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aih-tih-sc-a51633-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-a51633-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 3:56 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-a51633-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-a51633-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 20:42:03 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
78345950208	77403853988	10012	69395996574	5361078536	2337706263	309062603	0	0	0	5985996	241795869	1463463	0.024158	0.975842	0	0.896544	0.069261	0.030201	0.003993	0.965806	0.954192	0	0.530027	0.580393	0.720262	0.89567			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.29072
1	0.341006
2	0.406772
3	0.481962
4	0.558929
5	0.624004
6	0.683089
7	0.740555
8	0.792201
9	0.841368
10	0.884684
11	0.929279
12	0.969906
13	1.000537
14	1.020655
15	1.037602
16	1.057243
17	1.076859
18	1.087966
19	1.101444
20	1.114699
21	1.12803
22	1.136946
23	1.142168
24	1.146046
25	1.143898
26	1.145244
27	1.147681
28	1.148797
29	1.146632
30	1.147492
31	1.147527
32	1.146629
33	1.148936
34	1.149824
35	1.152888
36	1.146523
37	1.143907
38	1.154473
39	1.157591
40	1.15868
41	1.165938
42	1.175486
43	1.180063
44	1.181741
45	1.18614
46	1.184259
47	1.182537
48	1.174978
49	1.172219
50	1.166011
51	1.160191
52	1.154319
53	1.150739
54	1.154233
55	1.154122
56	1.145239
57	1.144049
58	1.141372
59	1.133774
60	1.131863
61	1.132511
62	1.136026
63	1.127342
64	1.130252
65	1.129672
66	1.120825
67	1.109708
68	1.100073
69	1.09216
70	1.082147
71	1.06624
72	1.059069
73	1.048905
74	1.039868
75	1.032702
76	1.021871
77	1.005165
78	0.994947
79	0.985546
80	0.972196
81	0.958178
82	0.938833
83	0.922749
84	0.911868
85	0.897149
86	0.881971
87	0.874285
88	0.859715
89	0.841422
90	0.824157
91	0.811358
92	0.791872
93	0.761875
94	0.736498
95	0.711171
96	0.68703
97	0.663801
98	0.633471
99	0.600329
100	0.56346