Input data and parameters 

Input

Analysis date: Sun Oct 29 01:50:04 GMT 2023
BAM file: SRX7354063.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): 39,530,128 / 39,501,661
Number of aligned pairs (without duplicates): 39,493,746
Total number of alignments: 86,917,844
Number of secondary alignments: 7,886,055
Number of non-unique alignments: 11,367,644
Aligned to genes: 66,539,512
Ambiguous alignments: 284,814
No feature assigned: 7,339,032
Missing chromosome in annotation: 1,386,842
Not aligned: 3,611,665

Reads genomic origin

Exonic: 66,539,512 / 90.07%
Intronic: 3,908,808 / 5.29%
Intergenic: 3,430,224 / 4.64%
Intronic/intergenic overlapping exon: 3,476,577 / 4.71%

Transcript coverage profile

5' bias: 0.09
3' bias: 0.11
5'-3' bias: 2.41

Junction analysis

Reads at junctions: 22,236,808
ACCT 5.95%
TCCT 5.73%
ATCT 4.79%
AGGT 3.87%
CCCT 3.61%
AGGA 2.78%
TCCC 2.76%
GCCT 2.61%
CGTA 2.45%
AGGC 2.24%
CCCA 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis