RNA-Seq QC report ----------------------------------- >>>>>>> Input bam file = SRX7354155.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) = 68,887,389 / 68,839,702 read pairs aligned = 68,835,029 total alignments = 148,517,519 secondary alignments = 10,790,428 non-unique alignments = 15,869,265 aligned to genes = 108,680,798 ambiguous alignments = 413,738 no feature assigned = 21,782,492 not aligned = 3,964,535 >>>>>>> Reads genomic origin exonic = 108,680,798 (83.3%) intronic = 12,698,113 (9.73%) intergenic = 9,084,379 (6.96%) overlapping exon = 5,075,380 (3.89%) >>>>>>> Transcript coverage profile 5' bias = 0.42 3' bias = 0.37 5'-3' bias = 1.51 >>>>>>> Junction analysis reads at junctions = 41,706,548 ACCT : 5.01% AGGT : 4.68% TCCT : 3.91% ATCT : 3.66% GCCT : 3.29% AGGA : 3.21% AGCT : 2.73% CCCT : 2.71% TTCT : 2.48% AGGC : 2.45% AGAT : 1.97%