## 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_Day1_adherentcells_DMSO_A70_S14.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day1_adherentcells_DMSO_A70_S14.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-NP_Day1_adherentcells_DMSO_A70_S14.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 19:17:30 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	241	17875888	0	0	121	2064244	5341	0.115479	71476150

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000263	14685043	0	14689366
2.0	1.779194	938580	5325	934931
3.0	2.385768	101906	8	101329
4.0	2.858123	29125	0	29054
5.0	3.225958	14303	0	14289
6.0	3.512401	8675	0	8674
7.0	3.735462	5619	0	5616
8.0	3.909165	3976	0	3975
9.0	4.044432	3077	0	3077
10.0	4.149768	2361	0	2357
11.0	4.231796	1904	0	1906
12.0	4.295673	1646	0	1642
13.0	4.345416	1330	0	1330
14.0	4.384152	1112	0	1117
15.0	4.414317	1019	0	1017
16.0	4.437807	864	0	863
17.0	4.456099	753	0	753
18.0	4.470344	667	0	671
19.0	4.481437	570	0	566
20.0	4.490075	542	0	543
21.0	4.496802	446	0	446
22.0	4.50204	478	0	475
23.0	4.50612	385	0	385
24.0	4.509296	372	0	375
25.0	4.51177	309	0	307
26.0	4.513696	301	0	300
27.0	4.515196	291	0	294
28.0	4.516364	268	0	265
29.0	4.517274	234	0	236
30.0	4.517983	221	0	218
31.0	4.518534	217	0	219
32.0	4.518964	185	0	184
33.0	4.519298	192	0	193
34.0	4.519559	167	0	166
35.0	4.519762	165	0	165
36.0	4.51992	147	0	147
37.0	4.520043	130	0	130
38.0	4.520138	145	0	145
39.0	4.520213	118	0	121
40.0	4.520271	123	0	121
41.0	4.520316	110	0	109
42.0	4.520352	108	0	108
43.0	4.520379	99	0	99
44.0	4.5204	100	0	100
45.0	4.520417	109	0	108
46.0	4.52043	82	0	85
47.0	4.52044	97	0	95
48.0	4.520448	84	0	83
49.0	4.520454	69	0	69
50.0	4.520459	63	0	63
51.0	4.520462	77	0	81
52.0	4.520465	77	0	73
53.0	4.520468	71	0	72
54.0	4.520469	66	0	66
55.0	4.520471	52	0	52
56.0	4.520472	57	0	56
57.0	4.520473	54	0	55
58.0	4.520473	62	0	62
59.0	4.520474	59	0	58
60.0	4.520474	51	0	52
61.0	4.520474	51	0	51
62.0	4.520475	49	0	48
63.0	4.520475	53	0	53
64.0	4.520475	32	0	32
65.0	4.520475	52	0	53
66.0	4.520475	31	0	31
67.0	4.520475	34	0	34
68.0	4.520475	39	0	38
69.0	4.520475	30	0	30
70.0	4.520475	30	0	31
71.0	4.520475	34	0	33
72.0	4.520475	38	0	38
73.0	4.520475	34	0	35
74.0	4.520476	30	0	30
75.0	4.520476	30	0	29
76.0	4.520476	27	0	29
77.0	4.520476	30	0	29
78.0	4.520476	37	0	36
