RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354093.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) = 34,363,830 / 34,335,618 read pairs aligned = 34,332,658 total alignments = 72,581,466 secondary alignments = 3,882,018 non-unique alignments = 6,591,576 aligned to genes = 57,633,537 ambiguous alignments = 165,409 no feature assigned = 7,930,936 not aligned = 5,652,016 >>>>>>> Reads genomic origin exonic = 57,633,537 (87.9%) intronic = 4,864,754 (7.42%) intergenic = 3,066,182 (4.68%) overlapping exon = 2,335,073 (3.56%) >>>>>>> Transcript coverage profile 5' bias = 0.31 3' bias = 0.17 5'-3' bias = 2.23 >>>>>>> Junction analysis reads at junctions = 15,853,368 ACCT : 5.34% AGGT : 4.93% AGGA : 3.68% ATCT : 3.65% TCCT : 3.43% GCCT : 2.9% AGCT : 2.72% CCCT : 2.38% AGGC : 2.36% AGAT : 2.31% TTCT : 2.11%