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659_cAd-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_cAd-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 1:10 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_cAd-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cAd-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 05:55:43 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
72832010982	71927995626	9564	65322854713	4780938104	1620180630	204012615	0	0	0	10501081	237442793	1097855	0.042353	0.957647	0	0.90817	0.066468	0.022525	0.002836	0.974638	0.962541	0	0.520676	0.500195	0.74946	0.756645			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.257281
1	0.29216
2	0.341072
3	0.396292
4	0.453429
5	0.507887
6	0.563676
7	0.615697
8	0.66932
9	0.722927
10	0.773618
11	0.824804
12	0.867184
13	0.904717
14	0.93831
15	0.968697
16	0.996648
17	1.024243
18	1.037857
19	1.049808
20	1.068186
21	1.08224
22	1.098687
23	1.106969
24	1.11556
25	1.120352
26	1.122881
27	1.131506
28	1.148075
29	1.150913
30	1.143823
31	1.143606
32	1.135965
33	1.152604
34	1.155513
35	1.164863
36	1.171259
37	1.176361
38	1.186079
39	1.18502
40	1.17476
41	1.175734
42	1.179577
43	1.185178
44	1.189064
45	1.198762
46	1.18913
47	1.186206
48	1.18549
49	1.186691
50	1.182756
51	1.172985
52	1.162636
53	1.162423
54	1.167125
55	1.171245
56	1.170035
57	1.172071
58	1.165957
59	1.161911
60	1.163695
61	1.166465
62	1.169193
63	1.165906
64	1.162452
65	1.159964
66	1.15847
67	1.153606
68	1.146994
69	1.139697
70	1.129687
71	1.115954
72	1.107317
73	1.096811
74	1.089177
75	1.080083
76	1.072938
77	1.064754
78	1.057467
79	1.047904
80	1.032033
81	1.017693
82	1.006831
83	0.992242
84	0.98148
85	0.958837
86	0.934051
87	0.921248
88	0.908752
89	0.894183
90	0.872668
91	0.838624
92	0.81499
93	0.787999
94	0.755888
95	0.721086
96	0.68302
97	0.65365
98	0.615447
99	0.576018
100	0.533084