RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354222.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) = 40,893,502 / 40,631,754 read pairs aligned = 40,611,840 total alignments = 87,391,881 secondary alignments = 5,866,625 non-unique alignments = 9,759,314 aligned to genes = 58,940,846 ambiguous alignments = 205,593 no feature assigned = 18,038,376 not aligned = 17,870,614 >>>>>>> Reads genomic origin exonic = 58,940,846 (76.57%) intronic = 8,827,496 (11.47%) intergenic = 9,210,880 (11.97%) overlapping exon = 3,676,854 (4.78%) >>>>>>> Transcript coverage profile 5' bias = 0.47 3' bias = 0.22 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 21,940,049 ACCT : 5.29% AGGT : 4.69% TCCT : 3.5% ATCT : 3.41% GCCT : 3.34% AGGA : 3.34% AGCT : 2.78% CCCT : 2.47% AGGC : 2.39% TTCT : 2.29% AGAT : 2.14%