Input data and parameters 

Input

Analysis date: Tue Oct 31 13:20:37 GMT 2023
BAM file: SRX7354405.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): 30,763,113 / 30,730,289
Number of aligned pairs (without duplicates): 30,725,787
Total number of alignments: 65,867,973
Number of secondary alignments: 4,374,571
Number of non-unique alignments: 7,355,850
Aligned to genes: 52,712,121
Ambiguous alignments: 188,842
No feature assigned: 5,326,374
Missing chromosome in annotation: 284,786
Not aligned: 9,694,352

Reads genomic origin

Exonic: 52,712,121 / 90.82%
Intronic: 3,204,950 / 5.52%
Intergenic: 2,121,424 / 3.66%
Intronic/intergenic overlapping exon: 1,751,488 / 3.02%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.19
5'-3' bias: 2.12

Junction analysis

Reads at junctions: 17,360,014
ACCT 5.37%
AGGT 4.53%
ATCT 3.78%
TCCT 3.58%
AGGA 3.35%
GCCT 3.11%
AGCT 2.55%
CCCT 2.45%
AGGC 2.34%
AGGG 2.15%
TTCT 2.02%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis