RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354368.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) = 37,170,428 / 37,141,768 read pairs aligned = 37,136,460 total alignments = 79,811,499 secondary alignments = 5,499,303 non-unique alignments = 8,850,688 aligned to genes = 59,896,902 ambiguous alignments = 241,323 no feature assigned = 10,393,799 not aligned = 3,059,134 >>>>>>> Reads genomic origin exonic = 59,896,902 (85.21%) intronic = 7,411,119 (10.54%) intergenic = 2,982,680 (4.24%) overlapping exon = 2,348,760 (3.34%) >>>>>>> Transcript coverage profile 5' bias = 0.5 3' bias = 0.23 5'-3' bias = 1.96 >>>>>>> Junction analysis reads at junctions = 21,483,991 ACCT : 5.37% AGGT : 4.65% AGGA : 3.53% ATCT : 3.51% TCCT : 3.41% GCCT : 2.8% AGCT : 2.75% TTCT : 2.4% CCCT : 2.37% AGGC : 2.35% AGAT : 2.34%