RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354380.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) = 32,475,923 / 32,454,361 read pairs aligned = 32,450,754 total alignments = 68,982,208 secondary alignments = 4,051,924 non-unique alignments = 6,742,741 aligned to genes = 54,667,406 ambiguous alignments = 181,723 no feature assigned = 7,130,079 not aligned = 3,222,682 >>>>>>> Reads genomic origin exonic = 54,667,406 (88.46%) intronic = 4,815,554 (7.79%) intergenic = 2,314,525 (3.75%) overlapping exon = 2,056,989 (3.33%) >>>>>>> Transcript coverage profile 5' bias = 0.34 3' bias = 0.21 5'-3' bias = 1.94 >>>>>>> Junction analysis reads at junctions = 19,038,012 ACCT : 5.25% AGGT : 4.55% ATCT : 3.56% AGGA : 3.52% TCCT : 3.4% GCCT : 3.21% AGCT : 2.88% AGGC : 2.35% AGAT : 2.27% CCCT : 2.26% TTCT : 2.08%