RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354107.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) = 48,135,034 / 48,096,378 read pairs aligned = 48,089,477 total alignments = 102,371,307 secondary alignments = 6,139,895 non-unique alignments = 10,105,013 aligned to genes = 81,728,412 ambiguous alignments = 258,134 no feature assigned = 9,824,937 not aligned = 7,546,390 >>>>>>> Reads genomic origin exonic = 81,728,412 (89.27%) intronic = 6,242,147 (6.82%) intergenic = 3,582,790 (3.91%) overlapping exon = 3,182,545 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.32 3' bias = 0.18 5'-3' bias = 1.99 >>>>>>> Junction analysis reads at junctions = 25,396,010 ACCT : 5.16% AGGT : 4.89% ATCT : 3.78% AGGA : 3.55% TCCT : 3.47% GCCT : 2.91% AGCT : 2.75% AGGC : 2.51% CCCT : 2.38% AGAT : 2.12% TTCT : 2.06%