Input data and parameters 

Input

Analysis date: Tue Oct 31 01:16:05 GMT 2023
BAM file: SRX7354369.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): 33,611,551 / 33,586,772
Number of aligned pairs (without duplicates): 33,581,637
Total number of alignments: 72,896,790
Number of secondary alignments: 5,698,467
Number of non-unique alignments: 8,773,058
Aligned to genes: 53,968,390
Ambiguous alignments: 219,442
No feature assigned: 9,283,782
Missing chromosome in annotation: 652,118
Not aligned: 3,771,281

Reads genomic origin

Exonic: 53,968,390 / 85.32%
Intronic: 7,108,273 / 11.24%
Intergenic: 2,175,509 / 3.44%
Intronic/intergenic overlapping exon: 1,840,045 / 2.91%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.22
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 19,284,399
ACCT 5.48%
AGGT 4.5%
TCCT 3.6%
ATCT 3.52%
AGGA 3.48%
GCCT 3.29%
AGCT 2.71%
CCCT 2.42%
AGGC 2.27%
AGAT 2.25%
TTCT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis