RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354134.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) = 37,391,266 / 37,365,278 read pairs aligned = 37,360,422 total alignments = 79,527,199 secondary alignments = 4,770,655 non-unique alignments = 8,240,486 aligned to genes = 62,097,508 ambiguous alignments = 192,412 no feature assigned = 8,730,368 not aligned = 5,957,702 >>>>>>> Reads genomic origin exonic = 62,097,508 (87.67%) intronic = 5,327,260 (7.52%) intergenic = 3,403,108 (4.8%) overlapping exon = 2,426,717 (3.43%) >>>>>>> Transcript coverage profile 5' bias = 0.27 3' bias = 0.17 5'-3' bias = 2.14 >>>>>>> Junction analysis reads at junctions = 19,049,154 ACCT : 5.51% AGGT : 4.75% AGGA : 3.62% ATCT : 3.6% TCCT : 3.34% GCCT : 3.13% AGCT : 2.68% AGGC : 2.39% CCCT : 2.38% AGAT : 2.3% TTCT : 2.17%