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RT4_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/RT4_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:54 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 RT4_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT RT4_FFPE_RNA_0001_B23LG7FLT4_2_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 28 22:44:26 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
75865500936	74981534655	56168	64565134814	5519819552	4319615977	576908144	0	0	0	6580796	229348764	1447392	0.027893	0.972107	0.000001	0.86108	0.073616	0.057609	0.007694	0.934696	0.923805	0	0.499381	0.54913	0.790476	0.758296			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.287609
1	0.322122
2	0.370789
3	0.429329
4	0.490226
5	0.551503
6	0.610362
7	0.662204
8	0.715932
9	0.76615
10	0.814745
11	0.858385
12	0.898206
13	0.92877
14	0.956454
15	0.98112
16	1.00298
17	1.027414
18	1.045684
19	1.060684
20	1.081018
21	1.098603
22	1.11963
23	1.134952
24	1.146365
25	1.148439
26	1.150012
27	1.155081
28	1.156376
29	1.156839
30	1.155328
31	1.156969
32	1.153567
33	1.156898
34	1.154857
35	1.155527
36	1.153202
37	1.152195
38	1.153217
39	1.156903
40	1.157248
41	1.152326
42	1.148279
43	1.149056
44	1.150919
45	1.151042
46	1.138086
47	1.133334
48	1.13482
49	1.145669
50	1.153312
51	1.152435
52	1.154959
53	1.160104
54	1.163596
55	1.160079
56	1.151509
57	1.148332
58	1.149421
59	1.14969
60	1.145978
61	1.147104
62	1.147801
63	1.142037
64	1.135256
65	1.129002
66	1.130005
67	1.122668
68	1.118468
69	1.111896
70	1.101426
71	1.092927
72	1.084422
73	1.074619
74	1.068496
75	1.067631
76	1.052486
77	1.039549
78	1.037307
79	1.027811
80	1.013542
81	0.999429
82	0.993294
83	0.979405
84	0.967068
85	0.961209
86	0.953083
87	0.944037
88	0.925686
89	0.908569
90	0.88374
91	0.861947
92	0.840727
93	0.816941
94	0.786022
95	0.753451
96	0.719432
97	0.683224
98	0.649252
99	0.615979
100	0.570798