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U118MG_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/U118MG_FFPE_RNA_0001_B23LG7FLT4_2_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0008_exp0011-e7be3c7a_b
Published
May 28, 2026 5:08 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 U118MG_FFPE_RNA_0001_B23LG7FLT4_2.Aligned.sortedByCoord.out.bam --OUTPUT U118MG_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 21:32:00 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
76185850037	75228133858	44495	67244334433	4734857436	2769445196	479452298	0	0	0	10967719	230499105	1426719	0.045421	0.954579	0.000001	0.893872	0.06294	0.036814	0.006373	0.956812	0.944784	0	0.506119	0.615194	0.740338	0.984163			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.326216
1	0.370218
2	0.425532
3	0.492977
4	0.554262
5	0.615075
6	0.680214
7	0.744342
8	0.8011
9	0.861705
10	0.907635
11	0.956736
12	1.003145
13	1.039708
14	1.072048
15	1.108338
16	1.134544
17	1.147665
18	1.154734
19	1.157769
20	1.176623
21	1.193793
22	1.200893
23	1.213196
24	1.213224
25	1.21102
26	1.212855
27	1.210865
28	1.204976
29	1.193777
30	1.19259
31	1.190007
32	1.18383
33	1.187
34	1.180643
35	1.18404
36	1.18106
37	1.174757
38	1.174362
39	1.171532
40	1.171439
41	1.169729
42	1.167184
43	1.167788
44	1.162466
45	1.161341
46	1.159065
47	1.156123
48	1.154608
49	1.157835
50	1.155382
51	1.158965
52	1.153781
53	1.152021
54	1.154664
55	1.155344
56	1.147534
57	1.142245
58	1.13171
59	1.119307
60	1.106518
61	1.100784
62	1.097384
63	1.092748
64	1.083674
65	1.07712
66	1.073445
67	1.064527
68	1.056766
69	1.049973
70	1.040541
71	1.028602
72	1.025267
73	1.011819
74	0.998423
75	0.990389
76	0.979925
77	0.958851
78	0.950259
79	0.943882
80	0.934344
81	0.922089
82	0.91096
83	0.891943
84	0.881556
85	0.872373
86	0.856405
87	0.841555
88	0.827984
89	0.810245
90	0.799259
91	0.777595
92	0.755254
93	0.733989
94	0.709484
95	0.686161
96	0.664649
97	0.636925
98	0.612162
99	0.584337
100	0.551125