RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354385.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) = 38,480,750 / 38,450,168 read pairs aligned = 38,446,171 total alignments = 81,522,038 secondary alignments = 4,591,120 non-unique alignments = 7,599,712 aligned to genes = 59,675,996 ambiguous alignments = 215,332 no feature assigned = 13,690,094 not aligned = 4,978,660 >>>>>>> Reads genomic origin exonic = 59,675,996 (81.34%) intronic = 8,587,705 (11.71%) intergenic = 5,102,389 (6.95%) overlapping exon = 2,866,811 (3.91%) >>>>>>> Transcript coverage profile 5' bias = 0.41 3' bias = 0.26 5'-3' bias = 1.82 >>>>>>> Junction analysis reads at junctions = 22,117,654 ACCT : 5.19% AGGT : 4.7% AGGA : 3.48% ATCT : 3.46% TCCT : 3.42% GCCT : 3.31% AGCT : 2.77% CCCT : 2.53% AGGC : 2.41% AGAT : 2.27% TTCT : 2.17%