## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S52F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S52F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S52F.dup_metrics.txt REMOVE_DUPLICATES=true    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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 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: Wed Mar 09 12:39:21 PST 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	2081980	15972939	10082539	12455124	792846	3061859	67896	0.203262	36759598

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003409	11650897	0	11699952
2.0	1.653188	952629	65042	911303
3.0	2.073968	146272	895	140364
4.0	2.346454	50956	143	50036
5.0	2.522908	26430	50	26144
6.0	2.637175	16609	17	16477
7.0	2.711171	11053	14	10942
8.0	2.759088	8102	4	8054
9.0	2.790119	6338	1	6254
10.0	2.810213	4792	4	4776
11.0	2.823226	3958	1	3934
12.0	2.831652	3283	1	3253
13.0	2.837109	2654	1	2643
14.0	2.840643	2232	2	2257
15.0	2.842931	2021	1	1968
16.0	2.844413	1643	1	1642
17.0	2.845373	1492	2	1478
18.0	2.845994	1238	2	1222
19.0	2.846396	1179	1	1169
20.0	2.846657	1035	0	1040
21.0	2.846826	869	0	879
22.0	2.846935	858	0	846
23.0	2.847006	816	1	796
24.0	2.847052	702	0	704
25.0	2.847081	695	0	705
26.0	2.8471	587	0	582
27.0	2.847113	533	0	514
28.0	2.847121	501	0	507
29.0	2.847126	464	0	459
30.0	2.84713	446	0	447
31.0	2.847132	402	0	403
32.0	2.847133	401	0	396
33.0	2.847134	358	0	356
34.0	2.847135	319	0	309
35.0	2.847135	277	0	277
36.0	2.847135	293	0	291
37.0	2.847135	258	0	272
38.0	2.847136	282	0	270
39.0	2.847136	232	0	223
40.0	2.847136	215	0	220
41.0	2.847136	213	0	197
42.0	2.847136	182	0	189
43.0	2.847136	185	0	195
44.0	2.847136	204	0	195
45.0	2.847136	179	0	182
46.0	2.847136	177	0	175
47.0	2.847136	138	0	138
48.0	2.847136	161	0	163
49.0	2.847136	152	0	139
50.0	2.847136	139	0	148
51.0	2.847136	140	0	140
52.0	2.847136	138	0	137
53.0	2.847136	124	0	117
54.0	2.847136	103	0	104
55.0	2.847136	115	0	123
56.0	2.847136	114	0	113
57.0	2.847136	91	0	90
58.0	2.847136	102	0	107
59.0	2.847136	101	0	88
60.0	2.847136	96	0	89
61.0	2.847136	80	0	84
62.0	2.847136	86	0	81
63.0	2.847136	74	0	86
64.0	2.847136	85	0	84
65.0	2.847136	77	0	76
66.0	2.847136	77	0	70
67.0	2.847136	73	0	69
68.0	2.847136	63	0	66
69.0	2.847136	70	0	75
70.0	2.847136	71	0	63
71.0	2.847136	48	0	53
72.0	2.847136	57	0	64
73.0	2.847136	50	0	40
74.0	2.847136	64	0	59
75.0	2.847136	52	0	57
76.0	2.847136	45	0	46
77.0	2.847136	56	0	59
78.0	2.847136	59	0	55
79.0	2.847136	39	0	36
80.0	2.847136	49	0	49
81.0	2.847136	43	0	42
82.0	2.847136	40	0	50
83.0	2.847136	45	0	43
84.0	2.847136	50	0	44
85.0	2.847136	41	0	48
86.0	2.847136	48	0	44
87.0	2.847136	46	0	40
88.0	2.847136	42	0	44
89.0	2.847136	43	0	46
90.0	2.847136	41	0	37
91.0	2.847136	30	0	26
92.0	2.847136	27	0	30
93.0	2.847136	31	0	33
94.0	2.847136	32	0	31
95.0	2.847136	29	0	25
96.0	2.847136	27	0	29
97.0	2.847136	33	0	41
98.0	2.847136	31	0	30
99.0	2.847136	35	0	30
100.0	2.847136	34	0	38
101.0	0	24	0	24
102.0	0	40	0	27
103.0	0	30	0	36
104.0	0	27	0	31
105.0	0	27	0	28
106.0	0	31	0	30
107.0	0	24	0	31
108.0	0	33	0	25
109.0	0	31	0	27
110.0	0	20	0	26
111.0	0	26	0	25
112.0	0	23	0	16
113.0	0	21	0	19
114.0	0	13	0	13
115.0	0	16	0	26
116.0	0	22	0	24
117.0	0	26	0	25
118.0	0	21	0	24
119.0	0	33	0	21
120.0	0	18	0	22
121.0	0	14	0	17
