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659_wQ-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0009_exp0010/B23MHV2LT4/nfcore_rnafusion__04da504a--20260522-114016/QC/picard/659_wQ-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp09_10-04da504a
Published
May 22, 2026 7:42 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 659_wQ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_wQ-T1-TRNA-1_B23MHV2LT4_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: Sat May 23 00:22:50 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
76226340434	75297863493	16167	68769391285	4508301451	1816817041	203337549	0	0	0	5162671	246446753	1700746	0.020519	0.979481	0	0.913298	0.059873	0.024128	0.0027	0.973171	0.961317	0	0.535723	0.485347	0.774099	0.707098			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.307945
1	0.339197
2	0.381606
3	0.429234
4	0.472511
5	0.514489
6	0.56791
7	0.613308
8	0.660822
9	0.708033
10	0.760822
11	0.81247
12	0.85732
13	0.895209
14	0.924217
15	0.948281
16	0.96825
17	0.983688
18	0.999992
19	1.017272
20	1.028731
21	1.040085
22	1.05963
23	1.073949
24	1.081354
25	1.085262
26	1.09326
27	1.103613
28	1.117698
29	1.124107
30	1.125317
31	1.128816
32	1.13219
33	1.140931
34	1.1385
35	1.144694
36	1.152492
37	1.15518
38	1.160653
39	1.163181
40	1.162036
41	1.166597
42	1.173946
43	1.182344
44	1.182297
45	1.180922
46	1.17742
47	1.175479
48	1.174106
49	1.172201
50	1.178104
51	1.175518
52	1.17562
53	1.169856
54	1.174178
55	1.174589
56	1.17922
57	1.177457
58	1.163176
59	1.154146
60	1.155704
61	1.157215
62	1.152863
63	1.144849
64	1.140397
65	1.146034
66	1.142198
67	1.137191
68	1.135038
69	1.127966
70	1.117263
71	1.109269
72	1.107275
73	1.104233
74	1.105806
75	1.105683
76	1.096163
77	1.095801
78	1.090231
79	1.08081
80	1.067636
81	1.055777
82	1.044817
83	1.019076
84	0.999185
85	0.981284
86	0.957396
87	0.942834
88	0.927606
89	0.913627
90	0.89777
91	0.876924
92	0.85184
93	0.822209
94	0.789825
95	0.756009
96	0.723791
97	0.690275
98	0.652282
99	0.614964
100	0.572164