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aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0021/A23YTGFLT4/nfcore_rnafusion__d2190e45--20260603-105009/QC/picard/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:34 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 aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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: Wed Jun 03 20:27:04 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
72615193624	71760772348	4374	65318763875	4485291655	1753890706	202821738	0	0	0	8260583	241777056	1012614	0.033037	0.966963	0	0.910229	0.062503	0.024441	0.002826	0.972733	0.961287	0	0.525635	0.519928	0.742134	0.81463			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.271439
1	0.308579
2	0.353921
3	0.415241
4	0.475937
5	0.536097
6	0.592406
7	0.640436
8	0.691507
9	0.739791
10	0.779964
11	0.819595
12	0.870995
13	0.918134
14	0.958756
15	0.990776
16	1.016299
17	1.040336
18	1.062358
19	1.075927
20	1.088456
21	1.104844
22	1.121703
23	1.142562
24	1.157603
25	1.163173
26	1.164596
27	1.165779
28	1.176727
29	1.178917
30	1.18202
31	1.179655
32	1.178268
33	1.180453
34	1.176541
35	1.184166
36	1.190518
37	1.181228
38	1.185352
39	1.181839
40	1.174716
41	1.175351
42	1.180061
43	1.191321
44	1.188997
45	1.193732
46	1.189822
47	1.185393
48	1.181816
49	1.184358
50	1.176389
51	1.171224
52	1.163357
53	1.170246
54	1.171954
55	1.169563
56	1.164297
57	1.167049
58	1.161294
59	1.143
60	1.131082
61	1.126928
62	1.123371
63	1.114698
64	1.113312
65	1.110038
66	1.106542
67	1.102658
68	1.102879
69	1.100394
70	1.0953
71	1.085717
72	1.08243
73	1.078825
74	1.072228
75	1.062606
76	1.054282
77	1.04475
78	1.036438
79	1.02079
80	1.003908
81	0.992769
82	0.983746
83	0.972619
84	0.968833
85	0.959904
86	0.942906
87	0.930193
88	0.908514
89	0.88838
90	0.855959
91	0.832758
92	0.808464
93	0.778428
94	0.747274
95	0.717867
96	0.685044
97	0.651036
98	0.610451
99	0.574448
100	0.538563