RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354289.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) = 52,631,495 / 52,605,509 read pairs aligned = 52,594,053 total alignments = 113,718,970 secondary alignments = 8,481,966 non-unique alignments = 13,419,243 aligned to genes = 90,554,612 ambiguous alignments = 393,234 no feature assigned = 8,391,253 not aligned = 2,217,064 >>>>>>> Reads genomic origin exonic = 90,554,612 (91.52%) intronic = 4,241,051 (4.29%) intergenic = 4,150,202 (4.19%) overlapping exon = 3,535,554 (3.57%) >>>>>>> Transcript coverage profile 5' bias = 0.1 3' bias = 0.14 5'-3' bias = 2.06 >>>>>>> Junction analysis reads at junctions = 23,820,891 ACCT : 4.85% AGGT : 4.59% TCCT : 4.41% ATCT : 4.22% CCCT : 3.47% AGGA : 3.32% AGGC : 2.36% AGCT : 2.13% GCCT : 2.13% TTCT : 1.97% AGAC : 1.84%