RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354055.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) = 51,044,481 / 51,001,192 read pairs aligned = 50,986,108 total alignments = 109,931,316 secondary alignments = 7,885,643 non-unique alignments = 12,852,376 aligned to genes = 84,936,466 ambiguous alignments = 330,641 no feature assigned = 11,116,317 not aligned = 2,076,971 >>>>>>> Reads genomic origin exonic = 84,936,466 (88.43%) intronic = 7,779,510 (8.1%) intergenic = 3,336,807 (3.47%) overlapping exon = 3,956,451 (4.12%) >>>>>>> Transcript coverage profile 5' bias = 0.48 3' bias = 0.25 5'-3' bias = 1.74 >>>>>>> Junction analysis reads at junctions = 31,922,768 ACCT : 5.49% AGGT : 4.59% ATCT : 3.69% GCCT : 3.62% TCCT : 3.56% AGGA : 3.2% CCCT : 2.69% AGCT : 2.66% AGGC : 2.38% TTCT : 2.26% AGAT : 1.97%