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tih_rna_sample_00015_23KKJ7LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0006/A23KKJ7LT4/nfcore_rnafusion_100M__5f1fa79--20260304-101508/QC/picard/tih_rna_sample_00015_23KKJ7LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0006-5f1fa79
Published
Mar 05, 2026 4:15 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_00015_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00015_23KKJ7LT4_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 Mar 05 23:00:12 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
26855693716	26425279843	41966	16786228719	2811426278	6210483707	617099173	0	0	0	2329558	60665541	324190	0.03698	0.96302	0.000002	0.635234	0.106392	0.235021	0.023353	0.741625	0.729739	0	0.489514	0.551237	0.754716	0.870883			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.312726
1	0.351219
2	0.404999
3	0.468834
4	0.526288
5	0.578354
6	0.641086
7	0.698059
8	0.759175
9	0.818802
10	0.869097
11	0.918036
12	0.966236
13	1.008169
14	1.038531
15	1.057847
16	1.08007
17	1.102704
18	1.113661
19	1.114978
20	1.116657
21	1.123209
22	1.13448
23	1.145529
24	1.152884
25	1.156792
26	1.153817
27	1.150353
28	1.151951
29	1.153756
30	1.163061
31	1.165837
32	1.172168
33	1.175886
34	1.177008
35	1.180249
36	1.180517
37	1.174137
38	1.17183
39	1.168024
40	1.164481
41	1.164897
42	1.169984
43	1.173802
44	1.175591
45	1.177649
46	1.174438
47	1.172573
48	1.167444
49	1.165852
50	1.163955
51	1.157059
52	1.153123
53	1.149897
54	1.149358
55	1.143816
56	1.135831
57	1.121191
58	1.111748
59	1.097457
60	1.089381
61	1.08718
62	1.084705
63	1.075372
64	1.065923
65	1.062095
66	1.061946
67	1.060144
68	1.059471
69	1.057515
70	1.052047
71	1.04455
72	1.046494
73	1.048074
74	1.048097
75	1.041587
76	1.034506
77	1.028812
78	1.031203
79	1.018431
80	1.006512
81	0.994303
82	0.983144
83	0.96713
84	0.958119
85	0.940851
86	0.918924
87	0.905621
88	0.890698
89	0.868677
90	0.843279
91	0.821739
92	0.795693
93	0.769757
94	0.745076
95	0.720207
96	0.695391
97	0.668975
98	0.638968
99	0.606956
100	0.569962