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Filename
FFPE_HD789_01_RNA_0002_23LGNLLT4_2_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0002/A23LGNLLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/FFPE_HD789_01_RNA_0002_23LGNLLT4_2_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0002_2cae617
Published
May 16, 2026 6:14 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_HD789_01_RNA_0002_23LGNLLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD789_01_RNA_0002_23LGNLLT4_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: Sat May 16 11:07:53 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
79814166998	79047181752	45972	69858616072	5509859239	3226173857	452486612	0	0	0	8804807	233618542	1507568	0.03632	0.96368	0.000001	0.883758	0.069703	0.040813	0.005724	0.953462	0.944299	0	0.492724	0.643044	0.737748	0.969256			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.294169
1	0.334939
2	0.387927
3	0.45386
4	0.527969
5	0.59481
6	0.659831
7	0.723822
8	0.786744
9	0.842494
10	0.888409
11	0.937541
12	0.987649
13	1.027586
14	1.062553
15	1.091456
16	1.125002
17	1.151637
18	1.162733
19	1.174131
20	1.193237
21	1.212421
22	1.222837
23	1.233061
24	1.231288
25	1.227044
26	1.226055
27	1.222231
28	1.219715
29	1.212178
30	1.204425
31	1.200848
32	1.201154
33	1.198832
34	1.195751
35	1.194725
36	1.188089
37	1.179536
38	1.170094
39	1.161664
40	1.160485
41	1.1614
42	1.157743
43	1.161143
44	1.157378
45	1.150152
46	1.13898
47	1.134572
48	1.131259
49	1.131239
50	1.126391
51	1.124657
52	1.123672
53	1.123113
54	1.12775
55	1.123913
56	1.112821
57	1.112932
58	1.108254
59	1.099716
60	1.095473
61	1.092437
62	1.093583
63	1.095162
64	1.087042
65	1.082981
66	1.0886
67	1.083167
68	1.075373
69	1.072085
70	1.063643
71	1.053793
72	1.048905
73	1.036518
74	1.026201
75	1.017565
76	1.007924
77	0.993267
78	0.98598
79	0.974207
80	0.957482
81	0.940342
82	0.931018
83	0.913045
84	0.896142
85	0.885433
86	0.870749
87	0.859022
88	0.84252
89	0.824574
90	0.810137
91	0.787869
92	0.765822
93	0.740595
94	0.711893
95	0.68584
96	0.661201
97	0.632374
98	0.60147
99	0.574559
100	0.538822