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aih-tih-sc-f6bb6f-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-f6bb6f-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:12 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-f6bb6f-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f6bb6f-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 20:58:57 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
75128524142	74295933928	4452	67608879278	4518755816	1963951791	204342591	0	0	0	5607162	244473617	1102430	0.022421	0.977579	0	0.909994	0.060821	0.026434	0.00275	0.970815	0.960057	0	0.518934	0.523164	0.740822	0.819322			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.278904
1	0.313679
2	0.369097
3	0.432495
4	0.490045
5	0.553627
6	0.616902
7	0.677186
8	0.738258
9	0.794421
10	0.839815
11	0.884039
12	0.928177
13	0.959239
14	0.994129
15	1.017274
16	1.047912
17	1.07236
18	1.082573
19	1.090757
20	1.099635
21	1.11294
22	1.125309
23	1.13914
24	1.140145
25	1.145438
26	1.147599
27	1.152469
28	1.160137
29	1.158457
30	1.163163
31	1.162598
32	1.160075
33	1.164944
34	1.160956
35	1.1699
36	1.180402
37	1.174771
38	1.168571
39	1.163186
40	1.163659
41	1.168393
42	1.170762
43	1.171547
44	1.170384
45	1.179117
46	1.181243
47	1.184167
48	1.185355
49	1.189144
50	1.191034
51	1.183374
52	1.175032
53	1.169002
54	1.169193
55	1.166564
56	1.166409
57	1.163809
58	1.158434
59	1.153954
60	1.150418
61	1.143765
62	1.145458
63	1.140517
64	1.139447
65	1.143049
66	1.136936
67	1.128581
68	1.11875
69	1.110832
70	1.093431
71	1.086043
72	1.075618
73	1.06535
74	1.055636
75	1.049524
76	1.037494
77	1.02347
78	1.022831
79	1.012065
80	0.996329
81	0.982872
82	0.972269
83	0.956152
84	0.938064
85	0.922735
86	0.899816
87	0.88871
88	0.871395
89	0.850924
90	0.831646
91	0.81225
92	0.78775
93	0.758325
94	0.726223
95	0.697504
96	0.665473
97	0.635611
98	0.60037
99	0.569943
100	0.529125