79.0	4.520476	25	0	25
80.0	4.520476	16	0	17
81.0	4.520476	25	0	24
82.0	4.520476	24	0	24
83.0	4.520476	26	0	26
84.0	4.520476	25	0	25
85.0	4.520476	20	0	21
86.0	4.520476	29	0	29
87.0	4.520476	23	0	23
88.0	4.520476	18	0	17
89.0	4.520476	16	0	16
90.0	4.520476	21	0	21
91.0	4.520476	14	0	14
92.0	4.520476	13	0	13
93.0	4.520476	12	0	13
94.0	4.520476	26	0	25
95.0	4.520476	16	0	17
96.0	4.520476	23	0	22
97.0	4.520476	20	0	21
98.0	4.520476	14	0	13
99.0	4.520476	21	0	21
100.0	4.520476	7	0	8
101.0	0	19	0	18
102.0	0	20	0	20
103.0	0	15	0	16
104.0	0	12	0	12
105.0	0	16	0	15
106.0	0	11	0	11
107.0	0	11	0	12
108.0	0	17	0	16
109.0	0	17	0	20
110.0	0	16	0	13
111.0	0	14	0	15
112.0	0	16	0	15
113.0	0	13	0	13
114.0	0	11	0	11
115.0	0	16	0	16
116.0	0	14	0	14
117.0	0	15	0	15
118.0	0	11	0	11
119.0	0	13	0	13
120.0	0	8	0	8
121.0	0	9	0	9
122.0	0	8	0	8
123.0	0	11	0	11
124.0	0	9	0	9
125.0	0	11	0	12
126.0	0	5	0	5
127.0	0	14	0	13
128.0	0	10	0	10
129.0	0	8	0	10
130.0	0	8	0	7
131.0	0	6	0	5
132.0	0	12	0	13
133.0	0	10	0	9
134.0	0	8	0	9
135.0	0	6	0	5
136.0	0	2	0	2
137.0	0	10	0	10
138.0	0	5	0	5
139.0	0	6	0	6
140.0	0	6	0	6
141.0	0	6	0	6
142.0	0	6	0	7
143.0	0	8	0	8
144.0	0	5	0	4
145.0	0	8	0	8
146.0	0	7	0	8
147.0	0	7	0	7
148.0	0	11	0	10
149.0	0	5	0	6
150.0	0	2	0	2
151.0	0	4	0	4
152.0	0	8	0	7
153.0	0	8	0	9
154.0	0	4	0	3
155.0	0	2	0	2
156.0	0	6	0	6
157.0	0	6	0	6
158.0	0	11	0	11
159.0	0	3	0	4
160.0	0	5	0	5
161.0	0	5	0	5
162.0	0	8	0	7
163.0	0	4	0	4
164.0	0	4	0	4
165.0	0	4	0	4
166.0	0	6	0	6
167.0	0	3	0	3
168.0	0	3	0	4
169.0	0	4	0	4
170.0	0	6	0	5
171.0	0	3	0	3
172.0	0	8	0	8
173.0	0	10	0	10
174.0	0	8	0	8
175.0	0	3	0	3
176.0	0	6	0	6
177.0	0	6	0	6
178.0	0	3	0	3
179.0	0	1	0	1
180.0	0	5	0	6
181.0	0	3	0	2
182.0	0	3	0	4
183.0	0	1	0	2
184.0	0	7	0	5
185.0	0	5	0	5
186.0	0	4	0	4
187.0	0	3	0	3
188.0	0	4	0	4
189.0	0	1	0	1
190.0	0	4	0	4
191.0	0	3	0	3
192.0	0	3	0	4
193.0	0	7	0	6
194.0	0	4	0	4
195.0	0	4	0	4
196.0	0	4	0	4
197.0	0	2	0	3
198.0	0	5	0	4
199.0	0	1	0	1
200.0	0	3	0	3
201.0	0	4	0	4
203.0	0	4	0	4
204.0	0	3	0	3
205.0	0	3	0	3
206.0	0	5	0	5
207.0	0	2	0	2
208.0	0	5	0	5
209.0	0	4	0	4
210.0	0	2	0	2
211.0	0	5	0	5
212.0	0	3	0	3
213.0	0	1	0	1
214.0	0	2	0	2
215.0	0	3	0	3
216.0	0	2	0	3
217.0	0	2	0	1
218.0	0	1	0	1
220.0	0	5	0	5
221.0	0	2	0	2
223.0	0	1	0	1
224.0	0	2	0	2
225.0	0	3	0	3
226.0	0	3	0	3
227.0	0	2	0	2
228.0	0	2	0	2
229.0	0	2	0	2
230.0	0	1	0	1
232.0	0	2	0	2
233.0	0	2	0	2
