Input data and parameters 

Input

Analysis date: Mon Oct 30 11:44:12 GMT 2023
BAM file: SRX7354177.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): 85,815,572 / 85,668,977
Number of aligned pairs (without duplicates): 85,661,074
Total number of alignments: 182,304,534
Number of secondary alignments: 10,819,985
Number of non-unique alignments: 15,660,330
Aligned to genes: 135,504,293
Ambiguous alignments: 482,450
No feature assigned: 28,797,845
Missing chromosome in annotation: 1,859,616
Not aligned: 6,300,089

Reads genomic origin

Exonic: 135,504,293 / 82.47%
Intronic: 20,074,711 / 12.22%
Intergenic: 8,723,134 / 5.31%
Intronic/intergenic overlapping exon: 7,551,578 / 4.6%

Transcript coverage profile

5' bias: 0.57
3' bias: 0.19
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 63,886,526
ACCT 5.32%
AGGT 4.72%
GCCT 3.57%
AGGA 3.56%
TCCT 3.39%
ATCT 3.37%
AGCT 2.91%
CCCT 2.56%
AGGC 2.43%
AGAT 2.3%
TTCT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis