RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354236.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) = 36,441,553 / 36,427,076 read pairs aligned = 36,424,031 total alignments = 77,365,448 secondary alignments = 4,496,819 non-unique alignments = 7,589,668 aligned to genes = 61,923,542 ambiguous alignments = 222,453 no feature assigned = 7,369,929 not aligned = 2,743,845 >>>>>>> Reads genomic origin exonic = 61,923,542 (89.36%) intronic = 4,815,420 (6.95%) intergenic = 2,554,509 (3.69%) overlapping exon = 2,098,652 (3.03%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.18 5'-3' bias = 2.1 >>>>>>> Junction analysis reads at junctions = 20,132,021 ACCT : 5.36% AGGT : 4.9% ATCT : 3.79% AGGA : 3.65% TCCT : 3.56% GCCT : 2.95% AGCT : 2.77% CCCT : 2.5% AGGC : 2.38% AGAT : 2.32% TTCT : 2.18%