RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354343.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) = 46,486,442 / 46,468,917 read pairs aligned = 46,461,217 total alignments = 118,332,330 secondary alignments = 25,376,971 non-unique alignments = 23,237,134 aligned to genes = 74,638,325 ambiguous alignments = 312,368 no feature assigned = 9,357,783 not aligned = 2,593,917 >>>>>>> Reads genomic origin exonic = 74,638,325 (88.86%) intronic = 6,075,923 (7.23%) intergenic = 3,281,860 (3.91%) overlapping exon = 3,113,143 (3.71%) >>>>>>> Transcript coverage profile 5' bias = 0.2 3' bias = 0.21 5'-3' bias = 1.71 >>>>>>> Junction analysis reads at junctions = 23,088,997 ACCT : 5.23% AGGT : 4.48% ATCT : 4.29% TCCT : 4.26% CCCT : 3.25% GCCT : 3.18% AGGA : 3.05% AGGC : 2.32% AGCT : 2.17% TTCT : 2.17% GTCT : 1.76%