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Filename
786-O_FFPE_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/786-O_FFPE_RNA_0001_B23LG7FLT4_3_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:45 PM

Content

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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 786-O_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT 786-O_FFPE_RNA_0001_B23LG7FLT4_3_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: Thu May 28 22:29:51 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
74964079438	74079971155	59028	65474369033	5040942730	3074463386	490136978	0	0	0	6531206	231369619	1417014	0.027453	0.972547	0.000001	0.883834	0.068047	0.041502	0.006616	0.951881	0.940655	0	0.509273	0.578141	0.764816	0.855336			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.297736
1	0.331188
2	0.379438
3	0.436639
4	0.500038
5	0.561304
6	0.61818
7	0.675906
8	0.739715
9	0.804117
10	0.862205
11	0.919808
12	0.964654
13	1.002184
14	1.032229
15	1.053745
16	1.07288
17	1.097847
18	1.116062
19	1.134007
20	1.152822
21	1.171361
22	1.181655
23	1.192083
24	1.196881
25	1.193484
26	1.187563
27	1.18394
28	1.182724
29	1.177007
30	1.174966
31	1.181281
32	1.181988
33	1.180152
34	1.172985
35	1.171946
36	1.169153
37	1.161215
38	1.157221
39	1.155115
40	1.15503
41	1.158589
42	1.161375
43	1.159891
44	1.157449
45	1.166694
46	1.157979
47	1.156878
48	1.156025
49	1.154576
50	1.152926
51	1.150658
52	1.144114
53	1.136061
54	1.135961
55	1.135876
56	1.130668
57	1.1242
58	1.11862
59	1.11364
60	1.106086
61	1.107889
62	1.112487
63	1.110696
64	1.107122
65	1.104306
66	1.09972
67	1.096019
68	1.085825
69	1.080308
70	1.074263
71	1.064024
72	1.057376
73	1.049317
74	1.04111
75	1.034145
76	1.022546
77	1.01352
78	1.012612
79	1.001177
80	0.986403
81	0.975871
82	0.966282
83	0.946697
84	0.934436
85	0.922526
86	0.907263
87	0.892613
88	0.874626
89	0.857329
90	0.837414
91	0.814167
92	0.79211
93	0.767742
94	0.739822
95	0.709998
96	0.68125
97	0.658039
98	0.629745
99	0.598449
100	0.560268