File Info

Filename
RT4_FFPE_RNA_0001_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/RT4_FFPE_RNA_0001_B23LG7FLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:13 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 RT4_FFPE_RNA_0001_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT RT4_FFPE_RNA_0001_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 21:19:52 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
75795256144	74879729245	56699	64577735998	5558236053	4149912505	593787990	0	0	0	9775434	226481211	1423595	0.041376	0.958624	0.000001	0.862419	0.074229	0.055421	0.00793	0.936648	0.925335	0	0.506028	0.544408	0.785115	0.774817			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.294203
1	0.332174
2	0.38186
3	0.440013
4	0.501126
5	0.562504
6	0.623188
7	0.675142
8	0.72974
9	0.78013
10	0.829646
11	0.876374
12	0.917464
13	0.951205
14	0.977007
15	0.999281
16	1.020258
17	1.041651
18	1.058352
19	1.072167
20	1.092926
21	1.112018
22	1.134675
23	1.153029
24	1.165694
25	1.168669
26	1.168676
27	1.174991
28	1.177751
29	1.174625
30	1.171646
31	1.170662
32	1.166112
33	1.167302
34	1.162932
35	1.159868
36	1.156057
37	1.155809
38	1.15731
39	1.160858
40	1.159965
41	1.154504
42	1.14734
43	1.149632
44	1.152067
45	1.152881
46	1.141412
47	1.136627
48	1.136131
49	1.146112
50	1.153368
51	1.151985
52	1.154734
53	1.158669
54	1.158989
55	1.154483
56	1.147099
57	1.144543
58	1.144398
59	1.14434
60	1.138778
61	1.138948
62	1.141036
63	1.136628
64	1.130234
65	1.123104
66	1.123896
67	1.114991
68	1.107083
69	1.096543
70	1.084855
71	1.075322
72	1.067104
73	1.057737
74	1.053221
75	1.050259
76	1.035198
77	1.023905
78	1.018643
79	1.011191
80	0.998557
81	0.985
82	0.978228
83	0.963718
84	0.950936
85	0.944239
86	0.934954
87	0.925552
88	0.907062
89	0.890283
90	0.868251
91	0.847503
92	0.828295
93	0.805512
94	0.775273
95	0.744195
96	0.711852
97	0.676932
98	0.643997
99	0.610209
100	0.564737