RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354193.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) = 48,675,559 / 48,658,801 read pairs aligned = 48,655,482 total alignments = 103,498,641 secondary alignments = 6,164,281 non-unique alignments = 9,590,359 aligned to genes = 79,671,351 ambiguous alignments = 274,876 no feature assigned = 13,183,519 not aligned = 1,720,638 >>>>>>> Reads genomic origin exonic = 79,671,351 (85.8%) intronic = 8,715,007 (9.39%) intergenic = 4,468,512 (4.81%) overlapping exon = 3,295,311 (3.55%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.28 5'-3' bias = 1.66 >>>>>>> Junction analysis reads at junctions = 29,165,070 ACCT : 4.95% AGGT : 4.58% ATCT : 3.69% TCCT : 3.53% AGGA : 3.37% GCCT : 3.36% AGCT : 2.95% CCCT : 2.66% AGGC : 2.36% TTCT : 2.15% AGAT : 2.04%