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659_bNS-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0020/B23WHTKLT4/nfcore_rnafusion__3e501777--20260520-120107/QC/picard/659_bNS-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 1:16 AM

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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 659_bNS-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bNS-T1-TRNA-1_B23WHTKLT4_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: Thu May 21 05:55:53 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
77780834907	76944862038	2102	69864793821	5296016435	1590957792	193091888	0	0	0	12413275	234356351	1196408	0.050303	0.949697	0	0.907985	0.068829	0.020677	0.002509	0.976814	0.966315	0	0.523102	0.545896	0.725479	0.87614			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.265289
1	0.298852
2	0.34497
3	0.405315
4	0.471654
5	0.538253
6	0.596028
7	0.650879
8	0.709349
9	0.758114
10	0.80361
11	0.858504
12	0.918621
13	0.968322
14	0.996315
15	1.029313
16	1.055315
17	1.076286
18	1.098627
19	1.114652
20	1.125846
21	1.142101
22	1.157919
23	1.168031
24	1.170703
25	1.174801
26	1.176997
27	1.180681
28	1.187687
29	1.185889
30	1.181998
31	1.176532
32	1.167983
33	1.168671
34	1.160685
35	1.168438
36	1.17004
37	1.169677
38	1.17072
39	1.16974
40	1.167606
41	1.168434
42	1.180892
43	1.196445
44	1.199228
45	1.210771
46	1.213758
47	1.210313
48	1.204516
49	1.204636
50	1.203087
51	1.199038
52	1.192093
53	1.188431
54	1.185662
55	1.178962
56	1.170349
57	1.168556
58	1.159557
59	1.149499
60	1.143766
61	1.140468
62	1.144119
63	1.13497
64	1.126792
65	1.127016
66	1.122199
67	1.122528
68	1.120262
69	1.110192
70	1.093994
71	1.081106
72	1.072617
73	1.059512
74	1.042503
75	1.035622
76	1.025096
77	1.011183
78	1.006728
79	0.999439
80	0.983415
81	0.970318
82	0.96265
83	0.949155
84	0.92975
85	0.914054
86	0.892289
87	0.876179
88	0.8544
89	0.835607
90	0.818938
91	0.79857
92	0.775327
93	0.748353
94	0.7191
95	0.691123
96	0.659659
97	0.622855
98	0.585154
99	0.548952
100	0.512793