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aih-tih-sc-ac6a71-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__2cae617--20260515-145204/QC/picard/aih-tih-sc-ac6a71-R1_B23WHYVLT4_1_rna_metrics.txt
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dev_rna_exp0018_2-2cae617
Published
May 16, 2026 7:27 AM

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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-ac6a71-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-ac6a71-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: Sat May 16 11:54:46 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
76846636706	76032998083	2688	69074102806	4750532748	2027155745	181204096	0	0	0	2925007	245104235	1712165	0.011793	0.988207	0	0.908475	0.06248	0.026662	0.002383	0.970955	0.960675	0	0.55424	0.505195	0.719647	0.778602			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.276796
1	0.309741
2	0.364181
3	0.429276
4	0.479583
5	0.527644
6	0.586792
7	0.637674
8	0.682584
9	0.731137
10	0.781103
11	0.829979
12	0.882204
13	0.923302
14	0.961838
15	0.993798
16	1.021453
17	1.0399
18	1.06361
19	1.083664
20	1.104534
21	1.123108
22	1.138641
23	1.155457
24	1.158413
25	1.161977
26	1.168458
27	1.176909
28	1.189034
29	1.196422
30	1.199094
31	1.197134
32	1.195205
33	1.191532
34	1.184011
35	1.188035
36	1.194418
37	1.185291
38	1.185054
39	1.184862
40	1.183952
41	1.180458
42	1.177635
43	1.182411
44	1.183899
45	1.187615
46	1.176032
47	1.179259
48	1.176114
49	1.177687
50	1.184641
51	1.181697
52	1.172975
53	1.173349
54	1.17404
55	1.168576
56	1.165613
57	1.159426
58	1.151688
59	1.142957
60	1.140023
61	1.146338
62	1.145151
63	1.14388
64	1.14162
65	1.135303
66	1.124239
67	1.114955
68	1.109005
69	1.109195
70	1.101656
71	1.089666
72	1.084704
73	1.081327
74	1.078867
75	1.070648
76	1.055928
77	1.042711
78	1.036205
79	1.020161
80	1.004599
81	0.9895
82	0.975059
83	0.958694
84	0.94098
85	0.928585
86	0.911396
87	0.902181
88	0.883947
89	0.86111
90	0.835206
91	0.805098
92	0.783175
93	0.749859
94	0.723118
95	0.696754
96	0.665257
97	0.631594
98	0.596185
99	0.561999
100	0.524204