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aih-tih-sc-3377ac-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-3377ac-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-3377ac-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-3377ac-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 20:17:54 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
70099568881	69277243238	6448	63382596531	3910755819	1703646217	280238223	0	0	0	12365931	241123050	973623	0.048783	0.951217	0	0.914912	0.056451	0.024592	0.004045	0.971363	0.959968	0	0.573858	0.517182	0.68926	0.839231			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.304646
1	0.33734
2	0.392815
3	0.458387
4	0.519527
5	0.57139
6	0.631091
7	0.689033
8	0.743736
9	0.796808
10	0.845335
11	0.895679
12	0.944559
13	0.987677
14	1.021547
15	1.052768
16	1.077675
17	1.096692
18	1.114892
19	1.129231
20	1.142253
21	1.156823
22	1.173963
23	1.18634
24	1.18931
25	1.194379
26	1.201128
27	1.207641
28	1.213727
29	1.209789
30	1.200609
31	1.192904
32	1.189396
33	1.184264
34	1.167883
35	1.164797
36	1.1653
37	1.160044
38	1.161399
39	1.161305
40	1.158724
41	1.153932
42	1.151938
43	1.153737
44	1.153637
45	1.160685
46	1.156961
47	1.157535
48	1.152639
49	1.153209
50	1.148532
51	1.149217
52	1.150187
53	1.148378
54	1.149465
55	1.145531
56	1.145633
57	1.13655
58	1.131788
59	1.12234
60	1.116449
61	1.115412
62	1.106974
63	1.097468
64	1.102861
65	1.107896
66	1.101193
67	1.092368
68	1.08295
69	1.075301
70	1.068056
71	1.058078
72	1.052307
73	1.047907
74	1.041784
75	1.038762
76	1.029795
77	1.019323
78	1.009592
79	1.000905
80	0.989082
81	0.979362
82	0.970578
83	0.959488
84	0.948862
85	0.93585
86	0.913763
87	0.904885
88	0.888075
89	0.870456
90	0.841073
91	0.812628
92	0.779257
93	0.749896
94	0.720049
95	0.689209
96	0.66014
97	0.626069
98	0.587818
99	0.55016
100	0.514352