Input data and parameters 

Input

Analysis date: Tue Oct 31 09:30:33 GMT 2023
BAM file: SRX7354339.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): 32,049,898 / 32,028,457
Number of aligned pairs (without duplicates): 32,025,030
Total number of alignments: 68,888,402
Number of secondary alignments: 4,810,047
Number of non-unique alignments: 8,288,904
Aligned to genes: 53,790,206
Ambiguous alignments: 207,994
No feature assigned: 6,377,061
Missing chromosome in annotation: 224,237
Not aligned: 7,175,313

Reads genomic origin

Exonic: 53,790,206 / 89.4%
Intronic: 4,193,484 / 6.97%
Intergenic: 2,183,577 / 3.63%
Intronic/intergenic overlapping exon: 2,130,412 / 3.54%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.17
5'-3' bias: 2.39

Junction analysis

Reads at junctions: 18,463,519
ACCT 5.49%
AGGT 4.67%
ATCT 3.61%
AGGA 3.51%
TCCT 3.48%
GCCT 3.25%
AGCT 2.62%
CCCT 2.42%
AGGC 2.33%
AGAT 2.19%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis