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aih-tih-sc-ffabe0-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-ffabe0-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:39 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-ffabe0-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ffabe0-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 20:19:57 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
71106528555	70238701174	5292	63204324011	4714445221	2087254039	232672611	0	0	0	7992283	240975439	1040131	0.032102	0.967898	0	0.89985	0.06712	0.029717	0.003313	0.966971	0.955169	0	0.530911	0.454591	0.759698	0.724733			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.294114
1	0.325595
2	0.3781
3	0.437855
4	0.483336
5	0.521943
6	0.576405
7	0.623063
8	0.671727
9	0.714862
10	0.75396
11	0.803114
12	0.849295
13	0.886615
14	0.918211
15	0.948888
16	0.976524
17	1.002092
18	1.025834
19	1.042684
20	1.057235
21	1.072124
22	1.084556
23	1.09908
24	1.104484
25	1.112807
26	1.11927
27	1.122495
28	1.130514
29	1.129986
30	1.132648
31	1.132208
32	1.132961
33	1.139058
34	1.136378
35	1.143872
36	1.147372
37	1.146616
38	1.145962
39	1.144969
40	1.143819
41	1.140818
42	1.153018
43	1.163234
44	1.169615
45	1.172746
46	1.173103
47	1.178026
48	1.17656
49	1.178276
50	1.178835
51	1.181664
52	1.178693
53	1.177668
54	1.177376
55	1.175924
56	1.176636
57	1.171
58	1.163637
59	1.156179
60	1.150561
61	1.153544
62	1.155215
63	1.147215
64	1.148984
65	1.150309
66	1.144492
67	1.141622
68	1.144897
69	1.146035
70	1.136255
71	1.129414
72	1.122134
73	1.115289
74	1.109898
75	1.105044
76	1.094666
77	1.084102
78	1.078672
79	1.065811
80	1.052056
81	1.037314
82	1.025028
83	1.00489
84	0.988371
85	0.973195
86	0.953225
87	0.945076
88	0.928793
89	0.913059
90	0.887575
91	0.866039
92	0.842993
93	0.812297
94	0.779737
95	0.745272
96	0.70673
97	0.668861
98	0.628738
99	0.58806
100	0.550145