Input data and parameters 

Input

Analysis date: Tue Oct 31 09:25:10 GMT 2023
BAM file: SRX7354316.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): 54,714,946 / 54,636,432
Number of aligned pairs (without duplicates): 54,618,939
Total number of alignments: 116,346,291
Number of secondary alignments: 6,994,913
Number of non-unique alignments: 11,921,690
Aligned to genes: 87,826,865
Ambiguous alignments: 272,270
No feature assigned: 15,967,534
Missing chromosome in annotation: 357,932
Not aligned: 7,905,778

Reads genomic origin

Exonic: 87,826,865 / 84.62%
Intronic: 11,152,896 / 10.75%
Intergenic: 4,814,638 / 4.64%
Intronic/intergenic overlapping exon: 4,273,996 / 4.12%

Transcript coverage profile

5' bias: 0.27
3' bias: 0.14
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 25,961,223
ACCT 5.15%
AGGT 4.7%
ATCT 3.72%
AGGA 3.7%
TCCT 3.27%
GCCT 3.07%
AGCT 2.77%
AGAT 2.48%
AGGC 2.38%
CCCT 2.37%
TTCT 2.25%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis