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tih_rna_sample_00332_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_00332_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0005_5f1fa79
Published
Mar 09, 2026 6:38 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_00332_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00332_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 00:46:51 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
22543462467	21862661683	157258	19360138431	1135240087	1097346689	269779218	0	0	0	2084426	79403819	262931	0.025579	0.974421	0.000007	0.885534	0.051926	0.050193	0.01234	0.93746	0.90915	0	0.856116	0.412001	0.370942	0.913076			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.371164
1	0.408975
2	0.464328
3	0.536838
4	0.609299
5	0.6736
6	0.736493
7	0.802065
8	0.864001
9	0.914854
10	0.97812
11	1.066387
12	1.131403
13	1.176609
14	1.205199
15	1.217125
16	1.213581
17	1.215403
18	1.201966
19	1.205048
20	1.220886
21	1.228271
22	1.25085
23	1.266263
24	1.27669
25	1.285636
26	1.292975
27	1.301379
28	1.302933
29	1.299169
30	1.292922
31	1.294064
32	1.28945
33	1.275572
34	1.255088
35	1.249825
36	1.246546
37	1.226068
38	1.213047
39	1.19895
40	1.197851
41	1.200867
42	1.208561
43	1.218145
44	1.223325
45	1.210614
46	1.199769
47	1.198556
48	1.185145
49	1.16695
50	1.141007
51	1.144287
52	1.146892
53	1.144672
54	1.146401
55	1.1412
56	1.131477
57	1.106762
58	1.093405
59	1.07161
60	1.056491
61	1.059719
62	1.053731
63	1.031956
64	1.014578
65	1.002289
66	0.990681
67	0.98601
68	0.980171
69	0.97277
70	0.954511
71	0.936749
72	0.929685
73	0.926148
74	0.925683
75	0.909189
76	0.897271
77	0.891804
78	0.886012
79	0.86568
80	0.858375
81	0.852269
82	0.852229
83	0.842643
84	0.826153
85	0.811111
86	0.789004
87	0.773866
88	0.755698
89	0.7384
90	0.723978
91	0.705706
92	0.683163
93	0.655716
94	0.628355
95	0.60173
96	0.57483
97	0.548083
98	0.514495
99	0.483786
100	0.450863