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aih-tih-sc-573e21-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-573e21-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:35 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-573e21-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-573e21-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 20:16:01 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
74386384789	73585410287	3006	67173945680	4530258303	1583915502	297287796	0	0	0	5555287	247141186	1306585	0.021984	0.978016	0	0.91287	0.061565	0.021525	0.00404	0.974435	0.963943	0	0.555486	0.563273	0.679313	0.935212			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.312419
1	0.351427
2	0.407847
3	0.477668
4	0.541188
5	0.599003
6	0.65688
7	0.710086
8	0.77249
9	0.824149
10	0.876895
11	0.929539
12	0.982104
13	1.024836
14	1.054915
15	1.073353
16	1.097001
17	1.123817
18	1.138444
19	1.155971
20	1.170466
21	1.182282
22	1.195089
23	1.205406
24	1.212223
25	1.213477
26	1.215463
27	1.214444
28	1.215527
29	1.218416
30	1.2099
31	1.199478
32	1.183589
33	1.181714
34	1.178796
35	1.179622
36	1.177567
37	1.178696
38	1.185695
39	1.186718
40	1.190117
41	1.190455
42	1.198091
43	1.202715
44	1.195799
45	1.197703
46	1.1901
47	1.187047
48	1.178234
49	1.175733
50	1.16197
51	1.156512
52	1.14653
53	1.141939
54	1.136405
55	1.133987
56	1.127771
57	1.122576
58	1.11885
59	1.111516
60	1.10679
61	1.10827
62	1.113019
63	1.096039
64	1.091038
65	1.084771
66	1.07883
67	1.065833
68	1.057965
69	1.051762
70	1.043735
71	1.035459
72	1.031811
73	1.023705
74	1.013125
75	1.001661
76	0.995824
77	0.986473
78	0.982652
79	0.97612
80	0.96312
81	0.950487
82	0.938688
83	0.928283
84	0.915508
85	0.901481
86	0.87669
87	0.858625
88	0.836189
89	0.815045
90	0.796078
91	0.778967
92	0.749151
93	0.718824
94	0.68676
95	0.658772
96	0.635301
97	0.609788
98	0.577313
99	0.546777
100	0.510124