RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354342.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) = 39,258,126 / 39,223,657 read pairs aligned = 39,217,100 total alignments = 82,720,236 secondary alignments = 4,238,453 non-unique alignments = 7,101,497 aligned to genes = 65,369,703 ambiguous alignments = 216,867 no feature assigned = 9,789,173 not aligned = 9,131,441 >>>>>>> Reads genomic origin exonic = 65,369,703 (86.98%) intronic = 6,894,317 (9.17%) intergenic = 2,894,856 (3.85%) overlapping exon = 2,613,774 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.26 3' bias = 0.15 5'-3' bias = 1.92 >>>>>>> Junction analysis reads at junctions = 22,810,658 ACCT : 5.32% AGGT : 4.58% AGGA : 3.6% ATCT : 3.58% TCCT : 3.33% GCCT : 3.19% AGCT : 2.85% AGGC : 2.37% AGAT : 2.37% CCCT : 2.14% TTCT : 2.13%