## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-TA1uM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-TA1uM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-TA1uM_3.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Wed Oct 04 10:22:00 CEST 2023

## 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	1859	46063790	37044132	0	1725	10301465	0	0.223649	86981508

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	31550425	31550425
2.0	1.588851	3051715	3051715
3.0	1.935597	536457	536457
4.0	2.139779	198692	198692
5.0	2.260012	107193	107193
6.0	2.330811	67244	67244
7.0	2.372501	45797	45797
8.0	2.397051	33011	33011
9.0	2.411507	24919	24919
10.0	2.420019	19232	19232
11.0	2.425032	15614	15614
12.0	2.427983	12407	12407
13.0	2.429721	10355	10355
14.0	2.430745	8568	8568
15.0	2.431348	7155	7155
16.0	2.431702	6306	6306
17.0	2.431911	5404	5404
18.0	2.432034	4735	4735
19.0	2.432107	4184	4184
20.0	2.43215	3724	3724
21.0	2.432175	3238	3238
22.0	2.432189	2910	2910
23.0	2.432198	2568	2568
24.0	2.432203	2291	2291
25.0	2.432206	2197	2197
26.0	2.432208	1969	1969
27.0	2.432209	1738	1738
28.0	2.43221	1650	1650
29.0	2.43221	1504	1504
30.0	2.43221	1356	1356
31.0	2.43221	1300	1300
32.0	2.432211	1173	1173
33.0	2.432211	1096	1096
34.0	2.432211	986	986
35.0	2.432211	944	944
36.0	2.432211	840	840
37.0	2.432211	875	875
38.0	2.432211	796	796
39.0	2.432211	707	707
40.0	2.432211	652	652
41.0	2.432211	622	622
42.0	2.432211	608	608
43.0	2.432211	565	565
44.0	2.432211	552	552
45.0	2.432211	479	479
46.0	2.432211	534	534
47.0	2.432211	472	472
48.0	2.432211	412	412
49.0	2.432211	390	390
50.0	2.432211	419	419
51.0	2.432211	369	369
52.0	2.432211	366	366
53.0	2.432211	352	352
54.0	2.432211	314	314
55.0	2.432211	306	306
56.0	2.432211	284	284
57.0	2.432211	307	307
58.0	2.432211	278	278
59.0	2.432211	282	282
60.0	2.432211	244	244
61.0	2.432211	219	219
62.0	2.432211	200	200
63.0	2.432211	221	221
64.0	2.432211	228	228
65.0	2.432211	187	187
66.0	2.432211	200	200
67.0	2.432211	193	193
68.0	2.432211	173	173
69.0	2.432211	162	162
70.0	2.432211	170	170
71.0	2.432211	182	182
72.0	2.432211	162	162
73.0	2.432211	169	169
74.0	2.432211	152	152
75.0	2.432211	144	144
76.0	2.432211	133	133
77.0	2.432211	135	135
78.0	2.432211	142	142
79.0	2.432211	134	134
80.0	2.432211	120	120
81.0	2.432211	127	127
82.0	2.432211	90	90
