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aih-tih-sc-f26674-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-f26674-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:42 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-f26674-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f26674-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 20:20:03 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
73947553672	73106067716	6222	66523062190	4688445599	1701212967	193340738	0	0	0	3171542	246894291	1069286	0.012683	0.987317	0	0.909953	0.064132	0.02327	0.002645	0.974085	0.963	0	0.50988	0.544597	0.753747	0.79899			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.299857
1	0.335501
2	0.383452
3	0.439745
4	0.495844
5	0.539885
6	0.597875
7	0.647893
8	0.706083
9	0.757832
10	0.798254
11	0.839811
12	0.887811
13	0.928894
14	0.959719
15	0.993655
16	1.024573
17	1.045354
18	1.060048
19	1.078337
20	1.097889
21	1.112781
22	1.129661
23	1.147559
24	1.149095
25	1.149237
26	1.144276
27	1.139542
28	1.143174
29	1.149285
30	1.155348
31	1.153707
32	1.137445
33	1.134376
34	1.128081
35	1.126078
36	1.127798
37	1.12906
38	1.129341
39	1.125005
40	1.126198
41	1.127832
42	1.13325
43	1.136949
44	1.140522
45	1.159454
46	1.161117
47	1.168204
48	1.171089
49	1.176419
50	1.180954
51	1.179996
52	1.17655
53	1.181235
54	1.186602
55	1.178498
56	1.175084
57	1.173115
58	1.161243
59	1.157455
60	1.150706
61	1.15006
62	1.150035
63	1.150566
64	1.150199
65	1.150419
66	1.138912
67	1.125048
68	1.121387
69	1.117799
70	1.112061
71	1.101603
72	1.097616
73	1.092336
74	1.084452
75	1.071685
76	1.061278
77	1.055758
78	1.057242
79	1.044388
80	1.030012
81	1.015853
82	1.008169
83	0.995999
84	0.984049
85	0.972394
86	0.955945
87	0.940384
88	0.91805
89	0.897745
90	0.868707
91	0.83921
92	0.813475
93	0.779718
94	0.741968
95	0.707158
96	0.675329
97	0.644258
98	0.609512
99	0.577681
100	0.54345