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tih_rna_sample_00136_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/tih_rna_sample_00136_B23WHTKLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 1:07 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_00136_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00136_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 06:02:02 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
68785090233	68088713683	2906	61121446187	4774396235	1934682613	258185742	0	0	0	7635132	209976582	991465	0.035086	0.964914	0	0.897674	0.07012	0.028414	0.003792	0.967794	0.957996	0	0.502709	0.490061	0.776776	0.709312			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.302083
1	0.339805
2	0.387198
3	0.441462
4	0.500633
5	0.5573
6	0.605565
7	0.645257
8	0.692065
9	0.734208
10	0.773565
11	0.810936
12	0.849652
13	0.886791
14	0.918431
15	0.947233
16	0.97047
17	0.988393
18	1.003985
19	1.017985
20	1.035236
21	1.052377
22	1.071726
23	1.086807
24	1.092603
25	1.100096
26	1.107535
27	1.113642
28	1.117785
29	1.11661
30	1.116392
31	1.123628
32	1.126118
33	1.13548
34	1.136501
35	1.142217
36	1.142817
37	1.139803
38	1.138621
39	1.135489
40	1.13204
41	1.150171
42	1.140316
43	1.141645
44	1.148823
45	1.152702
46	1.14551
47	1.150147
48	1.14672
49	1.144076
50	1.15192
51	1.154193
52	1.155085
53	1.156527
54	1.156369
55	1.161623
56	1.170733
57	1.170959
58	1.167378
59	1.162356
60	1.159336
61	1.158298
62	1.153264
63	1.145678
64	1.138923
65	1.130272
66	1.128034
67	1.126819
68	1.128332
69	1.122853
70	1.123051
71	1.12968
72	1.133213
73	1.136632
74	1.119838
75	1.111369
76	1.099459
77	1.088929
78	1.084427
79	1.073934
80	1.059941
81	1.048047
82	1.039336
83	1.027673
84	1.013133
85	0.994473
86	0.974013
87	0.96514
88	0.946779
89	0.926485
90	0.904966
91	0.87971
92	0.858117
93	0.829937
94	0.801315
95	0.772569
96	0.740627
97	0.70309
98	0.657501
99	0.616023
100	0.574945