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V4_0001_RNA_0005_23H5VFLT4_s19_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0001_exp003/B23H5VFLT4/nfcore_rnafusion__3e501777--20260519-101300/QC/picard/V4_0001_RNA_0005_23H5VFLT4_s19_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0001_exp003_3e501777
Published
May 19, 2026 4:27 PM

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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 V4_0001_RNA_0005_23H5VFLT4_s19.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s19_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: Tue May 19 20:55:20 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
78244813404	77242445887	81600	61606446174	7297601926	7311661987	1026654200	0	0	0	5382371	216152423	1056207	0.024296	0.975704	0.000001	0.797572	0.094477	0.094659	0.013291	0.892049	0.880621	0	0.499649	0.60914	0.755404	0.877468			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.282775
1	0.324028
2	0.384586
3	0.453125
4	0.522981
5	0.589052
6	0.653202
7	0.716531
8	0.774346
9	0.83
10	0.873781
11	0.918939
12	0.964784
13	1.008087
14	1.041131
15	1.067866
16	1.092777
17	1.110034
18	1.120244
19	1.133482
20	1.149833
21	1.163739
22	1.174445
23	1.182304
24	1.192591
25	1.198286
26	1.202731
27	1.205389
28	1.20305
29	1.201524
30	1.195022
31	1.193706
32	1.183258
33	1.182041
34	1.176703
35	1.174082
36	1.17085
37	1.162378
38	1.15545
39	1.154103
40	1.151428
41	1.149391
42	1.150025
43	1.150724
44	1.148108
45	1.151179
46	1.145192
47	1.140074
48	1.139066
49	1.140812
50	1.141719
51	1.138003
52	1.132197
53	1.131933
54	1.136155
55	1.135104
56	1.13072
57	1.126111
58	1.12321
59	1.117218
60	1.115235
61	1.118743
62	1.116322
63	1.110111
64	1.108133
65	1.104997
66	1.099749
67	1.094869
68	1.088148
69	1.079778
70	1.070011
71	1.062283
72	1.058663
73	1.050846
74	1.046095
75	1.039483
76	1.026439
77	1.009295
78	1.007313
79	0.998956
80	0.977774
81	0.957672
82	0.947514
83	0.930558
84	0.91902
85	0.912424
86	0.897804
87	0.884145
88	0.865462
89	0.849004
90	0.82998
91	0.807677
92	0.785847
93	0.760414
94	0.732998
95	0.705826
96	0.676064
97	0.643213
98	0.611387
99	0.576009
100	0.534452