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aih-tih-sc-9e2647-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-9e2647-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:53 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-9e2647-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-9e2647-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 20:47:04 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
77203371934	76489850798	6000	68778750975	5253295140	2211738744	246059939	0	0	0	3752372	244130537	1203352	0.015138	0.984862	0	0.899188	0.06868	0.028915	0.003217	0.967868	0.958922	0	0.504177	0.576265	0.760598	0.872638			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.287891
1	0.322653
2	0.377168
3	0.443696
4	0.510766
5	0.575914
6	0.632305
7	0.680084
8	0.737518
9	0.780334
10	0.830929
11	0.884223
12	0.936992
13	0.978947
14	1.009081
15	1.037733
16	1.061996
17	1.088119
18	1.097769
19	1.115096
20	1.124497
21	1.136589
22	1.150145
23	1.160134
24	1.161128
25	1.166841
26	1.171789
27	1.171141
28	1.16678
29	1.167766
30	1.164749
31	1.163389
32	1.156556
33	1.157755
34	1.152735
35	1.152178
36	1.154918
37	1.156819
38	1.159548
39	1.158836
40	1.156891
41	1.157881
42	1.158885
43	1.161723
44	1.162285
45	1.162248
46	1.15621
47	1.163873
48	1.16323
49	1.162231
50	1.160921
51	1.157131
52	1.15523
53	1.15386
54	1.15926
55	1.161002
56	1.156983
57	1.153153
58	1.154437
59	1.149941
60	1.147041
61	1.14612
62	1.147391
63	1.138301
64	1.133007
65	1.128979
66	1.115794
67	1.108857
68	1.102827
69	1.095691
70	1.084353
71	1.076816
72	1.071367
73	1.066287
74	1.056357
75	1.050486
76	1.039907
77	1.025578
78	1.009075
79	1.001289
80	0.988065
81	0.976791
82	0.966824
83	0.954695
84	0.941
85	0.922629
86	0.904347
87	0.888826
88	0.871191
89	0.855057
90	0.838341
91	0.820734
92	0.795561
93	0.769916
94	0.743695
95	0.715315
96	0.684845
97	0.650373
98	0.613418
99	0.579096
100	0.536906