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tih_rna_sample_00017_23LGNLLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0002/A23LGNLLT4/nfcore_rnafusion_100M__5f1fa79--20260304-095416/QC/picard/tih_rna_sample_00017_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0002_5f1fa79
Published
Mar 09, 2026 2:52 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_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: Mon Mar 09 20:52:27 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
24655534298	24334650059	10238	21202985817	1565211123	1428765513	137677368	0	0	0	2633393	76627972	394311	0.033224	0.966776	0	0.871308	0.06432	0.058713	0.005658	0.935629	0.923452	0	0.560298	0.497138	0.716533	0.795325			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.309023
1	0.350665
2	0.406424
3	0.471416
4	0.526505
5	0.574439
6	0.630868
7	0.681753
8	0.739219
9	0.799067
10	0.846385
11	0.888517
12	0.932971
13	0.971564
14	1.007438
15	1.032171
16	1.053029
17	1.075431
18	1.085211
19	1.083466
20	1.091411
21	1.106556
22	1.120874
23	1.137625
24	1.145653
25	1.153846
26	1.156654
27	1.160495
28	1.172837
29	1.182844
30	1.185207
31	1.179101
32	1.174665
33	1.184582
34	1.19098
35	1.203819
36	1.212703
37	1.211175
38	1.205266
39	1.196718
40	1.191872
41	1.193582
42	1.194472
43	1.194743
44	1.195952
45	1.190859
46	1.180634
47	1.178079
48	1.173808
49	1.175576
50	1.170412
51	1.160728
52	1.156384
53	1.151966
54	1.158563
55	1.154106
56	1.153951
57	1.14757
58	1.140137
59	1.132251
60	1.128125
61	1.130226
62	1.12489
63	1.117604
64	1.113189
65	1.103293
66	1.089586
67	1.08056
68	1.070506
69	1.067647
70	1.0587
71	1.047668
72	1.044277
73	1.036269
74	1.02197
75	1.016651
76	1.004432
77	0.99935
78	0.993207
79	0.976036
80	0.968444
81	0.960253
82	0.95386
83	0.944305
84	0.933656
85	0.927524
86	0.919874
87	0.909113
88	0.891088
89	0.868637
90	0.842456
91	0.817449
92	0.795115
93	0.768368
94	0.741501
95	0.712035
96	0.679721
97	0.64582
98	0.613514
99	0.580416
100	0.545894