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dna_s752_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_rna_exp0034/B2372Y3LT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/dna_s752_rna_metrics.txt
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2.8 KB
Workflow Run
cgp_rna_exp0034_2cae617
Published
May 16, 2026 7:17 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 dna_s752.Aligned.sortedByCoord.out.bam --OUTPUT dna_s752_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 11:55:14 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
86064659891	85045925238	18483837	32429491472	18907300768	29768913256	3921735905	0	0	0	92626617	91048761	6129783	0.504295	0.495705	0.000217	0.381317	0.222319	0.350033	0.046113	0.603636	0.596491	0	0.374129	0.861422	0.799278	1.02309			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.777289
1	0.833888
2	0.864345
3	0.874127
4	0.873538
5	0.877525
6	0.880614
7	0.882767
8	0.884302
9	0.887352
10	0.889075
11	0.890299
12	0.889236
13	0.895529
14	0.901115
15	0.906559
16	0.907181
17	0.91068
18	0.910732
19	0.919844
20	0.925947
21	0.925424
22	0.926126
23	0.929581
24	0.931971
25	0.940194
26	0.945853
27	0.944892
28	0.947555
29	0.955987
30	0.961922
31	0.96634
32	0.978125
33	0.981979
34	0.981519
35	0.976593
36	0.982957
37	0.988608
38	0.995401
39	1.007238
40	1.015671
41	1.02039
42	1.020145
43	1.024081
44	1.018222
45	1.018473
46	1.023486
47	1.02892
48	1.029295
49	1.027592
50	1.029089
51	1.031397
52	1.036849
53	1.034274
54	1.042744
55	1.045633
56	1.048935
57	1.054437
58	1.061894
59	1.064323
60	1.068299
61	1.072464
62	1.071182
63	1.07436
64	1.075258
65	1.075133
66	1.079655
67	1.082288
68	1.082989
69	1.080765
70	1.083322
71	1.087681
72	1.093922
73	1.102687
74	1.107957
75	1.111124
76	1.112442
77	1.107794
78	1.109884
79	1.113334
80	1.112872
81	1.108606
82	1.100828
83	1.098503
84	1.102079
85	1.098382
86	1.100028
87	1.092426
88	1.08233
89	1.073009
90	1.066481
91	1.058056
92	1.047052
93	1.03579
94	1.016596
95	0.988893
96	0.953494
97	0.915013
98	0.866318
99	0.800375
100	0.737479