RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354332.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) = 45,707,210 / 45,654,997 read pairs aligned = 45,649,318 total alignments = 97,476,975 secondary alignments = 6,114,768 non-unique alignments = 10,229,321 aligned to genes = 76,545,582 ambiguous alignments = 264,051 no feature assigned = 10,006,434 not aligned = 8,856,645 >>>>>>> Reads genomic origin exonic = 76,545,582 (88.44%) intronic = 6,409,296 (7.41%) intergenic = 3,597,138 (4.16%) overlapping exon = 3,035,717 (3.51%) >>>>>>> Transcript coverage profile 5' bias = 0.37 3' bias = 0.21 5'-3' bias = 1.99 >>>>>>> Junction analysis reads at junctions = 23,513,927 ACCT : 5.34% AGGT : 4.72% ATCT : 3.9% AGGA : 3.6% TCCT : 3.51% GCCT : 3.23% CCCT : 2.68% AGCT : 2.63% AGGC : 2.41% AGAT : 2.26% TTCT : 2.23%