RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354361.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) = 26,929,969 / 26,913,475 read pairs aligned = 26,911,681 total alignments = 57,201,849 secondary alignments = 3,358,405 non-unique alignments = 5,703,861 aligned to genes = 44,822,964 ambiguous alignments = 155,899 no feature assigned = 6,341,256 not aligned = 1,221,126 >>>>>>> Reads genomic origin exonic = 44,822,964 (87.61%) intronic = 4,420,807 (8.64%) intergenic = 1,920,449 (3.75%) overlapping exon = 1,713,221 (3.35%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.22 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 14,353,434 ACCT : 5.27% AGGT : 4.6% ATCT : 3.74% TCCT : 3.54% AGGA : 3.53% GCCT : 3.23% AGCT : 2.71% CCCT : 2.47% AGGC : 2.36% AGAT : 2.24% TTCT : 2.09%