File Info

Filename
659_djb-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0009_exp0010/B23MHV2LT4/nfcore_rnafusion__04da504a--20260522-114016/QC/picard/659_djb-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp09_10-04da504a
Published
May 22, 2026 5:31 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 659_djb-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_djb-T1-TRNA-1_B23MHV2LT4_1_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: Fri May 22 22:11:24 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
72409376550	71571042174	8870	65306069487	4635088922	1431824670	198050225	0	0	0	12324019	234648112	1169978	0.0499	0.9501	0	0.912465	0.064762	0.020006	0.002767	0.977227	0.965913	0	0.595445	0.444946	0.735994	0.668648			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.272717
1	0.300595
2	0.344146
3	0.404033
4	0.457078
5	0.50355
6	0.553586
7	0.595029
8	0.649235
9	0.688731
10	0.724841
11	0.765885
12	0.823997
13	0.879515
14	0.92302
15	0.96053
16	0.989178
17	1.011865
18	1.025647
19	1.041095
20	1.058493
21	1.077312
22	1.096563
23	1.102581
24	1.111078
25	1.118721
26	1.12812
27	1.135131
28	1.147507
29	1.157242
30	1.167993
31	1.170521
32	1.167338
33	1.171433
34	1.16377
35	1.163428
36	1.156353
37	1.154123
38	1.151277
39	1.141682
40	1.136288
41	1.13879
42	1.145091
43	1.139767
44	1.137494
45	1.142457
46	1.146862
47	1.156712
48	1.160132
49	1.161837
50	1.171723
51	1.173347
52	1.171528
53	1.167459
54	1.17644
55	1.180252
56	1.178143
57	1.178831
58	1.165959
59	1.155157
60	1.15663
61	1.164165
62	1.165326
63	1.159782
64	1.151597
65	1.144002
66	1.134455
67	1.131972
68	1.129327
69	1.129525
70	1.126331
71	1.120343
72	1.115305
73	1.112894
74	1.111063
75	1.109693
76	1.106164
77	1.0996
78	1.096984
79	1.088573
80	1.074558
81	1.061623
82	1.045011
83	1.024772
84	1.012927
85	0.99623
86	0.971321
87	0.95793
88	0.940264
89	0.918287
90	0.896889
91	0.865379
92	0.843201
93	0.815012
94	0.78694
95	0.750318
96	0.710681
97	0.668766
98	0.624607
99	0.576926
100	0.528063