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tih_rna_sample_00087_B23WHTKLT4_2_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/tih_rna_sample_00087_B23WHTKLT4_2_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 2:44 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 tih_rna_sample_00087_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00087_B23WHTKLT4_2_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 07:12:06 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
77224640282	76429489988	4353	68849098877	5197970752	2087012327	295403679	0	0	0	9299406	236710813	1200645	0.037801	0.962199	0	0.900819	0.06801	0.027306	0.003865	0.968829	0.958853	0	0.49129	0.526627	0.781139	0.775157			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.297791
1	0.332938
2	0.378914
3	0.435985
4	0.495588
5	0.55786
6	0.613197
7	0.659905
8	0.7127
9	0.772259
10	0.818252
11	0.850982
12	0.889544
13	0.925878
14	0.951719
15	0.976578
16	0.997292
17	1.018989
18	1.034236
19	1.048393
20	1.068186
21	1.090855
22	1.103392
23	1.115824
24	1.126761
25	1.136504
26	1.145316
27	1.148273
28	1.152276
29	1.157059
30	1.156222
31	1.155738
32	1.160704
33	1.164442
34	1.15667
35	1.160234
36	1.162127
37	1.155633
38	1.158713
39	1.156342
40	1.148484
41	1.147575
42	1.146305
43	1.149837
44	1.153359
45	1.152244
46	1.145667
47	1.152651
48	1.157473
49	1.161725
50	1.172874
51	1.178337
52	1.184755
53	1.18705
54	1.187076
55	1.186457
56	1.184645
57	1.172634
58	1.165727
59	1.1644
60	1.162421
61	1.161084
62	1.154826
63	1.144301
64	1.136406
65	1.126211
66	1.115266
67	1.106664
68	1.101762
69	1.093425
70	1.081886
71	1.077744
72	1.073356
73	1.073533
74	1.072977
75	1.062262
76	1.052274
77	1.046968
78	1.048776
79	1.037923
80	1.022403
81	1.009957
82	1.000145
83	0.988814
84	0.979817
85	0.961102
86	0.945079
87	0.93381
88	0.9157
89	0.893477
90	0.868752
91	0.844472
92	0.823742
93	0.798742
94	0.76837
95	0.735107
96	0.703068
97	0.669724
98	0.633477
99	0.597048
100	0.557437