File Info

Filename
FFPE_V4_0001_RNA_0005_23KMKGLT4_28_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_28_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0001R_5f1fa79
Published
Mar 09, 2026 12:14 PM

Content

View in new tab 
## 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_28.Aligned.sortedByCoord.out.bam --OUTPUT FFPE_V4_0001_RNA_0005_23KMKGLT4_28_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 18:10:55 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
25179939820	24894101122	12249	21525848519	2037853335	1190736056	139650963	0	0	0	1870379	77490325	342961	0.023568	0.976432	0	0.864697	0.081861	0.047832	0.00561	0.946558	0.935812	0	0.510742	0.57395	0.773226	0.8267			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.277686
1	0.314765
2	0.367985
3	0.427761
4	0.490771
5	0.553704
6	0.616138
7	0.675784
8	0.726614
9	0.777922
10	0.820686
11	0.865496
12	0.915728
13	0.957209
14	0.986306
15	1.010876
16	1.034648
17	1.051745
18	1.072174
19	1.088412
20	1.100877
21	1.120731
22	1.134113
23	1.145416
24	1.153379
25	1.156482
26	1.163875
27	1.17205
28	1.17487
29	1.173204
30	1.17068
31	1.170759
32	1.161578
33	1.159115
34	1.153493
35	1.154862
36	1.156137
37	1.147249
38	1.139854
39	1.13679
40	1.127907
41	1.127265
42	1.132156
43	1.137581
44	1.13824
45	1.146494
46	1.149149
47	1.149197
48	1.148982
49	1.154783
50	1.160952
51	1.158761
52	1.156022
53	1.157023
54	1.157045
55	1.158296
56	1.157283
57	1.158104
58	1.155782
59	1.154247
60	1.154454
61	1.155555
62	1.152966
63	1.146096
64	1.144574
65	1.144594
66	1.142559
67	1.138998
68	1.130585
69	1.123146
70	1.112502
71	1.105001
72	1.101604
73	1.089891
74	1.081996
75	1.074537
76	1.062539
77	1.044909
78	1.035473
79	1.023414
80	1.005739
81	0.988388
82	0.98299
83	0.971291
84	0.95627
85	0.949047
86	0.935295
87	0.917274
88	0.897162
89	0.877257
90	0.853135
91	0.829327
92	0.806866
93	0.778397
94	0.747957
95	0.715214
96	0.679368
97	0.643985
98	0.609023
99	0.570758
100	0.525077