Input data and parameters 

Input

Analysis date: Tue Oct 31 09:03:13 GMT 2023
BAM file: SRX7354247.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): 38,363,422 / 38,313,731
Number of aligned pairs (without duplicates): 38,305,241
Total number of alignments: 81,450,009
Number of secondary alignments: 4,772,856
Number of non-unique alignments: 7,782,762
Aligned to genes: 62,118,412
Ambiguous alignments: 205,160
No feature assigned: 10,952,328
Missing chromosome in annotation: 391,347
Not aligned: 3,673,401

Reads genomic origin

Exonic: 62,118,412 / 85.01%
Intronic: 7,708,056 / 10.55%
Intergenic: 3,244,272 / 4.44%
Intronic/intergenic overlapping exon: 2,985,252 / 4.09%

Transcript coverage profile

5' bias: 0.44
3' bias: 0.17
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 21,511,206
ACCT 5.34%
AGGT 4.72%
ATCT 3.81%
AGGA 3.64%
GCCT 3.35%
TCCT 3.27%
AGCT 2.68%
CCCT 2.59%
AGGC 2.36%
AGAT 2.36%
TTCT 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