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tih_rna_sample_00079_23KKJ7LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0007/A23KKJ7LT4/nfcore_rnafusion_100M__5f1fa79--20260304-102235/QC/picard/tih_rna_sample_00079_23KKJ7LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0007-5f1fa79
Published
Mar 05, 2026 1:44 PM

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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 tih_rna_sample_00079_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00079_23KKJ7LT4_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 Mar 05 20:53:44 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
24099628147	22463814469	186429	15431363477	2368940566	3643983043	1019340954	0	0	0	1863593	57990145	447026	0.031136	0.968864	0.000008	0.686943	0.105456	0.162216	0.045377	0.792399	0.738613	0	0.676928	0.524199	0.558273	0.989128			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.36279
1	0.403537
2	0.467944
3	0.539164
4	0.618558
5	0.699316
6	0.761179
7	0.810162
8	0.853923
9	0.891451
10	0.938147
11	0.981516
12	1.02703
13	1.062928
14	1.088784
15	1.103995
16	1.119182
17	1.132643
18	1.1229
19	1.127912
20	1.140549
21	1.15337
22	1.158927
23	1.167406
24	1.179723
25	1.187266
26	1.188382
27	1.184479
28	1.177079
29	1.167872
30	1.162733
31	1.156521
32	1.154971
33	1.155988
34	1.153747
35	1.151288
36	1.146882
37	1.143516
38	1.152294
39	1.142956
40	1.142422
41	1.145876
42	1.152661
43	1.148322
44	1.145733
45	1.155928
46	1.153186
47	1.144617
48	1.138869
49	1.136527
50	1.132897
51	1.126171
52	1.122555
53	1.128918
54	1.136694
55	1.135001
56	1.126587
57	1.117357
58	1.117602
59	1.106318
60	1.094533
61	1.097084
62	1.091508
63	1.084574
64	1.085387
65	1.07928
66	1.076997
67	1.065444
68	1.059296
69	1.056803
70	1.046328
71	1.040362
72	1.042403
73	1.039748
74	1.029856
75	1.021621
76	1.017397
77	1.007085
78	1.00708
79	1.003136
80	0.993623
81	0.9772
82	0.955579
83	0.940893
84	0.929327
85	0.909712
86	0.885335
87	0.86413
88	0.842249
89	0.818302
90	0.794849
91	0.781671
92	0.744785
93	0.714539
94	0.692466
95	0.666873
96	0.642865
97	0.616015
98	0.577672
99	0.545591
100	0.505498