## htsjdk.samtools.metrics.StringHeader # CollectRnaSeqMetrics REF_FLAT=genes_refFlat RIBOSOMAL_INTERVALS=rRNA_intervalList_sorted STRAND_SPECIFICITY=NONE INPUT=2wk_ASNase1_primary_unique.bam OUTPUT=CollectRnaSeqMetrics/2wk_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 06:14:26 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 2758899638 2758786673 48394605 1649131800 682896589 140812746 237550933 0 0 0 11174803 11074842 73827 0.502246 0.497754 0.017542 0.597774 0.247535 0.051042 0.086107 0.845309 0.845275 0 0.445007 0.273401 0.277198 0.960137 ## HISTOGRAM java.lang.Integer normalized_position All_Reads.normalized_coverage 0 0.080407 1 0.130936 2 0.223708 3 0.329208 4 0.400341 5 0.486888 6 0.565679 7 0.629652 8 0.686479 9 0.735219 10 0.774863 11 0.814875 12 0.852905 13 0.883023 14 0.909089 15 0.938323 16 0.958039 17 0.978591 18 0.997778 19 1.014393 20 1.031567 21 1.045227 22 1.058295 23 1.066342 24 1.077619 25 1.094621 26 1.102243 27 1.120077 28 1.134164 29 1.143447 30 1.148253 31 1.161387 32 1.172833 33 1.182057 34 1.183774 35 1.19329 36 1.198571 37 1.206759 38 1.211462 39 1.219134 40 1.224662 41 1.229177 42 1.230045 43 1.230297 44 1.227533 45 1.225539 46 1.229377 47 1.228609 48 1.231482 49 1.233703 50 1.233134 51 1.232133 52 1.229533 53 1.232577 54 1.236428 55 1.23886 56 1.244035 57 1.243271 58 1.242393 59 1.244166 60 1.248235 61 1.24533 62 1.240297 63 1.237337 64 1.23687 65 1.229029 66 1.22113 67 1.212124 68 1.207816 69 1.206237 70 1.201234 71 1.200633 72 1.193756 73 1.187096 74 1.178703 75 1.165388 76 1.157077 77 1.146789 78 1.137264 79 1.130836 80 1.112769 81 1.094657 82 1.081291 83 1.065296 84 1.046919 85 1.023784 86 0.998422 87 0.967565 88 0.932827 89 0.887232 90 0.835307 91 0.783909 92 0.729173 93 0.664466 94 0.586472 95 0.496486 96 0.400918 97 0.295762 98 0.190215 99 0.100706 100 0.04749