83.0	2.432211	112	112
84.0	2.432211	114	114
85.0	2.432211	105	105
86.0	2.432211	107	107
87.0	2.432211	114	114
88.0	2.432211	104	104
89.0	2.432211	79	79
90.0	2.432211	84	84
91.0	2.432211	94	94
92.0	2.432211	91	91
93.0	2.432211	88	88
94.0	2.432211	69	69
95.0	2.432211	75	75
96.0	2.432211	87	87
97.0	2.432211	86	86
98.0	2.432211	91	91
99.0	2.432211	62	62
100.0	2.432211	76	76
101.0	0	77	77
102.0	0	70	70
103.0	0	69	69
104.0	0	73	73
105.0	0	63	63
106.0	0	64	64
107.0	0	54	54
108.0	0	66	66
109.0	0	59	59
110.0	0	54	54
111.0	0	70	70
112.0	0	52	52
113.0	0	65	65
114.0	0	58	58
115.0	0	41	41
116.0	0	44	44
117.0	0	56	56
118.0	0	41	41
119.0	0	49	49
120.0	0	51	51
121.0	0	47	47
122.0	0	30	30
123.0	0	53	53
124.0	0	45	45
125.0	0	37	37
126.0	0	51	51
127.0	0	43	43
128.0	0	28	28
129.0	0	38	38
130.0	0	29	29
131.0	0	28	28
132.0	0	40	40
133.0	0	37	37
134.0	0	38	38
135.0	0	32	32
136.0	0	35	35
137.0	0	27	27
138.0	0	41	41
139.0	0	35	35
140.0	0	33	33
141.0	0	32	32
142.0	0	31	31
143.0	0	30	30
144.0	0	29	29
145.0	0	28	28
146.0	0	27	27
147.0	0	39	39
148.0	0	29	29
149.0	0	23	23
150.0	0	33	33
151.0	0	28	28
152.0	0	31	31
153.0	0	18	18
154.0	0	29	29
155.0	0	23	23
156.0	0	28	28
157.0	0	19	19
158.0	0	18	18
159.0	0	24	24
160.0	0	24	24
161.0	0	17	17
162.0	0	13	13
163.0	0	19	19
164.0	0	27	27
165.0	0	17	17
166.0	0	27	27
167.0	0	22	22
168.0	0	21	21
169.0	0	18	18
170.0	0	17	17
171.0	0	27	27
172.0	0	15	15
173.0	0	21	21
174.0	0	17	17
175.0	0	24	24
176.0	0	21	21
177.0	0	21	21
178.0	0	14	14
179.0	0	19	19
180.0	0	24	24
181.0	0	18	18
182.0	0	24	24
183.0	0	22	22
184.0	0	11	11
185.0	0	16	16
186.0	0	13	13
187.0	0	17	17
188.0	0	15	15
189.0	0	18	18
190.0	0	15	15
191.0	0	10	10
192.0	0	16	16
193.0	0	14	14
194.0	0	18	18
195.0	0	19	19
196.0	0	12	12
197.0	0	14	14
198.0	0	12	12
199.0	0	16	16
200.0	0	14	14
201.0	0	13	13
202.0	0	15	15
203.0	0	15	15
204.0	0	9	9
205.0	0	12	12
206.0	0	15	15
207.0	0	14	14
208.0	0	15	15
209.0	0	17	17
210.0	0	13	13
211.0	0	11	11
212.0	0	22	22
213.0	0	18	18
214.0	0	8	8
215.0	0	10	10
216.0	0	14	14
217.0	0	17	17
218.0	0	15	15
219.0	0	8	8
220.0	0	7	7
221.0	0	6	6
222.0	0	12	12
223.0	0	7	7
224.0	0	11	11
225.0	0	6	6
226.0	0	4	4
227.0	0	13	13
228.0	0	9	9
229.0	0	12	12
230.0	0	4	4
231.0	0	11	11
232.0	0	8	8
233.0	0	9	9
234.0	0	6	6
235.0	0	5	5
236.0	0	8	8
237.0	0	8	8
238.0	0	7	7
239.0	0	9	9
240.0	0	8	8
241.0	0	9	9
