Input data and parameters 

Input

Analysis date: Tue Oct 31 10:21:25 GMT 2023
BAM file: SRX7354391.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): 40,672,443 / 40,633,648
Number of aligned pairs (without duplicates): 40,629,590
Total number of alignments: 86,572,214
Number of secondary alignments: 5,266,123
Number of non-unique alignments: 8,869,574
Aligned to genes: 66,829,164
Ambiguous alignments: 223,123
No feature assigned: 10,346,323
Missing chromosome in annotation: 304,030
Not aligned: 3,911,155

Reads genomic origin

Exonic: 66,829,164 / 86.59%
Intronic: 6,700,508 / 8.68%
Intergenic: 3,645,815 / 4.72%
Intronic/intergenic overlapping exon: 2,555,439 / 3.31%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.2
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 20,668,773
ACCT 5.42%
AGGT 4.57%
ATCT 3.65%
AGGA 3.49%
TCCT 3.46%
GCCT 3.4%
AGCT 2.7%
CCCT 2.36%
AGGC 2.34%
AGAT 2.21%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis