RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354293.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) = 29,193,752 / 29,176,535 read pairs aligned = 29,172,597 total alignments = 61,630,413 secondary alignments = 3,260,126 non-unique alignments = 5,400,306 aligned to genes = 48,729,914 ambiguous alignments = 147,920 no feature assigned = 7,122,336 not aligned = 3,859,059 >>>>>>> Reads genomic origin exonic = 48,729,914 (87.25%) intronic = 4,849,464 (8.68%) intergenic = 2,272,872 (4.07%) overlapping exon = 1,719,920 (3.08%) >>>>>>> Transcript coverage profile 5' bias = 0.3 3' bias = 0.13 5'-3' bias = 2.36 >>>>>>> Junction analysis reads at junctions = 14,955,335 ACCT : 5.41% AGGT : 4.74% ATCT : 3.83% AGGA : 3.65% TCCT : 3.63% GCCT : 3.02% AGCT : 2.63% AGGC : 2.36% CCCT : 2.34% AGAT : 2.26% TTCT : 2.21%