RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354229.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) = 44,844,239 / 44,797,146 read pairs aligned = 44,769,178 total alignments = 96,009,021 secondary alignments = 6,367,636 non-unique alignments = 9,800,127 aligned to genes = 73,782,606 ambiguous alignments = 305,705 no feature assigned = 11,336,793 not aligned = 1,449,497 >>>>>>> Reads genomic origin exonic = 73,782,606 (86.68%) intronic = 8,322,545 (9.78%) intergenic = 3,014,248 (3.54%) overlapping exon = 3,847,373 (4.52%) >>>>>>> Transcript coverage profile 5' bias = 0.47 3' bias = 0.23 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 28,163,303 ACCT : 5.04% AGGT : 4.7% ATCT : 3.65% TCCT : 3.6% AGGA : 3.43% GCCT : 3.02% AGCT : 2.77% CCCT : 2.66% AGGC : 2.39% AGAT : 2.06% TTCT : 2.06%