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Filename
Hs746T_FFPE_RNA_0001_B23LG7FLT4_2_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/Hs746T_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
Size
2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 6:18 PM

Content

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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_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT Hs746T_FFPE_RNA_0001_B23LG7FLT4_2_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 22:48:48 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
74816601244	73469374693	62578	64750911723	4958344967	3332904776	427150649	0	0	0	8635749	229952589	1406655	0.036195	0.963805	0.000001	0.881332	0.067489	0.045365	0.005814	0.948821	0.931735	0	0.511314	0.586698	0.758283	0.903962			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.287922
1	0.327028
2	0.373654
3	0.432055
4	0.502487
5	0.5738
6	0.634907
7	0.696252
8	0.753895
9	0.804299
10	0.851669
11	0.902692
12	0.946849
13	0.985934
14	1.018419
15	1.051446
16	1.075847
17	1.100706
18	1.111025
19	1.122902
20	1.147307
21	1.170067
22	1.18364
23	1.194353
24	1.207498
25	1.209947
26	1.21331
27	1.212932
28	1.211878
29	1.207481
30	1.207892
31	1.208393
32	1.205413
33	1.204347
34	1.198329
35	1.19672
36	1.193
37	1.185272
38	1.186629
39	1.184389
40	1.182765
41	1.179074
42	1.177409
43	1.176574
44	1.171103
45	1.171103
46	1.164103
47	1.157642
48	1.154775
49	1.155987
50	1.149437
51	1.143972
52	1.142282
53	1.142232
54	1.145265
55	1.14288
56	1.13711
57	1.134639
58	1.124478
59	1.115036
60	1.112942
61	1.108084
62	1.106322
63	1.10305
64	1.09728
65	1.096128
66	1.089427
67	1.078873
68	1.069267
69	1.063652
70	1.059824
71	1.052435
72	1.051855
73	1.041179
74	1.028285
75	1.024843
76	1.01796
77	1.007459
78	1.000017
79	0.991644
80	0.973918
81	0.955856
82	0.943614
83	0.92715
84	0.912825
85	0.903353
86	0.884172
87	0.871129
88	0.860031
89	0.840235
90	0.823326
91	0.800945
92	0.77639
93	0.75264
94	0.726082
95	0.7017
96	0.675465
97	0.647296
98	0.617455
99	0.58675
100	0.550932