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659_cfy-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_cfy-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 1:02 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_cfy-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cfy-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 05:55:54 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
77911922224	77171731373	2936	70668625383	4952332142	1345474319	205296593	0	0	0	14178736	233572837	1130056	0.05723	0.94277	0	0.915732	0.064173	0.017435	0.00266	0.979905	0.970595	0	0.511925	0.495948	0.708657	0.833555			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.267447
1	0.301139
2	0.348962
3	0.404847
4	0.467031
5	0.525171
6	0.580856
7	0.632389
8	0.687351
9	0.736033
10	0.779101
11	0.824135
12	0.874524
13	0.915138
14	0.938699
15	0.967991
16	1.003228
17	1.034564
18	1.056547
19	1.073938
20	1.093725
21	1.116577
22	1.135536
23	1.148623
24	1.158593
25	1.160278
26	1.162788
27	1.163839
28	1.173962
29	1.174113
30	1.177662
31	1.181642
32	1.176137
33	1.180146
34	1.179891
35	1.181537
36	1.18198
37	1.18508
38	1.19545
39	1.197478
40	1.199092
41	1.203686
42	1.208643
43	1.215968
44	1.217795
45	1.217681
46	1.213199
47	1.215203
48	1.213421
49	1.216145
50	1.216261
51	1.207963
52	1.204534
53	1.204113
54	1.206085
55	1.201787
56	1.193601
57	1.190897
58	1.183918
59	1.170791
60	1.169909
61	1.17237
62	1.175835
63	1.164953
64	1.15582
65	1.148407
66	1.147555
67	1.131544
68	1.126456
69	1.119447
70	1.111211
71	1.100907
72	1.094156
73	1.081092
74	1.065017
75	1.054139
76	1.042647
77	1.022819
78	1.012275
79	0.99562
80	0.979154
81	0.963103
82	0.946298
83	0.929172
84	0.913047
85	0.894374
86	0.87114
87	0.854919
88	0.838347
89	0.819135
90	0.805416
91	0.790905
92	0.769915
93	0.745659
94	0.718092
95	0.690535
96	0.663722
97	0.632563
98	0.597223
99	0.566201
100	0.529283