RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354176.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) = 54,054,724 / 54,021,877 read pairs aligned = 54,017,634 total alignments = 115,095,605 secondary alignments = 7,019,004 non-unique alignments = 11,428,245 aligned to genes = 89,095,457 ambiguous alignments = 272,508 no feature assigned = 13,685,732 not aligned = 3,817,363 >>>>>>> Reads genomic origin exonic = 89,095,457 (86.68%) intronic = 8,506,016 (8.28%) intergenic = 5,179,716 (5.04%) overlapping exon = 3,673,528 (3.57%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.19 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 26,635,579 ACCT : 5.43% AGGT : 4.74% AGGA : 3.62% ATCT : 3.59% TCCT : 3.46% GCCT : 3.31% AGCT : 2.62% AGGC : 2.41% CCCT : 2.39% AGAT : 2.25% TTCT : 2.21%