122.0	0	22	0	16
123.0	0	13	0	13
124.0	0	22	0	24
125.0	0	16	0	17
126.0	0	19	0	13
127.0	0	12	0	15
128.0	0	22	0	23
129.0	0	10	0	13
130.0	0	16	0	15
131.0	0	16	0	15
132.0	0	20	0	19
133.0	0	17	0	15
134.0	0	11	0	14
135.0	0	9	0	7
136.0	0	13	0	9
137.0	0	12	0	13
138.0	0	12	0	13
139.0	0	17	0	21
140.0	0	16	0	16
141.0	0	15	0	14
142.0	0	13	0	9
143.0	0	14	0	16
144.0	0	11	0	10
145.0	0	7	0	5
146.0	0	8	0	11
147.0	0	14	0	12
148.0	0	7	0	11
149.0	0	12	0	9
150.0	0	9	0	6
151.0	0	7	0	8
152.0	0	6	0	4
153.0	0	7	0	15
154.0	0	15	0	10
155.0	0	8	0	13
156.0	0	9	0	12
157.0	0	16	0	11
158.0	0	14	0	12
159.0	0	6	0	7
160.0	0	11	0	7
161.0	0	9	0	10
162.0	0	10	0	11
163.0	0	6	0	10
164.0	0	10	0	6
165.0	0	9	0	9
166.0	0	4	0	4
167.0	0	10	0	6
168.0	0	4	0	7
169.0	0	6	0	7
170.0	0	4	0	8
171.0	0	10	0	7
172.0	0	7	0	2
173.0	0	3	0	5
174.0	0	3	0	6
175.0	0	7	0	5
176.0	0	5	0	6
177.0	0	10	0	6
178.0	0	3	0	9
179.0	0	7	0	9
180.0	0	9	0	4
181.0	0	7	0	7
182.0	0	9	0	7
183.0	0	4	0	6
184.0	0	4	0	4
185.0	0	6	0	5
186.0	0	6	0	4
187.0	0	5	0	11
188.0	0	5	0	1
189.0	0	4	0	6
190.0	0	7	0	7
191.0	0	7	0	5
192.0	0	3	0	5
193.0	0	4	0	0
194.0	0	2	0	8
195.0	0	13	0	10
196.0	0	5	0	6
197.0	0	6	0	4
198.0	0	5	0	6
199.0	0	2	0	2
200.0	0	6	0	3
201.0	0	8	0	7
202.0	0	0	0	3
203.0	0	4	0	4
204.0	0	6	0	6
205.0	0	3	0	3
206.0	0	3	0	5
207.0	0	6	0	6
208.0	0	4	0	6
209.0	0	4	0	9
210.0	0	6	0	3
211.0	0	9	0	5
212.0	0	7	0	6
213.0	0	7	0	7
214.0	0	5	0	2
215.0	0	3	0	3
216.0	0	4	0	4
217.0	0	2	0	2
218.0	0	2	0	4
219.0	0	4	0	9
220.0	0	10	0	6
221.0	0	4	0	3
222.0	0	6	0	2
223.0	0	2	0	4
224.0	0	1	0	5
225.0	0	7	0	6
226.0	0	4	0	3
227.0	0	2	0	7
228.0	0	11	0	7
229.0	0	4	0	2
230.0	0	2	0	2
231.0	0	3	0	5
232.0	0	6	0	7
233.0	0	4	0	3
234.0	0	5	0	4
235.0	0	3	0	6
236.0	0	5	0	2
237.0	0	5	0	4
238.0	0	1	0	3
239.0	0	4	0	4
240.0	0	3	0	1
241.0	0	4	0	5
242.0	0	3	0	2
243.0	0	4	0	3
244.0	0	2	0	1
245.0	0	2	0	2
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248.0	0	4	0	2
249.0	0	1	0	3
250.0	0	3	0	3
251.0	0	6	0	5
252.0	0	2	0	2
253.0	0	3	0	3
254.0	0	4	0	2
255.0	0	1	0	1
256.0	0	0	0	1
257.0	0	2	0	1
258.0	0	0	0	3
259.0	0	1	0	2
260.0	0	4	0	3
261.0	0	2	0	2
262.0	0	6	0	3
263.0	0	2	0	2
264.0	0	1	0	4
265.0	0	3	0	2
266.0	0	2	0	3
267.0	0	2	0	2
268.0	0	2	0	1
269.0	0	2	0	2
270.0	0	3	0	2
271.0	0	2	0	2
272.0	0	2	0	1
273.0	0	1	0	2
274.0	0	3	0	2
275.0	0	2	0	2
276.0	0	1	0	3
277.0	0	2	0	0
278.0	0	0	0	1
279.0	0	1	0	3
280.0	0	2	0	2
281.0	0	4	0	2
282.0	0	2	0	3
283.0	0	3	0	3
284.0	0	3	0	2
285.0	0	1	0	1
286.0	0	1	0	2
287.0	0	2	0	1
288.0	0	3	0	3
289.0	0	2	0	2
290.0	0	1	0	1
291.0	0	3	0	4
292.0	0	2	0	3
293.0	0	2	0	1
294.0	0	3	0	0
295.0	0	1	0	2
296.0	0	0	0	2
297.0	0	1	0	3
298.0	0	5	0	5
299.0	0	2	0	2
300.0	0	3	0	1
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303.0	0	1	0	1
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305.0	0	1	0	1
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308.0	0	1	0	0
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310.0	0	1	0	4
311.0	0	2	0	2
312.0	0	3	0	3
313.0	0	3	0	1
314.0	0	2	0	3
315.0	0	3	0	1
316.0	0	1	0	2
317.0	0	1	0	2
318.0	0	2	0	0
319.0	0	2	0	4
320.0	0	2	0	1
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382.0	0	0	0	1
384.0	0	1	0	0
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386.0	0	1	0	2
387.0	0	1	0	1
388.0	0	1	0	1
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390.0	0	1	0	2
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