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dna_s747_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_s747_rna_metrics.txt
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2.8 KB
Workflow Run
cgp_rna_exp0034_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 dna_s747.Aligned.sortedByCoord.out.bam --OUTPUT dna_s747_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 09:54:35 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
86152477358	85075077602	19176394	31413073030	19117070031	30560181843	3965576304	0	0	0	90255466	88887700	6842545	0.503818	0.496182	0.000225	0.369239	0.224708	0.359214	0.046613	0.593948	0.58652	0	0.37248	0.858715	0.813744	1.00639			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.778332
1	0.834824
2	0.864761
3	0.875311
4	0.874304
5	0.875385
6	0.878064
7	0.879993
8	0.882929
9	0.888614
10	0.891879
11	0.895769
12	0.892611
13	0.899555
14	0.903511
15	0.909178
16	0.909415
17	0.91249
18	0.911906
19	0.9198
20	0.924201
21	0.922216
22	0.921844
23	0.927111
24	0.927441
25	0.934058
26	0.939543
27	0.939679
28	0.938867
29	0.945328
30	0.950373
31	0.954098
32	0.960474
33	0.963857
34	0.962255
35	0.961706
36	0.964817
37	0.967038
38	0.97083
39	0.979886
40	0.98722
41	0.995503
42	0.998248
43	1.002589
44	1.005336
45	1.007365
46	1.013889
47	1.020356
48	1.020578
49	1.019912
50	1.022425
51	1.026625
52	1.033666
53	1.031469
54	1.040537
55	1.04534
56	1.050647
57	1.059717
58	1.067958
59	1.073228
60	1.081185
61	1.08646
62	1.084217
63	1.088282
64	1.088831
65	1.087139
66	1.090476
67	1.093453
68	1.093406
69	1.090716
70	1.091707
71	1.096078
72	1.102692
73	1.112143
74	1.117606
75	1.118452
76	1.119912
77	1.11706
78	1.116256
79	1.117183
80	1.115794
81	1.110552
82	1.104949
83	1.105876
84	1.108708
85	1.105757
86	1.107008
87	1.099616
88	1.090776
89	1.082736
90	1.077523
91	1.068134
92	1.056718
93	1.043127
94	1.024012
95	0.998318
96	0.963489
97	0.925621
98	0.877512
99	0.812627
100	0.75019