RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354050.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) = 77,380,415 / 77,301,187 read pairs aligned = 77,296,257 total alignments = 164,415,769 secondary alignments = 9,734,167 non-unique alignments = 16,163,047 aligned to genes = 132,389,326 ambiguous alignments = 413,044 no feature assigned = 14,638,973 not aligned = 9,619,044 >>>>>>> Reads genomic origin exonic = 132,389,326 (90.04%) intronic = 8,397,168 (5.71%) intergenic = 6,241,805 (4.25%) overlapping exon = 5,189,232 (3.53%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.17 5'-3' bias = 2.02 >>>>>>> Junction analysis reads at junctions = 47,613,401 ACCT : 5.39% AGGT : 4.71% AGGA : 3.66% ATCT : 3.48% TCCT : 3.35% GCCT : 3.16% AGCT : 2.73% AGGC : 2.43% AGAT : 2.35% CCCT : 2.3% TTCT : 2.11%