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tih_rna_sample_00176_23KKJ7LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0006/A23KKJ7LT4/nfcore_rnafusion_100M__5f1fa79--20260304-101508/QC/picard/tih_rna_sample_00176_23KKJ7LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp0006-5f1fa79
Published
Mar 05, 2026 4:27 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 tih_rna_sample_00176_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00176_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 23:03:49 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
23740368692	22637391897	285942	14137405006	2542193601	5137413571	820093777	0	0	0	3506171	49055112	364568	0.066706	0.933294	0.000013	0.624516	0.112301	0.226944	0.036227	0.736816	0.702584	0	0.677598	0.460719	0.503879	1.073804			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.32635
1	0.380741
2	0.462215
3	0.534331
4	0.599784
5	0.665943
6	0.727874
7	0.788554
8	0.845859
9	0.900254
10	0.9546
11	1.003695
12	1.046047
13	1.087316
14	1.119521
15	1.131446
16	1.120432
17	1.13176
18	1.130479
19	1.135727
20	1.141254
21	1.150799
22	1.166242
23	1.176279
24	1.18782
25	1.196945
26	1.200443
27	1.195859
28	1.196095
29	1.179559
30	1.171233
31	1.164748
32	1.163252
33	1.161162
34	1.152204
35	1.152407
36	1.153458
37	1.152815
38	1.149133
39	1.161381
40	1.179514
41	1.187835
42	1.188873
43	1.191489
44	1.183819
45	1.172622
46	1.167871
47	1.171895
48	1.163552
49	1.161273
50	1.144844
51	1.143244
52	1.141611
53	1.128574
54	1.135345
55	1.120733
56	1.10052
57	1.089378
58	1.089787
59	1.086545
60	1.087882
61	1.095922
62	1.097383
63	1.083203
64	1.077838
65	1.072432
66	1.068149
67	1.059799
68	1.052044
69	1.048201
70	1.035345
71	1.027179
72	1.026009
73	1.021169
74	1.007944
75	0.998817
76	0.99311
77	0.992903
78	0.981197
79	0.968638
80	0.961883
81	0.953598
82	0.938016
83	0.918598
84	0.908204
85	0.898272
86	0.887701
87	0.875584
88	0.849783
89	0.818446
90	0.792177
91	0.773617
92	0.742709
93	0.708095
94	0.685873
95	0.663413
96	0.637969
97	0.611485
98	0.572336
99	0.535034
100	0.543858