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aih-tih-sc-13a2f6-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-13a2f6-R1_B23WHYVLT4_1_rna_metrics.txt
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dev_rna_exp0018_2-fd1be10
Published
May 14, 2026 5:49 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-13a2f6-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-13a2f6-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 23:51:45 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
22519672807	22145912641	6070	20080912231	1360900826	627099113	76994401	0	0	0	2965540	78951744	513249	0.036202	0.963798	0	0.906755	0.061452	0.028317	0.003477	0.968206	0.952137	0	0.637354	0.402024	0.723733	0.516415			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.27785
1	0.302331
2	0.342509
3	0.397111
4	0.443588
5	0.481719
6	0.529636
7	0.569513
8	0.621567
9	0.674765
10	0.720151
11	0.766781
12	0.819244
13	0.862864
14	0.896957
15	0.923463
16	0.947788
17	0.972941
18	0.991332
19	1.009156
20	1.026415
21	1.043089
22	1.055437
23	1.06662
24	1.071988
25	1.082543
26	1.084257
27	1.087913
28	1.101819
29	1.106151
30	1.106056
31	1.115783
32	1.124449
33	1.133057
34	1.131766
35	1.130491
36	1.134316
37	1.137941
38	1.142925
39	1.140531
40	1.136201
41	1.139712
42	1.147332
43	1.147682
44	1.14499
45	1.154987
46	1.159026
47	1.171633
48	1.173592
49	1.179314
50	1.207347
51	1.215797
52	1.222857
53	1.225203
54	1.229003
55	1.221289
56	1.21523
57	1.199066
58	1.180899
59	1.173563
60	1.17282
61	1.166507
62	1.163633
63	1.156919
64	1.157903
65	1.158343
66	1.149538
67	1.144801
68	1.142764
69	1.138352
70	1.129349
71	1.126027
72	1.124558
73	1.123979
74	1.123289
75	1.123122
76	1.119155
77	1.111098
78	1.101718
79	1.089059
80	1.078213
81	1.069526
82	1.059567
83	1.046794
84	1.034689
85	1.014192
86	0.98933
87	0.984892
88	0.973787
89	0.96426
90	0.943615
91	0.911308
92	0.881929
93	0.842519
94	0.806089
95	0.767128
96	0.721258
97	0.686621
98	0.635601
99	0.583292
100	0.535164