RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354340.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) = 38,571,961 / 38,542,026 read pairs aligned = 38,538,312 total alignments = 82,483,363 secondary alignments = 5,369,376 non-unique alignments = 8,869,599 aligned to genes = 66,456,211 ambiguous alignments = 269,011 no feature assigned = 6,484,329 not aligned = 5,625,105 >>>>>>> Reads genomic origin exonic = 66,456,211 (91.11%) intronic = 3,723,038 (5.1%) intergenic = 2,761,291 (3.79%) overlapping exon = 2,405,398 (3.3%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.21 5'-3' bias = 1.64 >>>>>>> Junction analysis reads at junctions = 20,684,999 ACCT : 5.43% AGGT : 4.5% ATCT : 4.46% TCCT : 4.1% GCCT : 3.57% CCCT : 3.01% AGGA : 3.01% AGCT : 2.36% TTCT : 2.36% AGGC : 2.26% AGAA : 1.78%