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aih-tih-sc-377071-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-377071-R1_A23YTGFLT4_1_rna_metrics.txt
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:20 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-377071-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-377071-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 20:16:56 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
76965054414	76132579890	5596	67895701627	5660685880	2280430602	295756185	0	0	0	3763471	241372347	1267191	0.015353	0.984647	0	0.891809	0.074353	0.029953	0.003885	0.966162	0.955711	0	0.503144	0.542589	0.779448	0.794253			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.271173
1	0.304607
2	0.349067
3	0.408964
4	0.476623
5	0.541345
6	0.601493
7	0.659116
8	0.718597
9	0.771734
10	0.816121
11	0.861083
12	0.909176
13	0.952171
14	0.978932
15	1.001328
16	1.034153
17	1.055546
18	1.070134
19	1.083427
20	1.098245
21	1.113336
22	1.125999
23	1.13641
24	1.148395
25	1.15379
26	1.158148
27	1.16319
28	1.166351
29	1.168193
30	1.172382
31	1.168026
32	1.156724
33	1.159007
34	1.155353
35	1.15244
36	1.15262
37	1.153842
38	1.167238
39	1.168854
40	1.169954
41	1.171284
42	1.176484
43	1.185546
44	1.187171
45	1.201816
46	1.199721
47	1.200241
48	1.197387
49	1.19866
50	1.184874
51	1.182184
52	1.177699
53	1.177278
54	1.174215
55	1.163916
56	1.155528
57	1.150337
58	1.14274
59	1.134565
60	1.127398
61	1.128944
62	1.136747
63	1.136329
64	1.138219
65	1.133095
66	1.123306
67	1.111956
68	1.107725
69	1.10035
70	1.089899
71	1.08253
72	1.074544
73	1.066683
74	1.059683
75	1.055746
76	1.048135
77	1.039047
78	1.036322
79	1.026293
80	1.008447
81	0.994756
82	0.983101
83	0.970492
84	0.956954
85	0.941346
86	0.918311
87	0.901337
88	0.880662
89	0.864022
90	0.84542
91	0.830438
92	0.807789
93	0.779448
94	0.746197
95	0.712113
96	0.67922
97	0.64958
98	0.615207
99	0.580394
100	0.543486