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aih-tih-sc-2e5fe9-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-2e5fe9-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:10 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-2e5fe9-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2e5fe9-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 20:45:00 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
77385739606	76546169305	2218	68781351492	5629855427	1894645765	240314403	0	0	0	4808860	243540021	1441001	0.019363	0.980637	0	0.89856	0.073548	0.024752	0.003139	0.972109	0.961562	0	0.494207	0.611465	0.747605	0.934123			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.278901
1	0.323379
2	0.386652
3	0.460208
4	0.528783
5	0.594485
6	0.654106
7	0.714617
8	0.778182
9	0.827059
10	0.873964
11	0.919526
12	0.961902
13	0.998405
14	1.036825
15	1.061068
16	1.087749
17	1.110948
18	1.125583
19	1.146843
20	1.165186
21	1.185317
22	1.198422
23	1.207804
24	1.206078
25	1.199686
26	1.197978
27	1.195489
28	1.194987
29	1.193144
30	1.187423
31	1.184415
32	1.17635
33	1.174347
34	1.176194
35	1.17678
36	1.180235
37	1.178318
38	1.180008
39	1.177838
40	1.178818
41	1.178779
42	1.182149
43	1.179971
44	1.170835
45	1.177873
46	1.172524
47	1.168505
48	1.164466
49	1.167824
50	1.161979
51	1.155125
52	1.152539
53	1.148457
54	1.148384
55	1.146717
56	1.138481
57	1.133615
58	1.126307
59	1.111002
60	1.105099
61	1.102576
62	1.105482
63	1.104929
64	1.105896
65	1.108698
66	1.100445
67	1.087492
68	1.076773
69	1.06606
70	1.058102
71	1.050962
72	1.042142
73	1.032315
74	1.021917
75	1.012691
76	1.006157
77	0.992053
78	0.989208
79	0.982135
80	0.963209
81	0.949803
82	0.939692
83	0.926444
84	0.912598
85	0.900437
86	0.883222
87	0.868358
88	0.8485
89	0.829409
90	0.810407
91	0.791857
92	0.768977
93	0.742519
94	0.713797
95	0.686158
96	0.659505
97	0.636828
98	0.605549
99	0.575369
100	0.541623