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659_bhK-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_bhK-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 1:56 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_bhK-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bhK-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 04:34:30 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
78562352925	77743573757	1692	70680091036	5201335263	1665882523	196263243	0	0	0	13013376	242379369	1112787	0.050954	0.949046	0	0.909144	0.066904	0.021428	0.002524	0.976048	0.965875	0	0.497735	0.503121	0.76502	0.720206			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.306717
1	0.341058
2	0.384659
3	0.433304
4	0.479189
5	0.523098
6	0.575654
7	0.62441
8	0.67057
9	0.714025
10	0.75803
11	0.805548
12	0.850411
13	0.89124
14	0.921237
15	0.945338
16	0.968034
17	0.99171
18	1.008816
19	1.026229
20	1.048585
21	1.071281
22	1.094015
23	1.103181
24	1.109877
25	1.111957
26	1.116717
27	1.12624
28	1.129425
29	1.130226
30	1.132867
31	1.136744
32	1.130556
33	1.137801
34	1.1409
35	1.150896
36	1.160504
37	1.1575
38	1.15928
39	1.160177
40	1.161461
41	1.162678
42	1.167604
43	1.176517
44	1.177586
45	1.184374
46	1.18097
47	1.180798
48	1.180327
49	1.183136
50	1.184905
51	1.179281
52	1.176952
53	1.177107
54	1.177921
55	1.177714
56	1.177525
57	1.178462
58	1.168815
59	1.164066
60	1.161126
61	1.163572
62	1.168589
63	1.161984
64	1.154143
65	1.150985
66	1.159218
67	1.159554
68	1.158515
69	1.150987
70	1.134617
71	1.122757
72	1.117068
73	1.109259
74	1.106579
75	1.100376
76	1.084042
77	1.067647
78	1.057227
79	1.042357
80	1.02886
81	1.016249
82	1.01233
83	0.999165
84	0.984279
85	0.966426
86	0.940506
87	0.923564
88	0.910258
89	0.891849
90	0.872843
91	0.84387
92	0.819584
93	0.797001
94	0.7672
95	0.738658
96	0.706544
97	0.680889
98	0.64529
99	0.607312
100	0.568544