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aih-tih-sc-92d360-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-92d360-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-92d360-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-92d360-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 20:08:54 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
55126782540	54482741964	12694	49495532009	3200908998	1589629196	196659067	0	0	0	6988550	189230412	770438	0.035616	0.964384	0	0.908463	0.058751	0.029177	0.00361	0.967213	0.955914	0	0.567581	0.504957	0.724825	0.742781			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.310351
1	0.337152
2	0.397022
3	0.462781
4	0.510492
5	0.552713
6	0.603959
7	0.646605
8	0.698077
9	0.742783
10	0.786583
11	0.835985
12	0.881411
13	0.917777
14	0.956718
15	0.985764
16	1.011175
17	1.030504
18	1.037785
19	1.053091
20	1.064315
21	1.074112
22	1.091347
23	1.114526
24	1.126311
25	1.130777
26	1.127548
27	1.135695
28	1.145345
29	1.14244
30	1.143453
31	1.150781
32	1.159456
33	1.160885
34	1.149983
35	1.153529
36	1.153613
37	1.150706
38	1.154314
39	1.15963
40	1.157523
41	1.155312
42	1.157709
43	1.164071
44	1.16428
45	1.164227
46	1.160729
47	1.16592
48	1.162768
49	1.16339
50	1.157311
51	1.15553
52	1.155244
53	1.156796
54	1.166982
55	1.167918
56	1.167196
57	1.163716
58	1.154271
59	1.143677
60	1.14201
61	1.146206
62	1.151372
63	1.148954
64	1.163785
65	1.175376
66	1.1686
67	1.164766
68	1.160216
69	1.151467
70	1.147653
71	1.137857
72	1.12782
73	1.11764
74	1.108321
75	1.099079
76	1.079239
77	1.066172
78	1.05407
79	1.038567
80	1.01878
81	1.006404
82	0.994746
83	0.983651
84	0.972006
85	0.957816
86	0.93764
87	0.922596
88	0.903082
89	0.884218
90	0.860243
91	0.840137
92	0.811276
93	0.776845
94	0.738939
95	0.705223
96	0.669355
97	0.632651
98	0.591039
99	0.552466
100	0.51469