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aih-tih-sc-38a0a3-R1_A23WJ53LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0019/A23WJ53LT4/nfcore_rnafusion__3e501777--20260519-110950/QC/picard/aih-tih-sc-38a0a3-R1_A23WJ53LT4_1_rna_metrics.txt
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dev_rna_exp0019_2-3e501777
Published
May 19, 2026 4:40 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-38a0a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-38a0a3-R1_A23WJ53LT4_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: Tue May 19 21:25:02 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
75878725273	75116782526	876	68708717130	4429949975	1804923439	173191106	0	0	0	6982266	242796225	1328753	0.027954	0.972046	0	0.914692	0.058974	0.024028	0.002306	0.973666	0.963889	0	0.51612	0.503479	0.703022	0.783482			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.290247
1	0.325503
2	0.373045
3	0.430941
4	0.486862
5	0.537719
6	0.592986
7	0.646189
8	0.703615
9	0.755237
10	0.800106
11	0.84669
12	0.892409
13	0.931146
14	0.965363
15	1.001614
16	1.02984
17	1.055194
18	1.072818
19	1.094258
20	1.11398
21	1.131562
22	1.147956
23	1.163031
24	1.175328
25	1.178145
26	1.174484
27	1.179069
28	1.185463
29	1.184111
30	1.183616
31	1.181021
32	1.172191
33	1.172215
34	1.167358
35	1.175089
36	1.175382
37	1.176061
38	1.176693
39	1.175882
40	1.16948
41	1.170728
42	1.176238
43	1.18607
44	1.188582
45	1.194957
46	1.18666
47	1.185602
48	1.183283
49	1.179245
50	1.181802
51	1.175287
52	1.165166
53	1.166654
54	1.170378
55	1.175077
56	1.173037
57	1.169207
58	1.159041
59	1.15166
60	1.142842
61	1.137744
62	1.141617
63	1.12981
64	1.128508
65	1.123815
66	1.117967
67	1.110226
68	1.107663
69	1.102377
70	1.092954
71	1.081938
72	1.075889
73	1.075142
74	1.066525
75	1.056854
76	1.049005
77	1.041783
78	1.035913
79	1.025666
80	1.010248
81	0.993306
82	0.979384
83	0.96325
84	0.94296
85	0.925974
86	0.905431
87	0.892617
88	0.871591
89	0.84932
90	0.827796
91	0.809198
92	0.780775
93	0.749225
94	0.720507
95	0.691708
96	0.663536
97	0.631326
98	0.595929
99	0.562551
100	0.529317