## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919931.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919931.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919931.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/tmp]    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 Nov 02 15:35:17 CET 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	0	10358857	1748858	0	0	1857888	0	0.179353	25311064

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7600304	7600304
2.0	1.66414	616517	616517
3.0	2.105222	135659	135659
4.0	2.398163	54816	54816
5.0	2.592716	28676	28676
6.0	2.721927	17092	17092
7.0	2.807741	11091	11091
8.0	2.864734	7627	7627
9.0	2.902585	5446	5446
10.0	2.927723	4037	4037
11.0	2.944419	3032	3032
12.0	2.955507	2325	2325
13.0	2.962871	1944	1944
14.0	2.967762	1637	1637
15.0	2.97101	1276	1276
16.0	2.973167	1094	1094
17.0	2.9746	861	861
18.0	2.975551	769	769
19.0	2.976183	637	637
20.0	2.976603	569	569
21.0	2.976882	471	471
22.0	2.977067	413	413
23.0	2.97719	425	425
24.0	2.977271	340	340
25.0	2.977326	288	288
26.0	2.977362	233	233
27.0	2.977386	209	209
28.0	2.977401	222	222
29.0	2.977412	199	199
30.0	2.977419	183	183
31.0	2.977424	152	152
32.0	2.977427	155	155
33.0	2.977429	141	141
34.0	2.97743	122	122
35.0	2.977431	127	127
36.0	2.977432	99	99
37.0	2.977432	89	89
38.0	2.977432	98	98
39.0	2.977432	80	80
40.0	2.977433	92	92
41.0	2.977433	68	68
42.0	2.977433	63	63
43.0	2.977433	60	60
44.0	2.977433	54	54
45.0	2.977433	44	44
46.0	2.977433	49	49
47.0	2.977433	44	44
48.0	2.977433	40	40
49.0	2.977433	41	41
50.0	2.977433	35	35
51.0	2.977433	41	41
52.0	2.977433	33	33
53.0	2.977433	30	30
54.0	2.977433	28	28
55.0	2.977433	27	27
56.0	2.977433	25	25
57.0	2.977433	25	25
58.0	2.977433	29	29
59.0	2.977433	28	28
60.0	2.977433	22	22
61.0	2.977433	16	16
62.0	2.977433	20	20
63.0	2.977433	18	18
64.0	2.977433	17	17
65.0	2.977433	13	13
66.0	2.977433	18	18
67.0	2.977433	12	12
68.0	2.977433	16	16
69.0	2.977433	16	16
70.0	2.977433	15	15
71.0	2.977433	11	11
72.0	2.977433	21	21
73.0	2.977433	13	13
74.0	2.977433	9	9
75.0	2.977433	5	5
76.0	2.977433	13	13
77.0	2.977433	11	11
78.0	2.977433	15	15
79.0	2.977433	8	8
80.0	2.977433	10	10
81.0	2.977433	8	8
82.0	2.977433	7	7
83.0	2.977433	8	8
84.0	2.977433	11	11
85.0	2.977433	5	5
86.0	2.977433	6	6
87.0	2.977433	10	10
88.0	2.977433	10	10
89.0	2.977433	6	6
90.0	2.977433	6	6
91.0	2.977433	5	5
92.0	2.977433	8	8
93.0	2.977433	6	6
94.0	2.977433	6	6
95.0	2.977433	3	3
96.0	2.977433	7	7
97.0	2.977433	10	10
98.0	2.977433	6	6
99.0	2.977433	4	4
100.0	2.977433	1	1
101.0	0	5	5
102.0	0	5	5
103.0	0	1	1
104.0	0	5	5
105.0	0	2	2
106.0	0	4	4
107.0	0	3	3
108.0	0	3	3
109.0	0	8	8
110.0	0	1	1
111.0	0	5	5
112.0	0	5	5
113.0	0	4	4
115.0	0	5	5
116.0	0	3	3
117.0	0	3	3
118.0	0	1	1
119.0	0	3	3
120.0	0	3	3
121.0	0	3	3
122.0	0	5	5
123.0	0	2	2
124.0	0	4	4
125.0	0	2	2
127.0	0	1	1
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
132.0	0	1	1
133.0	0	3	3
134.0	0	4	4
135.0	0	2	2
137.0	0	2	2
139.0	0	1	1
141.0	0	1	1
142.0	0	1	1
143.0	0	4	4
144.0	0	1	1
145.0	0	3	3
146.0	0	1	1
147.0	0	1	1
148.0	0	4	4
149.0	0	1	1
150.0	0	3	3
152.0	0	1	1
154.0	0	1	1
155.0	0	1	1
156.0	0	1	1
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
161.0	0	3	3
162.0	0	1	1
163.0	0	3	3
166.0	0	1	1
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	1	1
176.0	0	2	2
178.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	1	1
187.0	0	2	2
188.0	0	1	1
193.0	0	1	1
194.0	0	2	2
195.0	0	2	2
200.0	0	3	3
203.0	0	1	1
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
209.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	2	2
220.0	0	1	1
230.0	0	1	1
231.0	0	1	1
235.0	0	2	2
236.0	0	2	2
238.0	0	1	1
245.0	0	1	1
252.0	0	1	1
267.0	0	1	1
271.0	0	1	1
272.0	0	1	1
273.0	0	1	1
276.0	0	1	1
278.0	0	1	1
279.0	0	1	1
288.0	0	1	1
295.0	0	1	1
299.0	0	1	1
302.0	0	1	1
303.0	0	1	1
304.0	0	1	1
312.0	0	1	1
322.0	0	1	1
328.0	0	2	2
360.0	0	1	1
366.0	0	1	1
374.0	0	1	1
381.0	0	1	1
382.0	0	1	1
407.0	0	1	1
422.0	0	1	1
424.0	0	1	1
433.0	0	1	1
437.0	0	1	1
444.0	0	1	1
464.0	0	1	1
472.0	0	1	1
474.0	0	1	1
518.0	0	1	1
524.0	0	1	1
577.0	0	1	1
604.0	0	1	1
1120.0	0	1	1
1246.0	0	1	1
1685.0	0	1	1