RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354405.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) = 30,763,113 / 30,730,289 read pairs aligned = 30,725,787 total alignments = 65,867,973 secondary alignments = 4,374,571 non-unique alignments = 7,355,850 aligned to genes = 52,712,121 ambiguous alignments = 188,842 no feature assigned = 5,326,374 not aligned = 9,694,352 >>>>>>> Reads genomic origin exonic = 52,712,121 (90.82%) intronic = 3,204,950 (5.52%) intergenic = 2,121,424 (3.66%) overlapping exon = 1,751,488 (3.02%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.19 5'-3' bias = 2.12 >>>>>>> Junction analysis reads at junctions = 17,360,014 ACCT : 5.37% AGGT : 4.53% ATCT : 3.78% TCCT : 3.58% AGGA : 3.35% GCCT : 3.11% AGCT : 2.55% CCCT : 2.45% AGGC : 2.34% AGGG : 2.15% TTCT : 2.02%