RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354330.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) = 44,876,832 / 44,805,443 read pairs aligned = 44,797,715 total alignments = 95,887,429 secondary alignments = 6,205,154 non-unique alignments = 9,616,604 aligned to genes = 73,211,538 ambiguous alignments = 261,017 no feature assigned = 12,007,032 not aligned = 14,309,273 >>>>>>> Reads genomic origin exonic = 73,211,538 (85.91%) intronic = 7,214,591 (8.47%) intergenic = 4,792,441 (5.62%) overlapping exon = 3,276,302 (3.84%) >>>>>>> Transcript coverage profile 5' bias = 0.43 3' bias = 0.29 5'-3' bias = 1.74 >>>>>>> Junction analysis reads at junctions = 26,028,734 ACCT : 5.18% AGGT : 4.77% TCCT : 3.66% ATCT : 3.65% AGGA : 3.47% GCCT : 3.01% AGCT : 2.75% CCCT : 2.63% AGGC : 2.43% TTCT : 2.14% AGAT : 2.13%