## 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_Day12_supernatant_TA_A73_S10.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day12_supernatant_TA_A73_S10.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-NP_Day12_supernatant_TA_A73_S10.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 19:22:41 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	278	17348780	0	0	158	2225669	5273	0.128293	61821301

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000263	13647354	0	13651376
2.0	1.755772	1228884	5269	1225803
3.0	2.326414	150751	2	149944
4.0	2.757426	39012	0	38917
5.0	3.082973	17597	0	17580
6.0	3.328862	10068	0	10064
7.0	3.514584	6508	0	6498
8.0	3.654861	4378	0	4379
9.0	3.760814	3152	0	3155
10.0	3.840842	2342	0	2340
11.0	3.901287	1769	0	1762
12.0	3.946942	1376	0	1379
13.0	3.981426	1089	0	1086
14.0	4.007471	934	0	932
15.0	4.027144	895	0	896
16.0	4.042003	695	0	694
17.0	4.053226	535	0	537
18.0	4.061703	503	0	502
19.0	4.068106	389	0	388
20.0	4.072942	325	0	324
21.0	4.076594	312	0	314
22.0	4.079353	258	0	256
23.0	4.081437	247	0	247
24.0	4.083011	247	0	248
25.0	4.0842	207	0	207
26.0	4.085098	196	0	196
27.0	4.085776	176	0	176
28.0	4.086288	166	0	165
29.0	4.086675	152	0	152
30.0	4.086967	124	0	125
31.0	4.087188	119	0	119
32.0	4.087355	126	0	125
33.0	4.087481	109	0	109
34.0	4.087576	92	0	93
35.0	4.087648	87	0	86
36.0	4.087702	82	0	83
37.0	4.087743	89	0	88
38.0	4.087774	62	0	62
39.0	4.087797	58	0	58
40.0	4.087815	62	0	62
41.0	4.087828	54	0	55
42.0	4.087838	55	0	55
43.0	4.087846	46	0	45
44.0	4.087852	44	0	44
45.0	4.087856	47	0	48
46.0	4.087859	50	0	49
47.0	4.087862	40	0	40
48.0	4.087864	37	0	38
49.0	4.087865	33	0	32
50.0	4.087866	35	0	35
51.0	4.087867	43	0	43
52.0	4.087867	33	0	33
53.0	4.087868	29	0	31
54.0	4.087868	33	0	31
55.0	4.087868	23	0	24
56.0	4.087869	30	0	29
57.0	4.087869	22	0	23
58.0	4.087869	29	0	28
59.0	4.087869	19	0	20
60.0	4.087869	24	0	23
61.0	4.087869	26	0	27
62.0	4.087869	23	0	22
63.0	4.087869	14	0	14
64.0	4.087869	23	0	23
65.0	4.087869	26	0	26
66.0	4.087869	10	0	10
67.0	4.087869	11	0	11
68.0	4.087869	13	0	14
69.0	4.087869	17	0	16
70.0	4.087869	13	0	13
71.0	4.087869	17	0	17
72.0	4.087869	11	0	11
73.0	4.087869	14	0	14
74.0	4.087869	10	0	10
75.0	4.087869	10	0	10
76.0	4.087869	15	0	15
77.0	4.087869	9	0	9
78.0	4.087869	11	0	11
79.0	4.087869	10	0	10
80.0	4.087869	11	0	11
81.0	4.087869	15	0	15
82.0	4.087869	14	0	14
83.0	4.087869	10	0	10
84.0	4.087869	6	0	6
85.0	4.087869	5	0	5
86.0	4.087869	8	0	8
87.0	4.087869	7	0	7
88.0	4.087869	9	0	9
89.0	4.087869	9	0	9
90.0	4.087869	8	0	8
91.0	4.087869	5	0	5
92.0	4.087869	13	0	13
93.0	4.087869	10	0	10
94.0	4.087869	15	0	15
95.0	4.087869	8	0	8
96.0	4.087869	4	0	4
97.0	4.087869	4	0	4
