Input data and parameters 

Input

Analysis date: Mon Oct 30 20:26:21 GMT 2023
BAM file: SRX7354243.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): 48,630,098 / 48,581,987
Number of aligned pairs (without duplicates): 48,570,598
Total number of alignments: 103,895,805
Number of secondary alignments: 6,683,720
Number of non-unique alignments: 10,743,495
Aligned to genes: 83,213,850
Ambiguous alignments: 331,531
No feature assigned: 9,000,876
Missing chromosome in annotation: 606,053
Not aligned: 11,984,909

Reads genomic origin

Exonic: 83,213,850 / 90.24%
Intronic: 5,023,006 / 5.45%
Intergenic: 3,977,870 / 4.31%
Intronic/intergenic overlapping exon: 3,500,552 / 3.8%

Transcript coverage profile

5' bias: 0.15
3' bias: 0.16
5'-3' bias: 2.01

Junction analysis

Reads at junctions: 29,500,473
ACCT 5.08%
TCCT 4.83%
AGGT 4.55%
ATCT 4.45%
CCCT 3.33%
AGGA 3.24%
GCCT 2.47%
TTCT 2.25%
AGGC 2.16%
AGCT 2.15%
AGAA 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis