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aih-tih-sc-bbc28d-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-bbc28d-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:35 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-bbc28d-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-bbc28d-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 21:12:41 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
44925567191	44273932656	10216	38797730059	3897651982	1330891022	247649377	0	0	0	3879978	163329020	651757	0.023204	0.976796	0	0.876311	0.088035	0.03006	0.005594	0.964346	0.950358	0	0.58164	0.493559	0.74947	0.769421			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.242796
1	0.2799
2	0.330387
3	0.389282
4	0.452137
5	0.514285
6	0.576758
7	0.632761
8	0.689544
9	0.741277
10	0.785519
11	0.833261
12	0.887893
13	0.940239
14	0.976299
15	1.008755
16	1.031426
17	1.054011
18	1.068438
19	1.079357
20	1.088692
21	1.103005
22	1.116793
23	1.129257
24	1.131945
25	1.140189
26	1.137632
27	1.140113
28	1.147755
29	1.14511
30	1.143029
31	1.142764
32	1.138019
33	1.140225
34	1.128544
35	1.134719
36	1.138975
37	1.140536
38	1.146451
39	1.144894
40	1.139484
41	1.142605
42	1.151576
43	1.153675
44	1.157633
45	1.166714
46	1.169591
47	1.172767
48	1.16869
49	1.168723
50	1.172836
51	1.173786
52	1.163658
53	1.167007
54	1.173532
55	1.175522
56	1.171607
57	1.16382
58	1.152376
59	1.147507
60	1.139644
61	1.141064
62	1.14908
63	1.13852
64	1.144332
65	1.149159
66	1.141769
67	1.13347
68	1.132547
69	1.127489
70	1.11692
71	1.107744
72	1.109351
73	1.104949
74	1.09754
75	1.088877
76	1.081414
77	1.077993
78	1.0705
79	1.059247
80	1.049466
81	1.038728
82	1.026162
83	1.013157
84	0.99292
85	0.971749
86	0.952374
87	0.940342
88	0.921401
89	0.90958
90	0.886863
91	0.862101
92	0.833571
93	0.800849
94	0.764838
95	0.723899
96	0.682448
97	0.643686
98	0.600733
99	0.556561
100	0.516047