RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354159.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) = 42,291,419 / 42,204,373 read pairs aligned = 42,193,568 total alignments = 91,808,775 secondary alignments = 7,312,983 non-unique alignments = 10,951,641 aligned to genes = 71,391,544 ambiguous alignments = 314,096 no feature assigned = 8,080,574 not aligned = 10,989,214 >>>>>>> Reads genomic origin exonic = 71,391,544 (89.83%) intronic = 4,658,783 (5.86%) intergenic = 3,421,791 (4.31%) overlapping exon = 3,937,813 (4.95%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.1 5'-3' bias = 2.32 >>>>>>> Junction analysis reads at junctions = 22,436,340 TCCT : 6.03% ACCT : 5.48% ATCT : 4.83% CCCT : 3.92% AGGT : 3.88% AGGA : 2.72% GCCT : 2.31% TCCC : 2.27% AGGC : 2.22% GTCT : 2.14% TTCT : 1.94%