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aih-tih-sc-150e73-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-150e73-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:43 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-150e73-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-150e73-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 20:35:00 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
72575460523	71642422858	9630	64456995367	5102803977	1843583736	239030148	0	0	0	5849081	240071332	1333089	0.023784	0.976216	0	0.899704	0.071226	0.025733	0.003336	0.97093	0.958448	0	0.564195	0.539492	0.665454	0.879973			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.262673
1	0.306731
2	0.372526
3	0.442219
4	0.512492
5	0.583201
6	0.640798
7	0.69666
8	0.755861
9	0.802081
10	0.851243
11	0.906811
12	0.961498
13	1.006286
14	1.02991
15	1.050071
16	1.077518
17	1.101623
18	1.119163
19	1.139822
20	1.16229
21	1.175872
22	1.178597
23	1.182203
24	1.190037
25	1.187217
26	1.182374
27	1.179324
28	1.176631
29	1.179306
30	1.183794
31	1.179313
32	1.166105
33	1.169626
34	1.166615
35	1.168348
36	1.167649
37	1.167362
38	1.172609
39	1.166939
40	1.163335
41	1.165403
42	1.173264
43	1.175172
44	1.171938
45	1.185631
46	1.182465
47	1.177555
48	1.172617
49	1.16888
50	1.166399
51	1.159839
52	1.146235
53	1.146181
54	1.149461
55	1.148913
56	1.141083
57	1.133303
58	1.127765
59	1.121113
60	1.120576
61	1.123014
62	1.132874
63	1.12048
64	1.11942
65	1.118495
66	1.109384
67	1.104839
68	1.100265
69	1.094833
70	1.081369
71	1.061663
72	1.058643
73	1.055593
74	1.048191
75	1.044398
76	1.036744
77	1.024696
78	1.013315
79	1.004232
80	0.989771
81	0.973195
82	0.952114
83	0.936858
84	0.918852
85	0.903147
86	0.88382
87	0.871505
88	0.860112
89	0.842919
90	0.823168
91	0.80883
92	0.782406
93	0.750742
94	0.715717
95	0.681228
96	0.651545
97	0.618577
98	0.574431
99	0.537416
100	0.499844