Input data and parameters 

Input

Analysis date: Sun Oct 29 13:02:07 GMT 2023
BAM file: SRX7354190.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): 51,415,388 / 51,403,402
Number of aligned pairs (without duplicates): 51,349,523
Total number of alignments: 112,213,115
Number of secondary alignments: 9,394,325
Number of non-unique alignments: 13,576,579
Aligned to genes: 86,421,407
Ambiguous alignments: 292,615
No feature assigned: 10,220,054
Missing chromosome in annotation: 1,702,460
Not aligned: 2,526,802

Reads genomic origin

Exonic: 86,421,407 / 89.42%
Intronic: 6,281,743 / 6.5%
Intergenic: 3,938,311 / 4.08%
Intronic/intergenic overlapping exon: 4,194,631 / 4.34%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.24
5'-3' bias: 2.08

Junction analysis

Reads at junctions: 27,884,925
ACCT 5.22%
AGGT 4.62%
ATCT 4.15%
TCCT 4.13%
AGGA 3.25%
GCCT 3.19%
CCCT 3.02%
AGCT 2.42%
TTCT 2.31%
AGGC 2.3%
AGAA 1.86%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis