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659_bQZ-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0020/B23WHTKLT4/nfcore_rnafusion__3e501777--20260520-120107/QC/picard/659_bQZ-T1-TRNA-1_B23WHTKLT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0020-3e501777
Published
May 21, 2026 1:03 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_bQZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_bQZ-T1-TRNA-1_B23WHTKLT4_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: Thu May 21 05:55:48 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
70550828151	69668060294	7410	63013702836	4756875722	1674487775	222986551	0	0	0	12800596	217432407	1076650	0.055598	0.944402	0	0.904485	0.068279	0.024035	0.003201	0.972764	0.960592	0	0.528801	0.51339	0.711217	0.803124			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.285165
1	0.322206
2	0.374159
3	0.433445
4	0.487028
5	0.54052
6	0.602017
7	0.657722
8	0.714997
9	0.765462
10	0.810404
11	0.854388
12	0.901613
13	0.942454
14	0.973079
15	1.001199
16	1.022042
17	1.041802
18	1.057527
19	1.076574
20	1.099321
21	1.119698
22	1.141172
23	1.153399
24	1.163098
25	1.170283
26	1.172694
27	1.177818
28	1.180748
29	1.175032
30	1.165876
31	1.163285
32	1.158234
33	1.164769
34	1.166625
35	1.170532
36	1.173272
37	1.175077
38	1.179783
39	1.180805
40	1.171493
41	1.174995
42	1.183623
43	1.185904
44	1.187598
45	1.185934
46	1.17571
47	1.17029
48	1.168166
49	1.167492
50	1.168673
51	1.159587
52	1.151621
53	1.154713
54	1.164648
55	1.172468
56	1.170823
57	1.162915
58	1.156777
59	1.151495
60	1.149263
61	1.151014
62	1.155096
63	1.151695
64	1.152196
65	1.149998
66	1.148947
67	1.142949
68	1.140562
69	1.1309
70	1.114174
71	1.103308
72	1.093431
73	1.086865
74	1.078296
75	1.071425
76	1.063289
77	1.04523
78	1.034106
79	1.023976
80	1.007773
81	0.990324
82	0.973931
83	0.960462
84	0.940399
85	0.920224
86	0.901093
87	0.887242
88	0.868605
89	0.846462
90	0.824123
91	0.801557
92	0.771453
93	0.741249
94	0.717651
95	0.689384
96	0.659883
97	0.622188
98	0.584603
99	0.550499
100	0.514286