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FFPE_V4_0001_RNA_0005_23KMKGLT4_40_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_40_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0001R_5f1fa79
Published
Mar 09, 2026 12:02 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_0005_23KMKGLT4_40.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_40_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 17:59:55 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
24994499617	24698390260	15856	21282776515	2054321677	1216897283	144378929	0	0	0	1685323	77402552	328520	0.021309	0.978691	0.000001	0.861707	0.083176	0.04927	0.005846	0.944883	0.933689	0	0.531021	0.536758	0.754075	0.774661			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.285495
1	0.319259
2	0.366821
3	0.422453
4	0.483858
5	0.546964
6	0.610186
7	0.670994
8	0.72471
9	0.776161
10	0.819437
11	0.867743
12	0.915098
13	0.958051
14	0.986263
15	1.011626
16	1.038432
17	1.057719
18	1.064214
19	1.079273
20	1.094351
21	1.111777
22	1.125891
23	1.139186
24	1.146666
25	1.152245
26	1.160499
27	1.168543
28	1.176427
29	1.179364
30	1.174496
31	1.177032
32	1.170702
33	1.170334
34	1.166508
35	1.166731
36	1.166323
37	1.158789
38	1.14988
39	1.140675
40	1.131825
41	1.127777
42	1.128066
43	1.127254
44	1.121534
45	1.127997
46	1.123808
47	1.117775
48	1.116625
49	1.12453
50	1.128142
51	1.127286
52	1.125213
53	1.127131
54	1.131828
55	1.136616
56	1.137479
57	1.139169
58	1.139744
59	1.140235
60	1.142309
61	1.15039
62	1.148949
63	1.14209
64	1.139949
65	1.140033
66	1.13698
67	1.130195
68	1.121286
69	1.114918
70	1.105378
71	1.099878
72	1.102512
73	1.094569
74	1.090365
75	1.084957
76	1.073536
77	1.056783
78	1.050487
79	1.040954
80	1.023808
81	1.004215
82	0.996915
83	0.98243
84	0.971374
85	0.965747
86	0.95359
87	0.93685
88	0.91673
89	0.900403
90	0.878609
91	0.854168
92	0.831253
93	0.802109
94	0.767311
95	0.732544
96	0.696647
97	0.661524
98	0.62552
99	0.585243
100	0.54072