RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354294.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) = 34,593,274 / 34,576,478 read pairs aligned = 34,573,819 total alignments = 73,369,404 secondary alignments = 4,199,652 non-unique alignments = 6,892,288 aligned to genes = 57,625,501 ambiguous alignments = 223,138 no feature assigned = 8,323,379 not aligned = 1,433,794 >>>>>>> Reads genomic origin exonic = 57,625,501 (87.38%) intronic = 6,115,455 (9.27%) intergenic = 2,207,924 (3.35%) overlapping exon = 2,190,900 (3.32%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.18 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 19,560,796 ACCT : 5.49% AGGT : 4.65% ATCT : 3.57% AGGA : 3.56% TCCT : 3.35% GCCT : 3.34% AGCT : 2.74% CCCT : 2.41% AGGC : 2.4% AGAT : 2.28% TTCT : 2.17%