RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354211.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) = 37,325,262 / 37,301,759 read pairs aligned = 37,298,503 total alignments = 79,710,118 secondary alignments = 5,083,097 non-unique alignments = 8,268,978 aligned to genes = 62,159,195 ambiguous alignments = 184,407 no feature assigned = 8,635,007 not aligned = 3,748,421 >>>>>>> Reads genomic origin exonic = 62,159,195 (87.8%) intronic = 5,454,367 (7.7%) intergenic = 3,180,640 (4.49%) overlapping exon = 2,287,536 (3.23%) >>>>>>> Transcript coverage profile 5' bias = 0.4 3' bias = 0.16 5'-3' bias = 2.18 >>>>>>> Junction analysis reads at junctions = 17,997,211 ACCT : 5.36% AGGT : 4.95% AGGA : 3.75% ATCT : 3.49% TCCT : 3.35% GCCT : 3.1% AGCT : 2.75% AGGC : 2.46% CCCT : 2.37% AGAT : 2.31% TTCT : 2.11%