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tih_rna_sample_00121_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_00121_B23WHTKLT4_2_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 1:02 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_00121_B23WHTKLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00121_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 05:43:04 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
77526248970	76707832116	3454	69240864606	5091134189	2148360858	227469009	0	0	0	6110430	242926248	1084712	0.024536	0.975464	0	0.902657	0.06637	0.028007	0.002965	0.969028	0.958798	0	0.501041	0.518258	0.753563	0.778687			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.319506
1	0.351654
2	0.402163
3	0.458743
4	0.503026
5	0.544951
6	0.602317
7	0.654067
8	0.702629
9	0.750695
10	0.798477
11	0.845264
12	0.887921
13	0.926761
14	0.959841
15	0.988329
16	1.013669
17	1.03263
18	1.050527
19	1.06896
20	1.084422
21	1.097238
22	1.114795
23	1.129354
24	1.139277
25	1.143524
26	1.147963
27	1.152747
28	1.158989
29	1.160548
30	1.16582
31	1.170925
32	1.171543
33	1.179249
34	1.180277
35	1.187234
36	1.188899
37	1.187101
38	1.191089
39	1.186996
40	1.183879
41	1.177761
42	1.178302
43	1.185146
44	1.181533
45	1.185832
46	1.184394
47	1.17976
48	1.173671
49	1.171504
50	1.159193
51	1.154311
52	1.1479
53	1.151315
54	1.149299
55	1.145583
56	1.145497
57	1.143657
58	1.137398
59	1.134757
60	1.128652
61	1.127657
62	1.127684
63	1.123718
64	1.118278
65	1.116513
66	1.114053
67	1.113672
68	1.115076
69	1.108055
70	1.098346
71	1.09114
72	1.084017
73	1.075862
74	1.074817
75	1.070505
76	1.061941
77	1.049704
78	1.043634
79	1.032142
80	1.01586
81	1.003792
82	0.994647
83	0.979048
84	0.965487
85	0.948823
86	0.924555
87	0.910533
88	0.891617
89	0.873588
90	0.852826
91	0.828803
92	0.804691
93	0.777225
94	0.750107
95	0.7223
96	0.689905
97	0.654217
98	0.618907
99	0.585196
100	0.551154