Input data and parameters 

Input

Analysis date: Sun Oct 29 12:25:27 GMT 2023
BAM file: SRX7354111.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): 42,412,643 / 42,348,916
Number of aligned pairs (without duplicates): 42,330,798
Total number of alignments: 89,880,843
Number of secondary alignments: 5,119,284
Number of non-unique alignments: 8,634,169
Aligned to genes: 69,555,711
Ambiguous alignments: 203,488
No feature assigned: 11,161,044
Missing chromosome in annotation: 326,431
Not aligned: 8,982,627

Reads genomic origin

Exonic: 69,555,711 / 86.17%
Intronic: 7,213,353 / 8.94%
Intergenic: 3,947,691 / 4.89%
Intronic/intergenic overlapping exon: 3,015,251 / 3.74%

Transcript coverage profile

5' bias: 0.24
3' bias: 0.16
5'-3' bias: 2.09

Junction analysis

Reads at junctions: 18,322,302
ACCT 5.32%
AGGT 4.73%
ATCT 3.79%
AGGA 3.61%
TCCT 3.48%
GCCT 2.89%
AGCT 2.64%
AGAT 2.47%
CCCT 2.44%
AGGC 2.42%
TTCT 2.21%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis