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Filename
V4_0001_RNA_0005_23H5VFLT4_s29_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0001/B23H5VFLT4/nfcore_rnafusion_100M__5f1fa79--20260304-093157/QC/picard/V4_0001_RNA_0005_23H5VFLT4_s29_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0001_5f1fa79
Published
Mar 04, 2026 3:26 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_s29.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s29_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: Wed Mar 04 22:22:12 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
25181496782	24811993967	48078	19472178789	2354854144	2633869463	351043493	0	0	0	2549979	69566692	340251	0.035359	0.964641	0.000002	0.784789	0.094908	0.106153	0.014148	0.879697	0.866789	0	0.517823	0.564636	0.740129	0.84844			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.297338
1	0.337638
2	0.40071
3	0.467302
4	0.533924
5	0.598589
6	0.662273
7	0.721159
8	0.771705
9	0.823792
10	0.863685
11	0.905661
12	0.949533
13	0.987741
14	1.018341
15	1.047094
16	1.070474
17	1.087719
18	1.093561
19	1.106921
20	1.125567
21	1.142682
22	1.159196
23	1.170173
24	1.180568
25	1.184365
26	1.187494
27	1.190797
28	1.192506
29	1.191229
30	1.186691
31	1.186624
32	1.177192
33	1.176355
34	1.169082
35	1.166272
36	1.165328
37	1.156164
38	1.147942
39	1.141552
40	1.134645
41	1.134898
42	1.135939
43	1.13555
44	1.134778
45	1.139246
46	1.136425
47	1.13358
48	1.13644
49	1.137792
50	1.140447
51	1.138069
52	1.134769
53	1.134942
54	1.134982
55	1.135072
56	1.137426
57	1.134426
58	1.131958
59	1.128497
60	1.129981
61	1.136101
62	1.134183
63	1.129515
64	1.128387
65	1.128529
66	1.121357
67	1.114867
68	1.103516
69	1.093789
70	1.082286
71	1.074652
72	1.072234
73	1.063303
74	1.059138
75	1.050145
76	1.038539
77	1.025339
78	1.018027
79	1.005634
80	0.985944
81	0.964182
82	0.953775
83	0.939331
84	0.927796
85	0.920855
86	0.904945
87	0.887111
88	0.86586
89	0.847685
90	0.827866
91	0.808854
92	0.791104
93	0.768359
94	0.742971
95	0.716175
96	0.684815
97	0.650397
98	0.615294
99	0.577806
100	0.534238