## 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_Day10_supernatant_TA_A71_S7.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day10_supernatant_TA_A71_S7.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-NP_Day10_supernatant_TA_A71_S7.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 19:22:21 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	207	14738284	0	0	105	3929934	4048	0.26665	22482131

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000194	8364601	0	8366774
2.0	1.519449	1923881	4041	1922897
3.0	1.789022	377475	2	376616
4.0	1.928972	74934	1	74706
5.0	2.001627	20378	0	20302
6.0	2.039346	9177	0	9164
7.0	2.058928	5765	0	5764
8.0	2.069095	4068	0	4061
9.0	2.074372	3267	0	3267
10.0	2.077112	2566	0	2568
11.0	2.078535	2093	0	2092
12.0	2.079273	1804	0	1806
13.0	2.079657	1425	0	1419
14.0	2.079856	1262	0	1264
15.0	2.079959	1073	0	1072
16.0	2.080013	913	0	916
17.0	2.080041	870	0	870
18.0	2.080055	748	0	744
19.0	2.080062	707	0	706
20.0	2.080066	596	0	597
21.0	2.080068	589	0	589
22.0	2.080069	527	0	528
23.0	2.08007	477	0	476
24.0	2.08007	441	0	444
25.0	2.08007	423	0	421
26.0	2.080071	370	0	369
27.0	2.080071	327	0	328
28.0	2.080071	311	0	310
29.0	2.080071	302	0	300
30.0	2.080071	298	0	301
31.0	2.080071	258	0	256
32.0	2.080071	239	0	242
33.0	2.080071	237	0	233
34.0	2.080071	232	0	234
35.0	2.080071	190	0	190
36.0	2.080071	167	0	167
37.0	2.080071	171	0	170
38.0	2.080071	191	0	191
39.0	2.080071	179	0	178
40.0	2.080071	182	0	185
41.0	2.080071	134	0	131
42.0	2.080071	141	0	142
43.0	2.080071	131	0	131
44.0	2.080071	133	0	132
45.0	2.080071	123	0	123
46.0	2.080071	116	0	117
47.0	2.080071	104	0	103
48.0	2.080071	93	0	93
49.0	2.080071	112	0	113
50.0	2.080071	79	0	79
51.0	2.080071	104	0	105
52.0	2.080071	78	0	78
53.0	2.080071	86	0	86
54.0	2.080071	97	0	98
55.0	2.080071	74	0	74
56.0	2.080071	63	0	61
57.0	2.080071	63	0	62
58.0	2.080071	57	0	58
59.0	2.080071	67	0	66
60.0	2.080071	58	0	60
61.0	2.080071	56	0	54
62.0	2.080071	52	0	52
63.0	2.080071	59	0	59
64.0	2.080071	70	0	73
65.0	2.080071	45	0	44
66.0	2.080071	51	0	49
67.0	2.080071	52	0	52
68.0	2.080071	44	0	44
69.0	2.080071	42	0	44
70.0	2.080071	51	0	51
71.0	2.080071	47	0	45
72.0	2.080071	37	0	38
73.0	2.080071	28	0	27
74.0	2.080071	51	0	53
75.0	2.080071	45	0	43
76.0	2.080071	29	0	32
77.0	2.080071	43	0	40
78.0	2.080071	46	0	47
79.0	2.080071	38	0	38
80.0	2.080071	41	0	41
81.0	2.080071	40	0	39
82.0	2.080071	30	0	30
83.0	2.080071	32	0	32
84.0	2.080071	33	0	33
85.0	2.080071	25	0	26
86.0	2.080071	32	0	32
87.0	2.080071	21	0	21
88.0	2.080071	19	0	19
