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tih_rna_sample_00226_23KKJ7LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0007/A23KKJ7LT4/nfcore_rnafusion_100M__5f1fa79--20260304-102235/QC/picard/tih_rna_sample_00226_23KKJ7LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0007-5f1fa79
Published
Mar 05, 2026 1:44 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 tih_rna_sample_00226_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00226_23KKJ7LT4_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 Mar 05 20:55:44 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
23278528083	21789794956	142759	15363818369	2562729040	2766123895	1096980893	0	0	0	2326628	58460364	410358	0.038275	0.961725	0.000007	0.705092	0.117611	0.126946	0.050344	0.822704	0.770089	0	0.89874	0.436783	0.273209	1.307044			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.420433
1	0.469332
2	0.541243
3	0.626716
4	0.718357
5	0.786507
6	0.839856
7	0.893325
8	0.955194
9	1.041385
10	1.11381
11	1.16431
12	1.216159
13	1.262943
14	1.29671
15	1.299487
16	1.292217
17	1.295895
18	1.276271
19	1.269425
20	1.281319
21	1.295101
22	1.29508
23	1.301649
24	1.313572
25	1.328446
26	1.341143
27	1.34043
28	1.325569
29	1.315449
30	1.301392
31	1.285658
32	1.263232
33	1.24017
34	1.216602
35	1.204377
36	1.193743
37	1.174984
38	1.159018
39	1.139227
40	1.143334
41	1.153991
42	1.163001
43	1.160113
44	1.156165
45	1.152488
46	1.137855
47	1.124531
48	1.110683
49	1.101771
50	1.096577
51	1.091591
52	1.083006
53	1.077283
54	1.080203
55	1.089581
56	1.091548
57	1.080318
58	1.069543
59	1.049429
60	1.040331
61	1.041101
62	1.032021
63	1.018873
64	1.012562
65	0.997854
66	0.97294
67	0.95406
68	0.947864
69	0.951165
70	0.943271
71	0.935438
72	0.932509
73	0.928689
74	0.928262
75	0.910886
76	0.897685
77	0.890558
78	0.884905
79	0.877925
80	0.870024
81	0.855677
82	0.835135
83	0.806456
84	0.793295
85	0.775412
86	0.746454
87	0.727312
88	0.710437
89	0.692299
90	0.669421
91	0.657914
92	0.6347
93	0.615807
94	0.597132
95	0.574738
96	0.554872
97	0.53266
98	0.506566
99	0.483381
100	0.455835