98.0	4.087869	6	0	6
99.0	4.087869	6	0	7
100.0	4.087869	9	0	8
101.0	0	7	0	7
102.0	0	9	0	9
103.0	0	4	0	4
104.0	0	5	0	5
105.0	0	6	0	6
106.0	0	7	0	7
107.0	0	5	0	5
108.0	0	5	0	5
109.0	0	6	0	7
110.0	0	8	0	7
111.0	0	8	0	8
112.0	0	3	0	3
113.0	0	3	0	3
114.0	0	6	0	6
115.0	0	5	0	5
116.0	0	3	0	3
117.0	0	8	0	8
118.0	0	10	0	11
119.0	0	5	0	4
120.0	0	9	0	9
121.0	0	2	0	2
122.0	0	5	0	5
123.0	0	3	0	3
124.0	0	2	0	2
125.0	0	4	0	4
126.0	0	4	0	4
127.0	0	4	0	4
128.0	0	4	0	4
129.0	0	3	0	3
130.0	0	5	0	5
131.0	0	4	0	4
132.0	0	3	0	3
133.0	0	5	0	5
134.0	0	4	0	4
135.0	0	4	0	4
136.0	0	2	0	2
137.0	0	2	0	2
139.0	0	1	0	1
140.0	0	2	0	2
141.0	0	3	0	3
142.0	0	2	0	2
143.0	0	3	0	3
144.0	0	1	0	1
145.0	0	5	0	5
146.0	0	3	0	3
147.0	0	1	0	1
148.0	0	1	0	1
149.0	0	1	0	1
151.0	0	1	0	1
152.0	0	1	0	1
153.0	0	4	0	4
154.0	0	1	0	1
155.0	0	2	0	2
157.0	0	1	0	1
158.0	0	1	0	1
159.0	0	2	0	2
160.0	0	4	0	4
162.0	0	0	0	1
163.0	0	4	0	3
165.0	0	1	0	3
166.0	0	3	0	1
168.0	0	1	0	1
169.0	0	1	0	1
170.0	0	1	0	1
171.0	0	2	0	2
172.0	0	1	0	1
173.0	0	2	0	2
174.0	0	1	0	1
175.0	0	2	0	3
176.0	0	3	0	2
177.0	0	2	0	2
178.0	0	1	0	1
180.0	0	2	0	2
181.0	0	3	0	3
183.0	0	4	0	4
187.0	0	1	0	1
188.0	0	2	0	2
191.0	0	2	0	2
192.0	0	3	0	3
193.0	0	3	0	3
194.0	0	2	0	2
195.0	0	1	0	1
197.0	0	2	0	2
202.0	0	1	0	1
203.0	0	3	0	3
204.0	0	2	0	2
206.0	0	2	0	2
207.0	0	1	0	1
208.0	0	1	0	1
210.0	0	2	0	2
211.0	0	1	0	1
214.0	0	1	0	1
218.0	0	2	0	2
219.0	0	3	0	3
222.0	0	1	0	1
223.0	0	1	0	1
224.0	0	2	0	2
225.0	0	1	0	1
229.0	0	2	0	2
232.0	0	1	0	1
233.0	0	2	0	2
234.0	0	1	0	1
237.0	0	1	0	1
241.0	0	0	0	1
242.0	0	2	0	1
249.0	0	1	0	1
250.0	0	1	0	1
251.0	0	1	0	1
253.0	0	2	0	2
255.0	0	2	0	2
258.0	0	1	0	1
265.0	0	0	0	1
266.0	0	1	0	0
270.0	0	1	0	1
273.0	0	1	0	1
275.0	0	1	0	1
277.0	0	1	0	1
278.0	0	1	0	1
283.0	0	1	0	1
284.0	0	1	0	1
285.0	0	1	0	1
286.0	0	1	0	1
289.0	0	1	0	1
290.0	0	2	0	2
291.0	0	1	0	1
294.0	0	1	0	1
305.0	0	1	0	1
309.0	0	1	0	1
314.0	0	2	0	2
315.0	0	1	0	1
317.0	0	1	0	1
320.0	0	1	0	1
327.0	0	1	0	1
330.0	0	1	0	1
332.0	0	1	0	1
336.0	0	1	0	1
345.0	0	1	0	1
348.0	0	1	0	1
349.0	0	1	0	1
350.0	0	0	0	1
351.0	0	1	0	0
357.0	0	1	0	1
358.0	0	2	0	2
359.0	0	1	0	1
362.0	0	1	0	1
363.0	0	2	0	2
364.0	0	2	0	2
366.0	0	1	0	1
368.0	0	1	0	1
375.0	0	3	0	3
378.0	0	1	0	1
387.0	0	1	0	1
408.0	0	2	0	2
422.0	0	1	0	1
424.0	0	1	0	2
425.0	0	1	0	1
426.0	0	1	0	0
437.0	0	1	0	1
454.0	0	1	0	1
456.0	0	1	0	1
460.0	0	1	0	1
463.0	0	1	0	1
469.0	0	1	0	1
479.0	0	1	0	1
483.0	0	1	0	1
494.0	0	1	0	1
521.0	0	1	0	1
537.0	0	0	0	1
538.0	0	1	0	0
562.0	0	2	0	2
606.0	0	1	0	1
612.0	0	1	0	1
621.0	0	1	0	1
622.0	0	1	0	1
709.0	0	1	0	1
712.0	0	1	0	1
717.0	0	1	0	1
753.0	0	1	0	1
780.0	0	1	0	1
800.0	0	1	0	1
903.0	0	1	0	1
906.0	0	0	0	1
907.0	0	1	0	0
1012.0	0	0	0	1
1013.0	0	1	0	0
1039.0	0	1	0	1
1053.0	0	1	0	1