RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354283.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) = 42,649,122 / 42,613,151 read pairs aligned = 42,608,922 total alignments = 90,274,213 secondary alignments = 5,011,940 non-unique alignments = 8,354,323 aligned to genes = 72,315,358 ambiguous alignments = 243,279 no feature assigned = 8,991,031 not aligned = 2,996,667 >>>>>>> Reads genomic origin exonic = 72,315,358 (88.94%) intronic = 5,750,993 (7.07%) intergenic = 3,240,038 (3.98%) overlapping exon = 2,943,711 (3.62%) >>>>>>> Transcript coverage profile 5' bias = 0.45 3' bias = 0.15 5'-3' bias = 2.11 >>>>>>> Junction analysis reads at junctions = 25,562,411 ACCT : 5.42% AGGT : 4.85% AGGA : 3.75% ATCT : 3.56% TCCT : 3.43% GCCT : 2.88% AGCT : 2.71% AGGC : 2.42% CCCT : 2.34% AGAT : 2.33% TTCT : 2.25%