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aih-tih-sc-776623-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-776623-R1_A23YTGFLT4_1_rna_metrics.txt
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2.8 KB
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dev_rna_exp0021-d2190e45
Published
Jun 03, 2026 4:12 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-776623-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-776623-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 21:07:54 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
73556341140	72647220877	3840	65618135527	4804799578	1970466781	253815151	0	0	0	11129059	236528845	1152286	0.044937	0.955063	0	0.903244	0.066139	0.027124	0.003494	0.969382	0.957401	0	0.644158	0.498391	0.58196	0.933675			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.294749
1	0.328718
2	0.379951
3	0.443522
4	0.499236
5	0.553726
6	0.622306
7	0.686543
8	0.753505
9	0.808454
10	0.862202
11	0.920415
12	0.972274
13	1.014869
14	1.043264
15	1.069804
16	1.090685
17	1.108063
18	1.121892
19	1.129024
20	1.144521
21	1.163241
22	1.178665
23	1.201602
24	1.223655
25	1.233905
26	1.234908
27	1.238074
28	1.244389
29	1.240665
30	1.240842
31	1.237499
32	1.228205
33	1.228768
34	1.222364
35	1.231614
36	1.236004
37	1.226056
38	1.219322
39	1.206899
40	1.1922
41	1.181897
42	1.178857
43	1.184256
44	1.186459
45	1.199304
46	1.198423
47	1.191031
48	1.181662
49	1.179142
50	1.189693
51	1.185919
52	1.179892
53	1.173436
54	1.175491
55	1.16944
56	1.16151
57	1.158617
58	1.14686
59	1.134355
60	1.126655
61	1.121337
62	1.118271
63	1.105891
64	1.097453
65	1.093305
66	1.085161
67	1.087095
68	1.085139
69	1.074364
70	1.062936
71	1.050101
72	1.039704
73	1.032697
74	1.019011
75	1.005273
76	0.991027
77	0.974978
78	0.9649
79	0.956264
80	0.941812
81	0.926378
82	0.916008
83	0.906316
84	0.892381
85	0.878756
86	0.857979
87	0.848297
88	0.832464
89	0.812548
90	0.785493
91	0.75591
92	0.723871
93	0.687462
94	0.65603
95	0.627121
96	0.595503
97	0.566596
98	0.536301
99	0.506024
100	0.472674