RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354192.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) = 40,015,316 / 39,966,036 read pairs aligned = 39,960,365 total alignments = 84,729,036 secondary alignments = 4,747,684 non-unique alignments = 7,949,656 aligned to genes = 65,714,212 ambiguous alignments = 205,206 no feature assigned = 10,595,464 not aligned = 9,884,664 >>>>>>> Reads genomic origin exonic = 65,714,212 (86.12%) intronic = 6,650,094 (8.71%) intergenic = 3,945,370 (5.17%) overlapping exon = 2,798,897 (3.67%) >>>>>>> Transcript coverage profile 5' bias = 0.33 3' bias = 0.18 5'-3' bias = 1.85 >>>>>>> Junction analysis reads at junctions = 21,151,392 ACCT : 5.6% AGGT : 4.65% AGGA : 3.51% ATCT : 3.5% GCCT : 3.29% TCCT : 3.26% AGCT : 2.8% CCCT : 2.47% AGAT : 2.41% AGGC : 2.36% TTCT : 2.19%