## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[larvae.sorted.bam] OUTPUT=larvae.markdup.sorted.bam METRICS_FILE=larvae.markdup.sorted.MarkDuplicates.metrics.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true TMP_DIR=[tmp] 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 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: Fri Mar 25 11:52:13 GMT 2022

## 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	60017	44576579	9216059	0	42459	34333764	0	0.770178	10384783

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	1874410	1874410
2.0	1.013671	1547662	1547662
3.0	1.013858	1512313	1512313
4.0	1.01386	1375348	1375348
5.0	1.01386	1146007	1146007
6.0	1.01386	878533	878533
7.0	1.01386	629447	629447
8.0	1.01386	427614	427614
9.0	1.01386	278531	278531
10.0	1.01386	176396	176396
11.0	1.01386	111495	111495
12.0	1.01386	71500	71500
13.0	1.01386	47324	47324
14.0	1.01386	32019	32019
15.0	1.01386	22830	22830
16.0	1.01386	16939	16939
17.0	1.01386	13004	13004
18.0	1.01386	10181	10181
19.0	1.01386	8390	8390
20.0	1.01386	6822	6822
21.0	1.01386	5706	5706
22.0	1.01386	4888	4888
23.0	1.01386	4120	4120
24.0	1.01386	3557	3557
25.0	1.01386	3201	3201
26.0	1.01386	2867	2867
27.0	1.01386	2481	2481
28.0	1.01386	2259	2259
29.0	1.01386	2011	2011
30.0	1.01386	1781	1781
31.0	1.01386	1618	1618
32.0	1.01386	1436	1436
33.0	1.01386	1306	1306
34.0	1.01386	1207	1207
35.0	1.01386	1060	1060
36.0	1.01386	1050	1050
37.0	1.01386	892	892
38.0	1.01386	879	879
39.0	1.01386	724	724
40.0	1.01386	714	714
41.0	1.01386	674	674
42.0	1.01386	619	619
43.0	1.01386	580	580
44.0	1.01386	522	522
45.0	1.01386	522	522
46.0	1.01386	472	472
47.0	1.01386	448	448
48.0	1.01386	415	415
49.0	1.01386	360	360
50.0	1.01386	331	331
51.0	1.01386	345	345
52.0	1.01386	305	305
53.0	1.01386	282	282
54.0	1.01386	276	276
55.0	1.01386	269	269
56.0	1.01386	233	233
57.0	1.01386	230	230
58.0	1.01386	230	230
59.0	1.01386	237	237
60.0	1.01386	191	191
61.0	1.01386	181	181
62.0	1.01386	196	196
63.0	1.01386	164	164
64.0	1.01386	140	140
65.0	1.01386	144	144
66.0	1.01386	141	141
67.0	1.01386	144	144
68.0	1.01386	125	125
69.0	1.01386	117	117
70.0	1.01386	117	117
71.0	1.01386	119	119
72.0	1.01386	111	111
73.0	1.01386	100	100
74.0	1.01386	92	92
75.0	1.01386	79	79
76.0	1.01386	100	100
77.0	1.01386	75	75
78.0	1.01386	82	82
79.0	1.01386	81	81
80.0	1.01386	73	73
81.0	1.01386	69	69
82.0	1.01386	65	65
83.0	1.01386	92	92
84.0	1.01386	68	68
85.0	1.01386	78	78
86.0	1.01386	50	50
87.0	1.01386	55	55
88.0	1.01386	61	61
89.0	1.01386	52	52
90.0	1.01386	49	49
91.0	1.01386	51	51
92.0	1.01386	39	39
93.0	1.01386	53	53
94.0	1.01386	44	44
95.0	1.01386	32	32
96.0	1.01386	39	39
97.0	1.01386	47	47
98.0	1.01386	41	41
99.0	1.01386	39	39
100.0	1.01386	41	41
101.0	0	26	26
