RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354231.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) = 38,119,584 / 38,089,682 read pairs aligned = 38,086,376 total alignments = 81,282,086 secondary alignments = 5,072,820 non-unique alignments = 8,301,638 aligned to genes = 63,716,105 ambiguous alignments = 237,206 no feature assigned = 8,683,383 not aligned = 5,145,444 >>>>>>> Reads genomic origin exonic = 63,716,105 (88.01%) intronic = 5,893,560 (8.14%) intergenic = 2,789,823 (3.85%) overlapping exon = 2,295,159 (3.17%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.18 5'-3' bias = 2 >>>>>>> Junction analysis reads at junctions = 23,099,454 ACCT : 5.66% AGGT : 4.83% AGGA : 3.77% TCCT : 3.46% ATCT : 3.43% GCCT : 2.89% AGCT : 2.82% AGGC : 2.46% AGAT : 2.44% CCCT : 2.38% TTCT : 2.24%