RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354179.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) = 36,770,141 / 36,731,997 read pairs aligned = 36,725,848 total alignments = 78,096,453 secondary alignments = 4,594,315 non-unique alignments = 7,595,099 aligned to genes = 61,051,104 ambiguous alignments = 242,409 no feature assigned = 8,932,455 not aligned = 9,214,754 >>>>>>> Reads genomic origin exonic = 61,051,104 (87.24%) intronic = 6,554,731 (9.37%) intergenic = 2,377,724 (3.4%) overlapping exon = 2,479,666 (3.54%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.2 5'-3' bias = 2.07 >>>>>>> Junction analysis reads at junctions = 23,169,242 ACCT : 5.35% AGGT : 4.84% AGGA : 3.6% ATCT : 3.59% TCCT : 3.41% GCCT : 2.92% AGCT : 2.73% CCCT : 2.46% AGGC : 2.45% AGAT : 2.26% TTCT : 2.16%