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659_SP-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0009_exp0010/B23MHV2LT4/nfcore_rnafusion__04da504a--20260522-114016/QC/picard/659_SP-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp09_10-04da504a
Published
May 22, 2026 7:32 PM

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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_SP-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_SP-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: Sat May 23 00:22:48 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
74400899641	73526611225	16145	66377979727	5251385428	1679252332	217977593	0	0	0	10327404	237867503	1250514	0.04161	0.95839	0	0.902775	0.071422	0.022839	0.002965	0.974196	0.962749	0	0.545432	0.494231	0.802626	0.664211			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.2553
1	0.287625
2	0.332609
3	0.387467
4	0.447165
5	0.503447
6	0.559059
7	0.611239
8	0.659644
9	0.702751
10	0.746005
11	0.790691
12	0.836313
13	0.880131
14	0.908472
15	0.931005
16	0.951999
17	0.974888
18	0.98751
19	1.001405
20	1.01705
21	1.034122
22	1.051189
23	1.068026
24	1.06854
25	1.073563
26	1.082335
27	1.087248
28	1.102637
29	1.110265
30	1.114653
31	1.121986
32	1.126987
33	1.133628
34	1.134591
35	1.140543
36	1.144157
37	1.144373
38	1.145245
39	1.145499
40	1.147643
41	1.150887
42	1.151767
43	1.15679
44	1.163585
45	1.170576
46	1.176672
47	1.180785
48	1.175463
49	1.182383
50	1.198958
51	1.198144
52	1.19848
53	1.194017
54	1.190037
55	1.183971
56	1.181457
57	1.176459
58	1.170941
59	1.172727
60	1.175175
61	1.180462
62	1.179157
63	1.175143
64	1.167096
65	1.160271
66	1.152058
67	1.154897
68	1.155655
69	1.149132
70	1.141535
71	1.135306
72	1.127941
73	1.116204
74	1.111196
75	1.102141
76	1.091663
77	1.084112
78	1.074666
79	1.064205
80	1.052984
81	1.046076
82	1.039562
83	1.029505
84	1.016471
85	1.00143
86	0.978224
87	0.96515
88	0.955117
89	0.944189
90	0.926577
91	0.890856
92	0.868507
93	0.834409
94	0.79986
95	0.769656
96	0.736449
97	0.711588
98	0.673808
99	0.631139
100	0.586584