Input data and parameters 

Input

Analysis date: Tue Oct 31 09:22:02 GMT 2023
BAM file: SRX7354276.markdup.sorted.bam
Counting algorithm: uniquely-mapped-reads
GTF file: gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf
Number of bases for 5'-3' bias computation: 100
Number of transcripts for 5'-3' bias computation: 1,000
Paired-end sequencing: yes
Protocol: strand-specific-reverse
Sorting performed: yes

Summary 

Reads alignment

Number of mapped reads (left/right): 47,724,956 / 47,487,891
Number of aligned pairs (without duplicates): 47,449,698
Total number of alignments: 113,422,231
Number of secondary alignments: 18,209,384
Number of non-unique alignments: 16,834,182
Aligned to genes: 67,603,730
Ambiguous alignments: 225,244
No feature assigned: 21,076,458
Missing chromosome in annotation: 7,682,617
Not aligned: 24,589,517

Reads genomic origin

Exonic: 67,603,730 / 76.23%
Intronic: 11,272,500 / 12.71%
Intergenic: 9,803,958 / 11.06%
Intronic/intergenic overlapping exon: 4,394,135 / 4.96%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.21
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 22,132,105
ACCT 5.14%
AGGT 4.68%
ATCT 3.6%
TCCT 3.53%
AGGA 3.37%
GCCT 3.29%
AGCT 2.72%
CCCT 2.58%
AGGC 2.39%
TTCT 2.26%
AGAT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis