RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354223.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) = 38,739,783 / 38,712,185 read pairs aligned = 38,707,237 total alignments = 82,306,634 secondary alignments = 4,854,666 non-unique alignments = 8,203,238 aligned to genes = 67,238,165 ambiguous alignments = 250,829 no feature assigned = 6,333,840 not aligned = 5,575,590 >>>>>>> Reads genomic origin exonic = 67,238,165 (91.39%) intronic = 3,833,122 (5.21%) intergenic = 2,500,718 (3.4%) overlapping exon = 2,511,626 (3.41%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.21 5'-3' bias = 1.64 >>>>>>> Junction analysis reads at junctions = 22,673,084 ACCT : 5.45% AGGT : 4.74% ATCT : 3.61% TCCT : 3.47% AGGA : 3.36% GCCT : 3.18% AGCT : 2.59% AGGC : 2.41% TTCT : 2.32% CCCT : 2.31% AGAT : 2.1%