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Filename
22Rv1_FFPE_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0011/B23LG7FLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0011-2cae617
Published
May 16, 2026 1:54 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 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3_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 08:40:16 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
2783493764	2656532186	287432	2132599602	236291649	233795966	53557537	0	0	0	1051056	8841250	72271	0.10625	0.89375	0.000108	0.802776	0.088947	0.088008	0.020161	0.891723	0.85105	0	0.84501	0.33767	0.429097	0.542658			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.346115
1	0.385099
2	0.444356
3	0.506786
4	0.571284
5	0.644299
6	0.712896
7	0.7846
8	0.851349
9	0.906349
10	0.937696
11	0.968439
12	1.002592
13	1.0336
14	1.061555
15	1.068016
16	1.076085
17	1.068767
18	1.068878
19	1.075212
20	1.085802
21	1.103306
22	1.117909
23	1.133375
24	1.139429
25	1.146958
26	1.153062
27	1.165615
28	1.1848
29	1.189459
30	1.198642
31	1.197124
32	1.196318
33	1.208692
34	1.192772
35	1.195618
36	1.200848
37	1.190612
38	1.180619
39	1.164591
40	1.158835
41	1.157133
42	1.160995
43	1.166972
44	1.171696
45	1.17476
46	1.178643
47	1.195773
48	1.195579
49	1.18741
50	1.168279
51	1.158374
52	1.152649
53	1.147318
54	1.147638
55	1.147762
56	1.139395
57	1.130511
58	1.120862
59	1.102633
60	1.107952
61	1.111297
62	1.101203
63	1.090963
64	1.092295
65	1.089472
66	1.093877
67	1.0837
68	1.075856
69	1.073416
70	1.063371
71	1.043198
72	1.043781
73	1.050447
74	1.049965
75	1.038728
76	1.030074
77	1.023122
78	1.004969
79	0.988657
80	0.979884
81	0.966139
82	0.936219
83	0.922781
84	0.91281
85	0.901568
86	0.883265
87	0.869952
88	0.849792
89	0.833242
90	0.812667
91	0.787805
92	0.742163
93	0.697292
94	0.666826
95	0.643108
96	0.618857
97	0.587605
98	0.55443
99	0.521034
100	0.518339