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659_djb-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0020/B23WHTKLT4/nfcore_rnafusion__3e501777--20260520-120107/QC/picard/659_djb-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 1:02 AM

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## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT 659_djb-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_djb-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt --TMP_DIR ./tmp --MINIMUM_LENGTH 500 --RRNA_FRAGMENT_PERCENTAGE 0.8 --METRIC_ACCUMULATION_LEVEL ALL_READS --END_BIAS_BASES 100 --ASSUME_SORTED true --STOP_AFTER 0 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu May 21 05:45:57 GMT 2026

## METRICS CLASS	picard.analysis.RnaSeqMetrics
PF_BASES	PF_ALIGNED_BASES	RIBOSOMAL_BASES	CODING_BASES	UTR_BASES	INTRONIC_BASES	INTERGENIC_BASES	IGNORED_READS	CORRECT_STRAND_READS	INCORRECT_STRAND_READS	NUM_R1_TRANSCRIPT_STRAND_READS	NUM_R2_TRANSCRIPT_STRAND_READS	NUM_UNEXPLAINED_READS	PCT_R1_TRANSCRIPT_STRAND_READS	PCT_R2_TRANSCRIPT_STRAND_READS	PCT_RIBOSOMAL_BASES	PCT_CODING_BASES	PCT_UTR_BASES	PCT_INTRONIC_BASES	PCT_INTERGENIC_BASES	PCT_MRNA_BASES	PCT_USABLE_BASES	PCT_CORRECT_STRAND_READS	MEDIAN_CV_COVERAGE	MEDIAN_5PRIME_BIAS	MEDIAN_3PRIME_BIAS	MEDIAN_5PRIME_TO_3PRIME_BIAS	SAMPLE	LIBRARY	READ_GROUP
75854840620	75017973543	4448	68374620050	4827003646	1589918403	226426996	0	0	0	15020538	231209975	978845	0.061002	0.938998	0	0.911443	0.064345	0.021194	0.003018	0.975788	0.965022	0	0.513746	0.472824	0.784141	0.671356			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.301346
1	0.327584
2	0.368923
3	0.419907
4	0.464606
5	0.504904
6	0.552186
7	0.591233
8	0.639334
9	0.679676
10	0.715339
11	0.756069
12	0.808276
13	0.858478
14	0.903165
15	0.939534
16	0.968204
17	0.990235
18	1.004346
19	1.019783
20	1.041086
21	1.058224
22	1.078821
23	1.086475
24	1.095152
25	1.101793
26	1.105797
27	1.107878
28	1.116673
29	1.124208
30	1.131058
31	1.132557
32	1.131963
33	1.141078
34	1.139416
35	1.1463
36	1.143712
37	1.139369
38	1.140159
39	1.138799
40	1.136925
41	1.139956
42	1.144875
43	1.142169
44	1.14329
45	1.147236
46	1.152355
47	1.167807
48	1.175191
49	1.178778
50	1.186504
51	1.18618
52	1.18143
53	1.176177
54	1.176877
55	1.182302
56	1.184883
57	1.186083
58	1.180835
59	1.171447
60	1.169261
61	1.179614
62	1.181775
63	1.178514
64	1.175
65	1.173122
66	1.17457
67	1.174913
68	1.173102
69	1.167569
70	1.154878
71	1.147659
72	1.141091
73	1.138939
74	1.133642
75	1.126601
76	1.120026
77	1.104607
78	1.09987
79	1.090385
80	1.078139
81	1.063188
82	1.053285
83	1.031714
84	1.0175
85	0.999851
86	0.975126
87	0.959463
88	0.937851
89	0.911728
90	0.885364
91	0.857235
92	0.832978
93	0.807138
94	0.774623
95	0.738595
96	0.701364
97	0.662757
98	0.621397
99	0.574779
100	0.531343