## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/star/GRCh37-NP_Day19_adherent_DMSO_A65_S2.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day19_adherent_DMSO_A65_S2.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-NP_Day19_adherent_DMSO_A65_S2.samtools-coordinate.metrics.txt    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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 REMOVE_DUPLICATES=false 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=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: Tue Aug 31 19:16:33 CEST 2021

## 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	132	16562195	0	0	69	5934078	4470	0.358291	17185598

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.00016	7122383	0	7124114
2.0	1.381691	2454815	4450	2454486
3.0	1.527233	736237	10	735540
4.0	1.582753	198135	0	197686
5.0	1.603932	53981	0	53802
6.0	1.612011	18229	0	18189
7.0	1.615093	8444	0	8424
8.0	1.616269	5126	0	5120
9.0	1.616717	3539	0	3534
10.0	1.616888	2882	0	2880
11.0	1.616953	2209	0	2216
12.0	1.616978	1799	0	1793
13.0	1.616988	1522	0	1520
14.0	1.616991	1279	0	1279
15.0	1.616993	1170	0	1170
16.0	1.616993	976	0	977
17.0	1.616994	885	0	885
18.0	1.616994	807	0	806
19.0	1.616994	746	0	749
20.0	1.616994	672	0	670
21.0	1.616994	568	0	567
22.0	1.616994	576	0	575
23.0	1.616994	486	0	486
24.0	1.616994	406	0	407
25.0	1.616994	400	0	398
26.0	1.616994	393	0	394
27.0	1.616994	374	0	374
28.0	1.616994	357	0	358
29.0	1.616994	322	0	320
30.0	1.616994	310	0	311
31.0	1.616994	276	0	274
32.0	1.616994	251	0	252
33.0	1.616994	257	0	260
34.0	1.616994	268	0	266
35.0	1.616994	227	0	227
36.0	1.616994	191	0	190
37.0	1.616994	218	0	217
38.0	1.616994	197	0	197
39.0	1.616994	167	0	167
40.0	1.616994	190	0	190
41.0	1.616994	147	0	147
42.0	1.616994	174	0	174
43.0	1.616994	156	0	159
44.0	1.616994	169	0	167
45.0	1.616994	140	0	144
46.0	1.616994	132	0	127
47.0	1.616994	133	0	136
48.0	1.616994	127	0	124
49.0	1.616994	123	0	123
50.0	1.616994	104	0	106
51.0	1.616994	112	0	113
52.0	1.616994	114	0	112
53.0	1.616994	95	0	95
54.0	1.616994	94	0	95
55.0	1.616994	86	0	84
56.0	1.616994	82	0	83
57.0	1.616994	79	0	79
58.0	1.616994	109	0	108
59.0	1.616994	76	0	78
60.0	1.616994	70	0	70
61.0	1.616994	68	0	67
62.0	1.616994	72	0	71
63.0	1.616994	65	0	68
64.0	1.616994	67	0	65
65.0	1.616994	60	0	59
66.0	1.616994	73	0	74
67.0	1.616994	60	0	60
68.0	1.616994	67	0	66
69.0	1.616994	50	0	50
70.0	1.616994	50	0	52
71.0	1.616994	48	0	46
72.0	1.616994	50	0	52
73.0	1.616994	70	0	69
74.0	1.616994	42	0	42
75.0	1.616994	47	0	47
76.0	1.616994	55	0	55
77.0	1.616994	45	0	44
78.0	1.616994	37	0	37
79.0	1.616994	44	0	44
80.0	1.616994	50	0	52
81.0	1.616994	34	0	32
82.0	1.616994	31	0	31
83.0	1.616994	44	0	46
84.0	1.616994	35	0	34
85.0	1.616994	34	0	34
86.0	1.616994	26	0	26
87.0	1.616994	39	0	38
