RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354096.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) = 55,529,928 / 55,490,400 read pairs aligned = 55,484,401 total alignments = 119,426,315 secondary alignments = 8,405,987 non-unique alignments = 13,986,788 aligned to genes = 92,240,458 ambiguous alignments = 319,090 no feature assigned = 12,300,535 not aligned = 5,226,298 >>>>>>> Reads genomic origin exonic = 92,240,458 (88.23%) intronic = 6,870,606 (6.57%) intergenic = 5,429,929 (5.19%) overlapping exon = 3,443,769 (3.29%) >>>>>>> Transcript coverage profile 5' bias = 0.28 3' bias = 0.2 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 29,007,850 ACCT : 5.26% AGGT : 4.91% AGGA : 3.65% TCCT : 3.64% ATCT : 3.52% GCCT : 2.73% AGCT : 2.68% CCCT : 2.53% AGGC : 2.41% TTCT : 2.25% AGAT : 2.17%