242.0	0	7	7
243.0	0	5	5
244.0	0	10	10
245.0	0	5	5
246.0	0	10	10
247.0	0	7	7
248.0	0	9	9
249.0	0	8	8
250.0	0	4	4
251.0	0	7	7
252.0	0	9	9
253.0	0	8	8
254.0	0	7	7
255.0	0	10	10
256.0	0	6	6
257.0	0	5	5
258.0	0	9	9
259.0	0	7	7
260.0	0	8	8
261.0	0	6	6
262.0	0	4	4
263.0	0	7	7
264.0	0	7	7
265.0	0	6	6
266.0	0	5	5
267.0	0	6	6
268.0	0	3	3
269.0	0	5	5
270.0	0	8	8
271.0	0	7	7
272.0	0	5	5
273.0	0	9	9
274.0	0	5	5
275.0	0	5	5
276.0	0	3	3
277.0	0	2	2
278.0	0	3	3
279.0	0	6	6
280.0	0	6	6
281.0	0	4	4
282.0	0	3	3
283.0	0	4	4
284.0	0	6	6
285.0	0	6	6
286.0	0	5	5
287.0	0	7	7
288.0	0	4	4
289.0	0	5	5
290.0	0	7	7
291.0	0	6	6
292.0	0	6	6
293.0	0	4	4
294.0	0	4	4
295.0	0	3	3
296.0	0	4	4
297.0	0	9	9
298.0	0	4	4
299.0	0	5	5
300.0	0	8	8
301.0	0	8	8
302.0	0	3	3
303.0	0	4	4
304.0	0	4	4
305.0	0	6	6
306.0	0	4	4
307.0	0	2	2
308.0	0	7	7
309.0	0	4	4
310.0	0	3	3
311.0	0	5	5
312.0	0	3	3
313.0	0	3	3
314.0	0	7	7
315.0	0	6	6
316.0	0	6	6
317.0	0	6	6
318.0	0	4	4
319.0	0	3	3
320.0	0	7	7
321.0	0	7	7
322.0	0	2	2
323.0	0	7	7
324.0	0	3	3
325.0	0	2	2
326.0	0	3	3
327.0	0	6	6
328.0	0	6	6
329.0	0	5	5
330.0	0	4	4
331.0	0	4	4
332.0	0	9	9
333.0	0	5	5
334.0	0	5	5
335.0	0	4	4
336.0	0	2	2
337.0	0	5	5
338.0	0	2	2
339.0	0	3	3
340.0	0	2	2
341.0	0	3	3
342.0	0	6	6
343.0	0	8	8
344.0	0	9	9
345.0	0	4	4
346.0	0	3	3
347.0	0	4	4
348.0	0	3	3
349.0	0	3	3
350.0	0	1	1
351.0	0	3	3
352.0	0	5	5
353.0	0	4	4
354.0	0	2	2
355.0	0	3	3
356.0	0	5	5
357.0	0	5	5
358.0	0	3	3
359.0	0	2	2
360.0	0	4	4
361.0	0	4	4
362.0	0	3	3
363.0	0	3	3
364.0	0	6	6
365.0	0	3	3
366.0	0	5	5
367.0	0	3	3
368.0	0	3	3
369.0	0	2	2
370.0	0	3	3
371.0	0	3	3
372.0	0	5	5
373.0	0	6	6
374.0	0	2	2
375.0	0	2	2
376.0	0	6	6
377.0	0	1	1
378.0	0	3	3
379.0	0	3	3
380.0	0	4	4
381.0	0	1	1
382.0	0	2	2
383.0	0	2	2
385.0	0	3	3
386.0	0	2	2
387.0	0	2	2
388.0	0	4	4
389.0	0	2	2
391.0	0	4	4
392.0	0	4	4
393.0	0	4	4
394.0	0	3	3
395.0	0	1	1
396.0	0	2	2
397.0	0	4	4
398.0	0	4	4
399.0	0	1	1
400.0	0	3	3
401.0	0	2	2
402.0	0	8	8
403.0	0	4	4
404.0	0	4	4
405.0	0	2	2
407.0	0	2	2
408.0	0	2	2
409.0	0	2	2
411.0	0	3	3
412.0	0	1	1
413.0	0	1	1
414.0	0	3	3
416.0	0	3	3
419.0	0	2	2
420.0	0	1	1
421.0	0	3	3
422.0	0	3	3
423.0	0	3	3
424.0	0	3	3
425.0	0	3	3
426.0	0	1	1
427.0	0	2	2
428.0	0	3	3
429.0	0	2	2
430.0	0	7	7
431.0	0	1	1
432.0	0	3	3
433.0	0	2	2
434.0	0	4	4
435.0	0	2	2
436.0	0	1	1
438.0	0	1	1
439.0	0	4	4
442.0	0	2	2
443.0	0	4	4