88.0	1.616994	29	0	30
89.0	1.616994	30	0	30
90.0	1.616994	39	0	38
91.0	1.616994	39	0	39
92.0	1.616994	24	0	24
93.0	1.616994	27	0	27
94.0	1.616994	23	0	23
95.0	1.616994	24	0	24
96.0	1.616994	21	0	22
97.0	1.616994	35	0	34
98.0	1.616994	32	0	32
99.0	1.616994	27	0	28
100.0	1.616994	26	0	27
101.0	0	33	0	31
102.0	0	17	0	18
103.0	0	25	0	24
104.0	0	20	0	20
105.0	0	18	0	20
106.0	0	21	0	19
107.0	0	27	0	27
108.0	0	18	0	21
109.0	0	16	0	14
110.0	0	22	0	21
111.0	0	27	0	27
112.0	0	18	0	18
113.0	0	14	0	14
114.0	0	24	0	24
115.0	0	16	0	16
116.0	0	13	0	15
117.0	0	25	0	26
118.0	0	26	0	23
119.0	0	23	0	23
120.0	0	22	0	23
121.0	0	17	0	17
122.0	0	10	0	9
123.0	0	22	0	22
124.0	0	15	0	15
125.0	0	12	0	13
126.0	0	19	0	18
127.0	0	17	0	17
128.0	0	16	0	16
129.0	0	14	0	16
130.0	0	15	0	15
131.0	0	19	0	17
132.0	0	8	0	9
133.0	0	12	0	11
134.0	0	12	0	12
135.0	0	12	0	13
136.0	0	14	0	13
137.0	0	12	0	14
138.0	0	14	0	13
139.0	0	10	0	10
140.0	0	16	0	15
141.0	0	11	0	11
142.0	0	7	0	7
143.0	0	14	0	14
144.0	0	11	0	11
145.0	0	7	0	9
146.0	0	12	0	11
147.0	0	14	0	13
148.0	0	14	0	14
149.0	0	11	0	12
150.0	0	9	0	8
151.0	0	9	0	9
152.0	0	15	0	15
153.0	0	9	0	9
154.0	0	9	0	10
155.0	0	10	0	9
156.0	0	6	0	6
157.0	0	12	0	12
158.0	0	11	0	11
159.0	0	12	0	12
160.0	0	8	0	8
161.0	0	5	0	6
162.0	0	12	0	11
163.0	0	7	0	7
164.0	0	8	0	8
165.0	0	10	0	11
166.0	0	7	0	6
167.0	0	3	0	3
168.0	0	5	0	5
169.0	0	8	0	10
170.0	0	10	0	8
171.0	0	7	0	7
172.0	0	4	0	4
173.0	0	8	0	8
174.0	0	5	0	5
175.0	0	10	0	10
176.0	0	8	0	8
177.0	0	1	0	1
178.0	0	9	0	9
179.0	0	4	0	4
180.0	0	12	0	13
181.0	0	8	0	7
182.0	0	5	0	5
183.0	0	4	0	5
184.0	0	4	0	3
185.0	0	7	0	7
186.0	0	3	0	3
187.0	0	8	0	8
188.0	0	5	0	5
189.0	0	10	0	11
190.0	0	6	0	5
192.0	0	3	0	3
193.0	0	6	0	6
194.0	0	11	0	11
195.0	0	7	0	8
196.0	0	8	0	7
197.0	0	5	0	5
198.0	0	6	0	7
199.0	0	5	0	4
200.0	0	4	0	4
201.0	0	5	0	6
202.0	0	6	0	5
203.0	0	5	0	5
204.0	0	2	0	2
205.0	0	7	0	7
206.0	0	6	0	6
207.0	0	4	0	4
208.0	0	2	0	2
209.0	0	5	0	5
210.0	0	3	0	4
211.0	0	4	0	3
212.0	0	4	0	4
213.0	0	5	0	5
214.0	0	2	0	3
215.0	0	7	0	6
216.0	0	1	0	1
217.0	0	4	0	5
218.0	0	1	0	0
219.0	0	2	0	2
220.0	0	4	0	4
221.0	0	5	0	5
222.0	0	1	0	1
223.0	0	3	0	3
224.0	0	2	0	3
225.0	0	5	0	4
226.0	0	5	0	5
227.0	0	5	0	5
228.0	0	7	0	7
229.0	0	4	0	5
230.0	0	2	0	3
231.0	0	6	0	5
232.0	0	3	0	2
233.0	0	6	0	6
234.0	0	3	0	3
235.0	0	1	0	1
236.0	0	3	0	3
237.0	0	2	0	3
238.0	0	4	0	3
239.0	0	6	0	6
240.0	0	4	0	4
241.0	0	0	0	1
242.0	0	5	0	4
243.0	0	4	0	5
244.0	0	4	0	3
246.0	0	4	0	4
247.0	0	2	0	2
248.0	0	2	0	2
249.0	0	3	0	3
250.0	0	4	0	4
251.0	0	5	0	5
252.0	0	3	0	3
253.0	0	4	0	4
254.0	0	1	0	1
255.0	0	1	0	1
256.0	0	8	0	8
257.0	0	4	0	4
258.0	0	2	0	2
259.0	0	4	0	5
260.0	0	5	0	4
261.0	0	6	0	6
262.0	0	1	0	1
264.0	0	1	0	1
265.0	0	1	0	1
266.0	0	1	0	2
267.0	0	6	0	5
268.0	0	4	0	5
269.0	0	3	0	2
270.0	0	3	0	3
271.0	0	6	0	6
272.0	0	4	0	4
273.0	0	3	0	4
274.0	0	5	0	4
275.0	0	4	0	4
