RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354323.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) = 36,019,904 / 35,981,957 read pairs aligned = 35,977,352 total alignments = 77,028,351 secondary alignments = 5,026,490 non-unique alignments = 8,620,465 aligned to genes = 58,961,636 ambiguous alignments = 207,409 no feature assigned = 8,971,461 not aligned = 7,788,733 >>>>>>> Reads genomic origin exonic = 58,961,636 (86.79%) intronic = 6,153,327 (9.06%) intergenic = 2,818,134 (4.15%) overlapping exon = 2,577,411 (3.79%) >>>>>>> Transcript coverage profile 5' bias = 0.38 3' bias = 0.2 5'-3' bias = 1.98 >>>>>>> Junction analysis reads at junctions = 22,293,640 ACCT : 5.55% AGGT : 4.68% ATCT : 3.65% AGGA : 3.47% GCCT : 3.36% TCCT : 3.34% AGCT : 2.66% AGGC : 2.38% CCCT : 2.37% AGAT : 2.25% TTCT : 2.11%