444.0	0	1	1
445.0	0	1	1
446.0	0	5	5
447.0	0	3	3
448.0	0	2	2
449.0	0	2	2
450.0	0	6	6
452.0	0	1	1
453.0	0	3	3
454.0	0	2	2
455.0	0	2	2
456.0	0	2	2
457.0	0	4	4
458.0	0	1	1
459.0	0	5	5
461.0	0	5	5
462.0	0	1	1
463.0	0	1	1
464.0	0	3	3
466.0	0	2	2
467.0	0	2	2
469.0	0	2	2
470.0	0	3	3
471.0	0	1	1
472.0	0	1	1
473.0	0	1	1
475.0	0	1	1
476.0	0	2	2
477.0	0	2	2
478.0	0	3	3
479.0	0	3	3
481.0	0	2	2
482.0	0	2	2
483.0	0	1	1
486.0	0	2	2
487.0	0	2	2
488.0	0	3	3
489.0	0	4	4
490.0	0	2	2
491.0	0	2	2
492.0	0	1	1
496.0	0	2	2
497.0	0	1	1
499.0	0	1	1
501.0	0	2	2
502.0	0	2	2
503.0	0	2	2
504.0	0	1	1
506.0	0	2	2
507.0	0	1	1
509.0	0	2	2
511.0	0	1	1
512.0	0	2	2
516.0	0	2	2
517.0	0	3	3
518.0	0	3	3
520.0	0	2	2
522.0	0	1	1
524.0	0	1	1
526.0	0	2	2
528.0	0	2	2
529.0	0	1	1
530.0	0	1	1
531.0	0	1	1
532.0	0	2	2
533.0	0	2	2
538.0	0	1	1
539.0	0	5	5
540.0	0	2	2
541.0	0	1	1
543.0	0	1	1
544.0	0	1	1
545.0	0	1	1
546.0	0	1	1
547.0	0	1	1
549.0	0	1	1
552.0	0	1	1
553.0	0	1	1
554.0	0	2	2
555.0	0	1	1
557.0	0	1	1
558.0	0	2	2
559.0	0	4	4
560.0	0	1	1
567.0	0	1	1
568.0	0	1	1
570.0	0	1	1
571.0	0	4	4
573.0	0	1	1
574.0	0	1	1
576.0	0	2	2
577.0	0	3	3
578.0	0	1	1
579.0	0	1	1
580.0	0	2	2
581.0	0	1	1
582.0	0	2	2
583.0	0	2	2
584.0	0	1	1
587.0	0	1	1
588.0	0	2	2
592.0	0	3	3
593.0	0	3	3
596.0	0	1	1
597.0	0	1	1
598.0	0	1	1
600.0	0	1	1
603.0	0	1	1
606.0	0	1	1
607.0	0	1	1
608.0	0	2	2
609.0	0	3	3
610.0	0	2	2
612.0	0	1	1
615.0	0	2	2
618.0	0	1	1
619.0	0	2	2
620.0	0	2	2
627.0	0	1	1
628.0	0	1	1
629.0	0	1	1
630.0	0	1	1
633.0	0	1	1
635.0	0	3	3
636.0	0	1	1
637.0	0	4	4
639.0	0	1	1
642.0	0	1	1
643.0	0	1	1
645.0	0	1	1
646.0	0	1	1
647.0	0	1	1
648.0	0	1	1
649.0	0	1	1
650.0	0	1	1
651.0	0	1	1
652.0	0	1	1
653.0	0	2	2
654.0	0	3	3
655.0	0	2	2
656.0	0	1	1
658.0	0	1	1
659.0	0	1	1
662.0	0	2	2
664.0	0	2	2
669.0	0	1	1
672.0	0	1	1
674.0	0	2	2
677.0	0	1	1
678.0	0	1	1
680.0	0	1	1
681.0	0	1	1
682.0	0	1	1
684.0	0	1	1
686.0	0	2	2
687.0	0	1	1
691.0	0	2	2
693.0	0	1	1
696.0	0	1	1
698.0	0	1	1
700.0	0	1	1
704.0	0	2	2
710.0	0	3	3
711.0	0	1	1
712.0	0	2	2
713.0	0	1	1
714.0	0	1	1
715.0	0	1	1
717.0	0	1	1
718.0	0	2	2
722.0	0	2	2
723.0	0	2	2
724.0	0	1	1
726.0	0	1	1
730.0	0	3	3
731.0	0	1	1
732.0	0	1	1
733.0	0	1	1
738.0	0	1	1
740.0	0	1	1
742.0	0	1	1
743.0	0	1	1
746.0	0	2	2
749.0	0	1	1
751.0	0	1	1
761.0	0	1	1
762.0	0	1	1
764.0	0	2	2
768.0	0	1	1
769.0	0	1	1
770.0	0	1	1
771.0	0	1	1
775.0	0	1	1
