Input data and parameters 

Input

Analysis date: Tue Oct 31 01:25:20 GMT 2023
BAM file: SRX7354308.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): 35,229,330 / 35,184,606
Number of aligned pairs (without duplicates): 35,181,118
Total number of alignments: 75,243,595
Number of secondary alignments: 4,829,659
Number of non-unique alignments: 8,154,856
Aligned to genes: 58,393,474
Ambiguous alignments: 204,378
No feature assigned: 8,169,029
Missing chromosome in annotation: 321,858
Not aligned: 4,455,770

Reads genomic origin

Exonic: 58,393,474 / 87.73%
Intronic: 5,111,403 / 7.68%
Intergenic: 3,057,626 / 4.59%
Intronic/intergenic overlapping exon: 2,177,958 / 3.27%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.19
5'-3' bias: 2.1

Junction analysis

Reads at junctions: 16,811,769
ACCT 5.17%
AGGT 4.8%
ATCT 3.81%
AGGA 3.57%
TCCT 3.37%
GCCT 3.16%
AGCT 2.77%
CCCT 2.54%
AGGC 2.44%
AGAT 2.33%
TTCT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis