## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_PBS2_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_PBS2_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 06:14:25 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 2724946165 2724810537 47375795 1643873294 619928625 152410648 261222175 0 0 0 10902971 10764566 71473 0.503194 0.496806 0.017387 0.603298 0.227513 0.055934 0.095868 0.830811 0.830769 0 0.434866 0.305879 0.254318 1.160557 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.087646 1 0.144292 2 0.24811 3 0.366063 4 0.448561 5 0.541119 6 0.623299 7 0.688309 8 0.74406 9 0.790339 10 0.829406 11 0.865807 12 0.90131 13 0.934426 14 0.961235 15 0.988545 16 1.007758 17 1.027915 18 1.045203 19 1.058236 20 1.073477 21 1.086576 22 1.100052 23 1.110742 24 1.119693 25 1.131807 26 1.14077 27 1.149459 28 1.163968 29 1.175233 30 1.181405 31 1.193474 32 1.202727 33 1.211073 34 1.210561 35 1.217897 36 1.221403 37 1.228606 38 1.237307 39 1.244433 40 1.247622 41 1.252775 42 1.252135 43 1.249074 44 1.245965 45 1.24478 46 1.246266 47 1.243016 48 1.240462 49 1.23846 50 1.23754 51 1.237944 52 1.235692 53 1.235376 54 1.237431 55 1.23525 56 1.234688 57 1.227432 58 1.224141 59 1.223832 60 1.22699 61 1.220468 62 1.211994 63 1.207032 64 1.208695 65 1.20418 66 1.189763 67 1.174843 68 1.167412 69 1.161822 70 1.158385 71 1.158876 72 1.152546 73 1.146316 74 1.137843 75 1.123827 76 1.107875 77 1.095484 78 1.085755 79 1.07682 80 1.057045 81 1.041617 82 1.028921 83 1.015016 84 0.992829 85 0.971241 86 0.936861 87 0.906879 88 0.870226 89 0.825671 90 0.77889 91 0.73241 92 0.680719 93 0.619892 94 0.545693 95 0.462251 96 0.371335 97 0.273347 98 0.176994 99 0.094574 100 0.045347