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aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0019/A23WJ53LT4/nfcore_rnafusion__3e501777--20260519-110950/QC/picard/aih-tih-sc-1ffee4-R1_A23WJ53LT4_1_rna_metrics.txt
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dev_rna_exp0019_2-3e501777
Published
May 19, 2026 4:36 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-1ffee4-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-1ffee4-R1_A23WJ53LT4_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: Tue May 19 21:27:01 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
70288261222	69543476475	802	63235436038	4351098748	1764229019	192711868	0	0	0	3697590	224471272	1132055	0.016205	0.983795	0	0.909294	0.062567	0.025369	0.002771	0.97186	0.961562	0	0.501853	0.527412	0.765576	0.766835			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.299112
1	0.334122
2	0.378387
3	0.428767
4	0.475682
5	0.523554
6	0.583801
7	0.635548
8	0.684949
9	0.731088
10	0.777052
11	0.824825
12	0.87091
13	0.91036
14	0.941111
15	0.974292
16	1.004229
17	1.032608
18	1.052928
19	1.064106
20	1.079661
21	1.100407
22	1.12147
23	1.138269
24	1.147292
25	1.157347
26	1.167538
27	1.174314
28	1.180648
29	1.17865
30	1.183143
31	1.183584
32	1.173439
33	1.174645
34	1.170475
35	1.17669
36	1.174093
37	1.168439
38	1.166104
39	1.163253
40	1.159681
41	1.154857
42	1.156473
43	1.159645
44	1.164222
45	1.17639
46	1.174118
47	1.179837
48	1.176875
49	1.176542
50	1.181741
51	1.178224
52	1.172991
53	1.169907
54	1.170637
55	1.172575
56	1.171637
57	1.167866
58	1.160256
59	1.146945
60	1.137747
61	1.135607
62	1.137664
63	1.129002
64	1.13214
65	1.134958
66	1.128775
67	1.121993
68	1.119197
69	1.112974
70	1.100545
71	1.090165
72	1.085401
73	1.082809
74	1.075336
75	1.067939
76	1.058217
77	1.039504
78	1.029848
79	1.021943
80	1.009835
81	0.998209
82	0.991719
83	0.977048
84	0.963836
85	0.952705
86	0.932488
87	0.916992
88	0.895384
89	0.8777
90	0.858869
91	0.840058
92	0.814133
93	0.789288
94	0.758734
95	0.731908
96	0.700659
97	0.6675
98	0.63107
99	0.5955
100	0.560051