RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354077.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) = 77,080,409 / 76,937,265 read pairs aligned = 76,926,539 total alignments = 163,471,885 secondary alignments = 9,454,211 non-unique alignments = 14,747,971 aligned to genes = 127,773,214 ambiguous alignments = 464,162 no feature assigned = 19,359,488 not aligned = 12,614,118 >>>>>>> Reads genomic origin exonic = 127,773,214 (86.84%) intronic = 12,508,592 (8.5%) intergenic = 6,850,896 (4.66%) overlapping exon = 6,118,082 (4.16%) >>>>>>> Transcript coverage profile 5' bias = 0.49 3' bias = 0.25 5'-3' bias = 1.87 >>>>>>> Junction analysis reads at junctions = 53,602,932 ACCT : 5.15% AGGT : 4.77% TCCT : 3.54% AGGA : 3.44% ATCT : 3.36% GCCT : 3.12% AGCT : 2.81% CCCT : 2.53% AGGC : 2.41% AGAT : 2.18% TTCT : 2.17%