## 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_no_replicates/star/GRCh38.p13-D12_supernatant_DMSO_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_DMSO_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_DMSO_2.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: Fri Oct 06 01:09:45 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	2431	47602548	45025310	0	2227	10525779	0	0.221136	91107195

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	32568919	32568919
2.0	1.593042	3238037	3238037
3.0	1.944742	630750	630750
4.0	2.153314	216422	216422
5.0	2.277007	109923	109923
6.0	2.350361	67322	67322
7.0	2.393864	45691	45691
8.0	2.419663	32815	32815
9.0	2.434962	24182	24182
10.0	2.444036	18845	18845
11.0	2.449417	15037	15037
12.0	2.452608	12301	12301
13.0	2.4545	9906	9906
14.0	2.455623	8329	8329
15.0	2.456288	7051	7051
16.0	2.456683	6117	6117
17.0	2.456917	5286	5286
18.0	2.457056	4544	4544
19.0	2.457138	4009	4009
20.0	2.457187	3566	3566
21.0	2.457216	3145	3145
22.0	2.457233	2767	2767
23.0	2.457243	2581	2581
24.0	2.457249	2234	2234
25.0	2.457253	2015	2015
26.0	2.457255	1839	1839
27.0	2.457256	1741	1741
28.0	2.457257	1580	1580
29.0	2.457258	1486	1486
30.0	2.457258	1311	1311
31.0	2.457258	1173	1173
32.0	2.457258	1084	1084
33.0	2.457258	1048	1048
34.0	2.457258	928	928
35.0	2.457258	911	911
36.0	2.457258	890	890
37.0	2.457258	821	821
38.0	2.457258	789	789
39.0	2.457258	731	731
40.0	2.457258	649	649
41.0	2.457258	655	655
42.0	2.457258	566	566
43.0	2.457258	560	560
44.0	2.457258	528	528
45.0	2.457258	514	514
46.0	2.457258	485	485
47.0	2.457258	465	465
48.0	2.457258	384	384
49.0	2.457258	401	401
50.0	2.457258	392	392
51.0	2.457258	377	377
52.0	2.457258	329	329
53.0	2.457258	324	324
54.0	2.457258	322	322
55.0	2.457258	271	271
56.0	2.457258	308	308
57.0	2.457258	261	261
58.0	2.457258	273	273
59.0	2.457258	267	267
60.0	2.457258	252	252
61.0	2.457258	226	226
62.0	2.457258	217	217
63.0	2.457258	264	264
64.0	2.457258	214	214
65.0	2.457258	216	216
66.0	2.457258	214	214
67.0	2.457258	183	183
68.0	2.457258	157	157
69.0	2.457258	142	142
70.0	2.457258	173	173
71.0	2.457258	159	159
72.0	2.457258	166	166
73.0	2.457258	157	157
74.0	2.457258	166	166
75.0	2.457258	142	142
