Input data and parameters 

Input

Analysis date: Tue Oct 31 09:29:52 GMT 2023
BAM file: SRX7354327.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): 38,589,868 / 38,541,275
Number of aligned pairs (without duplicates): 38,534,944
Total number of alignments: 82,976,778
Number of secondary alignments: 5,845,635
Number of non-unique alignments: 9,607,361
Aligned to genes: 64,189,427
Ambiguous alignments: 230,023
No feature assigned: 8,452,255
Missing chromosome in annotation: 497,712
Not aligned: 10,529,167

Reads genomic origin

Exonic: 64,189,427 / 88.36%
Intronic: 5,303,880 / 7.3%
Intergenic: 3,148,375 / 4.33%
Intronic/intergenic overlapping exon: 2,416,819 / 3.33%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.2
5'-3' bias: 2

Junction analysis

Reads at junctions: 19,813,294
ACCT 5.55%
AGGT 4.86%
ATCT 3.6%
TCCT 3.53%
AGGA 3.52%
GCCT 3.13%
CCCT 2.57%
AGCT 2.55%
AGGC 2.41%
AGAT 2.17%
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