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659_dfA-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__2cae617--20260515-145204/QC/picard/659_dfA-T1-TRNA-1_B23MHV2LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp09_10-2cae617
Published
May 16, 2026 6:13 AM

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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_dfA-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_dfA-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 16 11:00:31 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
77274392175	76406707349	9617	69384318416	5447156699	1346515911	228706706	0	0	0	3180318	243644549	1828842	0.012885	0.987115	0	0.908092	0.071292	0.017623	0.002993	0.979384	0.968386	0	0.49508	0.564028	0.743301	0.842966			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.287115
1	0.322206
2	0.373152
3	0.437848
4	0.504578
5	0.56312
6	0.621175
7	0.674684
8	0.726474
9	0.772726
10	0.817567
11	0.859473
12	0.902949
13	0.93871
14	0.969956
15	0.995943
16	1.016334
17	1.035084
18	1.049623
19	1.061344
20	1.079486
21	1.096779
22	1.109516
23	1.125836
24	1.136491
25	1.140572
26	1.143305
27	1.146307
28	1.148977
29	1.151211
30	1.146455
31	1.142946
32	1.142335
33	1.149657
34	1.148798
35	1.152161
36	1.161237
37	1.158909
38	1.157537
39	1.152209
40	1.147438
41	1.149371
42	1.150608
43	1.152254
44	1.154979
45	1.152503
46	1.14443
47	1.147186
48	1.148248
49	1.156878
50	1.162175
51	1.159185
52	1.158542
53	1.159725
54	1.168992
55	1.172171
56	1.172235
57	1.172857
58	1.166199
59	1.156907
60	1.156042
61	1.162368
62	1.160588
63	1.150872
64	1.149258
65	1.152365
66	1.145663
67	1.133991
68	1.131965
69	1.122112
70	1.109267
71	1.102307
72	1.097589
73	1.093051
74	1.088578
75	1.078463
76	1.064952
77	1.051061
78	1.045856
79	1.040177
80	1.025363
81	1.012058
82	1.001123
83	0.984398
84	0.970488
85	0.957913
86	0.941129
87	0.926222
88	0.906284
89	0.88838
90	0.865393
91	0.838122
92	0.806778
93	0.769189
94	0.740304
95	0.713056
96	0.676637
97	0.637319
98	0.601349
99	0.566556
100	0.5248