76.0	2.457258	153	153
77.0	2.457258	137	137
78.0	2.457258	112	112
79.0	2.457258	131	131
80.0	2.457258	116	116
81.0	2.457258	121	121
82.0	2.457258	119	119
83.0	2.457258	130	130
84.0	2.457258	124	124
85.0	2.457258	105	105
86.0	2.457258	88	88
87.0	2.457258	90	90
88.0	2.457258	122	122
89.0	2.457258	102	102
90.0	2.457258	94	94
91.0	2.457258	101	101
92.0	2.457258	90	90
93.0	2.457258	76	76
94.0	2.457258	80	80
95.0	2.457258	75	75
96.0	2.457258	74	74
97.0	2.457258	83	83
98.0	2.457258	62	62
99.0	2.457258	72	72
100.0	2.457258	52	52
101.0	0	68	68
102.0	0	63	63
103.0	0	77	77
104.0	0	71	71
105.0	0	61	61
106.0	0	62	62
107.0	0	60	60
108.0	0	53	53
109.0	0	54	54
110.0	0	62	62
111.0	0	42	42
112.0	0	55	55
113.0	0	50	50
114.0	0	52	52
115.0	0	50	50
116.0	0	47	47
117.0	0	46	46
118.0	0	41	41
119.0	0	40	40
120.0	0	44	44
121.0	0	38	38
122.0	0	48	48
123.0	0	52	52
124.0	0	45	45
125.0	0	40	40
126.0	0	28	28
127.0	0	25	25
128.0	0	40	40
129.0	0	54	54
130.0	0	42	42
131.0	0	41	41
132.0	0	33	33
133.0	0	37	37
134.0	0	31	31
135.0	0	33	33
136.0	0	33	33
137.0	0	38	38
138.0	0	37	37
139.0	0	27	27
140.0	0	30	30
141.0	0	39	39
142.0	0	35	35
143.0	0	28	28
144.0	0	37	37
145.0	0	15	15
146.0	0	25	25
147.0	0	21	21
148.0	0	27	27
149.0	0	30	30
150.0	0	25	25
151.0	0	25	25
152.0	0	31	31
153.0	0	26	26
154.0	0	25	25
155.0	0	26	26
156.0	0	20	20
157.0	0	21	21
158.0	0	15	15
159.0	0	23	23
160.0	0	23	23
161.0	0	21	21
162.0	0	35	35
163.0	0	25	25
164.0	0	12	12
165.0	0	16	16
166.0	0	8	8
167.0	0	18	18
168.0	0	16	16
169.0	0	19	19
170.0	0	20	20
171.0	0	14	14
172.0	0	19	19
173.0	0	21	21
174.0	0	28	28
175.0	0	15	15
176.0	0	15	15
177.0	0	13	13
178.0	0	17	17
179.0	0	12	12
180.0	0	27	27
181.0	0	24	24
182.0	0	13	13
183.0	0	14	14
184.0	0	19	19
185.0	0	11	11
186.0	0	16	16
187.0	0	11	11
188.0	0	14	14
189.0	0	11	11
190.0	0	17	17
191.0	0	12	12
192.0	0	17	17
193.0	0	11	11
194.0	0	12	12
195.0	0	10	10
196.0	0	15	15
197.0	0	18	18
198.0	0	19	19
199.0	0	12	12
200.0	0	16	16
201.0	0	14	14
202.0	0	8	8
203.0	0	17	17
204.0	0	7	7
205.0	0	15	15
206.0	0	13	13
207.0	0	16	16
208.0	0	22	22
209.0	0	10	10
210.0	0	10	10
211.0	0	10	10
212.0	0	12	12
213.0	0	18	18
214.0	0	5	5
215.0	0	15	15
216.0	0	13	13
217.0	0	11	11
218.0	0	7	7
219.0	0	11	11
220.0	0	10	10
221.0	0	6	6
