Input data and parameters 

Input

Analysis date: Sun Oct 29 11:54:05 GMT 2023
BAM file: SRX7354092.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): 41,736,374 / 41,709,084
Number of aligned pairs (without duplicates): 41,704,046
Total number of alignments: 89,927,303
Number of secondary alignments: 6,481,845
Number of non-unique alignments: 10,382,599
Aligned to genes: 65,579,389
Ambiguous alignments: 270,606
No feature assigned: 13,085,651
Missing chromosome in annotation: 609,058
Not aligned: 4,842,098

Reads genomic origin

Exonic: 65,579,389 / 83.37%
Intronic: 8,763,168 / 11.14%
Intergenic: 4,322,483 / 5.49%
Intronic/intergenic overlapping exon: 2,638,502 / 3.35%

Transcript coverage profile

5' bias: 0.5
3' bias: 0.33
5'-3' bias: 1.6

Junction analysis

Reads at junctions: 24,128,720
ACCT 5.09%
AGGT 4.68%
TCCT 3.64%
AGGA 3.43%
ATCT 3.34%
GCCT 3.19%
AGCT 2.79%
CCCT 2.55%
AGGC 2.42%
AGAT 2.21%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis