## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P10-female_nonbleached_K5.sorted.bam] OUTPUT=P10-female_nonbleached_K5.sorted.dedup.bam METRICS_FILE=P10-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 16:49:16 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	1338765	31035040	0	2706575	728334	7675908	1272320	0.253595	58841413

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.032492	18351545	0	18974099
2.0	1.641783	3540253	976019	3254532
3.0	2.001336	936770	109051	756546
4.0	2.213514	301646	18265	216462
5.0	2.338723	113356	3737	75502
6.0	2.412611	48628	995	31589
7.0	2.456214	23272	268	15639
8.0	2.481945	12584	89	8932
9.0	2.497129	7740	29	5925
10.0	2.506089	5113	18	3993
11.0	2.511377	3534	16	2935
12.0	2.514497	2503	6	2134
13.0	2.516339	1956	5	1725
14.0	2.517425	1453	2	1315
15.0	2.518067	1258	2	1048
16.0	2.518445	952	1	823
17.0	2.518668	770	1	721
18.0	2.5188	681	2	652
19.0	2.518878	610	2	477
20.0	2.518924	483	0	442
21.0	2.518951	415	1	363
22.0	2.518967	345	0	332
23.0	2.518976	295	3	295
24.0	2.518982	260	0	221
25.0	2.518985	238	0	212
26.0	2.518987	180	0	155
27.0	2.518988	162	1	160
28.0	2.518989	176	1	140
29.0	2.518989	147	0	137
30.0	2.518989	141	0	119
31.0	2.51899	122	0	112
32.0	2.51899	117	1	91
33.0	2.51899	87	0	89
34.0	2.51899	93	0	89
35.0	2.51899	76	0	73
36.0	2.51899	77	0	76
37.0	2.51899	73	0	59
38.0	2.51899	53	1	51
39.0	2.51899	62	0	49
40.0	2.51899	51	0	48
41.0	2.51899	38	0	35
42.0	2.51899	31	0	33
43.0	2.51899	55	0	31
44.0	2.51899	29	0	36
45.0	2.51899	35	0	41
46.0	2.51899	32	1	28
47.0	2.51899	31	0	22
48.0	2.51899	36	0	26
49.0	2.51899	29	0	20
50.0	2.51899	16	0	17
51.0	2.51899	19	1	19
52.0	2.51899	17	0	25
53.0	2.51899	17	0	16
54.0	2.51899	20	1	24
55.0	2.51899	24	0	13
56.0	2.51899	22	0	23
57.0	2.51899	21	0	15
58.0	2.51899	13	0	21
59.0	2.51899	16	0	15
60.0	2.51899	21	0	11
61.0	2.51899	12	1	9
62.0	2.51899	14	0	17
63.0	2.51899	11	0	11
64.0	2.51899	13	0	7
65.0	2.51899	10	0	10
66.0	2.51899	12	0	8
67.0	2.51899	9	0	9
68.0	2.51899	7	0	12
69.0	2.51899	11	0	6
70.0	2.51899	8	0	5
71.0	2.51899	4	0	7
72.0	2.51899	9	0	10
73.0	2.51899	4	0	7
74.0	2.51899	6	0	4
75.0	2.51899	6	0	4
76.0	2.51899	7	0	2
77.0	2.51899	4	0	6
78.0	2.51899	9	0	4
79.0	2.51899	1	0	5
80.0	2.51899	3	0	8
81.0	2.51899	7	0	6
82.0	2.51899	6	0	0
83.0	2.51899	4	0	2
84.0	2.51899	3	0	3
85.0	2.51899	3	0	1
86.0	2.51899	5	0	6
87.0	2.51899	2	0	7
88.0	2.51899	5	0	7
89.0	2.51899	5	0	6
90.0	2.51899	4	0	1
91.0	2.51899	5	0	3
92.0	2.51899	3	0	1
93.0	2.51899	5	0	2
94.0	2.51899	2	0	4
95.0	2.51899	3	0	5
96.0	2.51899	1	0	3
97.0	2.51899	1	0	5
98.0	2.51899	8	0	2
99.0	2.51899	4	0	2
100.0	2.51899	3	0	4
101.0	0	2	0	2
102.0	0	3	0	1
103.0	0	2	0	3
104.0	0	2	0	1
105.0	0	5	0	0
106.0	0	4	0	2
107.0	0	3	0	3
108.0	0	0	0	2
109.0	0	1	0	1
110.0	0	0	0	1
111.0	0	2	0	1
112.0	0	2	0	1
113.0	0	1	0	1
114.0	0	1	0	2
116.0	0	1	0	0
117.0	0	1	0	1
118.0	0	3	0	1
119.0	0	1	0	1
120.0	0	1	0	1
121.0	0	1	0	1
122.0	0	1	0	0
123.0	0	1	0	2
124.0	0	1	0	0
125.0	0	2	0	2
126.0	0	1	0	2
127.0	0	1	0	0
129.0	0	2	0	1
130.0	0	1	0	0
131.0	0	1	0	0
132.0	0	0	0	3
133.0	0	1	0	1
136.0	0	0	0	1
137.0	0	0	0	1
138.0	0	1	0	1
139.0	0	3	0	0
140.0	0	0	0	2
141.0	0	1	0	0
142.0	0	2	0	0
143.0	0	1	0	0
144.0	0	1	0	0
146.0	0	0	0	1
148.0	0	2	0	1
150.0	0	1	0	1
152.0	0	0	0	1
155.0	0	0	0	1
156.0	0	2	0	0
163.0	0	0	0	1
167.0	0	2	0	0
168.0	0	0	0	2
171.0	0	0	0	1
174.0	0	1	0	0
175.0	0	0	0	1
176.0	0	1	0	0
177.0	0	1	0	1
178.0	0	1	0	0
183.0	0	1	0	1
184.0	0	1	0	0
185.0	0	0	0	1
187.0	0	0	0	1
192.0	0	1	0	0
194.0	0	1	0	0
196.0	0	0	0	1
200.0	0	1	0	0
201.0	0	0	0	1
212.0	0	0	0	1
218.0	0	1	0	0
219.0	0	1	0	0
222.0	0	0	0	1
229.0	0	1	0	0
234.0	0	0	0	1
243.0	0	0	0	1
244.0	0	1	0	0
253.0	0	1	0	0
256.0	0	0	0	1
262.0	0	0	0	1
263.0	0	1	0	0
264.0	0	0	0	1
266.0	0	1	0	0
267.0	0	0	0	1
275.0	0	1	0	0
312.0	0	1	0	0
317.0	0	0	0	1
324.0	0	1	0	0
373.0	0	0	0	1
389.0	0	1	0	0
409.0	0	0	0	1
419.0	0	1	0	0
446.0	0	0	0	1
456.0	0	0	0	1
472.0	0	1	0	0
474.0	0	1	0	0
477.0	0	0	0	1
497.0	0	0	0	1
504.0	0	1	0	0
519.0	0	1	0	0
554.0	0	0	0	1
585.0	0	1	0	0
590.0	0	0	0	1
594.0	0	0	0	1
631.0	0	1	0	0
640.0	0	1	0	0
763.0	0	0	0	1
780.0	0	0	0	1
816.0	0	1	0	0
840.0	0	1	0	0