89.0	2.080071	23	0	23
90.0	2.080071	34	0	34
91.0	2.080071	23	0	23
92.0	2.080071	28	0	28
93.0	2.080071	22	0	21
94.0	2.080071	15	0	15
95.0	2.080071	25	0	25
96.0	2.080071	19	0	19
97.0	2.080071	21	0	21
98.0	2.080071	21	0	21
99.0	2.080071	19	0	19
100.0	2.080071	20	0	20
101.0	0	19	0	19
102.0	0	18	0	18
103.0	0	26	0	27
104.0	0	18	0	17
105.0	0	15	0	16
106.0	0	16	0	15
107.0	0	14	0	16
108.0	0	22	0	20
109.0	0	26	0	26
110.0	0	17	0	17
111.0	0	16	0	17
112.0	0	16	0	16
113.0	0	18	0	18
114.0	0	15	0	16
115.0	0	16	0	14
116.0	0	12	0	12
117.0	0	10	0	10
118.0	0	12	0	12
119.0	0	16	0	16
120.0	0	13	0	13
121.0	0	9	0	9
122.0	0	14	0	14
123.0	0	16	0	16
124.0	0	7	0	7
125.0	0	11	0	12
126.0	0	11	0	10
127.0	0	10	0	10
128.0	0	8	0	8
129.0	0	8	0	8
130.0	0	6	0	7
131.0	0	9	0	8
132.0	0	12	0	12
133.0	0	9	0	9
134.0	0	13	0	13
135.0	0	6	0	6
136.0	0	9	0	9
137.0	0	15	0	16
138.0	0	9	0	8
139.0	0	5	0	7
140.0	0	12	0	10
141.0	0	13	0	13
142.0	0	9	0	9
143.0	0	3	0	3
144.0	0	10	0	10
145.0	0	9	0	9
146.0	0	8	0	8
147.0	0	7	0	7
148.0	0	8	0	8
149.0	0	4	0	4
150.0	0	8	0	8
151.0	0	3	0	3
152.0	0	8	0	8
153.0	0	9	0	9
154.0	0	3	0	3
155.0	0	6	0	6
156.0	0	9	0	9
157.0	0	3	0	3
158.0	0	7	0	7
159.0	0	6	0	6
160.0	0	11	0	12
161.0	0	10	0	10
162.0	0	6	0	5
163.0	0	5	0	5
164.0	0	5	0	5
165.0	0	4	0	4
166.0	0	6	0	9
167.0	0	9	0	6
168.0	0	6	0	6
169.0	0	2	0	2
170.0	0	1	0	1
171.0	0	5	0	5
172.0	0	10	0	10
173.0	0	8	0	9
174.0	0	6	0	6
175.0	0	4	0	4
176.0	0	8	0	8
177.0	0	9	0	9
178.0	0	1	0	0
179.0	0	4	0	4
180.0	0	8	0	8
181.0	0	6	0	6
182.0	0	2	0	2
183.0	0	3	0	3
184.0	0	6	0	6
185.0	0	8	0	8
186.0	0	6	0	6
187.0	0	5	0	5
188.0	0	1	0	2
189.0	0	7	0	6
190.0	0	8	0	8
191.0	0	5	0	5
192.0	0	3	0	3
193.0	0	6	0	6
194.0	0	5	0	5
195.0	0	2	0	2
196.0	0	6	0	6
197.0	0	2	0	2
198.0	0	3	0	3
199.0	0	7	0	7
200.0	0	2	0	2
201.0	0	4	0	4
202.0	0	2	0	2
203.0	0	3	0	3
205.0	0	2	0	3
206.0	0	7	0	6
207.0	0	3	0	4
208.0	0	4	0	3
209.0	0	2	0	2
210.0	0	7	0	7
211.0	0	6	0	7
212.0	0	7	0	6
213.0	0	6	0	6
214.0	0	2	0	2
215.0	0	3	0	3
216.0	0	5	0	6
217.0	0	2	0	2
218.0	0	3	0	2
219.0	0	2	0	2
220.0	0	5	0	5
221.0	0	6	0	6
222.0	0	3	0	4
223.0	0	3	0	2
224.0	0	3	0	3
225.0	0	5	0	5
226.0	0	4	0	4
227.0	0	2	0	2
228.0	0	2	0	2
229.0	0	4	0	4
230.0	0	4	0	4
231.0	0	2	0	2
232.0	0	7	0	7
233.0	0	4	0	4
234.0	0	0	0	1
235.0	0	1	0	0
236.0	0	4	0	4
237.0	0	6	0	6
238.0	0	2	0	2
239.0	0	2	0	2
240.0	0	1	0	1
241.0	0	2	0	2
242.0	0	2	0	2
243.0	0	1	0	1
244.0	0	2	0	2
246.0	0	2	0	2
247.0	0	2	0	2
248.0	0	4	0	4
249.0	0	1	0	1
250.0	0	3	0	3
253.0	0	3	0	4
254.0	0	4	0	3
255.0	0	1	0	1
256.0	0	3	0	3
257.0	0	1	0	1
258.0	0	1	0	1
259.0	0	2	0	3
260.0	0	3	0	2
261.0	0	4	0	4
262.0	0	1	0	1
