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tih_rna_sample_00417_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_00417_23LGNLLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0002_5f1fa79
Published
Mar 09, 2026 2:20 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_00417_23LGNLLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00417_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 20:02:46 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
24614957118	24260844106	73471	20869294037	1649694416	1545495959	196286223	0	0	0	3606529	75306386	537879	0.045703	0.954297	0.000003	0.860205	0.067998	0.063703	0.008091	0.928203	0.91485	0	0.521029	0.461885	0.787292	0.677182			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.322391
1	0.355751
2	0.398473
3	0.447234
4	0.484007
5	0.516379
6	0.568175
7	0.61402
8	0.659467
9	0.702328
10	0.742585
11	0.775808
12	0.809043
13	0.84455
14	0.873711
15	0.907672
16	0.930574
17	0.958492
18	0.980916
19	0.995825
20	1.008621
21	1.022377
22	1.041796
23	1.058542
24	1.06892
25	1.078091
26	1.087355
27	1.100545
28	1.107243
29	1.104702
30	1.111486
31	1.114029
32	1.117717
33	1.122981
34	1.124266
35	1.131811
36	1.143506
37	1.146911
38	1.151728
39	1.147302
40	1.142801
41	1.142625
42	1.147812
43	1.154825
44	1.161165
45	1.167489
46	1.175393
47	1.177952
48	1.176515
49	1.177804
50	1.17807
51	1.175938
52	1.177435
53	1.173378
54	1.172388
55	1.164292
56	1.15805
57	1.159044
58	1.153013
59	1.145334
60	1.14478
61	1.149438
62	1.149692
63	1.147433
64	1.147531
65	1.145109
66	1.143256
67	1.138004
68	1.131418
69	1.132882
70	1.130177
71	1.123993
72	1.118424
73	1.113523
74	1.105466
75	1.102926
76	1.097299
77	1.090682
78	1.085471
79	1.076718
80	1.070879
81	1.065788
82	1.053574
83	1.038375
84	1.033806
85	1.021621
86	1.004932
87	0.998094
88	0.981555
89	0.961549
90	0.940022
91	0.919536
92	0.885548
93	0.851628
94	0.824055
95	0.794454
96	0.760261
97	0.724976
98	0.687374
99	0.649996
100	0.605056