RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354370.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) = 36,010,493 / 35,966,609 read pairs aligned = 35,945,505 total alignments = 77,885,943 secondary alignments = 5,908,841 non-unique alignments = 9,901,506 aligned to genes = 60,770,952 ambiguous alignments = 260,415 no feature assigned = 6,553,372 not aligned = 3,460,168 >>>>>>> Reads genomic origin exonic = 60,770,952 (90.27%) intronic = 3,803,671 (5.65%) intergenic = 2,749,701 (4.08%) overlapping exon = 2,956,712 (4.39%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.22 5'-3' bias = 2.18 >>>>>>> Junction analysis reads at junctions = 20,368,782 ACCT : 5.5% TCCT : 4.9% ATCT : 4.58% AGGT : 4.16% CCCT : 3.33% GCCT : 3.32% AGGA : 2.84% TTCT : 2.33% AGCT : 2.2% AGGC : 2.18% TCCC : 2.03%