RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354114.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) = 66,094,328 / 66,036,400 read pairs aligned = 66,030,416 total alignments = 140,408,542 secondary alignments = 8,277,814 non-unique alignments = 12,731,072 aligned to genes = 105,866,826 ambiguous alignments = 417,785 no feature assigned = 20,327,486 not aligned = 6,184,588 >>>>>>> Reads genomic origin exonic = 105,866,826 (83.89%) intronic = 13,218,117 (10.47%) intergenic = 7,109,369 (5.63%) overlapping exon = 4,960,922 (3.93%) >>>>>>> Transcript coverage profile 5' bias = 0.44 3' bias = 0.29 5'-3' bias = 1.66 >>>>>>> Junction analysis reads at junctions = 42,584,929 ACCT : 5.18% AGGT : 4.71% GCCT : 3.7% TCCT : 3.51% ATCT : 3.49% AGGA : 3.38% AGCT : 2.81% CCCT : 2.77% AGGC : 2.51% TTCT : 2.21% AGAT : 2.13%