Input data and parameters 

Input

Analysis date: Sun Oct 29 01:48:56 GMT 2023
BAM file: SRX7354122.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): 47,503,427 / 47,469,385
Number of aligned pairs (without duplicates): 47,457,110
Total number of alignments: 103,108,919
Number of secondary alignments: 8,136,107
Number of non-unique alignments: 12,584,288
Aligned to genes: 80,039,500
Ambiguous alignments: 321,738
No feature assigned: 9,186,051
Missing chromosome in annotation: 977,342
Not aligned: 4,500,566

Reads genomic origin

Exonic: 80,039,500 / 89.7%
Intronic: 5,846,675 / 6.55%
Intergenic: 3,339,376 / 3.74%
Intronic/intergenic overlapping exon: 3,163,504 / 3.55%

Transcript coverage profile

5' bias: 0.25
3' bias: 0.24
5'-3' bias: 1.62

Junction analysis

Reads at junctions: 23,976,346
ACCT 5.11%
AGGT 4.6%
ATCT 4.17%
TCCT 4.13%
AGGA 3.21%
GCCT 2.95%
CCCT 2.94%
AGCT 2.3%
AGGC 2.21%
TTCT 2.19%
AGAA 1.9%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis