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FFPE_HD789_01_RNA_13_A23YTGFLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/FFPE_HD789_01_RNA_13_A23YTGFLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
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 FFPE_HD789_01_RNA_13_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_HD789_01_RNA_13_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 20:13:05 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
79407815385	78713344590	3891	71512996344	5249264206	1730910983	220169166	0	0	0	3162682	245363471	1452223	0.012726	0.987274	0	0.908524	0.066688	0.02199	0.002797	0.975213	0.966684	0	0.48518	0.623674	0.753534	0.881479			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.270579
1	0.311568
2	0.366736
3	0.436354
4	0.51253
5	0.585423
6	0.650211
7	0.714125
8	0.772673
9	0.825529
10	0.873645
11	0.920594
12	0.969124
13	1.006146
14	1.03126
15	1.054943
16	1.077455
17	1.101985
18	1.116387
19	1.131807
20	1.150258
21	1.164376
22	1.168097
23	1.170705
24	1.172872
25	1.169996
26	1.172146
27	1.170915
28	1.167915
29	1.162043
30	1.155763
31	1.152264
32	1.146552
33	1.145367
34	1.143381
35	1.148217
36	1.148617
37	1.146571
38	1.141914
39	1.138195
40	1.136371
41	1.140653
42	1.144337
43	1.14775
44	1.148318
45	1.147168
46	1.139774
47	1.13704
48	1.137912
49	1.139403
50	1.141165
51	1.138602
52	1.137589
53	1.140909
54	1.147159
55	1.1474
56	1.143082
57	1.145792
58	1.147776
59	1.1403
60	1.139272
61	1.137252
62	1.135511
63	1.129658
64	1.122006
65	1.118131
66	1.124914
67	1.123305
68	1.120712
69	1.116431
70	1.105662
71	1.099112
72	1.096002
73	1.086296
74	1.07807
75	1.072079
76	1.060449
77	1.04136
78	1.031379
79	1.021851
80	0.99686
81	0.977343
82	0.969091
83	0.953027
84	0.934233
85	0.916624
86	0.897314
87	0.883672
88	0.867789
89	0.846693
90	0.830564
91	0.806962
92	0.780524
93	0.753595
94	0.725198
95	0.696484
96	0.663695
97	0.627989
98	0.589141
99	0.55278
100	0.517005