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SkinN_FFPE_L04_RNA_01_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/SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:58 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 SkinN_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT SkinN_FFPE_L04_RNA_01_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 22:38:54 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
65699774023	64408551876	68327	57503225957	3951400314	2405168432	548688846	0	0	0	13521829	221408848	1276664	0.057557	0.942443	0.000001	0.892789	0.061349	0.037342	0.008519	0.954138	0.935386	0	0.829445	0.351681	0.442953	0.927271			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.346179
1	0.379623
2	0.437992
3	0.502589
4	0.548428
5	0.594598
6	0.658157
7	0.717703
8	0.784476
9	0.836059
10	0.873427
11	0.901661
12	0.929575
13	0.965425
14	0.996285
15	1.018742
16	1.029859
17	1.0369
18	1.045121
19	1.054833
20	1.077442
21	1.093182
22	1.09918
23	1.106456
24	1.115747
25	1.125744
26	1.132399
27	1.140361
28	1.151237
29	1.145564
30	1.1411
31	1.148892
32	1.156331
33	1.17
34	1.153712
35	1.157289
36	1.177074
37	1.19208
38	1.203158
39	1.19859
40	1.189029
41	1.200708
42	1.193611
43	1.190714
44	1.189544
45	1.189928
46	1.19078
47	1.202628
48	1.19449
49	1.185982
50	1.186204
51	1.188134
52	1.176317
53	1.170015
54	1.168308
55	1.157247
56	1.147475
57	1.14866
58	1.144275
59	1.145724
60	1.16683
61	1.170244
62	1.165526
63	1.141607
64	1.128419
65	1.118375
66	1.111068
67	1.100609
68	1.095654
69	1.080229
70	1.061983
71	1.052128
72	1.04825
73	1.044032
74	1.043775
75	1.037621
76	1.038126
77	1.041234
78	1.035844
79	1.024011
80	1.005375
81	0.987581
82	0.96958
83	0.961578
84	0.953295
85	0.939273
86	0.923831
87	0.915704
88	0.898945
89	0.881479
90	0.853568
91	0.819923
92	0.772527
93	0.730119
94	0.685148
95	0.648099
96	0.613444
97	0.57914
98	0.544112
99	0.507896
100	0.465669