RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354190.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) = 51,415,388 / 51,403,402 read pairs aligned = 51,349,523 total alignments = 112,213,115 secondary alignments = 9,394,325 non-unique alignments = 13,576,579 aligned to genes = 86,421,407 ambiguous alignments = 292,615 no feature assigned = 10,220,054 not aligned = 2,526,802 >>>>>>> Reads genomic origin exonic = 86,421,407 (89.42%) intronic = 6,281,743 (6.5%) intergenic = 3,938,311 (4.08%) overlapping exon = 4,194,631 (4.34%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.24 5'-3' bias = 2.08 >>>>>>> Junction analysis reads at junctions = 27,884,925 ACCT : 5.22% AGGT : 4.62% ATCT : 4.15% TCCT : 4.13% AGGA : 3.25% GCCT : 3.19% CCCT : 3.02% AGCT : 2.42% TTCT : 2.31% AGGC : 2.3% AGAA : 1.86%