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aih-tih-sc-a9fe91-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-a9fe91-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:34 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-a9fe91-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-a9fe91-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 20:19:03 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
76830009100	76004877996	4134	68658851322	5199169662	1935669744	211183134	0	0	0	10448378	239456849	1182596	0.041809	0.958191	0	0.903348	0.068406	0.025468	0.002779	0.971754	0.961317	0	0.51732	0.598292	0.721876	0.908545			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.272358
1	0.319336
2	0.383486
3	0.463149
4	0.542679
5	0.612083
6	0.675881
7	0.736855
8	0.791053
9	0.841685
10	0.890024
11	0.932303
12	0.969628
13	1.014346
14	1.050085
15	1.068635
16	1.085131
17	1.104701
18	1.123264
19	1.13821
20	1.153954
21	1.16478
22	1.170368
23	1.180389
24	1.185514
25	1.183753
26	1.183879
27	1.181976
28	1.179298
29	1.174525
30	1.172432
31	1.175577
32	1.175548
33	1.179443
34	1.17815
35	1.177574
36	1.177326
37	1.177361
38	1.182539
39	1.181808
40	1.166249
41	1.162339
42	1.168945
43	1.174936
44	1.16955
45	1.173342
46	1.167099
47	1.165026
48	1.159625
49	1.153698
50	1.15189
51	1.142315
52	1.140242
53	1.145492
54	1.153165
55	1.155217
56	1.144635
57	1.138549
58	1.134746
59	1.122723
60	1.118841
61	1.11651
62	1.116827
63	1.110265
64	1.101918
65	1.099506
66	1.093848
67	1.084128
68	1.075506
69	1.068073
70	1.05892
71	1.049228
72	1.040305
73	1.030899
74	1.022286
75	1.014741
76	1.007509
77	0.996139
78	0.982978
79	0.972045
80	0.956105
81	0.946267
82	0.935687
83	0.927008
84	0.918195
85	0.903653
86	0.885948
87	0.873741
88	0.856454
89	0.836312
90	0.813832
91	0.801482
92	0.777083
93	0.751091
94	0.727312
95	0.700384
96	0.6746
97	0.645349
98	0.611468
99	0.579826
100	0.547125