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659_bhK-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_bhK-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 5:27 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_bhK-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bhK-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: Fri May 22 21:18:43 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
74971178175	74033686285	11764	67516200571	4761550871	1577418720	178504359	0	0	0	11056939	244323988	1620378	0.043296	0.956704	0	0.911966	0.064316	0.021307	0.002411	0.976282	0.964074	0	0.532622	0.526496	0.77355	0.749701			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.304945
1	0.338892
2	0.386614
3	0.444044
4	0.495926
5	0.542516
6	0.598046
7	0.647839
8	0.693772
9	0.736054
10	0.780387
11	0.821573
12	0.85988
13	0.895101
14	0.923183
15	0.949546
16	0.974289
17	0.996077
18	1.008955
19	1.02114
20	1.037345
21	1.055759
22	1.074535
23	1.091789
24	1.105535
25	1.111274
26	1.120736
27	1.133618
28	1.147436
29	1.151593
30	1.156935
31	1.158964
32	1.154081
33	1.160134
34	1.154354
35	1.160257
36	1.163615
37	1.159223
38	1.154319
39	1.151638
40	1.149432
41	1.148973
42	1.152999
43	1.161711
44	1.158512
45	1.162162
46	1.159692
47	1.160117
48	1.164511
49	1.170109
50	1.171221
51	1.166476
52	1.165104
53	1.16469
54	1.16499
55	1.162682
56	1.15934
57	1.158679
58	1.150082
59	1.143707
60	1.142264
61	1.14056
62	1.143001
63	1.140448
64	1.140424
65	1.146009
66	1.154801
67	1.154557
68	1.152836
69	1.148011
70	1.134815
71	1.120097
72	1.115839
73	1.111256
74	1.104777
75	1.100558
76	1.088815
77	1.079911
78	1.073372
79	1.055648
80	1.038468
81	1.023842
82	1.019669
83	1.003314
84	0.982377
85	0.96534
86	0.942521
87	0.92941
88	0.924013
89	0.908195
90	0.888186
91	0.852831
92	0.825836
93	0.800768
94	0.7708
95	0.738279
96	0.705341
97	0.683754
98	0.649339
99	0.60987
100	0.569507