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Filename
FFPE_V4_0001_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008_exp0011/B23LG7FLT4/nfcore_rnafusion__e7be3c7a--20260528-111100/QC/picard/FFPE_V4_0001_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:34 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_V4_0001_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0001_B23LG7FLT4_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: Thu May 28 22:31:05 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
71994076008	71026416966	50991	59075160820	7668177300	3789610614	493417241	0	0	0	6070415	207428914	1413477	0.028433	0.971567	0.000001	0.831735	0.107962	0.053355	0.006947	0.939697	0.927067	0	0.518579	0.574039	0.740441	0.861951			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.271586
1	0.311231
2	0.375073
3	0.441407
4	0.510254
5	0.579045
6	0.647563
7	0.710991
8	0.765509
9	0.815424
10	0.860742
11	0.913085
12	0.962254
13	1.004056
14	1.037293
15	1.070111
16	1.097664
17	1.11185
18	1.123369
19	1.136858
20	1.153968
21	1.168967
22	1.177269
23	1.183771
24	1.192402
25	1.200371
26	1.204279
27	1.206508
28	1.202515
29	1.200204
30	1.191076
31	1.187688
32	1.17527
33	1.175735
34	1.17546
35	1.177934
36	1.179674
37	1.170671
38	1.162539
39	1.164026
40	1.16543
41	1.164079
42	1.164891
43	1.163613
44	1.15878
45	1.164349
46	1.163616
47	1.160991
48	1.154259
49	1.155883
50	1.158329
51	1.153982
52	1.147886
53	1.149087
54	1.15007
55	1.145204
56	1.140422
57	1.137532
58	1.129172
59	1.122028
60	1.122368
61	1.12595
62	1.124707
63	1.117884
64	1.115664
65	1.110522
66	1.103029
67	1.096785
68	1.084038
69	1.073674
70	1.060701
71	1.050083
72	1.044759
73	1.03751
74	1.032239
75	1.021856
76	1.009796
77	0.99643
78	0.9894
79	0.980887
80	0.96374
81	0.94449
82	0.936947
83	0.920467
84	0.909163
85	0.901416
86	0.889606
87	0.881072
88	0.865306
89	0.847373
90	0.828511
91	0.803312
92	0.781881
93	0.758967
94	0.734771
95	0.706444
96	0.67627
97	0.645804
98	0.613007
99	0.577364
100	0.534225