Input data and parameters 

Input

Analysis date: Sun Oct 29 01:41:45 GMT 2023
BAM file: SRX7354070.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): 39,418,647 / 39,398,841
Number of aligned pairs (without duplicates): 39,395,911
Total number of alignments: 84,010,913
Number of secondary alignments: 5,193,425
Number of non-unique alignments: 8,613,591
Aligned to genes: 66,857,187
Ambiguous alignments: 261,619
No feature assigned: 7,946,159
Missing chromosome in annotation: 332,357
Not aligned: 3,207,988

Reads genomic origin

Exonic: 66,857,187 / 89.38%
Intronic: 5,374,878 / 7.19%
Intergenic: 2,571,281 / 3.44%
Intronic/intergenic overlapping exon: 2,255,456 / 3.02%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.21
5'-3' bias: 1.77

Junction analysis

Reads at junctions: 22,476,620
ACCT 5.43%
AGGT 4.65%
ATCT 3.63%
TCCT 3.62%
AGGA 3.41%
GCCT 3.28%
AGCT 2.7%
CCCT 2.49%
AGGC 2.36%
AGAT 2.13%
TTCT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis