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Filename
FFPE_V4_0001_RNA_0005_23KMKGLT4_28_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0004/B23KMKGLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/FFPE_V4_0001_RNA_0005_23KMKGLT4_28_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0004_2cae617
Published
May 16, 2026 5:53 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_28.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_28_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: Sat May 16 09:51:45 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
73043660986	72232198988	37119	62462572046	5910806854	3449194727	409588242	0	0	0	5433492	224992031	974130	0.02358	0.97642	0.000001	0.864747	0.081831	0.047751	0.00567	0.946578	0.936062	0	0.512788	0.565187	0.769119	0.8325			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.278909
1	0.316987
2	0.370632
3	0.429338
4	0.491768
5	0.554641
6	0.617996
7	0.677684
8	0.727661
9	0.777617
10	0.819765
11	0.864148
12	0.913316
13	0.951795
14	0.979872
15	1.00407
16	1.027206
17	1.04362
18	1.064038
19	1.080378
20	1.091717
21	1.11041
22	1.124413
23	1.136077
24	1.143373
25	1.147729
26	1.156684
27	1.166146
28	1.169697
29	1.168318
30	1.165774
31	1.166441
32	1.158103
33	1.156733
34	1.152787
35	1.154457
36	1.155126
37	1.148191
38	1.141859
39	1.140342
40	1.132991
41	1.133501
42	1.138967
43	1.142971
44	1.142669
45	1.148764
46	1.148982
47	1.148391
48	1.148256
49	1.154238
50	1.160403
51	1.157785
52	1.154471
53	1.155624
54	1.1559
55	1.15726
56	1.15663
57	1.157314
58	1.154948
59	1.152851
60	1.154162
61	1.157366
62	1.154261
63	1.148325
64	1.147545
65	1.146129
66	1.143903
67	1.138946
68	1.130801
69	1.123774
70	1.113754
71	1.105268
72	1.100986
73	1.091418
74	1.086249
75	1.079174
76	1.065813
77	1.049143
78	1.041028
79	1.030601
80	1.009949
81	0.992983
82	0.987201
83	0.972299
84	0.957898
85	0.951214
86	0.938533
87	0.921856
88	0.902824
89	0.884268
90	0.860887
91	0.837189
92	0.812996
93	0.783461
94	0.750534
95	0.716695
96	0.680004
97	0.643932
98	0.608414
99	0.571343
100	0.527119