File Info

Filename
V4_0001_RNA_0005_23H5VFLT4_s33_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_s33_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0001_5f1fa79
Published
Mar 04, 2026 4:10 PM

Content

View in new tab 
## 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_s33.Aligned.sortedByCoord.out.bam --OUTPUT V4_0001_RNA_0005_23H5VFLT4_s33_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 23:06:17 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
26032826565	25735962334	38147	21031342665	2346111365	2091479058	266991099	0	0	0	1473853	73820134	370099	0.019575	0.980425	0.000001	0.817197	0.091161	0.081267	0.010374	0.908357	0.897999	0	0.490303	0.592072	0.759194	0.843587			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.267954
1	0.312028
2	0.37351
3	0.444359
4	0.515422
5	0.584245
6	0.649467
7	0.714893
8	0.770744
9	0.822444
10	0.866991
11	0.917205
12	0.963853
13	1.003465
14	1.031936
15	1.060442
16	1.078427
17	1.092642
18	1.110197
19	1.129332
20	1.141411
21	1.157776
22	1.166453
23	1.172417
24	1.180533
25	1.186469
26	1.189937
27	1.193772
28	1.190079
29	1.185435
30	1.180509
31	1.178519
32	1.172883
33	1.169367
34	1.166116
35	1.16534
36	1.163654
37	1.154999
38	1.149319
39	1.150236
40	1.148577
41	1.146481
42	1.14988
43	1.150899
44	1.150825
45	1.157857
46	1.157428
47	1.154774
48	1.153626
49	1.157521
50	1.164957
51	1.166284
52	1.163018
53	1.161119
54	1.161145
55	1.159858
56	1.151787
57	1.147152
58	1.139955
59	1.130511
60	1.127427
61	1.131225
62	1.126993
63	1.118583
64	1.114315
65	1.112331
66	1.109085
67	1.101562
68	1.092717
69	1.084523
70	1.072796
71	1.064356
72	1.061115
73	1.053517
74	1.046148
75	1.039142
76	1.024474
77	1.006548
78	1.004251
79	0.999268
80	0.982207
81	0.961625
82	0.950041
83	0.932347
84	0.919514
85	0.913011
86	0.899439
87	0.881776
88	0.861805
89	0.842554
90	0.827042
91	0.808289
92	0.786608
93	0.760026
94	0.729306
95	0.697795
96	0.667873
97	0.638056
98	0.606896
99	0.574625
100	0.533652