RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354255.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) = 45,572,320 / 45,536,597 read pairs aligned = 45,527,428 total alignments = 96,927,407 secondary alignments = 5,818,490 non-unique alignments = 9,072,807 aligned to genes = 76,087,009 ambiguous alignments = 250,992 no feature assigned = 10,846,445 not aligned = 3,871,977 >>>>>>> Reads genomic origin exonic = 76,087,009 (87.52%) intronic = 7,618,470 (8.76%) intergenic = 3,227,975 (3.71%) overlapping exon = 3,550,082 (4.08%) >>>>>>> Transcript coverage profile 5' bias = 0.29 3' bias = 0.15 5'-3' bias = 1.93 >>>>>>> Junction analysis reads at junctions = 24,048,279 ACCT : 5.57% AGGT : 4.6% ATCT : 3.72% TCCT : 3.58% AGGA : 3.42% GCCT : 3.27% AGCT : 2.5% CCCT : 2.45% AGGC : 2.31% TTCT : 2.07% AGAT : 2.04%