Input data and parameters 

Input

Analysis date: Mon Oct 30 23:15:53 GMT 2023
BAM file: SRX7354256.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): 37,203,698 / 37,186,377
Number of aligned pairs (without duplicates): 37,183,663
Total number of alignments: 79,228,672
Number of secondary alignments: 4,838,597
Number of non-unique alignments: 8,154,609
Aligned to genes: 62,331,193
Ambiguous alignments: 207,418
No feature assigned: 8,243,786
Missing chromosome in annotation: 291,666
Not aligned: 2,044,763

Reads genomic origin

Exonic: 62,331,193 / 88.32%
Intronic: 5,469,862 / 7.75%
Intergenic: 2,773,924 / 3.93%
Intronic/intergenic overlapping exon: 2,457,941 / 3.48%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.19
5'-3' bias: 2

Junction analysis

Reads at junctions: 19,930,593
ACCT 5.28%
AGGT 4.82%
AGGA 3.65%
ATCT 3.46%
TCCT 3.4%
GCCT 2.98%
AGCT 2.76%
AGGC 2.48%
CCCT 2.47%
AGAT 2.32%
TTCT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis