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aih-tih-sc-6473fb-R1_B23WHYVLT4_1_rna_metrics.txt
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s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/dev_rna_exp0018/B23WHYVLT4/nfcore_rnafusion__fd1be10--20260514-142812/QC/picard/aih-tih-sc-6473fb-R1_B23WHYVLT4_1_rna_metrics.txt
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dev_rna_exp0018_2-fd1be10
Published
May 14, 2026 5:51 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-6473fb-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-6473fb-R1_B23WHYVLT4_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: Thu May 14 23:33:02 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
23954438827	23638050574	2292	21478332427	1410271981	646257448	103186426	0	0	0	2540729	77044311	502793	0.031925	0.968075	0	0.908634	0.059661	0.02734	0.004365	0.968295	0.955506	0	0.625535	0.40144	0.667162	0.653732			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.26861
1	0.298879
2	0.345213
3	0.405471
4	0.464041
5	0.520424
6	0.575868
7	0.622272
8	0.67185
9	0.714847
10	0.750822
11	0.783838
12	0.829098
13	0.867333
14	0.90087
15	0.932889
16	0.956922
17	0.983705
18	0.996388
19	1.013112
20	1.03075
21	1.046711
22	1.065113
23	1.080709
24	1.094929
25	1.103478
26	1.109535
27	1.115059
28	1.126844
29	1.132376
30	1.138341
31	1.141102
32	1.142311
33	1.142112
34	1.146051
35	1.152689
36	1.155945
37	1.161208
38	1.172388
39	1.17024
40	1.169353
41	1.177146
42	1.182442
43	1.18965
44	1.192937
45	1.192862
46	1.181487
47	1.179317
48	1.174705
49	1.181708
50	1.195461
51	1.19289
52	1.189892
53	1.19614
54	1.192098
55	1.184952
56	1.182861
57	1.173199
58	1.17213
59	1.176158
60	1.181612
61	1.186468
62	1.190804
63	1.172581
64	1.164546
65	1.15893
66	1.145044
67	1.134966
68	1.134607
69	1.135546
70	1.134642
71	1.127564
72	1.120085
73	1.111594
74	1.108163
75	1.104122
76	1.097808
77	1.091508
78	1.081777
79	1.064281
80	1.049855
81	1.037074
82	1.020536
83	1.007039
84	0.995415
85	0.98098
86	0.966713
87	0.956468
88	0.937848
89	0.916431
90	0.882674
91	0.850618
92	0.82026
93	0.786348
94	0.756831
95	0.732999
96	0.699758
97	0.662042
98	0.620207
99	0.580235
100	0.541398