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aih-tih-sc-a03f86-R1_B23WHYVLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0018/B23WHYVLT4/nfcore_rnafusion__fd1be10--20260514-142812/QC/picard/aih-tih-sc-a03f86-R1_B23WHYVLT4_1_rna_metrics.txt
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dev_rna_exp0018_2-fd1be10
Published
May 14, 2026 5:48 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-a03f86-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-a03f86-R1_B23WHYVLT4_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: Thu May 14 23:37:22 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
25806220289	25527022435	1120	23110442862	1586159088	747838952	82580413	0	0	0	1419846	81669872	582274	0.017088	0.982912	0	0.905332	0.062136	0.029296	0.003235	0.967469	0.957002	0	0.552111	0.504728	0.738715	0.754985			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.298369
1	0.328856
2	0.369065
3	0.421198
4	0.467938
5	0.512926
6	0.570449
7	0.620325
8	0.667165
9	0.712448
10	0.756635
11	0.802113
12	0.846669
13	0.8855
14	0.91733
15	0.946148
16	0.96929
17	0.991003
18	1.009734
19	1.026719
20	1.043359
21	1.065268
22	1.088758
23	1.113214
24	1.126936
25	1.13466
26	1.141681
27	1.149174
28	1.159841
29	1.166005
30	1.173331
31	1.176829
32	1.179798
33	1.189266
34	1.184153
35	1.184808
36	1.188778
37	1.185064
38	1.187287
39	1.181052
40	1.179099
41	1.180858
42	1.184585
43	1.194683
44	1.197719
45	1.210044
46	1.211678
47	1.214048
48	1.208176
49	1.210545
50	1.208959
51	1.203707
52	1.198012
53	1.190776
54	1.187056
55	1.175227
56	1.17025
57	1.165059
58	1.159255
59	1.148427
60	1.139431
61	1.141889
62	1.143872
63	1.143381
64	1.147495
65	1.15167
66	1.138692
67	1.120564
68	1.115403
69	1.109851
70	1.098268
71	1.088251
72	1.083007
73	1.081778
74	1.079331
75	1.076913
76	1.059708
77	1.044962
78	1.04163
79	1.031972
80	1.023081
81	1.010713
82	0.994723
83	0.983067
84	0.972494
85	0.962073
86	0.942982
87	0.929263
88	0.909971
89	0.894051
90	0.871153
91	0.845256
92	0.815681
93	0.778592
94	0.74747
95	0.720527
96	0.689714
97	0.660503
98	0.623779
99	0.583214
100	0.543511