RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354376.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) = 29,692,001 / 29,673,584 read pairs aligned = 29,669,824 total alignments = 63,383,786 secondary alignments = 4,018,201 non-unique alignments = 6,524,804 aligned to genes = 51,186,047 ambiguous alignments = 178,441 no feature assigned = 5,140,704 not aligned = 2,349,751 >>>>>>> Reads genomic origin exonic = 51,186,047 (90.87%) intronic = 2,632,893 (4.67%) intergenic = 2,507,811 (4.45%) overlapping exon = 1,960,160 (3.48%) >>>>>>> Transcript coverage profile 5' bias = 0.18 3' bias = 0.16 5'-3' bias = 2.12 >>>>>>> Junction analysis reads at junctions = 14,191,689 ACCT : 5.43% AGGT : 4.68% ATCT : 4.21% TCCT : 4.14% AGGA : 3.22% GCCT : 2.89% CCCT : 2.83% TTCT : 2.32% AGGC : 2.25% AGCT : 2.14% AGAA : 1.87%