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aih-tih-sc-6cc13c-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-6cc13c-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-6cc13c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-6cc13c-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 20:17:08 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
71883143209	71060260778	4464	64396524449	4353455926	2046933034	263342905	0	0	0	11059742	243220325	1030424	0.043494	0.956506	0	0.906224	0.061264	0.028806	0.003706	0.967488	0.956413	0	0.538611	0.510681	0.735357	0.754116			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.296688
1	0.33196
2	0.375156
3	0.430918
4	0.482666
5	0.531531
6	0.592743
7	0.648215
8	0.702667
9	0.751414
10	0.79595
11	0.839392
12	0.880111
13	0.913522
14	0.948981
15	0.983401
16	1.013131
17	1.040663
18	1.062389
19	1.082681
20	1.10152
21	1.120985
22	1.135477
23	1.147841
24	1.15855
25	1.163083
26	1.168468
27	1.172304
28	1.1693
29	1.166367
30	1.172326
31	1.177413
32	1.169268
33	1.168755
34	1.158194
35	1.161206
36	1.164575
37	1.161912
38	1.156874
39	1.153057
40	1.15084
41	1.15399
42	1.151615
43	1.153628
44	1.152438
45	1.166949
46	1.169809
47	1.173916
48	1.170274
49	1.167252
50	1.168566
51	1.163141
52	1.153751
53	1.155172
54	1.160558
55	1.154629
56	1.153217
57	1.149266
58	1.140798
59	1.133765
60	1.125946
61	1.127176
62	1.129462
63	1.123565
64	1.126853
65	1.134096
66	1.135936
67	1.131439
68	1.130726
69	1.126468
70	1.11604
71	1.111452
72	1.103354
73	1.094862
74	1.088312
75	1.077706
76	1.05958
77	1.040269
78	1.032131
79	1.022476
80	1.011131
81	1.002402
82	0.99284
83	0.980884
84	0.967229
85	0.953604
86	0.935744
87	0.924166
88	0.903612
89	0.885954
90	0.869197
91	0.846538
92	0.816978
93	0.785436
94	0.754095
95	0.728099
96	0.697562
97	0.658364
98	0.617222
99	0.577068
100	0.532044