RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354164.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) = 41,627,353 / 41,601,806 read pairs aligned = 41,597,357 total alignments = 88,640,387 secondary alignments = 5,411,228 non-unique alignments = 9,007,875 aligned to genes = 70,031,403 ambiguous alignments = 239,677 no feature assigned = 8,960,517 not aligned = 3,569,389 >>>>>>> Reads genomic origin exonic = 70,031,403 (88.66%) intronic = 5,784,392 (7.32%) intergenic = 3,176,125 (4.02%) overlapping exon = 2,752,850 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.39 3' bias = 0.21 5'-3' bias = 1.91 >>>>>>> Junction analysis reads at junctions = 21,181,027 ACCT : 5.16% AGGT : 4.66% ATCT : 3.62% TCCT : 3.59% AGGA : 3.58% GCCT : 3% AGCT : 2.73% CCCT : 2.41% AGGC : 2.34% TTCT : 2.2% AGAT : 2.18%