Input data and parameters 

Input

Analysis date: Sun Oct 29 11:39:06 GMT 2023
BAM file: SRX7354123.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): 45,024,402 / 44,986,366
Number of aligned pairs (without duplicates): 44,957,766
Total number of alignments: 101,623,516
Number of secondary alignments: 11,612,748
Number of non-unique alignments: 13,014,608
Aligned to genes: 72,713,122
Ambiguous alignments: 270,558
No feature assigned: 11,845,704
Missing chromosome in annotation: 3,779,524
Not aligned: 2,173,854

Reads genomic origin

Exonic: 72,713,122 / 85.99%
Intronic: 8,729,747 / 10.32%
Intergenic: 3,115,957 / 3.68%
Intronic/intergenic overlapping exon: 3,556,107 / 4.21%

Transcript coverage profile

5' bias: 0.47
3' bias: 0.19
5'-3' bias: 1.91

Junction analysis

Reads at junctions: 28,119,339
ACCT 5.23%
AGGT 4.75%
AGGA 3.57%
TCCT 3.55%
ATCT 3.53%
GCCT 2.85%
AGCT 2.78%
CCCT 2.47%
AGGC 2.41%
AGAT 2.3%
TTCT 2.24%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis