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aih-tih-sc-f0dbdf-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-f0dbdf-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:39 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-f0dbdf-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-f0dbdf-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
74078246369	73219235164	8894	65995875240	5051348102	1895318686	276684242	0	0	0	8615289	238448131	1042466	0.034871	0.965129	0	0.901346	0.068989	0.025886	0.003779	0.970336	0.959083	0	0.545462	0.53887	0.701819	0.8582			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.272242
1	0.306668
2	0.370286
3	0.439501
4	0.512246
5	0.582366
6	0.644984
7	0.698484
8	0.754698
9	0.803542
10	0.843813
11	0.886943
12	0.932084
13	0.975242
14	1.005096
15	1.031079
16	1.058012
17	1.076148
18	1.082607
19	1.098022
20	1.111178
21	1.12448
22	1.145515
23	1.159327
24	1.169528
25	1.175073
26	1.178219
27	1.177789
28	1.176776
29	1.177042
30	1.182729
31	1.184524
32	1.179339
33	1.18569
34	1.178261
35	1.180758
36	1.182454
37	1.17726
38	1.172452
39	1.178011
40	1.177105
41	1.179915
42	1.177432
43	1.17569
44	1.176954
45	1.186162
46	1.182981
47	1.184288
48	1.183326
49	1.183448
50	1.181159
51	1.174212
52	1.162318
53	1.160157
54	1.162988
55	1.154257
56	1.140063
57	1.131608
58	1.123518
59	1.119791
60	1.111456
61	1.115003
62	1.111981
63	1.1076
64	1.102789
65	1.104697
66	1.106643
67	1.103257
68	1.097885
69	1.09002
70	1.07562
71	1.064568
72	1.062841
73	1.056823
74	1.052996
75	1.044471
76	1.035824
77	1.02408
78	1.017414
79	1.009202
80	0.990992
81	0.974616
82	0.963496
83	0.94943
84	0.932214
85	0.919088
86	0.901359
87	0.890662
88	0.877837
89	0.857952
90	0.832857
91	0.808535
92	0.787972
93	0.762626
94	0.729992
95	0.697321
96	0.667614
97	0.634577
98	0.600355
99	0.568392
100	0.533407