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aih-tih-sc-f2fa3a-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-f2fa3a-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:49 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-f2fa3a-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f2fa3a-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 20:30:59 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
68404020237	67507963961	7200	62026764738	3705734863	1582759820	192697340	0	0	0	9672219	241115053	853103	0.038567	0.961433	0	0.918807	0.054893	0.023446	0.002854	0.9737	0.960945	0	0.565091	0.445184	0.74194	0.75557			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.261847
1	0.289112
2	0.329862
3	0.386745
4	0.439295
5	0.48266
6	0.536284
7	0.586358
8	0.642524
9	0.696505
10	0.748539
11	0.798675
12	0.850077
13	0.895027
14	0.932419
15	0.969075
16	0.99749
17	1.022705
18	1.041046
19	1.057608
20	1.074579
21	1.092794
22	1.11297
23	1.130616
24	1.136892
25	1.145314
26	1.150011
27	1.154739
28	1.163582
29	1.16833
30	1.16797
31	1.167991
32	1.16174
33	1.166854
34	1.166086
35	1.177451
36	1.181515
37	1.183719
38	1.18482
39	1.182885
40	1.181928
41	1.183519
42	1.191456
43	1.197439
44	1.201868
45	1.208543
46	1.205822
47	1.201163
48	1.197342
49	1.197781
50	1.190929
51	1.185175
52	1.178177
53	1.180714
54	1.186329
55	1.188521
56	1.192493
57	1.1922
58	1.180141
59	1.169411
60	1.157017
61	1.152719
62	1.151371
63	1.142067
64	1.144203
65	1.140857
66	1.129884
67	1.127537
68	1.125963
69	1.119213
70	1.110509
71	1.104619
72	1.096653
73	1.088571
74	1.08069
75	1.075011
76	1.068292
77	1.059973
78	1.060557
79	1.051901
80	1.03307
81	1.012507
82	0.996656
83	0.975583
84	0.957899
85	0.942024
86	0.925348
87	0.921971
88	0.908527
89	0.893904
90	0.874192
91	0.846756
92	0.819949
93	0.78718
94	0.752706
95	0.718379
96	0.682668
97	0.64713
98	0.61188
99	0.575602
100	0.539931