RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354245.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) = 41,221,056 / 41,195,930 read pairs aligned = 41,192,887 total alignments = 88,541,497 secondary alignments = 6,124,511 non-unique alignments = 9,880,692 aligned to genes = 69,580,110 ambiguous alignments = 224,208 no feature assigned = 8,230,866 not aligned = 2,354,474 >>>>>>> Reads genomic origin exonic = 69,580,110 (89.42%) intronic = 5,015,738 (6.45%) intergenic = 3,215,128 (4.13%) overlapping exon = 2,511,066 (3.23%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.22 5'-3' bias = 1.81 >>>>>>> Junction analysis reads at junctions = 20,845,453 ACCT : 5.34% AGGT : 4.7% ATCT : 3.71% AGGA : 3.52% TCCT : 3.41% GCCT : 3.25% AGCT : 2.8% CCCT : 2.65% AGGC : 2.36% TTCT : 2.27% AGAT : 2.2%