RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354069.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) = 56,342,109 / 56,318,118 read pairs aligned = 56,311,546 total alignments = 120,771,362 secondary alignments = 8,111,135 non-unique alignments = 13,442,984 aligned to genes = 94,332,928 ambiguous alignments = 339,189 no feature assigned = 12,013,333 not aligned = 2,962,341 >>>>>>> Reads genomic origin exonic = 94,332,928 (88.7%) intronic = 8,642,927 (8.13%) intergenic = 3,370,406 (3.17%) overlapping exon = 4,103,193 (3.86%) >>>>>>> Transcript coverage profile 5' bias = 0.25 3' bias = 0.17 5'-3' bias = 1.91 >>>>>>> Junction analysis reads at junctions = 31,293,488 ACCT : 5.4% AGGT : 4.67% ATCT : 3.66% TCCT : 3.49% AGGA : 3.44% GCCT : 3.19% AGCT : 2.62% TTCT : 2.45% AGGC : 2.4% CCCT : 2.37% AGAT : 2.15%