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Filename
FFPE_V4_0001_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/FFPE_V4_0001_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 6:05 PM

Content

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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_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_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 22:48:54 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
76622868748	75715249872	10966	66327913145	7054609989	2023681412	309034360	0	0	0	2943155	236211073	1579125	0.012307	0.987693	0	0.876018	0.093173	0.026728	0.004082	0.969191	0.95771	0	0.551954	0.581538	0.699391	0.9033			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.259136
1	0.302447
2	0.370295
3	0.44168
4	0.516013
5	0.594867
6	0.674094
7	0.742671
8	0.80423
9	0.8607
10	0.909582
11	0.961258
12	1.011681
13	1.059159
14	1.092837
15	1.119298
16	1.140316
17	1.153225
18	1.165141
19	1.180307
20	1.194844
21	1.210039
22	1.225481
23	1.234733
24	1.240614
25	1.242196
26	1.245885
27	1.250565
28	1.243524
29	1.23817
30	1.228674
31	1.220295
32	1.197847
33	1.19446
34	1.190504
35	1.191924
36	1.189749
37	1.175276
38	1.15987
39	1.157179
40	1.149651
41	1.147062
42	1.14792
43	1.149333
44	1.150289
45	1.160114
46	1.159205
47	1.155104
48	1.148532
49	1.149469
50	1.152039
51	1.150902
52	1.144653
53	1.144731
54	1.148217
55	1.148406
56	1.143757
57	1.138941
58	1.13118
59	1.125151
60	1.122737
61	1.122917
62	1.115594
63	1.103966
64	1.094172
65	1.086352
66	1.082021
67	1.076373
68	1.065579
69	1.055418
70	1.045381
71	1.035109
72	1.028957
73	1.017508
74	1.010287
75	0.999634
76	0.988787
77	0.968935
78	0.960874
79	0.956937
80	0.928128
81	0.907144
82	0.897729
83	0.885387
84	0.872732
85	0.86004
86	0.845898
87	0.842329
88	0.831332
89	0.812077
90	0.796165
91	0.774782
92	0.755734
93	0.733192
94	0.70632
95	0.674702
96	0.641379
97	0.607742
98	0.56967
99	0.532217
100	0.495696