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659_bUW-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_bUW-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0020-3e501777
Published
May 21, 2026 1:03 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_bUW-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bUW-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 05:54:57 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
78807269468	78053649295	5463	71725273116	5096060718	1071082862	161227136	0	0	0	9017603	241295684	1155725	0.036025	0.963975	0	0.918923	0.065289	0.013722	0.002066	0.984212	0.9748	0	0.482696	0.552189	0.775682	0.825371			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.243553
1	0.279838
2	0.342751
3	0.411571
4	0.479491
5	0.552211
6	0.60822
7	0.656911
8	0.714154
9	0.766495
10	0.810052
11	0.851832
12	0.895972
13	0.937882
14	0.973731
15	1.005118
16	1.022823
17	1.044545
18	1.055179
19	1.068606
20	1.095603
21	1.116106
22	1.125561
23	1.134591
24	1.144932
25	1.146849
26	1.153404
27	1.153834
28	1.15655
29	1.157977
30	1.159744
31	1.157436
32	1.153298
33	1.155453
34	1.153196
35	1.160544
36	1.161288
37	1.158657
38	1.160704
39	1.160965
40	1.152397
41	1.151714
42	1.153459
43	1.16036
44	1.161171
45	1.173256
46	1.174028
47	1.175194
48	1.172031
49	1.172881
50	1.171811
51	1.1633
52	1.157945
53	1.154159
54	1.161506
55	1.16861
56	1.16741
57	1.16959
58	1.17089
59	1.157356
60	1.1479
61	1.149378
62	1.148569
63	1.144422
64	1.142493
65	1.144581
66	1.143275
67	1.138217
68	1.141392
69	1.138225
70	1.126713
71	1.115926
72	1.108215
73	1.1056
74	1.097652
75	1.087786
76	1.075098
77	1.051063
78	1.044974
79	1.037434
80	1.020136
81	1.008599
82	0.995733
83	0.983506
84	0.971129
85	0.954172
86	0.934938
87	0.915562
88	0.890601
89	0.868649
90	0.84697
91	0.825124
92	0.797524
93	0.765901
94	0.73573
95	0.702014
96	0.668815
97	0.63422
98	0.591401
99	0.553188
100	0.513576