263.0	0	2	0	2
265.0	0	2	0	2
266.0	0	3	0	3
267.0	0	1	0	1
269.0	0	2	0	2
270.0	0	1	0	1
271.0	0	1	0	1
272.0	0	3	0	3
273.0	0	1	0	1
274.0	0	4	0	4
275.0	0	1	0	1
277.0	0	1	0	1
278.0	0	2	0	2
279.0	0	0	0	1
280.0	0	2	0	1
282.0	0	3	0	3
285.0	0	1	0	1
286.0	0	1	0	1
287.0	0	1	0	1
288.0	0	1	0	2
289.0	0	2	0	2
290.0	0	1	0	1
291.0	0	2	0	1
293.0	0	4	0	5
294.0	0	3	0	2
295.0	0	1	0	1
297.0	0	1	0	1
299.0	0	1	0	2
300.0	0	2	0	1
301.0	0	2	0	2
302.0	0	1	0	1
303.0	0	1	0	1
304.0	0	2	0	2
305.0	0	2	0	2
306.0	0	3	0	3
307.0	0	1	0	1
308.0	0	2	0	2
309.0	0	3	0	3
310.0	0	2	0	2
311.0	0	1	0	1
312.0	0	1	0	1
314.0	0	3	0	3
315.0	0	2	0	2
316.0	0	1	0	1
318.0	0	0	0	1
319.0	0	1	0	0
321.0	0	1	0	1
322.0	0	1	0	1
325.0	0	4	0	4
327.0	0	1	0	1
329.0	0	2	0	2
334.0	0	1	0	1
335.0	0	2	0	2
337.0	0	1	0	1
338.0	0	1	0	1
339.0	0	1	0	1
340.0	0	0	0	1
341.0	0	3	0	2
342.0	0	1	0	1
346.0	0	1	0	1
347.0	0	2	0	2
348.0	0	1	0	1
349.0	0	2	0	2
352.0	0	1	0	1
353.0	0	2	0	2
355.0	0	1	0	1
360.0	0	1	0	1
361.0	0	1	0	1
363.0	0	1	0	1
366.0	0	1	0	1
367.0	0	1	0	1
368.0	0	1	0	1
373.0	0	1	0	1
374.0	0	1	0	1
375.0	0	1	0	1
376.0	0	2	0	2
378.0	0	3	0	3
380.0	0	0	0	1
381.0	0	1	0	0
383.0	0	1	0	1
384.0	0	0	0	1
385.0	0	1	0	0
387.0	0	2	0	2
389.0	0	1	0	1
392.0	0	1	0	1
395.0	0	1	0	1
401.0	0	2	0	2
405.0	0	1	0	1
406.0	0	1	0	1
410.0	0	1	0	1
411.0	0	3	0	3
421.0	0	1	0	1
423.0	0	1	0	1
424.0	0	2	0	2
431.0	0	1	0	1
434.0	0	1	0	1
440.0	0	2	0	2
443.0	0	0	0	1
444.0	0	2	0	1
447.0	0	1	0	1
460.0	0	1	0	1
467.0	0	1	0	1
471.0	0	1	0	2
472.0	0	2	0	1
474.0	0	1	0	1
478.0	0	1	0	1
480.0	0	1	0	1
481.0	0	1	0	1
482.0	0	3	0	3
483.0	0	1	0	1
485.0	0	1	0	1
489.0	0	1	0	1
499.0	0	1	0	1
502.0	0	1	0	1
503.0	0	1	0	1
506.0	0	2	0	2
509.0	0	1	0	1
511.0	0	1	0	1
512.0	0	1	0	1
514.0	0	1	0	1
521.0	0	1	0	1
526.0	0	1	0	1
539.0	0	1	0	1
540.0	0	1	0	1
541.0	0	1	0	1
545.0	0	1	0	1
556.0	0	1	0	1
563.0	0	1	0	1
566.0	0	1	0	2
567.0	0	1	0	0
573.0	0	1	0	1
591.0	0	1	0	1
597.0	0	1	0	1
601.0	0	1	0	1
604.0	0	1	0	1
607.0	0	1	0	1
621.0	0	1	0	1
633.0	0	1	0	1
647.0	0	1	0	1
650.0	0	0	0	1
651.0	0	1	0	0
657.0	0	1	0	1
699.0	0	1	0	1
715.0	0	1	0	1
727.0	0	1	0	1
738.0	0	1	0	1
739.0	0	2	0	2
742.0	0	1	0	2
743.0	0	1	0	0
761.0	0	1	0	1
779.0	0	0	0	1
780.0	0	1	0	0
784.0	0	1	0	1
835.0	0	1	0	1
845.0	0	0	0	1
846.0	0	1	0	0
881.0	0	1	0	1
884.0	0	0	0	1
885.0	0	1	0	0
886.0	0	0	0	1
887.0	0	1	0	0
897.0	0	1	0	1
930.0	0	1	0	1
942.0	0	1	0	1
1024.0	0	0	0	1
1025.0	0	1	0	0
1041.0	0	1	0	1
1065.0	0	1	0	1
1095.0	0	1	0	1
1140.0	0	1	0	1
1203.0	0	1	0	1
1290.0	0	0	0	1
1291.0	0	1	0	0
1442.0	0	1	0	1
1452.0	0	0	0	1
1453.0	0	1	0	0
1711.0	0	0	0	1
1712.0	0	1	0	0
1764.0	0	1	0	1
2191.0	0	0	0	1
2192.0	0	1	0	0