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tih_rna_sample_00017_23LGNLLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0005/A23LGNLLT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/tih_rna_sample_00017_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0005_2cae617
Published
May 16, 2026 6:14 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_00017_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00017_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 09:56:39 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
73970472418	73075685157	42481	63692412472	4694688806	4283299164	405242234	0	0	0	7936354	230357244	1146101	0.033305	0.966695	0.000001	0.871595	0.064244	0.058615	0.005546	0.935839	0.924519	0	0.563415	0.490799	0.716277	0.815545			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.309331
1	0.350661
2	0.405313
3	0.470784
4	0.5245
5	0.571921
6	0.627512
7	0.67952
8	0.734979
9	0.79318
10	0.839625
11	0.879953
12	0.923706
13	0.962981
14	0.998156
15	1.025319
16	1.047898
17	1.06956
18	1.079074
19	1.075601
20	1.081993
21	1.099826
22	1.115774
23	1.133006
24	1.14173
25	1.150512
26	1.155572
27	1.161058
28	1.175812
29	1.186739
30	1.190246
31	1.184739
32	1.18159
33	1.193844
34	1.199593
35	1.210092
36	1.21578
37	1.212709
38	1.207205
39	1.197493
40	1.193288
41	1.194952
42	1.196398
43	1.198088
44	1.19909
45	1.193631
46	1.182972
47	1.178837
48	1.174345
49	1.175018
50	1.170164
51	1.161233
52	1.155893
53	1.151187
54	1.154899
55	1.150605
56	1.151432
57	1.146718
58	1.138306
59	1.130011
60	1.125134
61	1.126169
62	1.120564
63	1.113572
64	1.110309
65	1.10141
66	1.086964
67	1.078968
68	1.069346
69	1.066623
70	1.057993
71	1.048117
72	1.044739
73	1.037954
74	1.025594
75	1.021499
76	1.009767
77	1.003821
78	0.997091
79	0.980642
80	0.972358
81	0.963154
82	0.956181
83	0.944688
84	0.931913
85	0.924087
86	0.917486
87	0.908951
88	0.893113
89	0.872155
90	0.85062
91	0.828126
92	0.805667
93	0.780256
94	0.747582
95	0.71594
96	0.684217
97	0.649364
98	0.615483
99	0.582192
100	0.547706