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aih-tih-sc-714733-R1_A23YTGFLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/aih-tih-sc-714733-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:39 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 aih-tih-sc-714733-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-714733-R1_A23YTGFLT4_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: Wed Jun 03 20:18:58 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
75463016653	74601377104	6978	67195666590	4929848750	2201861234	273993552	0	0	0	4000994	246181882	1107309	0.015992	0.984008	0	0.90073	0.066083	0.029515	0.003673	0.966812	0.955773	0	0.532342	0.489822	0.755242	0.754463			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.29683
1	0.329503
2	0.374337
3	0.428139
4	0.476682
5	0.525947
6	0.584671
7	0.639521
8	0.694172
9	0.744887
10	0.789861
11	0.833334
12	0.878094
13	0.921498
14	0.951365
15	0.976508
16	1.006889
17	1.032413
18	1.048479
19	1.065833
20	1.08667
21	1.106361
22	1.128049
23	1.143437
24	1.149887
25	1.155116
26	1.158264
27	1.162592
28	1.170305
29	1.172006
30	1.176513
31	1.182486
32	1.18362
33	1.183425
34	1.180653
35	1.187842
36	1.19635
37	1.193583
38	1.192905
39	1.182953
40	1.179929
41	1.178456
42	1.176073
43	1.180764
44	1.175887
45	1.176903
46	1.174399
47	1.169305
48	1.168558
49	1.167345
50	1.166994
51	1.168861
52	1.169374
53	1.16797
54	1.16225
55	1.158361
56	1.151843
57	1.147501
58	1.137339
59	1.128635
60	1.125685
61	1.129642
62	1.138096
63	1.130306
64	1.135476
65	1.138677
66	1.141855
67	1.138436
68	1.134476
69	1.122271
70	1.105524
71	1.089345
72	1.084702
73	1.083675
74	1.073628
75	1.063339
76	1.053414
77	1.044209
78	1.037123
79	1.023828
80	1.010132
81	0.993609
82	0.981313
83	0.970232
84	0.961135
85	0.947427
86	0.925766
87	0.915656
88	0.898299
89	0.87745
90	0.852812
91	0.838961
92	0.813882
93	0.780018
94	0.743829
95	0.712674
96	0.681916
97	0.649155
98	0.61297
99	0.578856
100	0.541531