102.0	0	30	30
103.0	0	21	21
104.0	0	28	28
105.0	0	31	31
106.0	0	24	24
107.0	0	38	38
108.0	0	26	26
109.0	0	21	21
110.0	0	24	24
111.0	0	27	27
112.0	0	24	24
113.0	0	16	16
114.0	0	25	25
115.0	0	25	25
116.0	0	19	19
117.0	0	25	25
118.0	0	22	22
119.0	0	18	18
120.0	0	17	17
121.0	0	23	23
122.0	0	23	23
123.0	0	11	11
124.0	0	18	18
125.0	0	15	15
126.0	0	17	17
127.0	0	15	15
128.0	0	17	17
129.0	0	16	16
130.0	0	12	12
131.0	0	9	9
132.0	0	14	14
133.0	0	12	12
134.0	0	16	16
135.0	0	16	16
136.0	0	16	16
137.0	0	12	12
138.0	0	8	8
139.0	0	10	10
140.0	0	15	15
141.0	0	10	10
142.0	0	12	12
143.0	0	9	9
144.0	0	11	11
145.0	0	10	10
146.0	0	11	11
147.0	0	10	10
148.0	0	9	9
149.0	0	7	7
150.0	0	5	5
151.0	0	5	5
152.0	0	5	5
153.0	0	4	4
154.0	0	7	7
155.0	0	5	5
156.0	0	7	7
157.0	0	7	7
158.0	0	6	6
159.0	0	4	4
160.0	0	5	5
161.0	0	5	5
162.0	0	10	10
163.0	0	7	7
164.0	0	15	15
165.0	0	6	6
166.0	0	8	8
167.0	0	7	7
168.0	0	2	2
169.0	0	4	4
170.0	0	6	6
171.0	0	2	2
172.0	0	7	7
173.0	0	6	6
174.0	0	2	2
175.0	0	6	6
176.0	0	7	7
178.0	0	9	9
179.0	0	7	7
180.0	0	4	4
181.0	0	8	8
182.0	0	8	8
183.0	0	3	3
184.0	0	8	8
185.0	0	3	3
186.0	0	2	2
187.0	0	3	3
188.0	0	4	4
189.0	0	3	3
190.0	0	2	2
191.0	0	1	1
192.0	0	3	3
193.0	0	2	2
194.0	0	6	6
195.0	0	2	2
196.0	0	2	2
197.0	0	5	5
198.0	0	1	1
199.0	0	7	7
200.0	0	1	1
202.0	0	1	1
203.0	0	2	2
204.0	0	3	3
205.0	0	1	1
206.0	0	5	5
207.0	0	2	2
208.0	0	3	3
209.0	0	3	3
210.0	0	4	4
212.0	0	1	1
213.0	0	3	3
214.0	0	4	4
215.0	0	2	2
216.0	0	1	1
217.0	0	2	2
218.0	0	1	1
219.0	0	2	2
220.0	0	4	4
221.0	0	2	2
222.0	0	2	2
223.0	0	2	2
224.0	0	5	5
225.0	0	1	1
226.0	0	3	3
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
230.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	2	2
236.0	0	1	1
237.0	0	2	2
239.0	0	2	2
240.0	0	2	2
241.0	0	2	2
242.0	0	1	1
243.0	0	3	3
244.0	0	2	2
246.0	0	2	2
248.0	0	1	1
249.0	0	1	1
251.0	0	2	2
252.0	0	1	1
253.0	0	1	1
255.0	0	1	1
256.0	0	1	1
257.0	0	2	2
259.0	0	1	1
260.0	0	1	1
261.0	0	2	2
262.0	0	2	2
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	1	1
268.0	0	2	2
269.0	0	1	1
270.0	0	3	3
274.0	0	1	1
278.0	0	1	1
279.0	0	2	2
280.0	0	1	1
281.0	0	1	1
282.0	0	1	1
283.0	0	2	2
289.0	0	1	1
291.0	0	1	1
294.0	0	1	1
295.0	0	1	1
296.0	0	2	2
300.0	0	1	1
303.0	0	1	1
306.0	0	1	1
308.0	0	1	1
309.0	0	1	1
312.0	0	1	1
313.0	0	1	1
319.0	0	1	1
325.0	0	2	2
331.0	0	2	2
333.0	0	1	1
335.0	0	1	1
337.0	0	1	1
344.0	0	1	1
349.0	0	1	1
351.0	0	1	1
355.0	0	1	1
364.0	0	2	2
366.0	0	1	1
367.0	0	2	2
369.0	0	1	1
370.0	0	2	2
372.0	0	1	1
375.0	0	1	1
381.0	0	2	2
390.0	0	1	1
394.0	0	1	1
395.0	0	1	1
399.0	0	1	1
415.0	0	1	1
418.0	0	1	1
430.0	0	1	1
438.0	0	1	1
446.0	0	1	1
458.0	0	1	1
462.0	0	2	2
483.0	0	1	1
490.0	0	1	1
508.0	0	1	1
543.0	0	1	1
545.0	0	1	1
557.0	0	1	1
602.0	0	1	1
639.0	0	1	1
688.0	0	1	1
781.0	0	1	1
900.0	0	1	1
951.0	0	1	1