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FFPE_V4_0001_RNA_0005_23KMKGLT4_39_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0001/B23KMKGLT4/nfcore_rnafusion_100M__5f1fa79--20260304-094520/QC/picard/FFPE_V4_0001_RNA_0005_23KMKGLT4_39_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0001R_5f1fa79
Published
Mar 09, 2026 11:59 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_0001_RNA_0005_23KMKGLT4_39.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_39_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: Mon Mar 09 17:59:49 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
24769578537	24472319934	30770	21164163889	2002661544	1167322559	138141172	0	0	0	1884297	77330367	326207	0.023787	0.976213	0.000001	0.86482	0.081834	0.0477	0.005645	0.946654	0.935293	0	0.537093	0.54329	0.754305	0.811199			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.283831
1	0.318281
2	0.365286
3	0.420469
4	0.484241
5	0.548318
6	0.610197
7	0.671911
8	0.723734
9	0.772047
10	0.816852
11	0.86564
12	0.912644
13	0.952217
14	0.981556
15	1.006751
16	1.032128
17	1.052871
18	1.066104
19	1.08351
20	1.098425
21	1.118582
22	1.135221
23	1.148739
24	1.15767
25	1.16346
26	1.171169
27	1.18105
28	1.18909
29	1.189145
30	1.184584
31	1.184313
32	1.17556
33	1.170936
34	1.166985
35	1.166243
36	1.164958
37	1.156336
38	1.145196
39	1.142062
40	1.134723
41	1.129476
42	1.132333
43	1.133999
44	1.128256
45	1.13507
46	1.133551
47	1.128753
48	1.128053
49	1.13547
50	1.139574
51	1.139043
52	1.137752
53	1.141269
54	1.146075
55	1.1478
56	1.147114
57	1.147319
58	1.144673
59	1.141906
60	1.143081
61	1.146923
62	1.14721
63	1.141665
64	1.139244
65	1.140159
66	1.135063
67	1.130395
68	1.122547
69	1.11442
70	1.104206
71	1.098851
72	1.09818
73	1.089247
74	1.083247
75	1.076252
76	1.063963
77	1.045941
78	1.03705
79	1.02709
80	1.013428
81	0.995886
82	0.989764
83	0.978101
84	0.966044
85	0.95969
86	0.945039
87	0.926814
88	0.907028
89	0.889125
90	0.867595
91	0.843429
92	0.819657
93	0.791228
94	0.759219
95	0.72576
96	0.690109
97	0.654926
98	0.619368
99	0.580844
100	0.535211