RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354142.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) = 44,340,367 / 44,316,511 read pairs aligned = 44,310,807 total alignments = 97,107,115 secondary alignments = 8,450,237 non-unique alignments = 13,339,540 aligned to genes = 73,334,836 ambiguous alignments = 244,639 no feature assigned = 9,169,008 not aligned = 2,417,198 >>>>>>> Reads genomic origin exonic = 73,334,836 (88.89%) intronic = 6,301,732 (7.64%) intergenic = 2,867,276 (3.48%) overlapping exon = 3,554,267 (4.31%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.19 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 22,498,601 ACCT : 5.26% AGGT : 4.72% ATCT : 3.65% AGGA : 3.58% TCCT : 3.5% GCCT : 3.04% AGCT : 2.66% CCCT : 2.41% AGGC : 2.33% AGAT : 2.18% TTCT : 2.15%