Input data and parameters 

Input

Analysis date: Sun Oct 29 01:03:42 GMT 2023
BAM file: SRX7354067.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): 29,642,191 / 29,621,753
Number of aligned pairs (without duplicates): 29,619,433
Total number of alignments: 63,408,166
Number of secondary alignments: 4,144,222
Number of non-unique alignments: 6,855,660
Aligned to genes: 49,777,067
Ambiguous alignments: 178,089
No feature assigned: 6,300,637
Missing chromosome in annotation: 296,713
Not aligned: 2,359,404

Reads genomic origin

Exonic: 49,777,067 / 88.76%
Intronic: 4,290,219 / 7.65%
Intergenic: 2,010,418 / 3.59%
Intronic/intergenic overlapping exon: 1,708,140 / 3.05%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.24
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 17,116,733
ACCT 5.55%
AGGT 4.48%
ATCT 3.63%
GCCT 3.59%
TCCT 3.44%
AGGA 3.33%
AGCT 2.7%
CCCT 2.5%
AGGC 2.37%
TTCT 2.21%
AGAT 2.08%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis