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FFPE_HD789_01_RNA_0012_B2372Y3LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_rna_exp0034/B2372Y3LT4/nfcore_rnafusion__2cae617--20260515-145204/QC/picard/FFPE_HD789_01_RNA_0012_B2372Y3LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
cgp_rna_exp0034_2cae617
Published
May 16, 2026 6:11 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 FFPE_HD789_01_RNA_0012_B2372Y3LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD789_01_RNA_0012_B2372Y3LT4_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 09:56:31 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
78088498619	77357442612	14040	69918096269	5194476618	1999636752	245218933	0	0	0	2611741	227857080	782546	0.011332	0.988668	0	0.903832	0.067149	0.025849	0.00317	0.970981	0.96189	0	0.489187	0.590232	0.752038	0.877444			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.258214
1	0.297888
2	0.346061
3	0.407211
4	0.479855
5	0.54596
6	0.608702
7	0.673156
8	0.734726
9	0.790895
10	0.841201
11	0.891679
12	0.940224
13	0.978626
14	1.013645
15	1.043354
16	1.074795
17	1.105875
18	1.121048
19	1.135063
20	1.153422
21	1.17507
22	1.188845
23	1.199531
24	1.205921
25	1.20718
26	1.210767
27	1.211845
28	1.213444
29	1.209357
30	1.20443
31	1.197789
32	1.192196
33	1.191831
34	1.186686
35	1.189787
36	1.190154
37	1.186406
38	1.180771
39	1.171376
40	1.169785
41	1.17101
42	1.169813
43	1.173556
44	1.174542
45	1.177461
46	1.16946
47	1.162038
48	1.159218
49	1.165254
50	1.172125
51	1.172883
52	1.170345
53	1.166586
54	1.169684
55	1.162662
56	1.151833
57	1.153785
58	1.158031
59	1.148336
60	1.141849
61	1.135701
62	1.13119
63	1.123426
64	1.113405
65	1.11151
66	1.119696
67	1.115455
68	1.104472
69	1.093825
70	1.080094
71	1.07104
72	1.063375
73	1.052676
74	1.047032
75	1.040777
76	1.027655
77	1.006867
78	1.000492
79	0.985771
80	0.96832
81	0.94889
82	0.935755
83	0.918564
84	0.900415
85	0.88667
86	0.866803
87	0.850864
88	0.832451
89	0.815376
90	0.802018
91	0.779827
92	0.757263
93	0.73424
94	0.709551
95	0.685958
96	0.664027
97	0.635829
98	0.606585
99	0.581029
100	0.545745