222.0	0	10	10
223.0	0	5	5
224.0	0	8	8
225.0	0	15	15
226.0	0	5	5
227.0	0	8	8
228.0	0	11	11
229.0	0	5	5
230.0	0	12	12
231.0	0	10	10
232.0	0	11	11
233.0	0	4	4
234.0	0	13	13
235.0	0	15	15
236.0	0	12	12
237.0	0	2	2
238.0	0	13	13
239.0	0	10	10
240.0	0	12	12
241.0	0	7	7
242.0	0	11	11
243.0	0	11	11
244.0	0	6	6
245.0	0	10	10
246.0	0	9	9
247.0	0	9	9
248.0	0	11	11
249.0	0	3	3
250.0	0	10	10
251.0	0	4	4
252.0	0	3	3
253.0	0	8	8
254.0	0	8	8
255.0	0	2	2
256.0	0	5	5
257.0	0	6	6
258.0	0	5	5
259.0	0	9	9
260.0	0	7	7
261.0	0	4	4
262.0	0	8	8
263.0	0	4	4
264.0	0	12	12
265.0	0	9	9
266.0	0	6	6
267.0	0	6	6
268.0	0	10	10
269.0	0	9	9
270.0	0	7	7
271.0	0	2	2
272.0	0	7	7
273.0	0	7	7
274.0	0	5	5
275.0	0	6	6
276.0	0	8	8
277.0	0	9	9
278.0	0	8	8
279.0	0	8	8
280.0	0	3	3
281.0	0	9	9
282.0	0	7	7
283.0	0	8	8
284.0	0	12	12
285.0	0	6	6
286.0	0	9	9
287.0	0	6	6
288.0	0	2	2
289.0	0	8	8
290.0	0	2	2
291.0	0	7	7
292.0	0	13	13
293.0	0	4	4
294.0	0	5	5
295.0	0	5	5
296.0	0	12	12
297.0	0	4	4
298.0	0	2	2
299.0	0	4	4
300.0	0	1	1
301.0	0	9	9
302.0	0	4	4
303.0	0	4	4
304.0	0	7	7
305.0	0	2	2
306.0	0	3	3
307.0	0	8	8
309.0	0	5	5
310.0	0	5	5
311.0	0	3	3
312.0	0	8	8
313.0	0	5	5
314.0	0	1	1
316.0	0	7	7
318.0	0	5	5
319.0	0	6	6
320.0	0	4	4
321.0	0	3	3
322.0	0	2	2
323.0	0	5	5
324.0	0	1	1
325.0	0	2	2
326.0	0	5	5
327.0	0	6	6
328.0	0	3	3
329.0	0	1	1
330.0	0	4	4
331.0	0	6	6
332.0	0	5	5
333.0	0	4	4
334.0	0	1	1
335.0	0	5	5
336.0	0	2	2
337.0	0	5	5
338.0	0	5	5
339.0	0	4	4
340.0	0	3	3
341.0	0	1	1
342.0	0	3	3
343.0	0	7	7
344.0	0	5	5
345.0	0	3	3
346.0	0	7	7
347.0	0	7	7
348.0	0	2	2
349.0	0	3	3
350.0	0	1	1
351.0	0	3	3
352.0	0	6	6
353.0	0	3	3
354.0	0	2	2
355.0	0	6	6
356.0	0	4	4
357.0	0	2	2
358.0	0	1	1
359.0	0	3	3
360.0	0	3	3
361.0	0	3	3
362.0	0	6	6
363.0	0	5	5
364.0	0	2	2
365.0	0	1	1
366.0	0	2	2
367.0	0	4	4
368.0	0	2	2
369.0	0	3	3
370.0	0	2	2
371.0	0	1	1
372.0	0	2	2
373.0	0	2	2
374.0	0	2	2
375.0	0	8	8
376.0	0	2	2
377.0	0	5	5
378.0	0	2	2
379.0	0	5	5
380.0	0	1	1
381.0	0	2	2
382.0	0	6	6
383.0	0	2	2
384.0	0	4	4
385.0	0	4	4
387.0	0	1	1
388.0	0	2	2
389.0	0	2	2
390.0	0	3	3
391.0	0	6	6
392.0	0	4	4
394.0	0	5	5
395.0	0	2	2
396.0	0	5	5
397.0	0	1	1
399.0	0	3	3
400.0	0	2	2
402.0	0	2	2
403.0	0	4	4
404.0	0	2	2
405.0	0	6	6
406.0	0	3	3
407.0	0	4	4
408.0	0	2	2
