Input data and parameters 

Input

Analysis date: Tue Oct 31 17:37:14 GMT 2023
BAM file: SRX7354412.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): 53,141,033 / 53,105,945
Number of aligned pairs (without duplicates): 53,099,626
Total number of alignments: 113,660,721
Number of secondary alignments: 7,413,743
Number of non-unique alignments: 12,252,572
Aligned to genes: 87,299,418
Ambiguous alignments: 326,254
No feature assigned: 13,220,336
Missing chromosome in annotation: 562,141
Not aligned: 10,103,186

Reads genomic origin

Exonic: 87,299,418 / 86.85%
Intronic: 8,752,604 / 8.71%
Intergenic: 4,467,732 / 4.44%
Intronic/intergenic overlapping exon: 3,501,089 / 3.48%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.19
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 29,198,266
ACCT 5.44%
AGGT 4.66%
ATCT 3.66%
TCCT 3.54%
AGGA 3.52%
GCCT 3.25%
AGCT 2.63%
CCCT 2.5%
AGGC 2.38%
AGAT 2.28%
TTCT 2.28%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis