RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354153.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) = 59,193,792 / 59,148,949 read pairs aligned = 59,143,194 total alignments = 125,818,125 secondary alignments = 7,475,384 non-unique alignments = 12,439,347 aligned to genes = 97,808,259 ambiguous alignments = 327,551 no feature assigned = 14,719,792 not aligned = 4,212,999 >>>>>>> Reads genomic origin exonic = 97,808,259 (86.92%) intronic = 9,256,216 (8.23%) intergenic = 5,463,576 (4.86%) overlapping exon = 4,035,873 (3.59%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.18 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 29,515,488 ACCT : 5.48% AGGT : 4.65% AGGA : 3.52% ATCT : 3.46% GCCT : 3.43% TCCT : 3.28% AGCT : 2.69% CCCT : 2.43% AGGC : 2.42% TTCT : 2.29% AGAT : 2.25%