409.0	0	5	5
410.0	0	3	3
413.0	0	4	4
415.0	0	2	2
416.0	0	4	4
417.0	0	4	4
418.0	0	4	4
420.0	0	1	1
421.0	0	3	3
422.0	0	1	1
423.0	0	1	1
424.0	0	2	2
425.0	0	2	2
426.0	0	1	1
427.0	0	3	3
428.0	0	1	1
429.0	0	4	4
430.0	0	2	2
431.0	0	2	2
432.0	0	2	2
433.0	0	1	1
434.0	0	1	1
435.0	0	5	5
436.0	0	2	2
437.0	0	1	1
438.0	0	2	2
439.0	0	1	1
440.0	0	2	2
441.0	0	2	2
442.0	0	3	3
445.0	0	6	6
446.0	0	2	2
447.0	0	2	2
448.0	0	2	2
449.0	0	3	3
450.0	0	3	3
451.0	0	1	1
452.0	0	1	1
453.0	0	1	1
455.0	0	1	1
456.0	0	3	3
457.0	0	3	3
458.0	0	5	5
460.0	0	1	1
461.0	0	1	1
462.0	0	2	2
463.0	0	2	2
464.0	0	3	3
465.0	0	1	1
466.0	0	3	3
467.0	0	1	1
468.0	0	2	2
469.0	0	2	2
471.0	0	2	2
472.0	0	1	1
475.0	0	1	1
476.0	0	3	3
477.0	0	3	3
478.0	0	1	1
479.0	0	3	3
480.0	0	1	1
484.0	0	4	4
485.0	0	2	2
486.0	0	3	3
487.0	0	1	1
489.0	0	2	2
491.0	0	2	2
492.0	0	1	1
493.0	0	2	2
494.0	0	1	1
496.0	0	1	1
498.0	0	3	3
499.0	0	1	1
500.0	0	5	5
501.0	0	1	1
502.0	0	1	1
503.0	0	1	1
505.0	0	1	1
506.0	0	2	2
507.0	0	1	1
508.0	0	2	2
509.0	0	3	3
510.0	0	4	4
511.0	0	3	3
512.0	0	3	3
514.0	0	4	4
515.0	0	1	1
516.0	0	1	1
517.0	0	1	1
518.0	0	1	1
519.0	0	2	2
520.0	0	2	2
521.0	0	1	1
522.0	0	1	1
524.0	0	3	3
525.0	0	2	2
526.0	0	2	2
527.0	0	2	2
528.0	0	2	2
529.0	0	1	1
530.0	0	1	1
533.0	0	2	2
534.0	0	1	1
535.0	0	2	2
536.0	0	2	2
540.0	0	1	1
541.0	0	2	2
542.0	0	1	1
543.0	0	1	1
544.0	0	1	1
545.0	0	1	1
546.0	0	1	1
548.0	0	2	2
549.0	0	1	1
550.0	0	1	1
551.0	0	1	1
552.0	0	2	2
553.0	0	1	1
554.0	0	2	2
556.0	0	1	1
557.0	0	1	1
558.0	0	1	1
559.0	0	4	4
560.0	0	1	1
561.0	0	2	2
562.0	0	2	2
564.0	0	1	1
565.0	0	1	1
566.0	0	2	2
567.0	0	1	1
568.0	0	1	1
571.0	0	1	1
574.0	0	2	2
575.0	0	1	1
576.0	0	1	1
578.0	0	1	1
580.0	0	1	1
581.0	0	1	1
582.0	0	1	1
583.0	0	1	1
587.0	0	2	2
588.0	0	1	1
589.0	0	1	1
590.0	0	2	2
591.0	0	1	1
592.0	0	3	3
594.0	0	1	1
595.0	0	1	1
597.0	0	1	1
598.0	0	1	1
599.0	0	3	3
600.0	0	1	1
602.0	0	1	1
603.0	0	2	2
604.0	0	1	1
606.0	0	2	2
608.0	0	1	1
609.0	0	1	1
610.0	0	1	1
613.0	0	1	1
614.0	0	1	1
615.0	0	1	1
616.0	0	1	1
619.0	0	1	1
620.0	0	1	1
621.0	0	1	1
626.0	0	1	1
629.0	0	1	1
632.0	0	1	1
633.0	0	1	1
634.0	0	1	1
635.0	0	1	1
637.0	0	1	1
638.0	0	1	1
639.0	0	1	1
644.0	0	1	1
645.0	0	2	2
649.0	0	1	1
650.0	0	1	1
653.0	0	1	1
658.0	0	2	2
659.0	0	1	1
660.0	0	1	1
663.0	0	2	2
