Input data and parameters 

Input

Analysis date: Mon Oct 30 22:36:56 GMT 2023
BAM file: SRX7354284.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): 30,942,860 / 30,912,396
Number of aligned pairs (without duplicates): 30,903,913
Total number of alignments: 65,593,417
Number of secondary alignments: 3,738,161
Number of non-unique alignments: 6,107,027
Aligned to genes: 53,030,121
Ambiguous alignments: 177,837
No feature assigned: 5,976,943
Missing chromosome in annotation: 301,489
Not aligned: 6,618,840

Reads genomic origin

Exonic: 53,030,121 / 89.87%
Intronic: 3,390,613 / 5.75%
Intergenic: 2,586,330 / 4.38%
Intronic/intergenic overlapping exon: 2,033,187 / 3.45%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.15
5'-3' bias: 2.28

Junction analysis

Reads at junctions: 16,695,825
ACCT 5.94%
AGGT 4.48%
ATCT 3.9%
TCCT 3.88%
GCCT 3.43%
AGGA 3.24%
CCCT 2.5%
AGCT 2.37%
AGGC 2.33%
TTCT 2.11%
AGAT 1.95%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis