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Filename
786-O_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008/B23LG7FLT4/nfcore_rnafusion_100M__1bb6229e--20260226-142939/QC/picard/786-O_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_1bb6229e
Published
Feb 26, 2026 11:16 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 786-O_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT 786-O_FFPE_RNA_0001_B23LG7FLT4_2_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: Fri Feb 27 06:49:39 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
25136370399	24843155713	17876	21914932842	1692312657	1070988287	164904051	0	0	0	2601687	76666380	472660	0.032821	0.967179	0.000001	0.882132	0.06812	0.04311	0.006638	0.950251	0.939167	0	0.504807	0.573462	0.762199	0.837678			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.293218
1	0.325607
2	0.375152
3	0.432705
4	0.496829
5	0.558557
6	0.614739
7	0.668843
8	0.732797
9	0.796571
10	0.850497
11	0.906843
12	0.952856
13	0.991657
14	1.020461
15	1.041081
16	1.060179
17	1.088326
18	1.109858
19	1.127537
20	1.144988
21	1.161944
22	1.174608
23	1.186241
24	1.189866
25	1.185781
26	1.177997
27	1.173736
28	1.175503
29	1.171496
30	1.171608
31	1.177424
32	1.179359
33	1.175993
34	1.170766
35	1.170405
36	1.171942
37	1.166073
38	1.162951
39	1.162215
40	1.161777
41	1.163292
42	1.168544
43	1.16895
44	1.164882
45	1.173826
46	1.166272
47	1.164482
48	1.163561
49	1.16202
50	1.160111
51	1.160515
52	1.154237
53	1.145621
54	1.14675
55	1.145949
56	1.140073
57	1.132872
58	1.127175
59	1.122244
60	1.113403
61	1.114128
62	1.119913
63	1.117802
64	1.111916
65	1.107901
66	1.102407
67	1.097049
68	1.087179
69	1.083779
70	1.077771
71	1.069074
72	1.063352
73	1.054655
74	1.046408
75	1.040961
76	1.030048
77	1.020574
78	1.018818
79	1.008356
80	0.994929
81	0.982099
82	0.969688
83	0.950294
84	0.936323
85	0.924321
86	0.906986
87	0.89211
88	0.873321
89	0.8554
90	0.836023
91	0.811715
92	0.787517
93	0.759849
94	0.732868
95	0.704298
96	0.675914
97	0.651901
98	0.622212
99	0.589609
100	0.552154