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aih-tih-sc-18a6f2-R1_B23WHYVLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0018/B23WHYVLT4/nfcore_rnafusion__fd1be10--20260514-142812/QC/picard/aih-tih-sc-18a6f2-R1_B23WHYVLT4_1_rna_metrics.txt
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dev_rna_exp0018_2-fd1be10
Published
May 14, 2026 5:57 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-18a6f2-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-18a6f2-R1_B23WHYVLT4_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: Thu May 14 23:46:52 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
22771144359	22463543452	3572	20272386910	1462712214	657863766	70576990	0	0	0	4186183	78402066	474262	0.050687	0.949313	0	0.902457	0.065115	0.029286	0.003142	0.967572	0.954502	0	0.632901	0.406362	0.709795	0.604216			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.274456
1	0.301319
2	0.342016
3	0.395097
4	0.435618
5	0.475151
6	0.527931
7	0.573689
8	0.617995
9	0.660768
10	0.708351
11	0.754951
12	0.809882
13	0.854807
14	0.890403
15	0.926392
16	0.955217
17	0.97489
18	0.986535
19	0.997937
20	1.015028
21	1.032739
22	1.054408
23	1.06879
24	1.076223
25	1.08455
26	1.091891
27	1.106469
28	1.128852
29	1.136325
30	1.136524
31	1.144927
32	1.145499
33	1.156898
34	1.158491
35	1.164101
36	1.177846
37	1.179291
38	1.178792
39	1.169529
40	1.165324
41	1.170103
42	1.176848
43	1.181327
44	1.181523
45	1.178991
46	1.174646
47	1.179948
48	1.179967
49	1.184515
50	1.200426
51	1.200159
52	1.195819
53	1.195416
54	1.192166
55	1.186062
56	1.188839
57	1.182791
58	1.176755
59	1.171596
60	1.169964
61	1.173714
62	1.183428
63	1.183015
64	1.185142
65	1.181445
66	1.169454
67	1.158978
68	1.153607
69	1.150187
70	1.141975
71	1.134065
72	1.130597
73	1.12049
74	1.119195
75	1.111817
76	1.098071
77	1.087499
78	1.081619
79	1.066002
80	1.053797
81	1.046788
82	1.038409
83	1.023471
84	1.008433
85	0.992312
86	0.972616
87	0.962112
88	0.947689
89	0.930676
90	0.909784
91	0.878763
92	0.852013
93	0.817031
94	0.782693
95	0.749205
96	0.712401
97	0.673956
98	0.635131
99	0.593557
100	0.551986