## htsjdk.samtools.metrics.StringHeader
# CollectRnaSeqMetrics --REF_FLAT ref_annot.gtf.refflat --RIBOSOMAL_INTERVALS ctat_ref_annot.interval_list --STRAND_SPECIFICITY NONE --INPUT rna_s1200_S21.Aligned.sortedByCoord.out.bam --OUTPUT rna_s1200_S21_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 21:56:50 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
2795883347 2772797282 300 2470896529 201902141 86792356 13205956 0 0 0 128383 8100715 41447 0.015601 0.984399 0 0.891121 0.072815 0.031301 0.004763 0.963936 0.955976 0 0.563571 0.543049 0.68164 0.755191
## HISTOGRAM java.lang.Integer
normalized_position All_Reads.normalized_coverage
0 0.309711
1 0.346553
2 0.40561
3 0.470656
4 0.537896
5 0.614158
6 0.684648
7 0.738329
8 0.789637
9 0.828806
10 0.866681
11 0.904154
12 0.940791
13 0.977607
14 1.009535
15 1.043883
16 1.072314
17 1.084224
18 1.091344
19 1.111463
20 1.129586
21 1.144436
22 1.153642
23 1.165019
24 1.179679
25 1.187506
26 1.195764
27 1.199859
28 1.200035
29 1.192135
30 1.179665
31 1.172731
32 1.161183
33 1.168447
34 1.168088
35 1.16902
36 1.172234
37 1.16216
38 1.154721
39 1.146874
40 1.134038
41 1.130972
42 1.139922
43 1.144444
44 1.143409
45 1.14165
46 1.140949
47 1.141277
48 1.137295
49 1.139882
50 1.150497
51 1.150395
52 1.14884
53 1.145621
54 1.147696
55 1.147571
56 1.152178
57 1.152211
58 1.146733
59 1.143444
60 1.141569
61 1.144566
62 1.138619
63 1.130625
64 1.120877
65 1.116734
66 1.115729
67 1.10746
68 1.100787
69 1.095879
70 1.090612
71 1.088397
72 1.088978
73 1.084292
74 1.077125
75 1.065958
76 1.055391
77 1.039038
78 1.029497
79 1.021956
80 0.998467
81 0.976544
82 0.960909
83 0.944819
84 0.922483
85 0.900228
86 0.870929
87 0.862738
88 0.860338
89 0.836321
90 0.815203
91 0.784223
92 0.759136
93 0.734634
94 0.705999
95 0.676786
96 0.6461
97 0.62318
98 0.581398
99 0.542495
100 0.501162