	0	0
257.0	0	1	0	0
258.0	0	0	0	1
259.0	0	0	0	1
263.0	0	1	0	0
267.0	0	0	0	2
268.0	0	2	0	0
272.0	0	1	0	0
282.0	0	0	0	1
285.0	0	1	0	0
294.0	0	0	0	1
302.0	0	1	0	0
312.0	0	0	0	1
315.0	0	0	0	1
317.0	0	1	0	0
329.0	0	1	0	1
333.0	0	2	0	1
336.0	0	0	0	1
339.0	0	1	0	0
394.0	0	0	0	1
410.0	0	1	0	0
414.0	0	0	0	1
416.0	0	1	0	1
437.0	0	1	0	0
441.0	0	1	0	1
473.0	0	0	0	1
474.0	0	1	0	0
489.0	0	0	0	1
490.0	0	1	0	0
682.0	0	1	0	1
898.0	0	1	0	1
927.0	0	0	0	1
928.0	0	1	0	0
1020.0	0	0	0	1
1022.0	0	1	0	0
9792.0	0	0	0	1
9807.0	0	0	0	1
9814.0	0	1	0	0
9823.0	0	1	0	0
9961.0	0	0	0	1
9985.0	0	1	0	0
15768.0	0	0	0	1
15815.0	0	1	0	0
21558.0	0	0	0	1
21630.0	0	1	0	0