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tih_rna_sample_00086_23KKJ7LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0006_exp0007/A23KKJ7LT4/nfcore_rnafusion__2cae617--20260513-145008/QC/picard/tih_rna_sample_00086_23KKJ7LT4_1_rna_metrics.txt
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2.8 KB
Workflow Run
dev_rna_exp06_07-2cae617
Published
May 16, 2026 7:00 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 tih_rna_sample_00086_23KKJ7LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT tih_rna_sample_00086_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: Sat May 16 11:55:03 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
74751760287	73263997871	238036	52967438028	7284934741	11804427539	1206959527	0	0	0	3300936	201929771	999224	0.016084	0.983916	0.000003	0.722967	0.099434	0.161122	0.016474	0.822401	0.806033	0	0.567239	0.523835	0.707469	0.900068			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.363802
1	0.400739
2	0.459156
3	0.517829
4	0.571231
5	0.624131
6	0.685728
7	0.740362
8	0.79764
9	0.847594
10	0.891596
11	0.934476
12	0.970775
13	1.008158
14	1.035444
15	1.060497
16	1.071854
17	1.082339
18	1.083858
19	1.090779
20	1.105071
21	1.116175
22	1.126974
23	1.130035
24	1.140521
25	1.143202
26	1.148639
27	1.157152
28	1.157903
29	1.144285
30	1.135737
31	1.141529
32	1.144992
33	1.152377
34	1.150369
35	1.155541
36	1.15679
37	1.14908
38	1.151511
39	1.14775
40	1.142677
41	1.14468
42	1.14782
43	1.155535
44	1.153323
45	1.152688
46	1.145358
47	1.142301
48	1.138262
49	1.138867
50	1.138433
51	1.137558
52	1.134201
53	1.136943
54	1.14392
55	1.141951
56	1.134194
57	1.128518
58	1.126707
59	1.120745
60	1.115202
61	1.117795
62	1.118775
63	1.111751
64	1.111394
65	1.117124
66	1.118653
67	1.111279
68	1.104046
69	1.090991
70	1.078634
71	1.06932
72	1.061762
73	1.05492
74	1.047569
75	1.041193
76	1.030693
77	1.017318
78	1.010733
79	1.007122
80	0.998381
81	0.987771
82	0.97253
83	0.957631
84	0.940282
85	0.920427
86	0.901381
87	0.884502
88	0.870533
89	0.852385
90	0.837419
91	0.817672
92	0.791673
93	0.764865
94	0.742369
95	0.719106
96	0.693409
97	0.663181
98	0.626515
99	0.589258
100	0.54548