## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1221_S42.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1221_S42_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 21:56:51 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
2754287345 2727550835 2380143 2400643463 197498918 94951215 32077096 0 0 0 82025 8016569 44319 0.010128 0.989872 0.000873 0.880146 0.072409 0.034812 0.01176 0.952555 0.943308 0 0.579755 0.568567 0.670525 0.715967
## HISTOGRAM java.lang.Integer
normalized_position All_Reads.normalized_coverage
0 0.31384
1 0.35613
2 0.432987
3 0.515289
4 0.587595
5 0.660486
6 0.726424
7 0.780129
8 0.829338
9 0.872901
10 0.909585
11 0.939608
12 0.975934
13 1.012808
14 1.036853
15 1.064561
16 1.084072
17 1.10147
18 1.109069
19 1.132917
20 1.151881
21 1.16543
22 1.174495
23 1.178809
24 1.186087
25 1.189214
26 1.192396
27 1.188338
28 1.186295
29 1.17864
30 1.160312
31 1.153343
32 1.14244
33 1.147909
34 1.149988
35 1.154553
36 1.15302
37 1.14338
38 1.135031
39 1.12947
40 1.121112
41 1.119347
42 1.12874
43 1.131274
44 1.135245
45 1.133415
46 1.131511
47 1.129232
48 1.12542
49 1.129481
50 1.140017
51 1.13864
52 1.138577
53 1.134826
54 1.137382
55 1.133095
56 1.131532
57 1.128972
58 1.124459
59 1.119512
60 1.114492
61 1.116643
62 1.111405
63 1.105245
64 1.098802
65 1.095564
66 1.094848
67 1.08728
68 1.080188
69 1.078516
70 1.07072
71 1.063914
72 1.056756
73 1.05226
74 1.043466
75 1.036107
76 1.033195
77 1.022765
78 1.01718
79 1.013339
80 0.997186
81 0.981692
82 0.966946
83 0.953471
84 0.935427
85 0.918758
86 0.89125
87 0.878174
88 0.875717
89 0.855333
90 0.837316
91 0.807179
92 0.787559
93 0.76148
94 0.727603
95 0.692064
96 0.655598
97 0.625537
98 0.577016
99 0.535906
100 0.494773