## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=M2WTM_1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/M2WTM_1_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 10:57:14 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 1229891775 1229776588 182691927 593464048 228705078 50908292 174007243 0 0 0 25948 10620312 23015 0.002437 0.997563 0.148557 0.482579 0.185973 0.041396 0.141495 0.668552 0.668489 0 0.887156 0.031753 0.632677 0.051742 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.031854 1 0.042497 2 0.073564 3 0.130644 4 0.179899 5 0.261975 6 0.366344 7 0.450476 8 0.516733 9 0.573791 10 0.617663 11 0.648299 12 0.720367 13 0.771286 14 0.798988 15 0.8033 16 0.814672 17 0.85638 18 0.885084 19 0.907847 20 0.936203 21 0.972609 22 0.975887 23 0.986667 24 1.002184 25 1.034647 26 1.060739 27 1.087415 28 1.112131 29 1.098925 30 1.116845 31 1.126908 32 1.138042 33 1.137906 34 1.170805 35 1.180625 36 1.183519 37 1.175237 38 1.152857 39 1.146183 40 1.165473 41 1.19501 42 1.196962 43 1.191695 44 1.183148 45 1.177694 46 1.174472 47 1.147437 48 1.151222 49 1.172497 50 1.172765 51 1.157667 52 1.149518 53 1.165865 54 1.171501 55 1.171168 56 1.178545 57 1.185344 58 1.210235 59 1.233026 60 1.24291 61 1.216236 62 1.187538 63 1.190001 64 1.179653 65 1.186101 66 1.169118 67 1.159982 68 1.157892 69 1.134328 70 1.125833 71 1.145868 72 1.149474 73 1.155589 74 1.125279 75 1.122586 76 1.123883 77 1.147326 78 1.135662 79 1.117373 80 1.108448 81 1.111042 82 1.121906 83 1.118585 84 1.124689 85 1.145571 86 1.14023 87 1.138583 88 1.161593 89 1.185412 90 1.175796 91 1.17962 92 1.184839 93 1.131948 94 1.070591 95 1.020285 96 0.968199 97 0.863177 98 0.667693 99 0.406591 100 0.155738