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aih-tih-sc-816ec7-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-816ec7-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:48 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-816ec7-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-816ec7-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 20:33:05 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
74653855755	73841441224	4424	66675998479	5087944951	1816026145	261467225	0	0	0	9993370	239902006	1174833	0.03999	0.96001	0	0.902962	0.068904	0.024594	0.003541	0.971865	0.961289	0	0.529583	0.573985	0.723481	0.898611			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.262531
1	0.305048
2	0.360451
3	0.429492
4	0.50086
5	0.569942
6	0.628123
7	0.688095
8	0.745031
9	0.796986
10	0.842651
11	0.885909
12	0.932684
13	0.97197
14	1.003408
15	1.031424
16	1.060189
17	1.081963
18	1.093951
19	1.109596
20	1.129077
21	1.144308
22	1.152967
23	1.165959
24	1.174323
25	1.174575
26	1.181405
27	1.187686
28	1.191242
29	1.187882
30	1.185232
31	1.18922
32	1.180114
33	1.182203
34	1.180658
35	1.184011
36	1.179898
37	1.17816
38	1.177604
39	1.177228
40	1.17237
41	1.170332
42	1.173826
43	1.172502
44	1.172563
45	1.185401
46	1.175466
47	1.172904
48	1.168956
49	1.166068
50	1.164947
51	1.156367
52	1.144841
53	1.139692
54	1.143075
55	1.143648
56	1.137332
57	1.131238
58	1.123521
59	1.117868
60	1.11426
61	1.114961
62	1.120412
63	1.114182
64	1.114326
65	1.116939
66	1.109985
67	1.103466
68	1.097736
69	1.096424
70	1.08907
71	1.080972
72	1.074284
73	1.066692
74	1.060403
75	1.055041
76	1.045729
77	1.034587
78	1.02546
79	1.01175
80	0.996769
81	0.982059
82	0.96835
83	0.95841
84	0.945914
85	0.93128
86	0.916648
87	0.90705
88	0.885555
89	0.862275
90	0.83717
91	0.817307
92	0.788046
93	0.759021
94	0.723001
95	0.686977
96	0.652082
97	0.615872
98	0.578536
99	0.543568
100	0.509431