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659_cIX-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_cIX-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 1:06 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_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cIX-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 04:33:33 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
77075420285	76318260545	4958	69532334030	4969912819	1553266361	262742377	0	0	0	12495695	230995725	1111221	0.051319	0.948681	0	0.911084	0.065121	0.020352	0.003443	0.976205	0.966615	0	0.515777	0.486679	0.719116	0.739453			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.316393
1	0.346712
2	0.395355
3	0.457725
4	0.506671
5	0.542489
6	0.588578
7	0.632997
8	0.681512
9	0.730261
10	0.772153
11	0.81687
12	0.860519
13	0.89906
14	0.932902
15	0.964068
16	0.996289
17	1.016697
18	1.030595
19	1.04504
20	1.065652
21	1.087467
22	1.105363
23	1.114133
24	1.121685
25	1.131237
26	1.135419
27	1.136658
28	1.149958
29	1.155073
30	1.156835
31	1.156252
32	1.157335
33	1.164237
34	1.164159
35	1.175091
36	1.181213
37	1.18214
38	1.185788
39	1.188334
40	1.175569
41	1.182803
42	1.190526
43	1.192826
44	1.198996
45	1.201151
46	1.192489
47	1.196736
48	1.204067
49	1.20873
50	1.206759
51	1.204146
52	1.196771
53	1.191537
54	1.193598
55	1.191443
56	1.173992
57	1.16762
58	1.158017
59	1.154505
60	1.156321
61	1.152694
62	1.145439
63	1.128021
64	1.125324
65	1.128249
66	1.120106
67	1.106299
68	1.095055
69	1.086669
70	1.076124
71	1.068912
72	1.067876
73	1.065481
74	1.058958
75	1.057087
76	1.055681
77	1.04897
78	1.042114
79	1.034157
80	1.019316
81	1.004046
82	0.988641
83	0.969842
84	0.958328
85	0.947563
86	0.933026
87	0.927316
88	0.911068
89	0.890449
90	0.864657
91	0.842942
92	0.81934
93	0.79057
94	0.757531
95	0.725481
96	0.69329
97	0.657183
98	0.617866
99	0.577452
100	0.535323