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tih_rna_sample_00500_23LGNLLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/tih_rna_sample_00500_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0005_2cae617
Published
May 16, 2026 7:05 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_00500_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00500_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: Sat May 16 11:55:25 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
78170932282	77286681944	51605	65329702827	5835886079	5496304609	624736824	0	0	0	9826688	227821625	839861	0.04135	0.95865	0.000001	0.845291	0.07551	0.071116	0.008083	0.9208	0.910384	0	0.512857	0.557635	0.765496	0.837366			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.319532
1	0.353193
2	0.406609
3	0.469481
4	0.520631
5	0.568165
6	0.623626
7	0.682673
8	0.736785
9	0.787931
10	0.834358
11	0.877063
12	0.919903
13	0.954413
14	0.984429
15	1.01627
16	1.048443
17	1.073429
18	1.092466
19	1.103182
20	1.116877
21	1.132876
22	1.144941
23	1.16559
24	1.17054
25	1.17295
26	1.177342
27	1.178864
28	1.178349
29	1.172484
30	1.175084
31	1.169603
32	1.168341
33	1.17116
34	1.167849
35	1.171972
36	1.167862
37	1.161757
38	1.160201
39	1.160293
40	1.159537
41	1.158252
42	1.159723
43	1.168416
44	1.169979
45	1.175057
46	1.170538
47	1.175896
48	1.178502
49	1.178964
50	1.176022
51	1.173257
52	1.168972
53	1.165218
54	1.167865
55	1.164903
56	1.161135
57	1.153307
58	1.142453
59	1.133345
60	1.123668
61	1.123551
62	1.116944
63	1.115093
64	1.110373
65	1.104087
66	1.100204
67	1.088957
68	1.081399
69	1.079407
70	1.070834
71	1.062106
72	1.051535
73	1.044591
74	1.033396
75	1.02631
76	1.014303
77	1.005383
78	1.001299
79	0.994721
80	0.987937
81	0.978833
82	0.973381
83	0.956235
84	0.944119
85	0.934991
86	0.916544
87	0.900839
88	0.882839
89	0.865706
90	0.843706
91	0.820977
92	0.797364
93	0.770205
94	0.742464
95	0.717346
96	0.692641
97	0.667025
98	0.635613
99	0.60301
100	0.563479