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dna_s718_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_s718_rna_metrics.txt
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2.8 KB
Workflow Run
cgp_rna_exp0034_2cae617
Published
May 16, 2026 6:18 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_s718.Aligned.sortedByCoord.out.bam --OUTPUT dna_s718_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 09:51:28 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
83108301774	81981296824	18472683	35425706561	16993432984	25759055052	3784629544	0	0	0	97892052	97584925	4972631	0.500786	0.499214	0.000225	0.432119	0.207284	0.314206	0.046165	0.639404	0.630733	0	0.436675	0.96417	0.766128	1.166788			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.882063
1	0.950574
2	0.989146
3	1.001513
4	1.00384
5	1.0051
6	1.009981
7	1.013252
8	1.016659
9	1.0153
10	1.009582
11	1.012978
12	1.007324
13	1.008189
14	1.00745
15	1.017029
16	1.021914
17	1.021644
18	1.022932
19	1.028664
20	1.030157
21	1.026585
22	1.027339
23	1.02725
24	1.02713
25	1.024902
26	1.020876
27	1.019247
28	1.010808
29	1.0042
30	1.003117
31	1.006602
32	1.012164
33	1.013189
34	1.011334
35	1.00558
36	0.998976
37	0.991741
38	0.990323
39	1.000337
40	1.005142
41	1.013423
42	1.01583
43	1.014932
44	1.011724
45	1.010647
46	1.011753
47	1.01293
48	1.009578
49	1.006481
50	1.008175
51	1.009793
52	1.011071
53	1.006374
54	1.008947
55	1.003826
56	1.002275
57	1.006731
58	1.015938
59	1.024412
60	1.03571
61	1.040926
62	1.040157
63	1.043622
64	1.043008
65	1.045767
66	1.050071
67	1.045395
68	1.041221
69	1.031672
70	1.027545
71	1.022693
72	1.022324
73	1.027465
74	1.028151
75	1.032182
76	1.036756
77	1.032124
78	1.021651
79	1.016568
80	1.013237
81	1.005253
82	0.9959
83	0.996557
84	1.003777
85	1.005283
86	1.007427
87	0.995489
88	0.979907
89	0.970995
90	0.967439
91	0.961569
92	0.956345
93	0.947412
94	0.932615
95	0.912152
96	0.883652
97	0.846219
98	0.800482
99	0.746057
100	0.694804