RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354233.markdup.sorted.bam gff file = gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf counting algorithm = uniquely-mapped-reads protocol = strand-specific-reverse 5'-3' bias region size = 100 5'-3' bias number of top transcripts = 1000 >>>>>>> Reads alignment reads aligned (left/right) = 35,441,710 / 35,420,204 read pairs aligned = 35,417,097 total alignments = 74,624,108 secondary alignments = 3,762,194 non-unique alignments = 6,244,653 aligned to genes = 58,085,125 ambiguous alignments = 185,103 no feature assigned = 9,843,018 not aligned = 2,047,928 >>>>>>> Reads genomic origin exonic = 58,085,125 (85.51%) intronic = 7,152,969 (10.53%) intergenic = 2,690,049 (3.96%) overlapping exon = 2,376,602 (3.5%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.13 5'-3' bias = 2.49 >>>>>>> Junction analysis reads at junctions = 18,484,905 ACCT : 5.5% AGGT : 4.73% ATCT : 3.62% AGGA : 3.6% TCCT : 3.54% GCCT : 3.05% AGCT : 2.68% AGGC : 2.39% AGAT : 2.3% CCCT : 2.22% TTCT : 2.11%