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Filename
Hs746T_FFPE_RNA_0001_23LG7FLT4_1_rna_metrics.txt
Full Path
s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0008/B23LG7FLT4/nfcore_rnafusion_100M__5f1fa793--20260303-130000/QC/picard/Hs746T_FFPE_RNA_0001_23LG7FLT4_1_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_5f1fa793
Published
Mar 03, 2026 6:51 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 Hs746T_FFPE_RNA_0001_23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT Hs746T_FFPE_RNA_0001_23LG7FLT4_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: Wed Mar 04 01:44:00 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
25298329320	24829103536	18188	21849064667	1723778151	1104433091	151809439	0	0	0	2985406	76350617	499720	0.03763	0.96237	0.000001	0.879978	0.069426	0.044481	0.006114	0.949404	0.931794	0	0.507385	0.594265	0.728854	0.958512			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.302387
1	0.34111
2	0.39052
3	0.450778
4	0.51625
5	0.58402
6	0.643744
7	0.705792
8	0.763172
9	0.814554
10	0.865404
11	0.918522
12	0.9664
13	1.006552
14	1.036497
15	1.067174
16	1.083941
17	1.104373
18	1.115806
19	1.13143
20	1.160954
21	1.18722
22	1.202401
23	1.209891
24	1.219984
25	1.221617
26	1.22453
27	1.224871
28	1.22167
29	1.213374
30	1.209958
31	1.209712
32	1.205434
33	1.203523
34	1.202141
35	1.200649
36	1.195108
37	1.192139
38	1.19368
39	1.189581
40	1.186839
41	1.18143
42	1.178933
43	1.178465
44	1.173686
45	1.171994
46	1.163129
47	1.154334
48	1.150573
49	1.151001
50	1.143491
51	1.139104
52	1.135017
53	1.132959
54	1.138068
55	1.137933
56	1.131511
57	1.128099
58	1.120405
59	1.111026
60	1.106934
61	1.101924
62	1.098801
63	1.093209
64	1.089071
65	1.087678
66	1.081481
67	1.070525
68	1.064115
69	1.05915
70	1.054424
71	1.04606
72	1.047451
73	1.037577
74	1.022678
75	1.019312
76	1.009408
77	0.995017
78	0.986522
79	0.97925
80	0.965363
81	0.949612
82	0.936318
83	0.919237
84	0.907325
85	0.897792
86	0.875545
87	0.858875
88	0.846027
89	0.826238
90	0.809177
91	0.787879
92	0.762364
93	0.740042
94	0.714115
95	0.690332
96	0.666293
97	0.639482
98	0.611373
99	0.582574
100	0.547487