## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=8wk_ASNase1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/8wk_ASNase1_metrics MINIMUM_LENGTH=500 RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Mar 09 06:14:35 EDT 2020 ## 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 3270041953 3269917245 61023599 2021626486 761944706 129807076 295515378 0 0 0 13410346 13285708 97757 0.502334 0.497666 0.018662 0.61825 0.233017 0.039697 0.090374 0.851267 0.851234 0 0.423521 0.305778 0.251835 1.200523 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.086549 1 0.14413 2 0.251345 3 0.366307 4 0.448669 5 0.548542 6 0.634751 7 0.702583 8 0.76029 9 0.808225 10 0.84641 11 0.881256 12 0.914404 13 0.945945 14 0.97028 15 0.99846 16 1.017896 17 1.038587 18 1.058682 19 1.076999 20 1.095663 21 1.108475 22 1.123909 23 1.134831 24 1.143775 25 1.157616 26 1.16888 27 1.180089 28 1.192431 29 1.202827 30 1.207903 31 1.218681 32 1.225583 33 1.228702 34 1.238424 35 1.244097 36 1.23838 37 1.242258 38 1.248021 39 1.253092 40 1.255035 41 1.252721 42 1.247687 43 1.245662 44 1.244229 45 1.24238 46 1.240418 47 1.23773 48 1.235515 49 1.233247 50 1.233561 51 1.230931 52 1.228129 53 1.229488 54 1.229695 55 1.226745 56 1.226202 57 1.220767 58 1.216404 59 1.217388 60 1.217939 61 1.213893 62 1.206436 63 1.20262 64 1.199854 65 1.188026 66 1.176429 67 1.165037 68 1.157283 69 1.150656 70 1.147409 71 1.141875 72 1.131963 73 1.123073 74 1.109606 75 1.092929 76 1.083485 77 1.070242 78 1.0619 79 1.055881 80 1.03816 81 1.020529 82 1.006108 83 0.989266 84 0.969848 85 0.947981 86 0.925713 87 0.895605 88 0.859838 89 0.816944 90 0.770431 91 0.723421 92 0.670075 93 0.61153 94 0.540789 95 0.458106 96 0.366562 97 0.269977 98 0.173871 99 0.091549 100 0.046045