784.0	0	1	1
785.0	0	1	1
787.0	0	1	1
793.0	0	1	1
795.0	0	1	1
796.0	0	1	1
798.0	0	1	1
804.0	0	1	1
805.0	0	1	1
808.0	0	1	1
809.0	0	1	1
820.0	0	1	1
821.0	0	1	1
822.0	0	1	1
824.0	0	1	1
830.0	0	2	2
834.0	0	1	1
840.0	0	1	1
844.0	0	2	2
852.0	0	1	1
854.0	0	1	1
858.0	0	1	1
864.0	0	1	1
868.0	0	1	1
876.0	0	1	1
877.0	0	1	1
879.0	0	1	1
880.0	0	1	1
886.0	0	1	1
889.0	0	1	1
890.0	0	1	1
892.0	0	1	1
896.0	0	3	3
902.0	0	1	1
903.0	0	1	1
905.0	0	1	1
909.0	0	1	1
911.0	0	1	1
913.0	0	1	1
917.0	0	1	1
921.0	0	1	1
924.0	0	2	2
925.0	0	1	1
927.0	0	1	1
928.0	0	1	1
929.0	0	1	1
930.0	0	1	1
931.0	0	1	1
932.0	0	1	1
935.0	0	3	3
938.0	0	1	1
940.0	0	1	1
941.0	0	1	1
947.0	0	1	1
956.0	0	1	1
957.0	0	1	1
959.0	0	1	1
973.0	0	1	1
974.0	0	1	1
981.0	0	2	2
983.0	0	1	1
985.0	0	1	1
992.0	0	1	1
994.0	0	1	1
1000.0	0	1	1
1003.0	0	1	1
1004.0	0	1	1
1005.0	0	1	1
1025.0	0	2	2
1029.0	0	1	1
1030.0	0	1	1
1033.0	0	1	1
1042.0	0	1	1
1044.0	0	1	1
1047.0	0	1	1
1060.0	0	1	1
1061.0	0	1	1
1070.0	0	1	1
1074.0	0	1	1
1080.0	0	1	1
1081.0	0	1	1
1087.0	0	1	1
1088.0	0	1	1
1091.0	0	1	1
1120.0	0	1	1
1130.0	0	1	1
1139.0	0	1	1
1141.0	0	1	1
1164.0	0	1	1
1182.0	0	1	1
1200.0	0	1	1
1203.0	0	1	1
1204.0	0	1	1
1217.0	0	1	1
1220.0	0	1	1
1223.0	0	2	2
1228.0	0	1	1
1229.0	0	1	1
1236.0	0	1	1
1249.0	0	2	2
1277.0	0	1	1
1294.0	0	1	1
1297.0	0	1	1
1307.0	0	1	1
1309.0	0	1	1
1313.0	0	1	1
1323.0	0	1	1
1324.0	0	1	1
1327.0	0	1	1
1333.0	0	2	2
1338.0	0	1	1
1357.0	0	1	1
1358.0	0	1	1
1361.0	0	2	2
1364.0	0	1	1
1394.0	0	1	1
1421.0	0	1	1
1423.0	0	1	1
1428.0	0	1	1
1436.0	0	1	1
1442.0	0	1	1
1443.0	0	1	1
1482.0	0	1	1
1483.0	0	1	1
1484.0	0	1	1
1494.0	0	1	1
1518.0	0	1	1
1533.0	0	1	1
1540.0	0	1	1
1556.0	0	1	1
1557.0	0	1	1
1563.0	0	1	1
1570.0	0	1	1
1574.0	0	1	1
1578.0	0	1	1
1585.0	0	1	1
1610.0	0	1	1
1672.0	0	1	1
1686.0	0	1	1
1688.0	0	1	1
1744.0	0	1	1
1758.0	0	1	1
1819.0	0	1	1
1845.0	0	1	1
1849.0	0	1	1
1868.0	0	1	1
1884.0	0	1	1
1885.0	0	1	1
1902.0	0	1	1
1923.0	0	1	1
1983.0	0	1	1
1988.0	0	1	1
1998.0	0	1	1
2144.0	0	1	1
2212.0	0	1	1
2225.0	0	1	1
2244.0	0	1	1
2252.0	0	1	1
2270.0	0	1	1
2290.0	0	1	1
2345.0	0	1	1
2470.0	0	1	1
2531.0	0	1	1
2596.0	0	1	1
2619.0	0	1	1
2690.0	0	1	1
2696.0	0	1	1
2828.0	0	1	1
2874.0	0	1	1
2946.0	0	1	1
3061.0	0	1	1
3150.0	0	1	1
3291.0	0	1	1
4517.0	0	1	1
4611.0	0	1	1
4787.0	0	1	1
4910.0	0	1	1
4961.0	0	1	1
5964.0	0	1	1
6626.0	0	1	1
7340.0	0	1	1
10838.0	0	1	1
12503.0	0	1	1