Input data and parameters 

Input

Analysis date: Tue Oct 31 01:27:41 GMT 2023
BAM file: SRX7354271.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): 41,483,626 / 41,451,093
Number of aligned pairs (without duplicates): 41,447,561
Total number of alignments: 87,736,408
Number of secondary alignments: 4,801,689
Number of non-unique alignments: 8,092,240
Aligned to genes: 71,296,545
Ambiguous alignments: 219,525
No feature assigned: 7,799,261
Missing chromosome in annotation: 328,837
Not aligned: 2,855,393

Reads genomic origin

Exonic: 71,296,545 / 90.14%
Intronic: 4,462,095 / 5.64%
Intergenic: 3,337,166 / 4.22%
Intronic/intergenic overlapping exon: 2,717,662 / 3.44%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.17
5'-3' bias: 2.28

Junction analysis

Reads at junctions: 23,632,681
ACCT 5.4%
AGGT 4.67%
AGGA 3.6%
ATCT 3.52%
TCCT 3.4%
GCCT 3.11%
AGCT 2.75%
AGGC 2.38%
AGAT 2.32%
CCCT 2.28%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis