Input data and parameters 

Input

Analysis date: Sun Oct 29 12:30:31 GMT 2023
BAM file: SRX7354050.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): 77,380,415 / 77,301,187
Number of aligned pairs (without duplicates): 77,296,257
Total number of alignments: 164,415,769
Number of secondary alignments: 9,734,167
Number of non-unique alignments: 16,163,047
Aligned to genes: 132,389,326
Ambiguous alignments: 413,044
No feature assigned: 14,638,973
Missing chromosome in annotation: 811,379
Not aligned: 9,619,044

Reads genomic origin

Exonic: 132,389,326 / 90.04%
Intronic: 8,397,168 / 5.71%
Intergenic: 6,241,805 / 4.25%
Intronic/intergenic overlapping exon: 5,189,232 / 3.53%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.17
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 47,613,401
ACCT 5.39%
AGGT 4.71%
AGGA 3.66%
ATCT 3.48%
TCCT 3.35%
GCCT 3.16%
AGCT 2.73%
AGGC 2.43%
AGAT 2.35%
CCCT 2.3%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis