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Filename
FFPE_V4_0002_RNA_0001_B23WHTKLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0020/B23WHTKLT4/nfcore_rnafusion__3e501777--20260520-120107/QC/picard/FFPE_V4_0002_RNA_0001_B23WHTKLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 2:26 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 FFPE_V4_0002_RNA_0001_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0002_RNA_0001_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 07:12:19 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
79938793133	79055730363	2026	69145605154	7317313025	2234381262	358428896	0	0	0	9681547	231681632	1312776	0.040112	0.959888	0	0.874644	0.092559	0.028263	0.004534	0.967203	0.956518	0	0.525476	0.556938	0.724549	0.783403			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.263262
1	0.303102
2	0.363857
3	0.424824
4	0.488145
5	0.556803
6	0.620632
7	0.678811
8	0.734334
9	0.790352
10	0.835017
11	0.885953
12	0.934495
13	0.978852
14	1.008444
15	1.036277
16	1.06245
17	1.079781
18	1.098175
19	1.118249
20	1.138061
21	1.155603
22	1.171807
23	1.18497
24	1.193802
25	1.200476
26	1.21103
27	1.213953
28	1.211453
29	1.211044
30	1.207331
31	1.207062
32	1.191191
33	1.192455
34	1.194089
35	1.193392
36	1.192309
37	1.183605
38	1.176121
39	1.170963
40	1.164361
41	1.165107
42	1.169048
43	1.170049
44	1.169231
45	1.179845
46	1.178535
47	1.172647
48	1.168279
49	1.166306
50	1.167548
51	1.163894
52	1.158265
53	1.15824
54	1.159101
55	1.158784
56	1.156417
57	1.147914
58	1.139741
59	1.136334
60	1.133539
61	1.134656
62	1.131186
63	1.119791
64	1.114762
65	1.114295
66	1.114505
67	1.112759
68	1.10505
69	1.092817
70	1.078905
71	1.067197
72	1.062556
73	1.053847
74	1.049313
75	1.041563
76	1.027823
77	1.010351
78	1.001695
79	0.992421
80	0.962962
81	0.939488
82	0.929689
83	0.915156
84	0.901403
85	0.891956
86	0.878156
87	0.874153
88	0.863778
89	0.84418
90	0.824473
91	0.803944
92	0.781275
93	0.757371
94	0.729484
95	0.700198
96	0.666471
97	0.634665
98	0.599233
99	0.561798
100	0.5237