234.0	0	1	0	1
235.0	0	1	0	1
236.0	0	2	0	3
237.0	0	3	0	3
238.0	0	3	0	2
239.0	0	2	0	2
240.0	0	3	0	3
241.0	0	3	0	4
242.0	0	2	0	1
243.0	0	1	0	1
244.0	0	1	0	1
245.0	0	3	0	3
246.0	0	1	0	1
247.0	0	1	0	1
248.0	0	1	0	1
251.0	0	2	0	2
252.0	0	1	0	1
253.0	0	2	0	2
255.0	0	2	0	2
256.0	0	2	0	2
257.0	0	3	0	4
258.0	0	5	0	4
260.0	0	3	0	3
261.0	0	1	0	1
262.0	0	1	0	2
263.0	0	2	0	1
265.0	0	2	0	2
266.0	0	2	0	2
267.0	0	1	0	1
268.0	0	1	0	1
271.0	0	2	0	2
272.0	0	1	0	1
274.0	0	2	0	2
276.0	0	1	0	1
277.0	0	2	0	2
279.0	0	1	0	1
282.0	0	2	0	2
285.0	0	2	0	3
286.0	0	3	0	2
290.0	0	1	0	1
292.0	0	1	0	1
293.0	0	2	0	2
295.0	0	1	0	1
296.0	0	0	0	1
297.0	0	1	0	0
298.0	0	3	0	3
300.0	0	0	0	1
301.0	0	1	0	1
302.0	0	1	0	0
303.0	0	2	0	2
305.0	0	1	0	1
306.0	0	1	0	1
307.0	0	1	0	1
308.0	0	1	0	1
309.0	0	1	0	1
310.0	0	1	0	1
311.0	0	1	0	1
313.0	0	1	0	1
314.0	0	2	0	2
315.0	0	2	0	2
316.0	0	1	0	1
317.0	0	3	0	3
318.0	0	1	0	1
320.0	0	1	0	1
321.0	0	2	0	2
322.0	0	1	0	2
323.0	0	2	0	1
324.0	0	1	0	1
326.0	0	2	0	2
327.0	0	1	0	1
329.0	0	2	0	2
330.0	0	3	0	3
332.0	0	0	0	1
333.0	0	3	0	2
334.0	0	2	0	2
336.0	0	0	0	1
337.0	0	2	0	1
338.0	0	2	0	2
339.0	0	2	0	2
343.0	0	1	0	1
344.0	0	2	0	2
348.0	0	2	0	2
349.0	0	3	0	3
351.0	0	1	0	1
356.0	0	1	0	1
357.0	0	1	0	1
364.0	0	1	0	1
366.0	0	3	0	3
369.0	0	1	0	1
370.0	0	1	0	1
372.0	0	1	0	1
373.0	0	1	0	1
374.0	0	1	0	1
376.0	0	1	0	1
379.0	0	1	0	1
381.0	0	1	0	1
388.0	0	1	0	1
389.0	0	0	0	1
390.0	0	1	0	1
391.0	0	1	0	0
392.0	0	0	0	1
393.0	0	1	0	0
398.0	0	1	0	1
399.0	0	1	0	1
400.0	0	1	0	1
405.0	0	1	0	2
406.0	0	1	0	0
412.0	0	1	0	1
424.0	0	0	0	2
425.0	0	2	0	0
426.0	0	1	0	1
435.0	0	1	0	1
438.0	0	1	0	1
448.0	0	1	0	1
449.0	0	1	0	1
452.0	0	2	0	2
455.0	0	1	0	1
459.0	0	2	0	3
460.0	0	2	0	1
465.0	0	1	0	1
469.0	0	1	0	1
476.0	0	0	0	1
477.0	0	1	0	0
478.0	0	1	0	1
479.0	0	1	0	1
480.0	0	1	0	1
482.0	0	1	0	1
488.0	0	1	0	1
520.0	0	1	0	1
530.0	0	1	0	1
534.0	0	0	0	1
535.0	0	1	0	0
538.0	0	1	0	1
541.0	0	0	0	1
543.0	0	1	0	0
548.0	0	1	0	1
560.0	0	1	0	1
566.0	0	1	0	1
603.0	0	1	0	1
605.0	0	2	0	2
625.0	0	1	0	1
631.0	0	1	0	1
639.0	0	1	0	1
659.0	0	1	0	1
661.0	0	1	0	1
698.0	0	1	0	1
700.0	0	1	0	1
703.0	0	0	0	1
704.0	0	1	0	0
710.0	0	1	0	1
723.0	0	0	0	1
724.0	0	1	0	0
741.0	0	1	0	1
762.0	0	0	0	1
763.0	0	1	0	0
769.0	0	1	0	1
874.0	0	0	0	1
875.0	0	1	0	0
891.0	0	1	0	1
893.0	0	1	0	1
896.0	0	0	0	1
897.0	0	1	0	0
915.0	0	1	0	1
963.0	0	1	0	1
1034.0	0	0	0	1
1035.0	0	1	0	0