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tih_rna_sample_00322_23LGNLLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion_100M__5f1fa79--20260304-095416/QC/picard/tih_rna_sample_00322_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0005_5f1fa79
Published
Mar 09, 2026 6:23 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 tih_rna_sample_00322_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00322_23LGNLLT4_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: Tue Mar 10 00:24:58 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
24250715759	22404880454	37461	19293065310	1828995614	1045782357	236999712	0	0	0	1338807	72584472	255795	0.018111	0.981889	0.000002	0.86111	0.081634	0.046677	0.010578	0.942744	0.870987	0	0.669312	0.514792	0.518067	1.000894			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.330709
1	0.374874
2	0.447096
3	0.524575
4	0.593528
5	0.656289
6	0.716059
7	0.765784
8	0.819095
9	0.867529
10	0.917929
11	0.959746
12	1.005521
13	1.047757
14	1.07139
15	1.099098
16	1.123741
17	1.140384
18	1.139589
19	1.137146
20	1.149234
21	1.168893
22	1.183737
23	1.194126
24	1.202395
25	1.209707
26	1.217505
27	1.221974
28	1.234466
29	1.244059
30	1.240418
31	1.228964
32	1.22137
33	1.219884
34	1.210194
35	1.210132
36	1.207666
37	1.203999
38	1.202811
39	1.189059
40	1.183829
41	1.182804
42	1.18831
43	1.188535
44	1.183773
45	1.177558
46	1.166132
47	1.162681
48	1.153127
49	1.156933
50	1.150537
51	1.14497
52	1.140521
53	1.132651
54	1.133929
55	1.124701
56	1.118798
57	1.116415
58	1.113637
59	1.111027
60	1.110159
61	1.115023
62	1.112885
63	1.100755
64	1.0917
65	1.088248
66	1.076697
67	1.06503
68	1.059816
69	1.057783
70	1.042204
71	1.030393
72	1.028939
73	1.018828
74	1.017282
75	0.999158
76	0.988607
77	0.97282
78	0.961091
79	0.943845
80	0.934128
81	0.918816
82	0.907518
83	0.888771
84	0.87647
85	0.866571
86	0.849645
87	0.828163
88	0.802688
89	0.779342
90	0.759612
91	0.736765
92	0.721341
93	0.698092
94	0.67311
95	0.648019
96	0.619038
97	0.588699
98	0.556516
99	0.525473
100	0.488837