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FFPE_V4_0001_RNA_0005_23KMKGLT4_3_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0001/B23KMKGLT4/nfcore_rnafusion_100M__5f1fa79--20260304-094520/QC/picard/FFPE_V4_0001_RNA_0005_23KMKGLT4_3_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0001R_5f1fa79
Published
Mar 09, 2026 11:59 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_V4_0001_RNA_0005_23KMKGLT4_3.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_3_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: Mon Mar 09 17:59:52 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
25019144485	24715306399	12738	21342848756	2171767950	1006604462	194072493	0	0	0	3695352	75702972	307292	0.046542	0.953458	0.000001	0.863548	0.087871	0.040728	0.007852	0.951419	0.939865	0	0.55299	0.625168	0.67201	0.945888			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.289782
1	0.331912
2	0.39756
3	0.473706
4	0.551995
5	0.627792
6	0.700197
7	0.76996
8	0.833195
9	0.893833
10	0.942585
11	0.992605
12	1.0374
13	1.075643
14	1.100182
15	1.12506
16	1.143674
17	1.155891
18	1.163547
19	1.178152
20	1.191336
21	1.204648
22	1.216047
23	1.219377
24	1.223761
25	1.226037
26	1.22876
27	1.225241
28	1.222789
29	1.214592
30	1.20835
31	1.202788
32	1.186624
33	1.18311
34	1.179994
35	1.174598
36	1.167122
37	1.159007
38	1.14914
39	1.143156
40	1.136747
41	1.135597
42	1.13851
43	1.134642
44	1.129721
45	1.135516
46	1.129832
47	1.123574
48	1.120759
49	1.119923
50	1.120985
51	1.11814
52	1.115952
53	1.115057
54	1.118179
55	1.115539
56	1.110302
57	1.103004
58	1.100136
59	1.098337
60	1.098147
61	1.108475
62	1.11202
63	1.103654
64	1.097746
65	1.095353
66	1.092544
67	1.08686
68	1.079477
69	1.073146
70	1.063823
71	1.055139
72	1.054522
73	1.044142
74	1.033874
75	1.024976
76	1.013654
77	0.994096
78	0.983714
79	0.977734
80	0.963639
81	0.945601
82	0.929948
83	0.911364
84	0.896759
85	0.890053
86	0.874656
87	0.856246
88	0.83406
89	0.812851
90	0.794652
91	0.774745
92	0.757527
93	0.732628
94	0.699088
95	0.666068
96	0.633976
97	0.598394
98	0.561096
99	0.520546
100	0.475482