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aih-tih-sc-49909d-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-49909d-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:42 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-49909d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-49909d-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 20:03:05 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
63552510665	62659742376	23934	56156450351	4469851654	1707955375	325461062	0	0	0	9015964	207893493	974048	0.041566	0.958434	0	0.896213	0.071335	0.027258	0.005194	0.967548	0.953956	0	0.625369	0.491596	0.670735	0.836157			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.240963
1	0.279889
2	0.339062
3	0.404899
4	0.469973
5	0.537049
6	0.599468
7	0.65591
8	0.718893
9	0.769251
10	0.812797
11	0.865438
12	0.915626
13	0.963601
14	1.004801
15	1.041811
16	1.063012
17	1.08706
18	1.100171
19	1.109001
20	1.125648
21	1.142914
22	1.15787
23	1.176441
24	1.181958
25	1.1889
26	1.196444
27	1.199827
28	1.209954
29	1.211073
30	1.200612
31	1.201028
32	1.198487
33	1.199217
34	1.19404
35	1.19346
36	1.191305
37	1.188591
38	1.185634
39	1.182246
40	1.170959
41	1.167091
42	1.168371
43	1.165483
44	1.160806
45	1.161823
46	1.152188
47	1.150806
48	1.145956
49	1.14248
50	1.144439
51	1.138191
52	1.125708
53	1.127057
54	1.128683
55	1.125607
56	1.124522
57	1.119513
58	1.115313
59	1.113719
60	1.120202
61	1.128206
62	1.134865
63	1.126363
64	1.117987
65	1.120393
66	1.122451
67	1.121667
68	1.121241
69	1.119429
70	1.109124
71	1.09479
72	1.094092
73	1.091653
74	1.084648
75	1.077209
76	1.06589
77	1.054899
78	1.03905
79	1.023286
80	1.009209
81	0.990279
82	0.976659
83	0.957565
84	0.941588
85	0.929131
86	0.907613
87	0.89641
88	0.880227
89	0.861752
90	0.841021
91	0.818568
92	0.794807
93	0.76613
94	0.729122
95	0.695377
96	0.661376
97	0.623911
98	0.582575
99	0.545695
100	0.504826