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aih-tih-sc-c35cc3-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-c35cc3-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:35 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-c35cc3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-c35cc3-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 20:04:47 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
59168878247	58425091230	7670	52180778586	4342564760	1657098801	244641413	0	0	0	5247376	203732988	794162	0.025109	0.974891	0	0.893123	0.074327	0.028363	0.004187	0.96745	0.955288	0	0.581012	0.427804	0.733893	0.681315			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.267198
1	0.29514
2	0.334443
3	0.384471
4	0.430057
5	0.476993
6	0.535392
7	0.588706
8	0.642996
9	0.692702
10	0.737379
11	0.783476
12	0.828036
13	0.867997
14	0.9045
15	0.941385
16	0.974724
17	1.000542
18	1.01743
19	1.036313
20	1.062707
21	1.089107
22	1.109878
23	1.127918
24	1.138006
25	1.147061
26	1.153074
27	1.16037
28	1.168029
29	1.172463
30	1.177556
31	1.178293
32	1.168934
33	1.179785
34	1.176526
35	1.180576
36	1.186488
37	1.184637
38	1.188217
39	1.186601
40	1.179662
41	1.176721
42	1.181597
43	1.184771
44	1.18664
45	1.201713
46	1.201633
47	1.204666
48	1.203401
49	1.196607
50	1.185468
51	1.185838
52	1.176922
53	1.172825
54	1.179239
55	1.176854
56	1.173567
57	1.166894
58	1.154977
59	1.147969
60	1.143675
61	1.141072
62	1.141822
63	1.135819
64	1.140175
65	1.147109
66	1.137382
67	1.130396
68	1.131989
69	1.127653
70	1.116296
71	1.105311
72	1.101604
73	1.099205
74	1.094176
75	1.086852
76	1.076398
77	1.07052
78	1.067776
79	1.053794
80	1.03815
81	1.026962
82	1.009466
83	0.998168
84	0.985937
85	0.970953
86	0.951478
87	0.946383
88	0.931639
89	0.914234
90	0.892157
91	0.868578
92	0.833982
93	0.798035
94	0.761359
95	0.724565
96	0.687381
97	0.650722
98	0.609483
99	0.568654
100	0.528765