RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354358.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) = 42,797,565 / 42,711,422 read pairs aligned = 42,699,579 total alignments = 93,329,116 secondary alignments = 7,820,129 non-unique alignments = 12,071,635 aligned to genes = 72,395,820 ambiguous alignments = 303,699 no feature assigned = 7,702,557 not aligned = 7,670,411 >>>>>>> Reads genomic origin exonic = 72,395,820 (90.38%) intronic = 5,017,387 (6.26%) intergenic = 2,685,170 (3.35%) overlapping exon = 3,132,959 (3.91%) >>>>>>> Transcript coverage profile 5' bias = 0.23 3' bias = 0.2 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 23,233,004 ACCT : 5.4% AGGT : 4.49% TCCT : 4.18% ATCT : 4.03% AGGA : 3.15% GCCT : 3.05% CCCT : 2.67% TTCT : 2.43% AGCT : 2.23% AGGC : 2.21% AGAT : 1.79%