RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354378.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) = 31,509,835 / 31,488,128 read pairs aligned = 31,484,352 total alignments = 66,851,293 secondary alignments = 3,853,330 non-unique alignments = 6,258,286 aligned to genes = 51,773,257 ambiguous alignments = 174,767 no feature assigned = 8,315,266 not aligned = 2,825,283 >>>>>>> Reads genomic origin exonic = 51,773,257 (86.16%) intronic = 5,801,773 (9.66%) intergenic = 2,513,493 (4.18%) overlapping exon = 2,111,905 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.22 5'-3' bias = 1.76 >>>>>>> Junction analysis reads at junctions = 16,724,217 ACCT : 5.33% AGGT : 4.72% ATCT : 3.59% AGGA : 3.52% TCCT : 3.27% GCCT : 3.2% AGCT : 2.83% AGGC : 2.43% CCCT : 2.39% AGAT : 2.32% TTCT : 2.17%