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aih-tih-sc-fe8311-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-fe8311-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:36 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-fe8311-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-fe8311-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 20:22:04 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
75249593558	74316440942	4612	66380617718	5720716171	1909071745	306030696	0	0	0	10616921	235785683	1027044	0.043088	0.956912	0	0.893216	0.076978	0.025688	0.004118	0.970194	0.958162	0	0.534654	0.51672	0.677516	0.851617			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.295987
1	0.330659
2	0.378554
3	0.435957
4	0.490667
5	0.536827
6	0.597528
7	0.659699
8	0.7174
9	0.766531
10	0.813456
11	0.863183
12	0.912909
13	0.961709
14	1.004252
15	1.037183
16	1.05968
17	1.072584
18	1.078061
19	1.087376
20	1.1002
21	1.117904
22	1.139532
23	1.157051
24	1.166968
25	1.175506
26	1.18411
27	1.190156
28	1.190776
29	1.190373
30	1.193677
31	1.195948
32	1.18962
33	1.186881
34	1.17735
35	1.179595
36	1.178712
37	1.175472
38	1.177966
39	1.176419
40	1.174989
41	1.170727
42	1.177353
43	1.18773
44	1.191956
45	1.194673
46	1.194612
47	1.195749
48	1.1904
49	1.192475
50	1.181564
51	1.175183
52	1.169258
53	1.162802
54	1.162346
55	1.163028
56	1.162053
57	1.153518
58	1.142373
59	1.13401
60	1.129277
61	1.129589
62	1.131366
63	1.124249
64	1.118068
65	1.113195
66	1.104857
67	1.099925
68	1.100792
69	1.093041
70	1.080547
71	1.072107
72	1.071713
73	1.063411
74	1.058482
75	1.050997
76	1.042702
77	1.029656
78	1.025096
79	1.014226
80	1.000592
81	0.984827
82	0.97604
83	0.95326
84	0.937627
85	0.921601
86	0.900065
87	0.888341
88	0.868124
89	0.845832
90	0.819778
91	0.797616
92	0.773789
93	0.748644
94	0.719985
95	0.691109
96	0.660323
97	0.628879
98	0.593246
99	0.55973
100	0.528228