RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354184.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) = 46,340,904 / 46,317,068 read pairs aligned = 46,309,534 total alignments = 100,184,925 secondary alignments = 7,526,953 non-unique alignments = 11,602,696 aligned to genes = 79,715,103 ambiguous alignments = 360,075 no feature assigned = 7,612,390 not aligned = 3,279,928 >>>>>>> Reads genomic origin exonic = 79,715,103 (91.28%) intronic = 4,113,998 (4.71%) intergenic = 3,498,392 (4.01%) overlapping exon = 3,713,368 (4.25%) >>>>>>> Transcript coverage profile 5' bias = 0.13 3' bias = 0.12 5'-3' bias = 2.33 >>>>>>> Junction analysis reads at junctions = 27,180,805 ACCT : 5.3% AGGT : 4.67% ATCT : 4.52% TCCT : 4.24% CCCT : 3.34% AGGA : 2.73% AGGC : 2.69% AGAC : 2.39% GCCT : 2.34% AGCT : 2.02% TTCT : 1.9%