664.0	0	2	2
666.0	0	1	1
668.0	0	1	1
669.0	0	2	2
675.0	0	1	1
677.0	0	3	3
680.0	0	1	1
681.0	0	1	1
689.0	0	1	1
695.0	0	1	1
696.0	0	1	1
700.0	0	1	1
701.0	0	3	3
702.0	0	1	1
705.0	0	1	1
707.0	0	1	1
709.0	0	1	1
719.0	0	1	1
721.0	0	1	1
727.0	0	1	1
729.0	0	1	1
730.0	0	1	1
731.0	0	1	1
732.0	0	1	1
736.0	0	1	1
740.0	0	2	2
741.0	0	1	1
743.0	0	1	1
744.0	0	2	2
746.0	0	1	1
749.0	0	2	2
753.0	0	1	1
755.0	0	3	3
756.0	0	1	1
761.0	0	1	1
763.0	0	2	2
765.0	0	1	1
770.0	0	1	1
773.0	0	2	2
776.0	0	1	1
778.0	0	1	1
782.0	0	2	2
784.0	0	2	2
790.0	0	1	1
793.0	0	1	1
795.0	0	1	1
802.0	0	1	1
804.0	0	1	1
806.0	0	1	1
809.0	0	1	1
815.0	0	1	1
817.0	0	1	1
818.0	0	1	1
824.0	0	1	1
832.0	0	1	1
846.0	0	1	1
847.0	0	1	1
850.0	0	1	1
853.0	0	2	2
854.0	0	1	1
859.0	0	1	1
862.0	0	1	1
875.0	0	1	1
877.0	0	1	1
883.0	0	1	1
887.0	0	1	1
888.0	0	1	1
891.0	0	1	1
894.0	0	1	1
902.0	0	2	2
905.0	0	1	1
906.0	0	1	1
910.0	0	1	1
913.0	0	1	1
914.0	0	1	1
915.0	0	2	2
917.0	0	1	1
920.0	0	1	1
932.0	0	1	1
933.0	0	1	1
934.0	0	1	1
935.0	0	1	1
941.0	0	1	1
942.0	0	1	1
947.0	0	1	1
951.0	0	1	1
958.0	0	1	1
966.0	0	1	1
973.0	0	1	1
985.0	0	1	1
986.0	0	1	1
993.0	0	1	1
1004.0	0	1	1
1006.0	0	1	1
1018.0	0	1	1
1031.0	0	1	1
1037.0	0	1	1
1042.0	0	1	1
1047.0	0	1	1
1074.0	0	1	1
1080.0	0	1	1
1084.0	0	1	1
1086.0	0	1	1
1094.0	0	1	1
1110.0	0	1	1
1118.0	0	1	1
1123.0	0	1	1
1147.0	0	1	1
1154.0	0	1	1
1164.0	0	1	1
1165.0	0	1	1
1179.0	0	1	1
1190.0	0	1	1
1196.0	0	1	1
1198.0	0	1	1
1206.0	0	1	1
1216.0	0	1	1
1264.0	0	1	1
1273.0	0	1	1
1279.0	0	1	1
1290.0	0	1	1
1307.0	0	1	1
1354.0	0	1	1
1360.0	0	1	1
1387.0	0	1	1
1397.0	0	2	2
1403.0	0	1	1
1416.0	0	1	1
1431.0	0	1	1
1434.0	0	1	1
1500.0	0	1	1
1516.0	0	1	1
1531.0	0	1	1
1570.0	0	1	1
1575.0	0	1	1
1591.0	0	1	1
1595.0	0	1	1
1597.0	0	1	1
1604.0	0	2	2
1623.0	0	1	1
1648.0	0	1	1
1693.0	0	1	1
1696.0	0	1	1
1700.0	0	1	1
1713.0	0	1	1
1720.0	0	1	1
1730.0	0	1	1
1733.0	0	1	1
1734.0	0	1	1
1749.0	0	1	1
1776.0	0	1	1
1778.0	0	1	1
1805.0	0	1	1
1822.0	0	1	1
1827.0	0	1	1
1849.0	0	1	1
1897.0	0	1	1
1947.0	0	1	1
1949.0	0	1	1
2034.0	0	1	1
2112.0	0	1	1
2163.0	0	1	1
2180.0	0	1	1
2192.0	0	1	1
2257.0	0	1	1
2382.0	0	1	1
2626.0	0	1	1
2658.0	0	1	1
2712.0	0	1	1
3130.0	0	1	1
3131.0	0	1	1
3225.0	0	1	1
3708.0	0	1	1
3711.0	0	1	1
4403.0	0	1	1
7049.0	0	1	1
9012.0	0	1	1