RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354374.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) = 52,753,753 / 52,708,450 read pairs aligned = 52,702,661 total alignments = 112,225,788 secondary alignments = 6,763,585 non-unique alignments = 11,409,808 aligned to genes = 86,304,505 ambiguous alignments = 313,791 no feature assigned = 13,818,934 not aligned = 5,949,749 >>>>>>> Reads genomic origin exonic = 86,304,505 (86.2%) intronic = 9,343,897 (9.33%) intergenic = 4,475,037 (4.47%) overlapping exon = 3,486,704 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.18 5'-3' bias = 1.74 >>>>>>> Junction analysis reads at junctions = 28,622,176 ACCT : 5.36% AGGT : 4.63% ATCT : 3.61% AGGA : 3.56% TCCT : 3.34% GCCT : 3.19% AGCT : 2.72% AGGC : 2.37% CCCT : 2.33% AGAT : 2.27% TTCT : 2.2%