RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354274.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) = 23,569,142 / 23,558,672 read pairs aligned = 23,555,663 total alignments = 54,185,546 secondary alignments = 7,057,732 non-unique alignments = 9,301,734 aligned to genes = 33,067,568 ambiguous alignments = 160,673 no feature assigned = 10,048,298 not aligned = 1,368,460 >>>>>>> Reads genomic origin exonic = 33,067,568 (76.69%) intronic = 5,031,996 (11.67%) intergenic = 5,016,302 (11.63%) overlapping exon = 1,551,098 (3.6%) >>>>>>> Transcript coverage profile 5' bias = 0.21 3' bias = 0.23 5'-3' bias = 2.08 >>>>>>> Junction analysis reads at junctions = 14,157,551 ACCT : 4.76% TCCT : 4.62% AGGT : 4.47% ATCT : 3.96% AGGA : 3.08% CCCT : 2.88% GCCT : 2.51% AGGC : 2.31% AGCT : 2.2% TTCT : 2.16% GTCT : 2.11%