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Filename
FFPE_V4_0001_RNA_0005_23KMKGLT4_11_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0001/B23KMKGLT4/nfcore_rnafusion_100M__5f1fa79--20260304-094520/QC/picard/FFPE_V4_0001_RNA_0005_23KMKGLT4_11_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0001R_5f1fa79
Published
Mar 09, 2026 12:02 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 FFPE_V4_0001_RNA_0005_23KMKGLT4_11.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_11_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: Mon Mar 09 17:59:22 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
25499659424	25201256278	10165	21895551729	2088270690	1073885337	143538357	0	0	0	1926085	77693853	329208	0.024191	0.975809	0	0.868828	0.082864	0.042612	0.005696	0.951692	0.940555	0	0.51171	0.575982	0.755254	0.851269			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.270342
1	0.309644
2	0.367576
3	0.434055
4	0.502571
5	0.569916
6	0.632717
7	0.694111
8	0.748638
9	0.800183
10	0.846594
11	0.89337
12	0.941313
13	0.984925
14	1.016594
15	1.043578
16	1.06187
17	1.076451
18	1.091364
19	1.110511
20	1.127448
21	1.145447
22	1.159825
23	1.169906
24	1.177845
25	1.181013
26	1.186366
27	1.191715
28	1.193658
29	1.192456
30	1.187819
31	1.184495
32	1.173408
33	1.170608
34	1.164869
35	1.163168
36	1.162227
37	1.153659
38	1.145259
39	1.14215
40	1.134519
41	1.131126
42	1.133913
43	1.13483
44	1.130045
45	1.138788
46	1.139089
47	1.13777
48	1.138368
49	1.145047
50	1.151259
51	1.147736
52	1.142755
53	1.141591
54	1.143025
55	1.143044
56	1.140041
57	1.137833
58	1.134472
59	1.126852
60	1.126365
61	1.133554
62	1.131753
63	1.1277
64	1.125967
65	1.126698
66	1.124478
67	1.121358
68	1.11479
69	1.106143
70	1.094526
71	1.085602
72	1.082552
73	1.072555
74	1.063403
75	1.055475
76	1.04367
77	1.024456
78	1.018923
79	1.011479
80	0.993494
81	0.974814
82	0.967598
83	0.953809
84	0.94207
85	0.937125
86	0.92436
87	0.908025
88	0.886463
89	0.867866
90	0.849909
91	0.828439
92	0.80635
93	0.779479
94	0.748249
95	0.717599
96	0.683413
97	0.648328
98	0.613192
99	0.572625
100	0.528335