276.0	0	3	0	3
277.0	0	1	0	1
278.0	0	1	0	1
279.0	0	3	0	3
280.0	0	3	0	3
281.0	0	2	0	2
282.0	0	3	0	3
283.0	0	3	0	4
284.0	0	3	0	2
285.0	0	1	0	1
286.0	0	3	0	4
287.0	0	4	0	3
288.0	0	1	0	1
289.0	0	2	0	2
290.0	0	2	0	2
291.0	0	1	0	1
292.0	0	2	0	2
293.0	0	1	0	1
294.0	0	4	0	4
295.0	0	5	0	5
297.0	0	1	0	1
298.0	0	1	0	1
299.0	0	1	0	1
301.0	0	3	0	3
302.0	0	2	0	2
303.0	0	2	0	3
304.0	0	2	0	1
306.0	0	1	0	1
307.0	0	3	0	3
308.0	0	1	0	1
309.0	0	1	0	1
310.0	0	2	0	2
311.0	0	1	0	1
312.0	0	3	0	3
313.0	0	2	0	2
314.0	0	3	0	3
315.0	0	3	0	3
316.0	0	2	0	2
317.0	0	1	0	1
318.0	0	2	0	2
319.0	0	2	0	2
320.0	0	3	0	4
321.0	0	3	0	2
323.0	0	2	0	3
324.0	0	4	0	3
325.0	0	1	0	1
327.0	0	6	0	6
328.0	0	2	0	2
329.0	0	1	0	1
330.0	0	1	0	1
332.0	0	2	0	2
334.0	0	2	0	2
336.0	0	3	0	3
337.0	0	2	0	2
338.0	0	1	0	1
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342.0	0	1	0	1
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344.0	0	3	0	3
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358.0	0	3	0	3
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360.0	0	1	0	0
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364.0	0	2	0	2
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368.0	0	1	0	1
370.0	0	1	0	1
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373.0	0	1	0	0
374.0	0	1	0	1
378.0	0	1	0	1
379.0	0	1	0	1
381.0	0	2	0	2
383.0	0	2	0	2
384.0	0	2	0	3
385.0	0	3	0	2
387.0	0	2	0	2
388.0	0	2	0	2
390.0	0	3	0	3
391.0	0	1	0	1
393.0	0	2	0	2
396.0	0	1	0	1
397.0	0	0	0	1
398.0	0	2	0	1
400.0	0	1	0	1
401.0	0	1	0	1
405.0	0	2	0	2
407.0	0	1	0	1
408.0	0	1	0	1
415.0	0	1	0	2
416.0	0	5	0	4
419.0	0	4	0	4
420.0	0	1	0	1
421.0	0	1	0	1
422.0	0	1	0	1
423.0	0	1	0	1
424.0	0	2	0	2
425.0	0	1	0	1
426.0	0	1	0	1
427.0	0	1	0	1
429.0	0	3	0	4
430.0	0	4	0	3
432.0	0	1	0	1
433.0	0	1	0	1
438.0	0	1	0	1
439.0	0	1	0	1
441.0	0	1	0	1
445.0	0	1	0	1
446.0	0	2	0	2
450.0	0	2	0	2
453.0	0	1	0	1
454.0	0	1	0	1
459.0	0	1	0	1
460.0	0	1	0	1
463.0	0	1	0	1
465.0	0	1	0	1
467.0	0	1	0	1
470.0	0	1	0	1
476.0	0	1	0	1
480.0	0	1	0	1
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491.0	0	1	0	1
496.0	0	1	0	1
499.0	0	0	0	1
500.0	0	2	0	1
502.0	0	1	0	1
503.0	0	1	0	1
506.0	0	1	0	1
509.0	0	2	0	2
514.0	0	2	0	2
522.0	0	1	0	1
526.0	0	1	0	1
534.0	0	1	0	1
536.0	0	1	0	1
537.0	0	1	0	1
540.0	0	1	0	1
541.0	0	1	0	1
542.0	0	1	0	1
543.0	0	1	0	1
545.0	0	1	0	1
546.0	0	2	0	2
547.0	0	2	0	2
549.0	0	1	0	1
556.0	0	1	0	1
558.0	0	1	0	1
563.0	0	1	0	1
566.0	0	1	0	1
568.0	0	0	0	1
569.0	0	2	0	1
573.0	0	1	0	1
579.0	0	1	0	1
595.0	0	1	0	1
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597.0	0	2	0	2
602.0	0	1	0	1
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661.0	0	0	0	1
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673.0	0	1	0	1
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715.0	0	0	0	1
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1651.0	0	1	0	0