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aih-tih-sc-d1f1a3-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-d1f1a3-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 4:01 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-d1f1a3-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT aih-tih-sc-d1f1a3-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 20:39:01 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
72226704517	71357771450	7156	64964277088	4372241008	1813660671	207585527	0	0	0	5307131	245406366	868772	0.021168	0.978832	0	0.910402	0.061272	0.025416	0.002909	0.971674	0.959985	0	0.555521	0.476649	0.739046	0.766071			

## HISTOGRAM	java.lang.Integer
normalized_position	All_Reads.normalized_coverage
0	0.285693
1	0.317808
2	0.363874
3	0.423126
4	0.477899
5	0.522343
6	0.58177
7	0.636029
8	0.69085
9	0.747706
10	0.800896
11	0.851978
12	0.900088
13	0.946374
14	0.986103
15	1.012176
16	1.033974
17	1.049972
18	1.059772
19	1.074798
20	1.086023
21	1.09681
22	1.109421
23	1.120045
24	1.129047
25	1.135548
26	1.136645
27	1.144315
28	1.158548
29	1.168167
30	1.173647
31	1.176366
32	1.166711
33	1.163283
34	1.153405
35	1.15742
36	1.155179
37	1.155055
38	1.158396
39	1.161991
40	1.158362
41	1.157624
42	1.168358
43	1.182737
44	1.191093
45	1.196784
46	1.197329
47	1.197107
48	1.191716
49	1.195134
50	1.185783
51	1.182075
52	1.177992
53	1.173323
54	1.167569
55	1.162199
56	1.159703
57	1.153505
58	1.140777
59	1.130052
60	1.123895
61	1.123076
62	1.118783
63	1.110644
64	1.107908
65	1.10832
66	1.102618
67	1.101578
68	1.103606
69	1.102344
70	1.092995
71	1.083117
72	1.079111
73	1.074613
74	1.072421
75	1.073179
76	1.068754
77	1.062478
78	1.056983
79	1.046643
80	1.030566
81	1.01465
82	1.001999
83	0.980747
84	0.966274
85	0.951364
86	0.930409
87	0.922299
88	0.907452
89	0.889677
90	0.868031
91	0.84605
92	0.821093
93	0.789073
94	0.758288
95	0.728457
96	0.694736
97	0.660016
98	0.622736
99	0.587443
100	0.547149