Input data and parameters 

Input

Analysis date: Tue Oct 31 09:53:53 GMT 2023
BAM file: SRX7354371.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): 38,763,882 / 38,729,948
Number of aligned pairs (without duplicates): 38,726,639
Total number of alignments: 84,718,154
Number of secondary alignments: 7,224,324
Number of non-unique alignments: 10,042,492
Aligned to genes: 64,829,228
Ambiguous alignments: 236,288
No feature assigned: 8,187,693
Missing chromosome in annotation: 1,422,453
Not aligned: 4,452,184

Reads genomic origin

Exonic: 64,829,228 / 88.79%
Intronic: 5,374,012 / 7.36%
Intergenic: 2,813,681 / 3.85%
Intronic/intergenic overlapping exon: 2,562,872 / 3.51%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.25
5'-3' bias: 1.75

Junction analysis

Reads at junctions: 20,415,271
ACCT 5.35%
AGGT 4.53%
ATCT 3.65%
TCCT 3.53%
GCCT 3.43%
AGGA 3.21%
TTCT 2.76%
CCCT 2.67%
AGCT 2.65%
AGGC 2.34%
AGAT 2.05%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis