RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354228.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) = 44,902,147 / 44,860,642 read pairs aligned = 44,840,145 total alignments = 95,210,306 secondary alignments = 5,447,517 non-unique alignments = 8,989,643 aligned to genes = 75,360,413 ambiguous alignments = 257,877 no feature assigned = 10,170,501 not aligned = 690,225 >>>>>>> Reads genomic origin exonic = 75,360,413 (88.11%) intronic = 6,511,971 (7.61%) intergenic = 3,658,530 (4.28%) overlapping exon = 3,640,492 (4.26%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.23 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 23,212,085 ACCT : 5.43% AGGT : 4.63% TCCT : 3.55% ATCT : 3.45% GCCT : 3.38% AGGA : 3.32% AGCT : 2.72% CCCT : 2.53% AGGC : 2.4% TTCT : 2.05% AGAT : 2%