RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354198.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) = 38,215,094 / 38,192,852 read pairs aligned = 38,190,131 total alignments = 81,210,745 secondary alignments = 4,802,799 non-unique alignments = 8,040,508 aligned to genes = 64,526,635 ambiguous alignments = 215,579 no feature assigned = 8,087,077 not aligned = 3,218,298 >>>>>>> Reads genomic origin exonic = 64,526,635 (88.86%) intronic = 5,282,114 (7.27%) intergenic = 2,804,963 (3.86%) overlapping exon = 2,364,879 (3.26%) >>>>>>> Transcript coverage profile 5' bias = 0.35 3' bias = 0.2 5'-3' bias = 2.12 >>>>>>> Junction analysis reads at junctions = 20,443,792 ACCT : 5.45% AGGT : 4.57% ATCT : 3.8% TCCT : 3.46% AGGA : 3.37% GCCT : 3.25% AGCT : 2.72% TTCT : 2.47% CCCT : 2.43% AGGC : 2.3% AGAT : 2.19%